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Installation error #498

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Jack-Lin-DS-AI opened this issue Sep 19, 2019 · 15 comments
Closed

Installation error #498

Jack-Lin-DS-AI opened this issue Sep 19, 2019 · 15 comments

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@Jack-Lin-DS-AI
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I'd like to install apex but failed. Any suggestions? Thank you.

$ pip install -v --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./
/lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/lib/python3.6/site-packages/pip/_internal/commands/install.py:243: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
  cmdoptions.check_install_build_global(options)
Created temporary directory: /tmp/pip-ephem-wheel-cache-8ib28pad
Created temporary directory: /tmp/pip-req-tracker-su9lkj72
Created requirements tracker '/tmp/pip-req-tracker-su9lkj72'
Created temporary directory: /tmp/pip-install-px208sk7
Processing /lab/cedar/home/lin/gitProjects/apex
  Created temporary directory: /tmp/pip-req-build-zfi8u8xr
  Added file:///lab/cedar/home/lin/gitProjects/apex to build tracker '/tmp/pip-req-tracker-su9lkj72'
    Running setup.py (path:/tmp/pip-req-build-zfi8u8xr/setup.py) egg_info for package from file:///lab/cedar/home/lin/gitProjects/apex
    Running command python setup.py egg_info
    torch.__version__  =  1.2.0
    running egg_info
    creating pip-egg-info/apex.egg-info
    writing pip-egg-info/apex.egg-info/PKG-INFO
    writing dependency_links to pip-egg-info/apex.egg-info/dependency_links.txt
    writing top-level names to pip-egg-info/apex.egg-info/top_level.txt
    writing manifest file 'pip-egg-info/apex.egg-info/SOURCES.txt'
    reading manifest file 'pip-egg-info/apex.egg-info/SOURCES.txt'
    writing manifest file 'pip-egg-info/apex.egg-info/SOURCES.txt'
    /tmp/pip-req-build-zfi8u8xr/setup.py:43: UserWarning: Option --pyprof not specified. Not installing PyProf dependencies!
      warnings.warn("Option --pyprof not specified. Not installing PyProf dependencies!")
  Source in /tmp/pip-req-build-zfi8u8xr has version 0.1, which satisfies requirement apex==0.1 from file:///lab/cedar/home/lin/gitProjects/apex
  Removed apex==0.1 from file:///lab/cedar/home/lin/gitProjects/apex from build tracker '/tmp/pip-req-tracker-su9lkj72'
Skipping bdist_wheel for apex, due to binaries being disabled for it.
Installing collected packages: apex
  Created temporary directory: /tmp/pip-record-mazj60_q
    Running command /lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-zfi8u8xr/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-zfi8u8xr/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-mazj60_q/install-record.txt --single-version-externally-managed --compile
    torch.__version__  =  1.2.0
    /tmp/pip-req-build-zfi8u8xr/setup.py:43: UserWarning: Option --pyprof not specified. Not installing PyProf dependencies!
      warnings.warn("Option --pyprof not specified. Not installing PyProf dependencies!")

    Compiling cuda extensions with
    nvcc: NVIDIA (R) Cuda compiler driver
    Copyright (c) 2005-2018 NVIDIA Corporation
    Built on Sat_Aug_25_21:08:01_CDT_2018
    Cuda compilation tools, release 10.0, V10.0.130
    from /usr/local/cuda/bin

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-zfi8u8xr/setup.py", line 100, in <module>
        check_cuda_torch_binary_vs_bare_metal(torch.utils.cpp_extension.CUDA_HOME)
      File "/tmp/pip-req-build-zfi8u8xr/setup.py", line 77, in check_cuda_torch_binary_vs_bare_metal
        "https://github.com/NVIDIA/apex/pull/323#discussion_r287021798.  "
    RuntimeError: Cuda extensions are being compiled with a version of Cuda that does not match the version used to compile Pytorch binaries.  Pytorch binaries were compiled with Cuda 9.2.148.
    In some cases, a minor-version mismatch will not cause later errors:  https://github.com/NVIDIA/apex/pull/323#discussion_r287021798.  You can try commenting out this check (at your own risk).
  Running setup.py install for apex ... error
Cleaning up...
  Removing source in /tmp/pip-req-build-zfi8u8xr
Removed build tracker '/tmp/pip-req-tracker-su9lkj72'
ERROR: Command errored out with exit status 1: /lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-zfi8u8xr/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-zfi8u8xr/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-mazj60_q/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
Exception information:
Traceback (most recent call last):
  File "/lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 188, in main
    status = self.run(options, args)
  File "/lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 407, in run
    use_user_site=options.use_user_site,
  File "/lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/lib/python3.6/site-packages/pip/_internal/req/__init__.py", line 58, in install_given_reqs
    **kwargs
  File "/lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 959, in install
    spinner=spinner,
  File "/lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/lib/python3.6/site-packages/pip/_internal/utils/misc.py", line 931, in call_subprocess
    raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /lab/cedar/home/lin/.conda/envs/monorepoCancerCommunity/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-zfi8u8xr/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-zfi8u8xr/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' --cpp_ext --cuda_ext install --record /tmp/pip-record-mazj60_q/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
1 location(s) to search for versions of pip:
* https://pypi.org/simple/pip/
Getting page https://pypi.org/simple/pip/
Found index url https://pypi.org/simple
Starting new HTTPS connection (1): pypi.org:443
https://pypi.org:443 "GET /simple/pip/ HTTP/1.1" 200 11972
Analyzing links from page https://pypi.org/simple/pip/
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Given no hashes to check 127 links for project 'pip': discarding no candidates
@ptrblck
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ptrblck commented Sep 19, 2019

Hi @ChihHsuLin,

your local CUDA installation does not match the version PyTorch is using.

RuntimeError: Cuda extensions are being compiled with a version of Cuda that does not match the version used to compile Pytorch binaries. Pytorch binaries were compiled with Cuda 9.2.148.
In some cases, a minor-version mismatch will not cause later errors: #323 (comment). You can try commenting out this check (at your own risk).

Since you are using CUDA10.0 as your local installation, you could install the PyTorch binaries using the matching CUDA version as described here.

@Jack-Lin-DS-AI
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Do you mean I need to reinstall PyTorch for CUDA 10.0?

@ptrblck
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ptrblck commented Sep 19, 2019 •
edited

Yes, that would be the easiest solution.

EDIT: Alternatively, you could of course install CUDA9.2, but I would rather keep the newer version.

@Jack-Lin-DS-AI
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I see. Thank you for letting me know. Let me try to reinstall the PyTorch.

@Jack-Lin-DS-AI
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It worked. Thank you.

@molyswu
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molyswu commented Sep 24, 2019

pip3 install -v --no-cache-dir --global-option="--pyprof" --global-option="--cpp_ext" --global-option="--cuda_ext" ./
/usr/local/lib/python3.5/dist-packages/pip/_internal/commands/install.py:243: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
cmdoptions.check_install_build_global(options)
Created temporary directory: /tmp/pip-ephem-wheel-cache-88s2o54e
Created temporary directory: /tmp/pip-req-tracker-c7pyojs0
Created requirements tracker '/tmp/pip-req-tracker-c7pyojs0'
Created temporary directory: /tmp/pip-install-fgs1v8k7
Processing /media/ai/sdc1/tools/apex
Created temporary directory: /tmp/pip-req-build-ewvg3b4p
Added file:///media/ai/sdc1/tools/apex to build tracker '/tmp/pip-req-tracker-c7pyojs0'
Running setup.py (path:/tmp/pip-req-build-ewvg3b4p/setup.py) egg_info for package from file:///media/ai/sdc1/tools/apex
Running command python setup.py egg_info
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-req-build-ewvg3b4p/setup.py", line 1, in
import torch
File "/usr/local/lib/python3.5/dist-packages/torch/init.py", line 81, in
from torch._C import *
ImportError: libmpi.so.1: cannot open shared object file: No such file or directory
Cleaning up...
Removing source in /tmp/pip-req-build-ewvg3b4p
Removed file:///media/ai/sdc1/tools/apex from build tracker '/tmp/pip-req-tracker-c7pyojs0'
Removed build tracker '/tmp/pip-req-tracker-c7pyojs0'
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Exception information:
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/cli/base_command.py", line 188, in main
status = self.run(options, args)
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/commands/install.py", line 345, in run
resolver.resolve(requirement_set)
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/legacy_resolve.py", line 196, in resolve
self._resolve_one(requirement_set, req)
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/legacy_resolve.py", line 359, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/legacy_resolve.py", line 307, in _get_abstract_dist_for
self.require_hashes
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/operations/prepare.py", line 215, in prepare_linked_requirement
finder, self.build_isolation,
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/distributions/source.py", line 79, in prepare_distribution_metadata
self.req.prepare_metadata()
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/req/req_install.py", line 551, in prepare_metadata
self.run_egg_info()
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/req/req_install.py", line 628, in run_egg_info
command_desc='python setup.py egg_info')
File "/usr/local/lib/python3.5/dist-packages/pip/_internal/utils/misc.py", line 931, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
1 location(s) to search for versions of pip:

@ptrblck
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ptrblck commented Sep 24, 2019

@molyswu How did you install PyTorch? Can you import torch successfully and create a dummy tensor?
The error points to a broken libmpi.so in PyTorch.

@molyswu
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molyswu commented Sep 26, 2019

Removed build tracker '/tmp/pip-req-tracker-unbw23dh'
ERROR: Command errored out with exit status 1: /home/ai/anaconda3/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-bax_1an2/setup.py'"'"'; file='"'"'/tmp/pip-req-build-bax_1an2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' --pyprof --cpp_ext --cuda_ext install --record /tmp/pip-record-74erabwc/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
Exception information:

@DangerousY
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Removed build tracker '/tmp/pip-req-tracker-unbw23dh'
ERROR: Command errored out with exit status 1: /home/ai/anaconda3/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-bax_1an2/setup.py'"'"'; file='"'"'/tmp/pip-req-build-bax_1an2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' --pyprof --cpp_ext --cuda_ext install --record /tmp/pip-record-74erabwc/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
Exception information:

I meet with this problem as well, have you solved it?

@molyswu
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molyswu commented Sep 28, 2019

It is working

@DNGros
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DNGros commented Oct 5, 2019 •
edited

Also had the this issue when using pytorch installed from conda without a global install of cuda on the machine. My guess is that this is because conda does not install nvcc. The fix for me:

  • Install cuda toolkit follow instructions at https://developer.nvidia.com/cuda-10.0-download-archive (What version you install depends on your pytorch version. I chose 10. Not sure if 10.1 is supported)
  • Make sure cuda/bin is on your path ( echo 'PATH=$PATH:/usr/local/cuda/bin' >> ~/.bashrc && source ~/.bashrc)
  • Install apex as described in readme
  • potentially reboot (I was getting "unknown cuda errors" which resolved after reboot).

Hopes this helps someone.

This isn't a big deal, but it might be useful to improve the error handling of the pip install script to check to make sure nvcc and such is properly installed before trying to install apex. Then a more helpful message could be given to conda users rather than and spewing a lot of unhelpful stuff to the terminal.

@DNGros DNGros mentioned this issue Oct 5, 2019
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@MicPie
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MicPie commented Dec 7, 2019 •
edited

Hi @ChihHsuLin,

your local CUDA installation does not match the version PyTorch is using.

RuntimeError: Cuda extensions are being compiled with a version of Cuda that does not match the version used to compile Pytorch binaries. Pytorch binaries were compiled with Cuda 9.2.148.
In some cases, a minor-version mismatch will not cause later errors: #323 (comment). You can try commenting out this check (at your own risk).

Since you are using CUDA10.0 as your local installation, you could install the PyTorch binaries using the matching CUDA version as described here.

Maybe this is helping others with the same problem (because it took me some time to figure it out, but maybe that is me):

Use conda install pytorch torchvision cudatoolkit=XY.Z -c pytorch and replace XY.Z with the right version to match your CUDA version.

This worked for me! :-)

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Hi @ChihHsuLin,
your local CUDA installation does not match the version PyTorch is using.

RuntimeError: Cuda extensions are being compiled with a version of Cuda that does not match the version used to compile Pytorch binaries. Pytorch binaries were compiled with Cuda 9.2.148.
In some cases, a minor-version mismatch will not cause later errors: #323 (comment). You can try commenting out this check (at your own risk).

Since you are using CUDA10.0 as your local installation, you could install the PyTorch binaries using the matching CUDA version as described here.

Maybe this is helping others with the same problem (because it took me some time to figure it out, but maybe that is me):

Use conda install pytorch torchvision cudatoolkit=XY.Z -c pytorch and replace XY.Z with the right version to match your CUDA version.

This worked for me! :-)

Hi,friend , can you post which [pytorch, torchvision, cudatoolkit] version you used ? I can not install apex-pytorch properly .
And what's your computer system version ? I'm using ubuntun19.04 .
Thanks .

@MicPie
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MicPie commented Dec 8, 2019

Hi,friend , can you post which [pytorch, torchvision, cudatoolkit] version you used ? I can not install apex-pytorch properly .
And what's your computer system version ? I'm using ubuntun19.04 .
Thanks .

On Ubuntu 18.04.3 LTS I used the version shown with nvcc --version, which was in my case 10.0, and then installed in my conda env with conda install pytorch torchvision cudatoolkit=10.0 -c pytorch pytorch with the matching cudatoolkit.

I hope that can help you!

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@MicPie Thanks for your tips , it's helpful !

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