[joss-review] tests #314

vsoch · 2021-05-20T03:46:38Z

It looks like tests aren't included in the release, and at least for HPC, installers would want to be able to run tests before moving forward. Have you considered adding them?

mviereck · 2021-05-20T10:19:31Z

In fact this is a requirement for the JOSS review to have automated or manual test instructions:
openjournals/joss-reviews#3295

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

mariojmdavid · 2021-05-28T12:15:47Z

this regards the devel3 branch
we will tackle this in the documentation since unit tests exist (we will make sure they are part of the release, and coverage of 79% at the moment, our Jenkins CI pipeline executes them
additionally there are 2 shell scripts
1 utils/udocker_test.sh
2 utils/udocker_test-run.sh

where almost all the commands of udocker are tested from the perspective of a user, the second script test udocker run with several images and all execution modes except singularity (S1)

jorge-lip · 2021-06-08T17:00:10Z

The have unit tests, integration tests, security tests with bandit and code style checking. We use Jenkins pipelines for our SQA.
They are under utils as Mario explained. The .sqa directory has the configurations for the Jenkins pipeline as code.
We tests the udocker functionalities we don't provide tests for specific applications or environments such as HPC.

vsoch · 2021-06-16T16:53:38Z

@jorge-lip great! Are there instructions anywhere for how a developer or interested user like myself could run the tests?

mariojmdavid · 2021-06-17T15:14:28Z

just did a commit with information about how to run tests, it's in section 9 of the installation manual
https://github.com/indigo-dc/udocker/blob/master/docs/installation_manual.md

vsoch · 2021-06-17T15:24:05Z

This is great! I had a few suggestions here -> #333

mariojmdavid · 2021-06-17T15:34:54Z

PR approved and merged

vsoch · 2021-06-17T15:36:36Z

I'm good with thew new additions - @mviereck when you've had a chance to take a look let me know, and if you are also good we can close the issue.

mviereck · 2021-06-17T21:08:45Z

I've tried to run the test as described:

virtualenv -p python3 ud3
source ud3/bin/activate
git clone https://github.com/indigo-dc/udocker.git
cd udocker
pip install -r requirements-dev.txt

I got a lot of errors at the pip install step:

$ pip install -r requirements-dev.txt 
Collecting pycurl>=7.15.5
  Downloading pycurl-7.43.0.6.tar.gz (222 kB)
     |████████████████████████████████| 222 kB 148 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-vfl_elow
         cwd: /tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py", line 236, in configure_unix
        p = subprocess.Popen((self.curl_config(), '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py", line 988, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py", line 649, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py", line 101, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_d24e0afcc1234c6e8f3614cb1e6cf277/setup.py", line 241, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/50/1a/35b1d8b8e4e23a234f1b17a8a40299fd550940b16866c9a1f2d47a04b969/pycurl-7.43.0.6.tar.gz#sha256=8301518689daefa53726b59ded6b48f33751c383cf987b0ccfbbc4ed40281325 (from https://pypi.org/simple/pycurl/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.43.0.5.tar.gz (216 kB)
     |████████████████████████████████| 216 kB 148 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-0ec9to67
         cwd: /tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py", line 233, in configure_unix
        p = subprocess.Popen((self.curl_config(), '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py", line 961, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py", line 623, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py", line 101, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_d2021d887aba41e986309ba1a9ad6f24/setup.py", line 238, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/ef/05/4b773f74f830a90a326b06f9b24e65506302ab049e825a3c0b60b1a6e26a/pycurl-7.43.0.5.tar.gz#sha256=ec7dd291545842295b7b56c12c90ffad2976cc7070c98d7b1517b7b6cd5994b3 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.43.0.4.tar.gz (215 kB)
     |████████████████████████████████| 215 kB 149 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-1tip3p9e
         cwd: /tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py", line 233, in configure_unix
        p = subprocess.Popen((self.curl_config(), '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py", line 957, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py", line 618, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py", line 101, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_a12a478de2c44e8ab5f563f3909d72a7/setup.py", line 238, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/0f/52/2c6951c4cd8a4e9288f2561eb9da1dc15b5d0f4e610a7e2acf39bc703281/pycurl-7.43.0.4.tar.gz#sha256=bdc308ff2a16ede41921cb0d88f51bd6cb5208c6478be9db579789e2e4db2528 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.43.0.3.tar.gz (215 kB)
     |████████████████████████████████| 215 kB 94 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-71g04xf5
         cwd: /tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py", line 228, in configure_unix
        p = subprocess.Popen((self.curl_config(), '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py", line 944, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py", line 606, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py", line 101, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_8342159dbc4c403b994ef0fac168da55/setup.py", line 233, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/ac/b3/0f3979633b7890bab6098d84c84467030b807a1e2b31f5d30103af5a71ca/pycurl-7.43.0.3.tar.gz#sha256=6f08330c5cf79fa8ef68b9912b9901db7ffd34b63e225dce74db56bb21deda8e (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.43.0.2.tar.gz (214 kB)
     |████████████████████████████████| 214 kB 28 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-s6cb76p9
         cwd: /tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py", line 222, in configure_unix
        p = subprocess.Popen((self.curl_config(), '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py", line 913, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py", line 582, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py", line 99, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_b156f0da2f0245b9aa9392ea7a2d185d/setup.py", line 227, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/e8/e4/0dbb8735407189f00b33d84122b9be52c790c7c3b25286826f4e1bdb7bde/pycurl-7.43.0.2.tar.gz#sha256=0f0cdfc7a92d4f2a5c44226162434e34f7d6967d3af416a6f1448649c09a25a4 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.43.0.1.tar.gz (195 kB)
     |████████████████████████████████| 195 kB 147 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-abw4yag8
         cwd: /tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py", line 103, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py", line 841, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py", line 508, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py", line 72, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_29c1f91bb14a46efa5eec5ca6bae66bc/setup.py", line 108, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/77/d9/d272b38e6e25d2686e22f6058820298dadead69340b1c57ff84c87ef81f0/pycurl-7.43.0.1.tar.gz#sha256=43231bf2bafde923a6d9bb79e2407342a5f3382c1ef0a3b2e491c6a4e50b91aa (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.43.0.tar.gz (182 kB)
     |████████████████████████████████| 182 kB 30 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-k1hx2drw
         cwd: /tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py", line 102, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py", line 823, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py", line 497, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py", line 71, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_7c5eb365935a4289b0f3447890044304/setup.py", line 107, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/12/3f/557356b60d8e59a1cce62ffc07ecc03e4f8a202c86adae34d895826281fb/pycurl-7.43.0.tar.gz#sha256=aa975c19b79b6aa6c0518c0cc2ae33528900478f0b500531dbcdbf05beec584c (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.21.5.tar.gz (170 kB)
     |████████████████████████████████| 170 kB 148 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-nhmgk35k
         cwd: /tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py", line 102, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py", line 743, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py", line 497, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py", line 71, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_d61383c0f9d4453c91753274b6705e52/setup.py", line 107, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/74/fa/37bc18e2f60100d9833cf008dca0861f6815cd1743c3b31a419bc6576ee3/pycurl-7.21.5.tar.gz#sha256=8a1e0eb55573388275a1d6c2534ca4cfca5d7fa772b99b505c08fa149b27aed0 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.5.3.tar.gz (154 kB)
     |████████████████████████████████| 154 kB 28 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-jaey4ki0
         cwd: /tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py", line 102, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py", line 731, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py", line 488, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py", line 71, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_e8ddb10fbcf14407923a3056284f5a03/setup.py", line 107, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/b4/a2/59761b58683967087aa131e1043b67d6b4675f0d0e68940c3b4d6f9df263/pycurl-7.19.5.3.tar.gz#sha256=24f6c4016b1dd2a5e29d1b025ac2ad61f80c17adfdcf8a7f47aefab63ace78d7 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.5.2.tar.gz (153 kB)
     |████████████████████████████████| 153 kB 148 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-a5cufd6i
         cwd: /tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py", line 102, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py", line 731, in <module>
        ext = get_extension(sys.argv, split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py", line 488, in get_extension
        ext_config = ExtensionConfiguration(argv)
      File "/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py", line 71, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_bdac16c5cd7b437ca42494f1c9efd2bf/setup.py", line 107, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/94/35/04e331a7a9e2fdea4b9cadcc23038bd56f80632065258c98730a199fd223/pycurl-7.19.5.2.tar.gz#sha256=98cc821555d152977fac99b6e5cb0f759275aabdf14e4928890c6fcc944ab736 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.5.1.tar.gz (142 kB)
     |████████████████████████████████| 142 kB 38 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-bzrxbre_
         cwd: /tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py", line 95, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py", line 634, in <module>
        ext = get_extension(split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py", line 392, in get_extension
        ext_config = ExtensionConfiguration()
      File "/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py", line 65, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_8854ca41112b42beaa42b1c0c1113015/setup.py", line 100, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/f9/fb/973d075babcd8cb101d964b898c7b148bb80275344d960c27532b5b35abf/pycurl-7.19.5.1.tar.gz#sha256=6e9770f80459757f73bd71af82fbb29cd398b38388cdf1beab31ea91a331bc6c (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.5.tar.gz (107 kB)
     |████████████████████████████████| 107 kB 119 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-fd48rsma
         cwd: /tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py", line 95, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py", line 634, in <module>
        ext = get_extension(split_extension_source=split_extension_source)
      File "/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py", line 392, in get_extension
        ext_config = ExtensionConfiguration()
      File "/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py", line 65, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_dc21198d314d4ae78206a94f8b00e626/setup.py", line 100, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/6c/48/13bad289ef6f4869b1d8fc11ae54de8cfb3cc4a2eb9f7419c506f763be46/pycurl-7.19.5.tar.gz#sha256=69a0aa7c9dddbfe4cebf4d1f674c490faccf739fc930d85d8990ce2fd0551a43 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.3.1.tar.gz (116 kB)
     |████████████████████████████████| 116 kB 148 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-l0x23bc8
         cwd: /tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/
    Complete output (22 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py", line 95, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py", line 563, in <module>
        ext = get_extension()
      File "/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py", line 368, in get_extension
        ext_config = ExtensionConfiguration()
      File "/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py", line 65, in __init__
        self.configure()
      File "/tmp/pip-install-gdqmopho/pycurl_98df6f37941044348bc448638e4caaf9/setup.py", line 100, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/22/e9/f3dc93a056957d80b5697f221dbb6a7c114f979bdfa7433bc8e89d723b0f/pycurl-7.19.3.1.tar.gz#sha256=c0d673fe99a9de07239eabe77c798f1b043f60c02afaec1430ceaf59d7501a4f (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.3.tar.gz (113 kB)
     |████████████████████████████████| 113 kB 150 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-l6qbrnj6
         cwd: /tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/
    Complete output (20 lines):
    Traceback (most recent call last):
      File "/tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/setup.py", line 175, in configure_unix
        p = subprocess.Popen((CURL_CONFIG, '--version'),
      File "/usr/lib/python3.9/subprocess.py", line 951, in __init__
        self._execute_child(args, executable, preexec_fn, close_fds,
      File "/usr/lib/python3.9/subprocess.py", line 1823, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'curl-config'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/setup.py", line 479, in <module>
        configure()
      File "/tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/setup.py", line 297, in configure
        configure_unix()
      File "/tmp/pip-install-gdqmopho/pycurl_d00726c5567c40aca6af141f6526d550/setup.py", line 180, in configure_unix
        raise ConfigurationError(msg)
    __main__.ConfigurationError: Could not run curl-config: [Errno 2] No such file or directory: 'curl-config'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/97/07/f96744c4d54b30f923194423c93215f71b62fd45d4626af7380ee5aac77c/pycurl-7.19.3.tar.gz#sha256=05e48835fe445ff327dcd373f49d9970e0b828a07cd4d08a23264507a742d616 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.0.3.tar.gz (90 kB)
     |█████████████████████▋          | 61 kB 155 kB/s eta 0:00:01

     |████████████████████████████████| 90 kB 32 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_494d1707aec24ee0abaef958c973b4d1/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_494d1707aec24ee0abaef958c973b4d1/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-j11xpmq3
         cwd: /tmp/pip-install-gdqmopho/pycurl_494d1707aec24ee0abaef958c973b4d1/
    Complete output (6 lines):
    /bin/sh: 1: curl-config: not found
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_494d1707aec24ee0abaef958c973b4d1/setup.py", line 133, in <module>
        raise Exception("`%s' not found -- please install the libcurl development files or specify --curl-config=/path/to/curl-config" % CURL_CONFIG)
    Exception: `curl-config' not found -- please install the libcurl development files or specify --curl-config=/path/to/curl-config
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/f7/42/1394c2aac756d8c75af612ee4476130e994d56b3fe097f213a1f5db5d272/pycurl-7.19.0.3.tar.gz#sha256=3293c990e076428bc7408c26c787af92fd531ef63976b1dc45f75eec7480b09a (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

  Downloading pycurl-7.19.0.2.tar.gz (89 kB)
     |████████████████████████████████| 89 kB 150 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_97bd07461e9b4562873dd9ced8c8d281/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_97bd07461e9b4562873dd9ced8c8d281/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-fqqfvev9
         cwd: /tmp/pip-install-gdqmopho/pycurl_97bd07461e9b4562873dd9ced8c8d281/
    Complete output (6 lines):
    /bin/sh: 1: curl-config: not found
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_97bd07461e9b4562873dd9ced8c8d281/setup.py", line 90, in <module>
        raise Exception("`%s' not found -- please install the libcurl development files or specify --curl-config=/path/to/curl-config" % CURL_CONFIG)
    Exception: `curl-config' not found -- please install the libcurl development files or specify --curl-config=/path/to/curl-config
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/08/79/576eaecd19f11a265cd8d10f339ecfd4b1033436e56e6f2625153a4b79aa/pycurl-7.19.0.2.tar.gz#sha256=7a9e793b9181654d5eef3f6d22c244c57d2b51d38feb4c1b71d68efda99b0547 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.0.1.tar.gz (86 kB)
     |████████████████████████████████| 86 kB 162 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_ae121ddb66594bc39f3ddd323942fdc9/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_ae121ddb66594bc39f3ddd323942fdc9/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-6hjmctjj
         cwd: /tmp/pip-install-gdqmopho/pycurl_ae121ddb66594bc39f3ddd323942fdc9/
    Complete output (6 lines):
    /bin/sh: 1: curl-config: not found
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_ae121ddb66594bc39f3ddd323942fdc9/setup.py", line 90, in <module>
        raise Exception("`%s' not found -- please install the libcurl development files or specify --curl-config=/path/to/curl-config" % CURL_CONFIG)
    Exception: `curl-config' not found -- please install the libcurl development files or specify --curl-config=/path/to/curl-config
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/17/11/79e2187232ffdb96c9c200f8fc82452f8631f659fd9bdd2acf4bf7991905/pycurl-7.19.0.1.tar.gz#sha256=8b14d91d7453c5d9a4cc8cd4e61ab9389298813028d10661bf2079ee06d676c8 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.19.0.tar.gz (70 kB)
     |████████████████████████████████| 70 kB 54 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_eb06c4bb4e6249dc96c00727a6b10741/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_eb06c4bb4e6249dc96c00727a6b10741/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-h4od2h58
         cwd: /tmp/pip-install-gdqmopho/pycurl_eb06c4bb4e6249dc96c00727a6b10741/
    Complete output (6 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_eb06c4bb4e6249dc96c00727a6b10741/setup.py", line 58
        print "FATAL: bad directory %s in environment variable %s" % (dir, envvar)
              ^
    SyntaxError: invalid syntax
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/11/73/abcfbbb6e1dd7087fa53042c301c056c11264e8a737a4688f834162d731e/pycurl-7.19.0.tar.gz#sha256=8ef0bf1c0e48f0d193ef8ac4ae4b3596a1e91b6cbf1ff1b25de769fe3782aeb6 (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
  Downloading pycurl-7.18.2.tar.gz (69 kB)
     |████████████████████████████████| 69 kB 155 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdqmopho/pycurl_f246786bf1fe4812baa3bea160672d32/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdqmopho/pycurl_f246786bf1fe4812baa3bea160672d32/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-os5i7diw
         cwd: /tmp/pip-install-gdqmopho/pycurl_f246786bf1fe4812baa3bea160672d32/
    Complete output (6 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-gdqmopho/pycurl_f246786bf1fe4812baa3bea160672d32/setup.py", line 58
        print "FATAL: bad directory %s in environment variable %s" % (dir, envvar)
              ^
    SyntaxError: invalid syntax
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/fe/8f/711d436c76938093dd10dae465ccee316c6241cfdada06c5cc3b5c1f74b8/pycurl-7.18.2.tar.gz#sha256=cda1085b7911ca802746d816f37d541165ad1e20c241d22e4c304ddb2bc81ffe (from https://pypi.org/simple/pycurl/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement pycurl>=7.15.5
ERROR: No matching distribution found for pycurl>=7.15.5

I could fix this installing libcurl4-gnutls-dev (debian) and several files are downloaded.
But than I ran into the next error:

[...]
Collecting lazy-object-proxy>=1.4.0
  Downloading lazy_object_proxy-1.6.0-cp39-cp39-manylinux1_x86_64.whl (57 kB)
     |████████████████████████████████| 57 kB 181 kB/s 
Collecting wrapt<1.13,>=1.11
  Downloading wrapt-1.12.1.tar.gz (27 kB)
Building wheels for collected packages: pycurl, wrapt
  Building wheel for pycurl (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/lauscher/bin/udocker/ud3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-lq38c8yv
       cwd: /tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/
  Complete output (20 lines):
  Using curl-config (libcurl 7.74.0)
  Using SSL library: GnuTLS
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.9
  creating build/lib.linux-x86_64-3.9/curl
  copying python/curl/__init__.py -> build/lib.linux-x86_64-3.9/curl
  running build_ext
  building 'pycurl' extension
  creating build/temp.linux-x86_64-3.9
  creating build/temp.linux-x86_64-3.9/src
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYCURL_VERSION="7.43.0.6" -DHAVE_CURL_SSL=1 -DHAVE_CURL_GNUTLS=1 -DHAVE_CURL_SSL=1 -I/home/lauscher/bin/udocker/ud3/include -I/usr/include/python3.9 -c src/docstrings.c -o build/temp.linux-x86_64-3.9/src/docstrings.o
  In file included from src/docstrings.c:4:
  src/pycurl.h:5:10: fatal error: Python.h: Datei oder Verzeichnis nicht gefunden
      5 | #include <Python.h>
        |          ^~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for pycurl
  Running setup.py clean for pycurl
  Building wheel for wrapt (setup.py) ... done
  Created wheel for wrapt: filename=wrapt-1.12.1-py3-none-any.whl size=19553 sha256=ddcca34ec6a4c573770fe44e5c31689702d9af97aa54826a19b7378a926448a3
  Stored in directory: /home/lauscher/.cache/pip/wheels/98/23/68/efe259aaca055e93b08e74fbe512819c69a2155c11ba3c0f10
Successfully built wrapt
Failed to build pycurl
Installing collected packages: pycparser, pyparsing, cffi, zipp, webencodings, urllib3, smmap, six, packaging, jeepney, idna, filelock, distlib, cryptography, chardet, certifi, appdirs, wrapt, virtualenv, toml, SecretStorage, requests, Pygments, py, pluggy, pbr, lazy-object-proxy, importlib-metadata, gitdb, docutils, bleach, tqdm, tox, stevedore, snowballstemmer, rfc3986, requests-toolbelt, readme-renderer, PyYAML, pkginfo, nose, mccabe, keyring, isort, iniconfig, GitPython, coverage, colorama, attrs, astroid, watchdog, twine, tox-travis, pytest-runner, pytest, pylint, pydocstyle, pycurl, pep8, nosexcover, mock, bandit
    Running setup.py install for pycurl ... error
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/bin/udocker/ud3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-r81lwub2/install-record.txt --single-version-externally-managed --compile --install-headers /home/lauscher/bin/udocker/ud3/include/site/python3.9/pycurl
         cwd: /tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/
    Complete output (20 lines):
    Using curl-config (libcurl 7.74.0)
    Using SSL library: GnuTLS
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.9
    creating build/lib.linux-x86_64-3.9/curl
    copying python/curl/__init__.py -> build/lib.linux-x86_64-3.9/curl
    running build_ext
    building 'pycurl' extension
    creating build/temp.linux-x86_64-3.9
    creating build/temp.linux-x86_64-3.9/src
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYCURL_VERSION="7.43.0.6" -DHAVE_CURL_SSL=1 -DHAVE_CURL_GNUTLS=1 -DHAVE_CURL_SSL=1 -I/home/lauscher/bin/udocker/ud3/include -I/usr/include/python3.9 -c src/docstrings.c -o build/temp.linux-x86_64-3.9/src/docstrings.o
    In file included from src/docstrings.c:4:
    src/pycurl.h:5:10: fatal error: Python.h: Datei oder Verzeichnis nicht gefunden
        5 | #include <Python.h>
          |          ^~~~~~~~~~
    compilation terminated.
    error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/lauscher/bin/udocker/ud3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4fdns7z8/pycurl_0bc854ef52c44900adffabdf651144b1/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-r81lwub2/install-record.txt --single-version-externally-managed --compile --install-headers /home/lauscher/bin/udocker/ud3/include/site/python3.9/pycurl Check the logs for full command output.

vsoch · 2021-06-17T21:59:19Z

@mviereck I tried the tests and they did work - do you have python-dev headers available? (I'm seeing a reference to Python.h). Although that's a bit of a strange dependency, probably one of the libraries needs it to build.

mviereck · 2021-06-17T22:36:41Z

@vsoch I've installed pyton3-dev and get a new error, now about missing gnutls.h.

Building wheels for collected packages: pycurl
  Building wheel for pycurl (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/lauscher/git/ud3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/setup.py'"'"'; __file__='"'"'/tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ccubbr8w
       cwd: /tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/
  Complete output (20 lines):
  Using curl-config (libcurl 7.74.0)
  Using SSL library: GnuTLS
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.9
  creating build/lib.linux-x86_64-3.9/curl
  copying python/curl/__init__.py -> build/lib.linux-x86_64-3.9/curl
  running build_ext
  building 'pycurl' extension
  creating build/temp.linux-x86_64-3.9
  creating build/temp.linux-x86_64-3.9/src
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYCURL_VERSION="7.43.0.6" -DHAVE_CURL_SSL=1 -DHAVE_CURL_GNUTLS=1 -DHAVE_CURL_SSL=1 -I/home/lauscher/git/ud3/include -I/usr/include/python3.9 -c src/docstrings.c -o build/temp.linux-x86_64-3.9/src/docstrings.o
  In file included from src/docstrings.c:4:
  src/pycurl.h:202:13: fatal error: gnutls/gnutls.h: Datei oder Verzeichnis nicht gefunden
    202 | #   include <gnutls/gnutls.h>
        |             ^~~~~~~~~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for pycurl
  Running setup.py clean for pycurl
Failed to build pycurl
Installing collected packages: pycparser, pyparsing, cffi, zipp, webencodings, urllib3, smmap, six, packaging, jeepney, idna, filelock, distlib, cryptography, chardet, certifi, appdirs, wrapt, virtualenv, toml, SecretStorage, requests, Pygments, py, pluggy, pbr, lazy-object-proxy, importlib-metadata, gitdb, docutils, bleach, tqdm, tox, stevedore, snowballstemmer, rfc3986, requests-toolbelt, readme-renderer, PyYAML, pkginfo, nose, mccabe, keyring, isort, iniconfig, GitPython, coverage, colorama, attrs, astroid, watchdog, twine, tox-travis, pytest-runner, pytest, pylint, pydocstyle, pycurl, pep8, nosexcover, mock, bandit
    Running setup.py install for pycurl ... error
    ERROR: Command errored out with exit status 1:
     command: /home/lauscher/git/ud3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/setup.py'"'"'; __file__='"'"'/tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8ive146d/install-record.txt --single-version-externally-managed --compile --install-headers /home/lauscher/git/ud3/include/site/python3.9/pycurl
         cwd: /tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/
    Complete output (20 lines):
    Using curl-config (libcurl 7.74.0)
    Using SSL library: GnuTLS
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.9
    creating build/lib.linux-x86_64-3.9/curl
    copying python/curl/__init__.py -> build/lib.linux-x86_64-3.9/curl
    running build_ext
    building 'pycurl' extension
    creating build/temp.linux-x86_64-3.9
    creating build/temp.linux-x86_64-3.9/src
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPYCURL_VERSION="7.43.0.6" -DHAVE_CURL_SSL=1 -DHAVE_CURL_GNUTLS=1 -DHAVE_CURL_SSL=1 -I/home/lauscher/git/ud3/include -I/usr/include/python3.9 -c src/docstrings.c -o build/temp.linux-x86_64-3.9/src/docstrings.o
    In file included from src/docstrings.c:4:
    src/pycurl.h:202:13: fatal error: gnutls/gnutls.h: Datei oder Verzeichnis nicht gefunden
      202 | #   include <gnutls/gnutls.h>
          |             ^~~~~~~~~~~~~~~~~
    compilation terminated.
    error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/lauscher/git/ud3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/setup.py'"'"'; __file__='"'"'/tmp/pip-install-3_3lzrpt/pycurl_457dc6203ed44295b24f9ca3ec174c00/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8ive146d/install-record.txt --single-version-externally-managed --compile --install-headers /home/lauscher/git/ud3/include/site/python3.9/pycurl Check the logs for full command output.

I could fix this with installing libgnutls28-dev.
Now this step completes.

The step

nosetests -v --with-coverage --cover-package=udocker tests/unit

shows several 'ok' and some errors. Because I don't know what is checked exactly (syntax and code style?), I can't assess its meaning.

The results of the further tests also tell me nothing, but seem to be ok:

pylint --rcfile=pylintrc --disable=R,C udocker
bandit -r udocker -f html -o bandit.html

Currently I run ./udocker_test.sh , it seems to take some time.

vsoch · 2021-06-17T23:28:31Z

Hmm, it probably would make sense to list the system dependencies somewhere or provide a container. I must have lucked out that I had them.

mariojmdavid · 2021-06-18T07:47:56Z

"Nose’s tagline is “nose extends unittest to make testing easier”.
It’s is a fairly well known python unit test framework, and can run doctests, unittests, and “no boilerplate” tests."
https://pythontesting.net/framework/nose/nose-introduction/

"Pylint is a Python static code analysis tool which looks for programming errors, helps enforcing a coding standard, sniffs for code smells and offers simple refactoring suggestions."
https://pypi.org/project/pylint/

"Bandit is a tool designed to find common security issues in Python code. To do this Bandit processes each file, builds an AST from it, and runs appropriate plugins against the AST nodes. Once Bandit has finished scanning all the files it generates a report."
https://pypi.org/project/bandit/

I hope this clarifies what tests are being preformed

mariojmdavid · 2021-06-18T07:58:23Z

./udocker_test.sh and ./udocker_test-run.sh it may take more or less time, it depends on the one hand on your internet bandwidth since both download docker images from dockerhub, and depend on you laptop or desktop performance, since they execute the CLI including running containers, import and exporting the containers etc., in my desktop
./udocker_test.sh took about 46 sec.
./udocker_test-run.sh took about 1min 33 sec

mviereck · 2021-06-18T08:25:48Z

./udocker_test.sh and ./udocker_test-run.sh it may take more or less time, it depends on the one hand on your internet bandwidth since both download docker images from dockerhub, I did not measure the time, but after about half an hour I put the laptop aside.

Yes, the internet bandwith was the bottleneck here.

udocker_test.sh showed one minor error:

tar img file exists https://download.ncg.ingrid.pt/webdav/udocker_test/centos7.tar
------------------------------------------------------------>
Error: failed to extract container: centos7.tar
Error: load failed
 
[FAIL]    T028: udocker load -i centos7.tar

It makes sense to collect all errors and show them altogether when the script has finished. I found this one scrolling through the output.

I hope this clarifies what tests are being preformed

Thank you! Yes that helps.
So nosetests, pylint and bandit run code checks, while udocker-test.sh and udocker_test-run.sh run tests on user level. This is basically said in the instructions, could however be a bit more pointed out.
The tests required by JOSS are fulfilled with the high level tests, the code checks are a nice bonus.

Hmm, it probably would make sense to list the system dependencies somewhere or provide a container.

A similar/additional thought: udocker-test.sh and udocker_test-run.sh must not have an already existing ~/.udocker. It would be good if the tests are possible nonetheless, either in a container or using another directory than ~/.udocker for the tests, maybe set with one of the environment variables to something like /tmp/udocker-test. That would allow to run the test scripts at any time.

jorge-lip · 2021-06-18T08:35:26Z

Many thanks for the suggestions we will address those in a future release.

mviereck · 2021-06-18T10:58:55Z

I've run udocker_test-run.sh and got some errors.
Likely caused by damaged image downloads caused by limited bandwith.
The same suggestion as above: Please collect the errors and print a summary at the end.
Looking only at the final output would currrently suggest that everything went well.
Even echo $? printed 0 although errors occured.

$ ./udocker_test-run.sh 
=============================================
* This script tests udocker run and options *
* and volume mount options                  *
=============================================
Info: creating repo: /home/lauscher/.udocker
Info: udocker command line interface 1.3.0
Info: searching for udockertools 1.2.8
Info: installing udockertools 1.2.8
Info: installation of udockertools successful
Error: invalid container id 
Error: invalid container id 
Error: invalid container id 
Info: deleting image: centos:7
Error: deleting image
Info: deleting image: ubuntu:18.04
Error: deleting image
Info: deleting image: java
Error: deleting image
Info: downloading layer sha256:2d473b07cdd5f0912cd6f1a703352c82b512407db6b05b43f2553732b55df3bc
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:5040bd2983909aa8896b9932438c3f1479d25ae837a5f6220242a264d0221f2d
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:fce5728aad85a763fe3c419db16885eb6f7a670a42824ea618414b8fb309ccde
Info: downloading layer sha256:76610ec20bf5892e24cebd4153c7668284aa1d1151b7c3b0c7d50c579aa5ce75
Info: downloading layer sha256:60170fec2151d2108ed1420625c51138434ba4e0223d3023353d3f32ffe3cfc2
Info: downloading layer sha256:e98f73de8f0d2ef292f58b004d67bc6e9ee779dcfaff7ebb3964649d4787b872
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:11f7af24ed9cf47597dd6cf9963bb3e9109c963f0135e869a9e9b4999fdc12a3
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: downloading layer sha256:49e2d6393f32abb1de7c9395c04c822ceb2287383d5a90998f7bd8dbfd43d48c
Info: downloading layer sha256:bb9cdec9c7f337940f7d872274353b66e118412cbfd433c711361bcf7922aea4
REPOSITORY
ubuntu:18.04                                                 .
centos:7                                                     .
java:latest                                                  .
c02f1b7f-2124-3322-be7b-7b2a5dca66b1
73474c75-0894-3b4a-99e2-ed56b0cffaf7
4d89fa47-3cb1-33c1-b623-0a2195cd31a9
CONTAINER ID                         P M NAMES              IMAGE               
4d89fa47-3cb1-33c1-b623-0a2195cd31a9 . W ['jv']             java:latest         
73474c75-0894-3b4a-99e2-ed56b0cffaf7 . W ['ub18']           ubuntu:18.04        
c02f1b7f-2124-3322-be7b-7b2a5dca66b1 . W ['c7']             centos:7            
====================
* Test udocker run *
====================
===================================== execmode = P1
execmode: P1
nvidiamode: False
 
[OK]    T006: udocker setup jv
------------------------------------------------------------>
 
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: java
proot info: vpid 2: terminated with signal 11
proot info: vpid 1: terminated with signal 11
 
[FAIL]    T007: udocker run jv java -version
------------------------------------------------------------>
execmode: P1
nvidiamode: False
 
[OK]    T008: udocker setup c7
------------------------------------------------------------>
 
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: env
TERM=xterm-256color
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PROOT_TMP_DIR=/tmp
USERNAME=root
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
SHLVL=0
container_names=c7
LOGNAME=root
USER=root
HOME=/root
container_execmode=P1
container_ruser=lauscher
PS1=c02f1b7f#
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
PWD=/root
 
[OK]    T009: udocker run c7 env|sort
------------------------------------------------------------>
execmode: P1
nvidiamode: False
 
[OK]    T010: udocker setup ub18
------------------------------------------------------------>
 
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: env
TERM=xterm-256color
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PROOT_TMP_DIR=/tmp
USERNAME=root
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
SHLVL=0
container_names=ub18
LOGNAME=root
USER=root
HOME=/root
container_execmode=P1
container_ruser=lauscher
PS1=73474c75#
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
PWD=/root
 
[OK]    T011: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = P2
 
[OK]    T006: udocker setup --execmode=P2 jv
------------------------------------------------------------>
 
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: java
proot info: vpid 2: terminated with signal 11
proot info: vpid 1: terminated with signal 11
 
[FAIL]    T007: udocker run jv java -version
------------------------------------------------------------>
 
[OK]    T012: udocker setup --execmode=P2 c7
------------------------------------------------------------>
 
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: env
TERM=xterm-256color
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PROOT_TMP_DIR=/tmp
USERNAME=root
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
SHLVL=0
container_names=c7
PROOT_NO_SECCOMP=1
LOGNAME=root
USER=root
HOME=/root
container_execmode=P2
container_ruser=lauscher
PS1=c02f1b7f#
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
PWD=/root
 
[OK]    T013: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T014: udocker setup --execmode=P2 ub18
------------------------------------------------------------>
 
 ****************************************************************************** 
 *                                                                            * 
 *               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                * 
 *                                                                            * 
 ****************************************************************************** 
 executing: env
TERM=xterm-256color
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PROOT_TMP_DIR=/tmp
USERNAME=root
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
SHLVL=0
container_names=ub18
PROOT_NO_SECCOMP=1
LOGNAME=root
USER=root
HOME=/root
container_execmode=P2
container_ruser=lauscher
PS1=73474c75#
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
PWD=/root
 
[OK]    T015: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = F1
 
[OK]    T016: udocker setup --execmode=F1 c7
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F1
HOME=/
PS1=c02f1b7f\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
TERM=xterm-256color
FAKECHROOT_DIR_MAP=/tmp/udocker-22737-af9ff3c4-7d20-3199-9c76-ab78126e0720-passwd!/etc/passwd:/tmp/udocker-22737-e5b03e5f-446b-31e5-a2b6-39f2cbe623b7-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
container_ruser=lauscher
container_names=c7
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-CentOS-7-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
FAKECHROOT_ELFLOADER=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64/ld-linux-x86-64.so.2
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T017: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T018: udocker setup --execmode=F1 ub18
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F1
HOME=/
PS1=73474c75\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
TERM=xterm-256color
FAKECHROOT_DIR_MAP=/tmp/udocker-22749-1f87db2b-1c7e-3fc9-bea3-438a2887d293-passwd!/etc/passwd:/tmp/udocker-22749-fcf69c43-f236-3bc0-be67-48d9a81da9c8-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
container_ruser=lauscher
container_names=ub18
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-Ubuntu-18-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
FAKECHROOT_ELFLOADER=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64/ld-linux-x86-64.so.2
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T019: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = F2
 
[OK]    T016: udocker setup --execmode=F2 c7
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F2
HOME=/
PS1=c02f1b7f\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
TERM=xterm-256color
FAKECHROOT_DIR_MAP=/tmp/udocker-22763-d73221dd-9ec4-353b-802d-49733bb6a25b-passwd!/etc/passwd:/tmp/udocker-22763-23c4bc2c-a7a7-33b3-80d4-d0c5e64541b2-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
LD_LIBRARY_REAL=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
FAKECHROOT_LIBRARY_ORIG=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
container_ruser=lauscher
container_names=c7
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-CentOS-7-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
FAKECHROOT_ELFLOADER=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64/ld-linux-x86-64.so.2
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T017: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T018: udocker setup --execmode=F2 ub18
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F2
HOME=/
PS1=73474c75\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
TERM=xterm-256color
FAKECHROOT_DIR_MAP=/tmp/udocker-22771-fec6f6c3-d58b-37e9-a431-cf3d2873a882-passwd!/etc/passwd:/tmp/udocker-22771-f9d2e067-15f5-38d5-9d2c-73b6f05d2e7d-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
LD_LIBRARY_REAL=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
FAKECHROOT_LIBRARY_ORIG=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
container_ruser=lauscher
container_names=ub18
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-Ubuntu-18-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
FAKECHROOT_ELFLOADER=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64/ld-linux-x86-64.so.2
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T019: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = F3
 
[OK]    T006: udocker setup --execmode=F3 jv
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                # 
 #                                                                            # 
 ############################################################################## 
 executing: java
openjdk version "1.8.0_111"
OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-2~bpo8+1-b14)
OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)
 
[OK]    T007: udocker run jv java -version
------------------------------------------------------------>
 
[OK]    T016: udocker setup --execmode=F3 c7
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F3
HOME=/
PS1=c02f1b7f\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
TERM=xterm-256color
FAKECHROOT_DIR_MAP=/tmp/udocker-25989-002088b0-e56d-31ff-95f6-f21874008577-passwd!/etc/passwd:/tmp/udocker-25989-b9c5e6a5-ed6c-30c8-9ea3-f2135e2e3ae6-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
LD_LIBRARY_REAL=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
FAKECHROOT_LIBRARY_ORIG=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
container_ruser=lauscher
container_names=c7
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-CentOS-7-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T017: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T018: udocker setup --execmode=F3 ub18
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F3
HOME=/
PS1=73474c75\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
TERM=xterm-256color
FAKECHROOT_DIR_MAP=/tmp/udocker-26581-a84646fe-b20f-373b-9443-b2ce5006110d-passwd!/etc/passwd:/tmp/udocker-26581-aeec5786-6df8-3391-9b88-1e2e4abb806b-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
LD_LIBRARY_REAL=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
FAKECHROOT_LIBRARY_ORIG=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
container_ruser=lauscher
container_names=ub18
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-Ubuntu-18-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T019: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = F4
 
[OK]    T006: udocker setup --execmode=F4 jv
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                # 
 #                                                                            # 
 ############################################################################## 
 executing: java
openjdk version "1.8.0_111"
OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-2~bpo8+1-b14)
OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)
 
[OK]    T007: udocker run jv java -version
------------------------------------------------------------>
 
[OK]    T016: udocker setup --execmode=F4 c7
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
FAKECHROOT_PATCH_PATCHELF=/home/lauscher/.udocker/bin/patchelf-x86_64
FAKECHROOT_PATCH_LAST_TIME=1624009865
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F4
HOME=/
PS1=c02f1b7f\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
TERM=xterm-256color
FAKECHROOT_PATCH_ELFLOADER=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64/ld-linux-x86-64.so.2
FAKECHROOT_DIR_MAP=/tmp/udocker-26614-b9c06096-f0a0-36fa-9e2c-f4a8724ca884-passwd!/etc/passwd:/tmp/udocker-26614-f70f9cf1-b2f8-3b6a-bb53-b4dd0d4cf1af-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
LD_LIBRARY_REAL=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
FAKECHROOT_LIBRARY_ORIG=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/libexec/coreutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/gconv:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/sasl2:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/nss:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/elfutils:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/python2.7/site-packages:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/openssl/engines:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/rtkaio:/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT/usr/lib64/libuser:.
container_ruser=lauscher
container_names=c7
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-CentOS-7-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T017: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T018: udocker setup --execmode=F4 ub18
------------------------------------------------------------>
 
 ############################################################################## 
 #                                                                            # 
 #               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                # 
 #                                                                            # 
 ############################################################################## 
 executing: env
FAKECHROOT_PATCH_PATCHELF=/home/lauscher/.udocker/bin/patchelf-x86_64
FAKECHROOT_PATCH_LAST_TIME=1624009882
LOGNAME=lauscher
USER=lauscher
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_execmode=F4
HOME=/
PS1=73474c75\$
LD_LIBRARY_PATH=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
TERM=xterm-256color
FAKECHROOT_PATCH_ELFLOADER=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64/ld-linux-x86-64.so.2
FAKECHROOT_DIR_MAP=/tmp/udocker-26625-7656cb58-13e4-34b8-b5e1-9c015be1372b-passwd!/etc/passwd:/tmp/udocker-26625-4aa4c036-4835-305d-864f-88f9a262abf3-group!/etc/group
SHLVL=0
FAKECHROOT_EXCLUDE_PATH=/dev:/proc:/sys:/etc/resolv.conf:/etc/host.conf:/lib/modules
LD_LIBRARY_REAL=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
FAKECHROOT_LIBRARY_ORIG=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib64:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT//lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/gconv:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/usr/lib/x86_64-linux-gnu/coreutils:/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT/lib/x86_64-linux-gnu:.
container_ruser=lauscher
container_names=ub18
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
USERNAME=lauscher
FAKECHROOT_BASE=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
LD_PRELOAD=/home/lauscher/.udocker/lib/libfakechroot-Ubuntu-18-x86_64.so
FAKECHROOT_EXPAND_SYMLINKS=none
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
PWD=/
FAKECHROOT_AF_UNIX_PATH=/tmp
PROOT_TMP_DIR=/tmp
FAKECHROOT=true
FAKECHROOT_VERSION=2.18.1
 
[OK]    T019: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = R1
 
[OK]    T006: udocker setup --execmode=R1 jv
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: java
openjdk version "1.8.0_111"
OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-2~bpo8+1-b14)
OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)
 
[OK]    T007: udocker run jv java -version
------------------------------------------------------------>
 
[OK]    T020: udocker setup --execmode=R1 c7
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: env
USERNAME=root
TERM=xterm-256color
PS1=c02f1b7f#
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
SHLVL=0
container_names=c7
LOGNAME=root
USER=root
HOME=/root
container_execmode=R1
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_ruser=lauscher
PROOT_TMP_DIR=/tmp
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
 
[OK]    T021: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T022: udocker setup --execmode=R1 ub18
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: env
USERNAME=root
TERM=xterm-256color
PS1=73474c75#
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
SHLVL=0
container_names=ub18
LOGNAME=root
USER=root
HOME=/root
container_execmode=R1
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_ruser=lauscher
PROOT_TMP_DIR=/tmp
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
 
[OK]    T023: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = R2
 
[OK]    T006: udocker setup --execmode=R2 jv
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: java
openjdk version "1.8.0_111"
OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-2~bpo8+1-b14)
OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)
 
[OK]    T007: udocker run jv java -version
------------------------------------------------------------>
 
[OK]    T024: udocker setup --execmode=R2 c7
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: env
USERNAME=root
TERM=xterm-256color
PS1=c02f1b7f#
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
SHLVL=0
container_names=c7
LOGNAME=root
USER=root
HOME=/root
container_execmode=R2
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_ruser=lauscher
PROOT_TMP_DIR=/tmp
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
PROOT_NO_SECCOMP=1
PWD=/root
 
[OK]    T025: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T026: udocker setup --execmode=R2 ub18
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: env
USERNAME=root
TERM=xterm-256color
PS1=73474c75#
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
SHLVL=0
container_names=ub18
LOGNAME=root
USER=root
HOME=/root
container_execmode=R2
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_ruser=lauscher
PROOT_TMP_DIR=/tmp
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
PROOT_NO_SECCOMP=1
PWD=/root
 
[OK]    T027: udocker run ub18 env|sort
------------------------------------------------------------>
===================================== execmode = R3
 
[OK]    T006: udocker setup --execmode=R3 jv
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING 4d89fa47-3cb1-33c1-b623-0a2195cd31a9                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: java
openjdk version "1.8.0_111"
OpenJDK Runtime Environment (build 1.8.0_111-8u111-b14-2~bpo8+1-b14)
OpenJDK 64-Bit Server VM (build 25.111-b14, mixed mode)
 
[OK]    T007: udocker run jv java -version
------------------------------------------------------------>
 
[OK]    T028: udocker setup --execmode=R3 c7
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING c02f1b7f-2124-3322-be7b-7b2a5dca66b1                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: env
USERNAME=root
TERM=xterm-256color
PS1=c02f1b7f#
container_uuid=c02f1b7f-2124-3322-be7b-7b2a5dca66b1
SHLVL=0
container_names=c7
LOGNAME=root
USER=root
HOME=/root
container_execmode=R3
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_ruser=lauscher
PROOT_TMP_DIR=/tmp
container_root=/home/lauscher/.udocker/containers/c02f1b7f-2124-3322-be7b-7b2a5dca66b1/ROOT
PROOT_NO_SECCOMP=1
PWD=/root
 
[OK]    T029: udocker run c7 env|sort
------------------------------------------------------------>
 
[OK]    T030: udocker setup --execmode=R3 ub18
------------------------------------------------------------>
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 %                                                                            % 
 %               STARTING 73474c75-0894-3b4a-99e2-ed56b0cffaf7                % 
 %                                                                            % 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 executing: env
USERNAME=root
TERM=xterm-256color
PS1=73474c75#
container_uuid=73474c75-0894-3b4a-99e2-ed56b0cffaf7
SHLVL=0
container_names=ub18
LOGNAME=root
USER=root
HOME=/root
container_execmode=R3
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
container_ruser=lauscher
PROOT_TMP_DIR=/tmp
container_root=/home/lauscher/.udocker/containers/73474c75-0894-3b4a-99e2-ed56b0cffaf7/ROOT
PROOT_NO_SECCOMP=1
PWD=/root
 
[OK]    T031: udocker run ub18 env|sort
------------------------------------------------------------>
$ echo $?
0

jorge-lip · 2021-06-18T15:43:37Z

The two test scripts have been improved to display a summary of the failed tests upon exit, when failures occur. The exit status also reflects the errors.

mviereck · 2021-06-18T18:31:15Z

The two test scripts have been improved to display a summary of the failed tests upon exit, when failures occur. The exit status also reflects the errors.

Great!
Just did a test run with udocker-test.sh. It shows some curl timeout errors, but overall success. Is that correct?

$ ./udocker_test.sh
=================================================
* This script tests all udocker CLI and options *
* except the run command and vol. mount options *
=================================================
Info: creating repo: /home/lauscher/.udocker
Info: udocker command line interface 1.3.0
Info: searching for udockertools 1.2.8
Info: installing udockertools 1.2.8
Info: installation of udockertools successful
/home/lauscher/.udocker/bin/proot-x86_64
 
[OK]    T001: udocker install
------------------------------------------------------------>
Info: udocker command line interface 1.3.0
Info: searching for udockertools 1.2.8
Info: installing udockertools 1.2.8
Info: installation of udockertools successful
 
[OK]    T002: udocker install --force
------------------------------------------------------------>

Syntax:
  udocker  [general_options] <command>  [command_options]  <command_args>

  udocker [-h|--help|help]        :Display this help and exits
  udocker [-V|--version|version]  :Display udocker and tarball version and exits

General options common to all commands must appear before the command:
  -D, --debug                   :Debug
  -q, --quiet                   :Less verbosity
  --insecure                    :Allow insecure non authenticated https
  --repo=<directory>            :Use repository at directory
  --allow-root                  :Allow execution by root NOT recommended
  --config=<conf_file>          :Use configuration <conf_file>

Commands:
  --help [command]              :Command specific help
  showconf                      :Print all configuration options

  search <repo/expression>      :Search dockerhub for container images
  pull <repo/image:tag>         :Pull container image from dockerhub
  create <repo/image:tag>       :Create container from a pulled image
  run <container_id|name>       :Execute created container
  run <repo/image:tag>          :Pull, create and execute container

  images -l                     :List container images
  ps -m -s                      :List created containers
  name <container_id> <name>    :Give name to container
  rmname <name>                 :Delete name from container
  rename <name> <new_name>      :Change container name
  clone <container_id>          :Duplicate container
  rm  <container-id|name>       :Delete container
  rmi <repo/image:tag>          :Delete image

  import <tar> <repo/image:tag> :Import tar file (exported by docker)
  import - <repo/image:tag>     :Import from stdin (exported by docker)
  export -o <tar> <container>   :Export container directory tree to file
  export - <container>          :Export container directory tree to stdin
  load -i <exported-image>      :Load image from file (saved by docker)
  load                          :Load image from stdin (saved by docker)
  save -o <imagefile> <repo/image:tag>  :Save image with layers to file

  inspect -p <repo/image:tag>   :Return low level information on image
  verify <repo/image:tag>       :Verify a pulled image

  protect <repo/image:tag>      :Protect repository
  unprotect <repo/image:tag>    :Unprotect repository
  protect <container>           :Protect container
  unprotect <container>         :Unprotect container

  mkrepo <top-repo-dir>         :Create another repository in location
  setup --execmode=<mode>       :Change container execution mode
  setup --nvidia                :Setup container to use nvidia GPU
  setup --purge                 :clean mountpoints and files created by udocker
  setup --fixperm               :attempt to fix file permissions

  login                         :Login into docker repository
  logout                        :Logout from docker repository

Examples:
  udocker search expression
  udocker search quay.io/expression
  udocker search --list-tags myimage
  udocker pull myimage:mytag
  udocker images
  udocker create --name=mycontainer  myimage:mytag
  udocker ps -m -s
  udocker inspect mycontainer
  udocker inspect -p mycontainer

  udocker run  mycontainer  cat /etc/redhat-release
  udocker run --hostauth --hostenv --bindhome  mycontainer
  udocker run --user=root  mycontainer  yum install firefox
  udocker run --hostauth --hostenv --bindhome mycontainer  firefox
  udocker run --entrypoint="" mycontainer  /bin/bash -i
  udocker run --entrypoint="/bin/bash" mycontainer -i

  udocker clone --name=anotherc mycontainer
  udocker rm anotherc

  udocker mkrepo /data/myrepo
  udocker --repo=/data/myrepo load -i docker-saved-repo.tar
  udocker --repo=/data/myrepo images
  udocker --repo=/data/myrepo run --user=$USER  myimage:mytag

  udocker export -o myimage.tar mycontainer
  udocker import myimage.tar mynewimage
  udocker create --name=mynewc mynewimage
  udocker export --clone -o mycontainer.tar mycontainer
  udocker import --clone mycontainer.tar

Notes:
 * by default the binaries, images and containers are placed in
      $HOME/.udocker
 * by default the following host directories are mounted in the
   container:
      /dev /proc /sys /etc/resolv.conf /etc/host.conf /etc/hostname
 * to prevent the mount of the above directories use:
      run  --nosysdirs  <container>
 * additional host directories to be mounted are specified with:
      run --volume=/data:/mnt --volume=/etc/hosts  <container>
      run --nosysdirs --volume=/dev --volume=/proc  <container>
 * udocker provides several execution modes that offer different
   approaches and technologies to execute containers, they
   can be selected using the setup command. See the setup help.
      udocker setup --execmode=F3 fedx
      udocker setup --execmode=R1 fedx
      udocker setup --execmode=S1 fedx
      udocker setup --help
 * udocker facilitates the usage of nvidia drivers within containers
      udocker setup --nvidia fedx

See: https://github.com/indigo-dc/udocker/blob/master/SUMMARY.md
            
 
[OK]    T003: udocker (with no options)
------------------------------------------------------------>
 
[OK]    T004: udocker help
------------------------------------------------------------>
 
[OK]    T005: udocker -h
------------------------------------------------------------>
--------------------------------------------------------------------------------
		Configuration options
docdir = None
invalid_host_env = ('VTE_VERSION',)
cmd = ['/bin/bash', '-i']
dockerio_index_url = https://hub.docker.com
cpu_affinity_exec_tools = (['numactl', '-C', '%s', '--'], ['taskset', '-c', '%s'])
proot_killonexit = True
lib_dirs_list_append = ('.',)
http_proxy = 
sysdirs_list = ('/dev', '/proc', '/sys', '/etc/resolv.conf', '/etc/host.conf', '/lib/modules')
use_proot_executable = UDOCKER
use_curl_executable = 
lib_dirs_list_x86_64 = ('/usr/lib/x86_64-linux-gnu', '/usr/lib64')
mountpoint_prefixes = ('/etc',)
tarball_release = 1.2.8
nvi_lib_list = ['libOpenCL.', 'libcuda.', 'libnvcuvid.', 'libnvidia-cfg.', 'libnvidia-compiler.', 'libnvidia-encode.', 'libnvidia-fatbinaryloader.', 'libnvidia-fbc.', 'libnvidia-ifr.', 'libnvidia-ml.', 'libnvidia-opencl.', 'libnvidia-ptxjitcompiler.', 'libnvidia-tls.', 'tls/libnvidia-tls.']
tmpdir = /tmp
nvi_etc_list = ['vulkan/icd.d/nvidia_icd.json', 'OpenCL/vendors/nvidia.icd']
keystore = keystore
dri_list = ('/usr/lib64/dri', '/lib64/dri', '/usr/lib/dri', '/lib/dri')
runc_nomqueue = None
http_agent = 
homedir = /home/lauscher/.udocker
fakechroot_expand_symlinks = none
lib_dirs_list_essential = ('/lib/x86_64-linux-gnu', '/usr/lib/x86_64-linux-gnu', '/lib64', '/usr/lib64', '/lib', '/usr/lib')
use_singularity_executable = 
libdir = None
tarball = https://download.ncg.ingrid.pt/webdav/udocker/udocker-englib-1.2.8.tar.gz https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-englib-1.2.8.tar.gz
nvi_dev_list = ['/dev/nvidia']
installretry = 3
dockerio_registry_url = https://registry.hub.docker.com
http_insecure = False
layersdir = None
config = udocker.conf
singularity_options = ['-w']
bindir = None
location = 
valid_host_env = ('TERM', 'PATH', 'PROOT_TMP_DIR')
verbose_level = 3
timeout = 12
proot_noseccomp = None
runc_capabilities = ['CAP_KILL', 'CAP_NET_BIND_SERVICE', 'CAP_CHOWN', 'CAP_DAC_OVERRIDE', 'CAP_FOWNER', 'CAP_FSETID', 'CAP_KILL', 'CAP_SETGID', 'CAP_SETUID', 'CAP_SETPCAP', 'CAP_NET_BIND_SERVICE', 'CAP_NET_RAW', 'CAP_SYS_CHROOT', 'CAP_MKNOD', 'CAP_AUDIT_WRITE', 'CAP_SETFCAP']
download_timeout = 1800
default_execution_mode = P1
ld_so_cache = /etc/ld.so.cache
installinfo = ['https://raw.githubusercontent.com/indigo-dc/udocker/master/messages']
use_runc_executable = 
fakechroot_so = None
autoinstall = True
docker_registries = {'docker.io': ['https://registry.hub.docker.com', 'https://hub.docker.com']}
topdir = /home/lauscher/.udocker
containersdir = None
root_path = /usr/sbin:/sbin:/usr/bin:/bin
reposdir = None
nvi_bin_list = ['nvidia-bug-report.sh', 'nvidia-cuda-mps-control', 'nvidia-cuda-mps-server', 'nvidia-debugdump', 'nvidia-installer', 'nvidia-persistenced', 'nvidia-settings', 'nvidia-smi', 'nvidia-uninstall', 'nvidia-xconfig']
user_path = /usr/local/bin:/usr/bin:/bin
ctimeout = 6
access_files = ('/sys/class/infiniband', '/dev/open-mx', '/dev/myri0', '/dev/myri1', '/dev/myri2', '/dev/myri3', '/dev/myri4', '/dev/myri5', '/dev/myri6', '/dev/myri7', '/dev/myri8', '/dev/myri9', '/dev/ipath', '/dev/kgni0', '/dev/mic/scif', '/dev/scif')
--------------------------------------------------------------------------------
 
[OK]    T006: udocker showconf
------------------------------------------------------------>
version: 1.3.0
tarball: https://download.ncg.ingrid.pt/webdav/udocker/udocker-englib-1.2.8.tar.gz https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-englib-1.2.8.tar.gz
tarball_release: 1.2.8
 
[OK]    T007: udocker version
------------------------------------------------------------>
Info: using curl executable 
version: 1.3.0
tarball: https://download.ncg.ingrid.pt/webdav/udocker/udocker-englib-1.2.8.tar.gz https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-englib-1.2.8.tar.gz
tarball_release: 1.2.8
 
[OK]    T008: udocker -D version
------------------------------------------------------------>
version: 1.3.0
tarball: https://download.ncg.ingrid.pt/webdav/udocker/udocker-englib-1.2.8.tar.gz https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-englib-1.2.8.tar.gz
tarball_release: 1.2.8
 
[OK]    T009: udocker --quiet version
------------------------------------------------------------>
version: 1.3.0
tarball: https://download.ncg.ingrid.pt/webdav/udocker/udocker-englib-1.2.8.tar.gz https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-englib-1.2.8.tar.gz
tarball_release: 1.2.8
 
[OK]    T010: udocker -q version
------------------------------------------------------------>
Info: using curl executable 
version: 1.3.0
tarball: https://download.ncg.ingrid.pt/webdav/udocker/udocker-englib-1.2.8.tar.gz https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-englib-1.2.8.tar.gz
tarball_release: 1.2.8
 
[OK]    T011: udocker --debug version
------------------------------------------------------------>
 
[OK]    T012: udocker -V
------------------------------------------------------------>
 
[OK]    T013: udocker --version
------------------------------------------------------------>
gromacs/gromacs                                             ---- GROMACS molecular dynamics simulations                                     5
gromacs/gmx-configurations                                  ---- GROMACS built in different configurations, used in builder pattern for     0
gromacs/ci-docs-llvm-master                                 ----                                                                            0
gromacs/cmake-3.13.0-llvm-8-tsan-master                     ----                                                                            0
gromacs/cmake-3.15.7-llvm-9-openmpi-master                  ----                                                                            0
gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master     ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi-master     ----                                                                            1
gromacs/ci-docs-llvm                                        ----                                                                            0
gromacs/cmake-3.17.2-oneapi-2021.1-beta08-master            ----                                                                            0
gromacs/fftw                                                ---- Containerized libfftw for use in containerized builds of GROMACS using     0
gromacs/ci-ubuntu-18.04-llvm-8-tsan                         ----                                                                            0
gromacs/cmake-3.15.7-llvm-9-openmpi                         ----                                                                            0
gromacs/ci-ubuntu-18.04-llvm-9                              ----                                                                            0
gromacs/cmake-3.17.2-oneapi-2021.1-beta09-master            ----                                                                            0
gromacs/ci-ubuntu-18.04-llvm-7-docs                         ----                                                                            0
gromacs/ci-ubuntu-18.04-gcc-8-cuda-11.0                     ----                                                                            0
gromacs/ci-ubuntu-18.04-gcc-7-oneapi-2021.1-beta09          ----                                                                            0
gromacs/ci-ubuntu-18.04-gcc-7                               ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-intelopencl-openmpi             ----                                                                            0
gromacs/cmake-3.13.0-llvm-8-tsan                            ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi-master     ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi-master        ----                                                                            0
gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi          ----                                                                            0
gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.0                    ----                                                                            0
gromacs/continuous-integration                              ---- Storage of images used for running CI jobs                                 0
gromacs/gitlab-runner                                       ----                                                                            0
gromacs/cmake-3.11.4-llvm-8-openmpi                         ----                                                                            0
gromacs/cmake-3.9.6-gcc-5-cuda-9.0-openmpi                  ----                                                                            0
gromacs/ci-clang-7                                          ----                                                                            0
gromacs/gitlab-runner-helper                                ----                                                                            0
gromacs/ci-gcc-7                                            ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-10.1-nvidiaopencl-clfft-openmpi     ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-tsan                            ----                                                                            0
gromacs/ci-docs-gcc                                         ----                                                                            0
gromacs/cmake-3.9.6-gcc-6-cuda-10.1-nvidiaopencl-clfft-openmpi     ----                                                                            0
gromacs/cmake-3.9.6-gcc-7-amdopencl-clfft-openmpi           ----                                                                            0
gromacs/base                                                ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-cuda-10.1-openmpi               ----                                                                            0
gromacs/ci-ubuntu-20.04-gcc-10                              ----                                                                            0
Error: in download: curl: (28) Operation timed out after 6000 milliseconds with 0 out of 0 bytes received

gromacs/ci-gcc-8                                            ----                                                                            0
gromacs/cmake-3.9.6-llvm-3.6-amdopencl-openmpi              ----                                                                            0
gromacs/ci-docs-clang                                       ----                                                                            0
gromacs/ci-clang-6                                          ----                                                                            0
gromacs/ci-clang-8                                          ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-10.1-openmpi                ----                                                                            0
gromacs/ci-gcc-8-cuda-10.2                                  ----                                                                            0
gromacs/cmake-3.13.0-llvm-9-amdopencl                       ----                                                                            0
gromacs/ci-ubuntu-18.04-llvm-8-cuda-11.0                    ----                                                                            0
gromacs/cmake-3.13.0-llvm-9-amdopencl-openmpi               ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-11.0-nvidiaopencl-clfft-openmpi     ----                                                                            0
gromacs/cmake-3.13.0-llvm-9-intelopencl-openmpi             ----                                                                            0
gromacs/cmake-3.9.6-gcc-9-cuda-10.0-openmpi                 ----                                                                            0
gromacs/ci-ubuntu-18.04-gcc-9                               ----                                                                            0
gromacs/cmake-3.9.6-llvm-8-amdopencl-openmpi                ----                                                                            0
gromacs/ci-gcc-5                                            ----                                                                            0
gromacs/ci-gcc-6                                            ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-cuda-10.0-openmpi               ----                                                                            0
gromacs/cmake-3.15.7-icc-19.1-openmpi                       ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-cuda-10.1-mpi                   ----                                                                            0
gromacs/cmake-3.11.4-llvm-3                                 ----                                                                            0
gromacs/cmake-3.13.0-llvm-9-intelopencl-openmpi-master      ----                                                                            0
gromacs/gmx-multimage                                       ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-10.1                        ----                                                                            0
gromacs/cmake-3.17.2-oneapi-2021.1-beta08                   ----                                                                            0
gromacs/ci-ubuntu-18.04-gcc-7-cuda-10.2                     ----                                                                            0
Error: in download: curl: (28) Operation timed out after 6000 milliseconds with 0 out of 0 bytes received

gromacs/cmake-3.9.6-gcc-6-cuda-10.1-opencl-clfft-mpi        ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-intel-opencl                    ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-cuda-10.0-openmpi-master        ----                                                                            0
gromacs/cmake-3.15.7-llvm-9                                 ----                                                                            0
gromacs/cmake-3.15.7-llvm-8-cuda-10.0-mpi                   ----                                                                            0
gromacs/ci-ubuntu-18.04-llvm-8-cuda-10.1                    ----                                                                            0
gromacs/cmake-3.13.0-gcc-7-cuda-9.0-mpi                     ----                                                                            0
gromacs/cmake-3.13.0-llvm-9-amdopencl-openmpi-master        ----                                                                            0
gromacs/cmake-3.13.0-llvm-9-intel-opencl                    ----                                                                            0
gromacs/cmake-3.15.7-gcc-8-cuda-10.1-opencl-clfft-mpi       ----                                                                            0
gromacs/cmake-3.9.6-gcc-5-cuda-9-mpi                        ----                                                                            0
gromacs/cmake-3.15.7-llvm-9-cuda-10.2-mpi                   ----                                                                            0
gromacs/cmake-3.9.6-gcc-9-cuda-10.0-mpi                     ----                                                                            0
 
[OK]    T014: udocker search -a
------------------------------------------------------------>
Info: downloading layer sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
 
[OK]    T015: udocker pull ubuntu:18.04
------------------------------------------------------------>
Error: in download: curl: (28) Operation timed out after 6000 milliseconds with 0 out of 0 bytes received

Info: downloading layer sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
 
[OK]    T016: udocker --insecure pull ubuntu:18.04
------------------------------------------------------------>
Info: verifying: ubuntu:18.04
Info: loading structure
Info: verifying layers
Info: layer ok: sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: layer ok: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: image Ok
 
[OK]    T017: udocker verify ubuntu:18.04
------------------------------------------------------------>
REPOSITORY
ubuntu:18.04                                                 .
 
[OK]    T018: udocker images
------------------------------------------------------------>
{
    "architecture": "amd64",
    "config": {
        "AttachStderr": false,
        "AttachStdin": false,
        "AttachStdout": false,
        "Cmd": [
            "bash"
        ],
        "Domainname": "",
        "Entrypoint": null,
        "Env": [
            "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
        ],
        "Hostname": "",
        "Image": "sha256:d207f9055fcf01ac5c8231b88b56098a667475e94547cedc334c8c7c2ef8f22b",
        "Labels": null,
        "OnBuild": null,
        "OpenStdin": false,
        "StdinOnce": false,
        "Tty": false,
        "User": "",
        "Volumes": null,
        "WorkingDir": ""
    },
    "container": "49ae0ef29bbebdcfb000569e222fd2ffbc8d8762ca8a9a419159a042c26377d1",
    "container_config": {
        "AttachStderr": false,
        "AttachStdin": false,
        "AttachStdout": false,
        "Cmd": [
            "/bin/sh",
            "-c",
            "#(nop) ",
            "CMD [\"bash\"]"
        ],
        "Domainname": "",
        "Entrypoint": null,
        "Env": [
            "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
        ],
        "Hostname": "49ae0ef29bbe",
        "Image": "sha256:d207f9055fcf01ac5c8231b88b56098a667475e94547cedc334c8c7c2ef8f22b",
        "Labels": {},
        "OnBuild": null,
        "OpenStdin": false,
        "StdinOnce": false,
        "Tty": false,
        "User": "",
        "Volumes": null,
        "WorkingDir": ""
    },
    "created": "2021-06-17T23:31:22.471354017Z",
    "docker_version": "19.03.12",
    "id": "7ec2fc34c6353200971345f1378d3c65adbb22d65182d3df19e8dccf64ab16b4",
    "os": "linux",
    "parent": "11374178a4566afd7c1017ef6338ce343308f0c051bfd403e09d6d83c430eefd",
    "throwaway": true
}
 
[OK]    T019: udocker inspect (image)
------------------------------------------------------------>
ContainerID = 1ce33a4c-3d57-3af1-aab5-64f71536555d
 
[OK]    T020: udocker create ubuntu:18.04
------------------------------------------------------------>
 
[OK]    T021: udocker create --name=ubuntu ubuntu:18.04
------------------------------------------------------------>
CONTAINER ID                         P M NAMES              IMAGE               
1ce33a4c-3d57-3af1-aab5-64f71536555d . W                    ubuntu:18.04        
741dd2d4-cb26-35f3-8c48-d04e028e5158 . W ['ubuntu']         ubuntu:18.04        
 
[OK]    T022: udocker ps
------------------------------------------------------------>
1ce33a4c-3d57-3af1-aab5-64f71536555d . W ['conti']          ubuntu:18.04        
 
[OK]    T023: udocker name 1ce33a4c-3d57-3af1-aab5-64f71536555d
------------------------------------------------------------>
Info: container name: conti removed.
1ce33a4c-3d57-3af1-aab5-64f71536555d . W                    ubuntu:18.04        
 
[OK]    T024: udocker rmname
------------------------------------------------------------>
{
    "architecture": "amd64",
    "config": {
        "AttachStderr": false,
        "AttachStdin": false,
        "AttachStdout": false,
        "Cmd": [
            "bash"
        ],
        "Domainname": "",
        "Entrypoint": null,
        "Env": [
            "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
        ],
        "Hostname": "",
        "Image": "sha256:d207f9055fcf01ac5c8231b88b56098a667475e94547cedc334c8c7c2ef8f22b",
        "Labels": null,
        "OnBuild": null,
        "OpenStdin": false,
        "StdinOnce": false,
        "Tty": false,
        "User": "",
        "Volumes": null,
        "WorkingDir": ""
    },
    "container": "49ae0ef29bbebdcfb000569e222fd2ffbc8d8762ca8a9a419159a042c26377d1",
    "container_config": {
        "AttachStderr": false,
        "AttachStdin": false,
        "AttachStdout": false,
        "Cmd": [
            "/bin/sh",
            "-c",
            "#(nop) ",
            "CMD [\"bash\"]"
        ],
        "Domainname": "",
        "Entrypoint": null,
        "Env": [
            "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
        ],
        "Hostname": "49ae0ef29bbe",
        "Image": "sha256:d207f9055fcf01ac5c8231b88b56098a667475e94547cedc334c8c7c2ef8f22b",
        "Labels": {},
        "OnBuild": null,
        "OpenStdin": false,
        "StdinOnce": false,
        "Tty": false,
        "User": "",
        "Volumes": null,
        "WorkingDir": ""
    },
    "created": "2021-06-17T23:31:22.471354017Z",
    "docker_version": "19.03.12",
    "id": "7ec2fc34c6353200971345f1378d3c65adbb22d65182d3df19e8dccf64ab16b4",
    "os": "linux",
    "parent": "11374178a4566afd7c1017ef6338ce343308f0c051bfd403e09d6d83c430eefd",
    "throwaway": true
}
 
[OK]    T025: udocker inspect (container 1ce33a4c-3d57-3af1-aab5-64f71536555d)
------------------------------------------------------------>
3670a0ac-91bb-33c1-8003-7d216071f8af
 
[OK]    T026: udocker clone --name=myclone 1ce33a4c-3d57-3af1-aab5-64f71536555d
------------------------------------------------------------>
Info: exporting to file myexportcont.tar
 
[OK]    T027: udocker export -o myexportcont.tar 1ce33a4c-3d57-3af1-aab5-64f71536555d
------------------------------------------------------------>
Info: deleting container: 1ce33a4c-3d57-3af1-aab5-64f71536555d
 
[OK]    T028: udocker rm 1ce33a4c-3d57-3af1-aab5-64f71536555d
------------------------------------------------------------>
execmode: P1
nvidiamode: False
 
[OK]    T029: udocker setup ubuntu
------------------------------------------------------------>
 
[OK]    T030: udocker mkrepo /home/lauscher/.udocker-test-h45y7k9X
------------------------------------------------------------>
Info: udocker command line interface 1.3.0
Info: searching for udockertools 1.2.8
Info: installing udockertools 1.2.8
Info: installation of udockertools successful
Error: in download: curl: (28) Resolving timed out after 6000 milliseconds

Info: downloading layer sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: downloading layer sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
 
[OK]    T031: udocker --repo=/home/lauscher/.udocker-test-h45y7k9X pull ubuntu:18.04
------------------------------------------------------------>
Info: verifying: ubuntu:18.04
Info: loading structure
Info: verifying layers
Info: layer ok: sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: layer ok: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: image Ok
 
[OK]    T032: udocker --repo=/home/lauscher/.udocker-test-h45y7k9X verify ubuntu:18.04
------------------------------------------------------------>
Info: verifying: ubuntu:18.04
Info: loading structure
Info: verifying layers
Info: layer ok: sha256:25fa05cd42bd8fabb25d2a6f3f8c9f7ab34637903d00fd2ed1c1d0fa980427dd
Info: layer ok: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Info: image Ok
 
[OK]    T033: udocker --repo=/home/lauscher/.udocker-test-h45y7k9X verify ubuntu:18.04
------------------------------------------------------------>
Download a docker tar img file https://download.ncg.ingrid.pt/webdav/udocker_test/centos7.tar
--2021-06-18 18:58:23--  https://download.ncg.ingrid.pt/webdav/udocker_test/centos7.tar
Auflösen des Hostnamens download.ncg.ingrid.pt (download.ncg.ingrid.pt)… 194.210.120.220
Verbindungsaufbau zu download.ncg.ingrid.pt (download.ncg.ingrid.pt)|194.210.120.220|:443 … verbunden.
HTTP-Anforderung gesendet, auf Antwort wird gewartet … 200 OK
Länge: 209612288 (200M) [application/x-tar]
Wird in »centos7.tar« gespeichert.

centos7.tar         100%[===================>] 199,90M  87,6KB/s    in 42m 18s 

2021-06-18 19:40:43 (80,7 KB/s) - »centos7.tar« gespeichert [209612288/209612288]

------------------------------------------------------------>
Info: adding layer: 90162fd7e6fcf45916ddd8c41753f5b98c6a31d0c9366719c34f98aafe705ea7
centos:7
 
[OK]    T034: udocker load -i centos7.tar
------------------------------------------------------------>
 
[OK]    T035: udocker protect ubuntu (container)
------------------------------------------------------------>
Error: container is protected
 
[OK]    T036: udocker rm ubuntu (try to remove protected container)
------------------------------------------------------------>
 
[OK]    T037: udocker unprotect ubuntu (container)
------------------------------------------------------------>
Info: deleting container: 741dd2d4-cb26-35f3-8c48-d04e028e5158
 
[OK]    T038: udocker rm ubuntu (try to remove unprotected container)
------------------------------------------------------------>
Download a docker tar container file https://download.ncg.ingrid.pt/webdav/udocker_test/centos7-cont.tar
--2021-06-18 19:40:44--  https://download.ncg.ingrid.pt/webdav/udocker_test/centos7-cont.tar
Auflösen des Hostnamens download.ncg.ingrid.pt (download.ncg.ingrid.pt)… 194.210.120.220
Verbindungsaufbau zu download.ncg.ingrid.pt (download.ncg.ingrid.pt)|194.210.120.220|:443 … verbunden.
HTTP-Anforderung gesendet, auf Antwort wird gewartet … 200 OK
Länge: 209604096 (200M) [application/x-tar]
Wird in »centos7-cont.tar« gespeichert.

centos7-cont.tar    100%[===================>] 199,89M   129KB/s    in 38m 54s 

2021-06-18 20:19:39 (87,7 KB/s) - »centos7-cont.tar« gespeichert [209604096/209604096]

------------------------------------------------------------>
Info: added layer 8fbc80884152233e7f4e3ec8067eff271d45cad0bf6343a8612f05d8d710bedd
 
[OK]    T039: udocker import centos7-cont.tar mycentos1:latest
------------------------------------------------------------>
353ddc33-c13b-3d51-8cc4-091892915bbd
 
[OK]    T040: udocker import --tocontainer --name=mycont centos7-cont.tar
------------------------------------------------------------>
Warning: check container content: f520345f-bbb1-3784-b2bf-0f62a9e748ff
f520345f-bbb1-3784-b2bf-0f62a9e748ff
 
[OK]    T041: udocker import --clone --name=clone_cont centos7-cont.tar
------------------------------------------------------------>
Info: deleting image: ubuntu:18.04
 
[OK]    T042: udocker rmi ubuntu:18.04
------------------------------------------------------------>
CONTAINER ID                         P M MOD NAMES              IMAGE               
353ddc33-c13b-3d51-8cc4-091892915bbd . W P1 ['mycont']         IMPORTED:unknown    
f520345f-bbb1-3784-b2bf-0f62a9e748ff . W P1 ['clone_cont']     CLONING:inprogress  
3670a0ac-91bb-33c1-8003-7d216071f8af . W P1 ['myclone']        ubuntu:18.04        
 
[OK]    T043: udocker ps -m
------------------------------------------------------------>
CONTAINER ID                         P M MOD SIZE NAMES              IMAGE               
353ddc33-c13b-3d51-8cc4-091892915bbd . W P1   213 ['mycont']         IMPORTED:unknown    
f520345f-bbb1-3784-b2bf-0f62a9e748ff . W P1     1 ['clone_cont']     CLONING:inprogress  
3670a0ac-91bb-33c1-8003-7d216071f8af . W P1    69 ['myclone']        ubuntu:18.04        
 
[OK]    T044: udocker ps -s -m
------------------------------------------------------------>
REPOSITORY
centos:7                                                     .
  /home/lauscher/.udocker/repos/centos/7
    /90162fd7e6fcf45916ddd8c41753f5b98c6a31d0c9366719c34f98aafe705ea7.json (1 MB)
    /container.json (1 MB)
    /90162fd7e6fcf45916ddd8c41753f5b98c6a31d0c9366719c34f98aafe705ea7.layer (199 MB)
mycentos1:latest                                             .
  /home/lauscher/.udocker/repos/mycentos1/latest
    /8fbc80884152233e7f4e3ec8067eff271d45cad0bf6343a8612f05d8d710bedd.json (1 MB)
    /8fbc80884152233e7f4e3ec8067eff271d45cad0bf6343a8612f05d8d710bedd.layer (199 MB)
 
[OK]    T045: udocker images -l
------------------------------------------------------------>
Clean up files containers and images used in the tests
Info: deleting container: 353ddc33-c13b-3d51-8cc4-091892915bbd
Info: deleting container: f520345f-bbb1-3784-b2bf-0f62a9e748ff
Info: deleting container: 3670a0ac-91bb-33c1-8003-7d216071f8af
Info: deleting image: mycentos1
Info: deleting image: centos:7
------------------------------------------------------------>
[OK]    All tests passed

jorge-lip · 2021-06-18T21:20:29Z

Yes it is alerting of some TCP connect timeouts which means that your network must have some problems.
There is recovery for these errors, the operations are retried and it completes ok.

mviereck · 2021-06-18T21:43:46Z

There is recovery for these errors, the operations are retried and it completes ok.

Great! docker and podman just drop hours of download on such failures.

So far I am good with the tests and we can close here.

If it helps you, I would run nosetests -v --with-coverage --cover-package=udocker tests/unit again to show you the error messages it produced here. I cannot assess if they are harmless or important.

Remaining possible improvements, but I won't insist:

More obvious differenciation between code tests and user level tests.
Ability to run user level tests even with existing ~/.udocker.

jorge-lip · 2021-06-19T16:58:10Z

Thanks, Yes please, send us those error messages.
Ok we will make the tests differentiation more clear in the documentation
Regarding the ~/.udocker the best approach is for the user himself to rename .udocker to something else, run the tests and then move back the directory. We can add that to the documentation as well.

mviereck · 2021-06-20T09:07:57Z

Thanks, Yes please, send us those error messages.

nose.log

mariojmdavid · 2021-06-21T12:53:44Z

those are error messages from the code itself when the unit test passes though the branch containing that message and not a real error from the test.
nonetheless I have set the message level to 0 so as not to show any messages from the code in the execution of the unit tests, that commit will be done soon

mariojmdavid · 2021-06-21T14:31:46Z

solved in latest commit to master, only affected the unit tests

mviereck · 2021-06-23T18:22:31Z

Regarding the ~/.udocker the best approach is for the user himself to rename .udocker to something else, run the tests and then move back the directory. We can add that to the documentation as well.

This would be a good addition. I tried to set UDOCKER_DIR to a different folder, but that did not help.

those are error messages from the code itself when the unit test passes though the branch containing that message and not a real error from the test.

ok, I understand.

nonetheless I have set the message level to 0 so as not to show any messages from the code in the execution of the unit tests, that commit will be done soon

Set in the way you think it's best. I did not want to enforce a change here, just tried to understand.

Thank you for all this, I am good with the tests.

mariojmdavid · 2021-06-30T12:55:30Z

as per the last comment we will close this issue

mariojmdavid closed this as completed Jun 30, 2021

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[joss-review] tests #314

[joss-review] tests #314

vsoch commented May 20, 2021

mviereck commented May 20, 2021

mariojmdavid commented May 28, 2021

jorge-lip commented Jun 8, 2021

vsoch commented Jun 16, 2021

mariojmdavid commented Jun 17, 2021

vsoch commented Jun 17, 2021

mariojmdavid commented Jun 17, 2021

vsoch commented Jun 17, 2021

mviereck commented Jun 17, 2021

vsoch commented Jun 17, 2021

mviereck commented Jun 17, 2021

vsoch commented Jun 17, 2021

mariojmdavid commented Jun 18, 2021

mariojmdavid commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 19, 2021

mviereck commented Jun 20, 2021

mariojmdavid commented Jun 21, 2021

mariojmdavid commented Jun 21, 2021

mviereck commented Jun 23, 2021

mariojmdavid commented Jun 30, 2021

[joss-review] tests #314

[joss-review] tests #314

Comments

vsoch commented May 20, 2021

mviereck commented May 20, 2021

mariojmdavid commented May 28, 2021

jorge-lip commented Jun 8, 2021

vsoch commented Jun 16, 2021

mariojmdavid commented Jun 17, 2021

vsoch commented Jun 17, 2021

mariojmdavid commented Jun 17, 2021

vsoch commented Jun 17, 2021

mviereck commented Jun 17, 2021

vsoch commented Jun 17, 2021

mviereck commented Jun 17, 2021

vsoch commented Jun 17, 2021

mariojmdavid commented Jun 18, 2021

mariojmdavid commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 18, 2021

mviereck commented Jun 18, 2021

jorge-lip commented Jun 19, 2021

mviereck commented Jun 20, 2021

mariojmdavid commented Jun 21, 2021

mariojmdavid commented Jun 21, 2021

mviereck commented Jun 23, 2021

mariojmdavid commented Jun 30, 2021