Numba is not detecting the icc_rt libraries when installed with pip

[sogoogos]

Hello, I am trying to take advantage of Intel SVML. However, installing icc_rt by using pip (through PyCharm) does not make numba utilizes it since numba -s says SVML is False as below. This instruction only gives a way to install with conda. Is there any way to do it without conda?

System info:
--------------------------------------------------------------------------------
__Time Stamp__
2019-10-15 07:41:22.709866

__Hardware Information__
Machine                                       : x86_64
CPU Name                                      : skylake
Number of accessible CPU cores                : 12
Listed accessible CPUs cores                  : 0-11
CFS restrictions                              : None
CPU Features                                  : 
64bit adx aes avx avx2 bmi bmi2 clflushopt cmov cx16 f16c fma fsgsbase invpcid
lzcnt mmx movbe pclmul popcnt prfchw rdrnd rdseed sahf sgx sse sse2 sse3 sse4.1
sse4.2 ssse3 xsave xsavec xsaveopt xsaves

__OS Information__
Platform                                      : Linux-5.0.0-31-generic-x86_64-with-Ubuntu-18.04-bionic
Release                                       : 5.0.0-31-generic
System Name                                   : Linux
Version                                       : #33~18.04.1-Ubuntu SMP Tue Oct 1 10:20:39 UTC 2019
OS specific info                              : Ubuntu18.04bionic
glibc info                                    : glibc 2.25

__Python Information__
Python Compiler                               : GCC 8.3.0
Python Implementation                         : CPython
Python Version                                : 3.6.8
Python Locale                                 : en_US UTF-8

__LLVM information__
LLVM version                                  : 8.0.0

__CUDA Information__
Found 1 CUDA devices
id 0    b'GeForce GTX 1050 Ti with Max-Q Design'                              [SUPPORTED]
                      compute capability: 6.1
                           pci device id: 0
                              pci bus id: 1
Summary:
	1/1 devices are supported
CUDA driver version                           : 10010
CUDA libraries:
Finding cublas from System
	ERROR: can't locate lib
Finding cusparse from System
	named  libcusparse.so.10.3.0.243
Finding cufft from System
	named  libcufft.so.10.1.1.243
Finding curand from System
	named  libcurand.so.10.1.1.243
Finding nvvm from System
	named  libnvvm.so.3.3.0
Finding libdevice from System
	searching for compute_20...	ok
	searching for compute_30...	ok
	searching for compute_35...	ok
	searching for compute_50...	ok

__ROC Information__
ROC available                                 : False
Error initialising ROC due to                 : No ROC toolchains found.
No HSA Agents found, encountered exception when searching:
Error at driver init: 
NUMBA_HSA_DRIVER /opt/rocm/lib/libhsa-runtime64.so is not a valid file path.  Note it must be a filepath of the .so/.dll/.dylib or the driver:

__SVML Information__
SVML state, config.USING_SVML                 : False
SVML library found and loaded                 : False
llvmlite using SVML patched LLVM              : True
SVML operational                              : False

__Threading Layer Information__
TBB Threading layer available                 : True
OpenMP Threading layer available              : False
+--> Disabled due to                          : Unknown import problem.
Workqueue Threading layer available           : True

__Numba Environment Variable Information__
None set.

__Conda Information__
ERROR: The install method you used for conda--probably either `pip install conda`
or `easy_install conda`--is not compatible with using conda as an application.
If your intention is to install conda as a standalone application, currently
supported install methods include the Anaconda installer and the miniconda
installer.  You can download the miniconda installer from
https://conda.io/miniconda.html.

Conda not present/not working.
Error was Command '['conda', 'info', '--json']' returned non-zero exit status 1.

--------------------------------------------------------------------------------
If requested, please copy and paste the information between
the dashed (----) lines, or from a given specific section as
appropriate.

=============================================================
IMPORTANT: Please ensure that you are happy with sharing the
contents of the information present, any information that you
wish to keep private you should remove before sharing.
=============================================================

[stuartarchibald]

Thanks for the report. I don't think there's a way to obtain this via pip, will add as a feature request. The package is available for download here: https://anaconda.org/numba/icc_rt

[stuartarchibald]

Apologies, I've interpreted this incorrectly! There's obviously icc_rt from Intel Corp https://pypi.org/project/icc-rt/ accessible via pip. I cannot reproduce the above:

$ conda create -n _tmp_issue4713 python=3.7
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.10
  latest version: 4.7.12

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: <anaconda3path>/envs/_tmp_issue4713

  added / updated specs:
    - python=3.7


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.8.28-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_2
  pip                pkgs/main/linux-64::pip-19.2.3-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate _tmp_issue4713
#
# To deactivate an active environment, use
#
#     $ conda deactivate


$ conda activate _tmp_issue4713

$ pip install numba icc_rt
Collecting numba
  Using cached https://files.pythonhosted.org/packages/57/66/7ebc88e87b4ddf9b1c204e24d467cb0d13a7a890ecb4f83d20949f768929/numba-0.46.0-cp37-cp37m-manylinux1_x86_64.whl
Collecting icc_rt
  Using cached https://files.pythonhosted.org/packages/1e/29/0ee89498c2b3e96620add5f4730d4e55e685b292a47aa67f52975fed9f71/icc_rt-2019.0-py2.py3-none-manylinux1_x86_64.whl
Collecting numpy (from numba)
  Using cached https://files.pythonhosted.org/packages/ba/e0/46e2f0540370f2661b044647fa447fef2ecbcc8f7cdb4329ca2feb03fb23/numpy-1.17.2-cp37-cp37m-manylinux1_x86_64.whl
Collecting llvmlite>=0.30.0dev0 (from numba)
  Using cached https://files.pythonhosted.org/packages/1f/3e/642ffb29ed35ca5e93f171ba327452bdee81ec76f2d711ef0f15b411928a/llvmlite-0.30.0-cp37-cp37m-manylinux1_x86_64.whl
Collecting intel-openmp (from icc_rt)
  Using cached https://files.pythonhosted.org/packages/ea/f0/b1bc380d90241ab37149ed526a2ae585f6780ba616bd670b57f0559be37b/intel_openmp-2019.0-py2.py3-none-manylinux1_x86_64.whl
Installing collected packages: numpy, llvmlite, numba, intel-openmp, icc-rt
Successfully installed icc-rt-2019.0 intel-openmp-2019.0 llvmlite-0.30.0 numba-0.46.0 numpy-1.17.2

$ numba -s

System info:
--------------------------------------------------------------------------------
__Time Stamp__
2019-10-16 08:26:57.263046

<snip>

__SVML Information__
SVML state, config.USING_SVML                 : True
SVML library found and loaded                 : True
llvmlite using SVML patched LLVM              : True
SVML operational                              : True

<snip>

__Current Conda Env__
_libgcc_mutex             0.1                        main  
ca-certificates           2019.8.28                     0  
certifi                   2019.9.11                py37_0  
icc-rt                    2019.0                   pypi_0    pypi
intel-openmp              2019.0                   pypi_0    pypi
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 9.1.0                hdf63c60_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
llvmlite                  0.30.0                   pypi_0    pypi
ncurses                   6.1                  he6710b0_1  
numba                     0.46.0                   pypi_0    pypi
numpy                     1.17.2                   pypi_0    pypi
openssl                   1.1.1d               h7b6447c_2  
pip                       19.2.3                   py37_0  
python                    3.7.4                h265db76_1  
readline                  7.0                  h7b6447c_5  
setuptools                41.4.0                   py37_0  
sqlite                    3.30.0               h7b6447c_0  
tk                        8.6.8                hbc83047_0  
wheel                     0.33.6                   py37_0  
xz                        5.2.4                h14c3975_4  
zlib                      1.2.11               h7b6447c_3  
--------------------------------------------------------------------------------

[stuartarchibald]

@sogoogos did you manage to find a way to reproduce this as I'm afraid I cannot? Thanks

[sogoogos]

Sorry about late reply! I actually still cannot configure it properly.

$ pip install numba icc_rt
Requirement already satisfied: numba in /home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages
Requirement already satisfied: icc_rt in /home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages
Requirement already satisfied: llvmlite>=0.30.0dev0 in /home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages (from numba)
Requirement already satisfied: numpy in /home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages (from numba)
Requirement already satisfied: intel-openmp in /home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages (from icc_rt)

$ numba -s
/home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages/numba/errors.py:137: UserWarning: Insufficiently recent colorama version found. Numba requires colorama >= 0.3.9
  warnings.warn(msg)
System info:
--------------------------------------------------------------------------------
__Time Stamp__
2019-10-22 15:06:01.286165

__Hardware Information__
Machine                                       : x86_64
CPU Name                                      : skylake
Number of accessible CPU cores                : 12
Listed accessible CPUs cores                  : 0-11
CFS restrictions                              : None
CPU Features                                  : 
64bit adx aes avx avx2 bmi bmi2 clflushopt cmov cx16 f16c fma fsgsbase invpcid
lzcnt mmx movbe pclmul popcnt prfchw rdrnd rdseed sahf sgx sse sse2 sse3 sse4.1
sse4.2 ssse3 xsave xsavec xsaveopt xsaves

__OS Information__
Platform                                      : Linux-5.0.0-31-generic-x86_64-with-Ubuntu-18.04-bionic
Release                                       : 5.0.0-31-generic
System Name                                   : Linux
Version                                       : #33~18.04.1-Ubuntu SMP Tue Oct 1 10:20:39 UTC 2019
OS specific info                              : Ubuntu18.04bionic
glibc info                                    : glibc 2.25

__Python Information__
Python Compiler                               : GCC 8.3.0
Python Implementation                         : CPython
Python Version                                : 3.6.8
Python Locale                                 : en_US UTF-8

__LLVM information__
LLVM version                                  : 8.0.0

__CUDA Information__
Found 1 CUDA devices
id 0    b'GeForce GTX 1050 Ti with Max-Q Design'                              [SUPPORTED]
                      compute capability: 6.1
                           pci device id: 0
                              pci bus id: 1
Summary:
	1/1 devices are supported
CUDA driver version                           : 10010
CUDA libraries:
Finding cublas from System
	ERROR: can't locate lib
Finding cusparse from System
	named  libcusparse.so.10.3.0.243
Finding cufft from System
	named  libcufft.so.10.1.1.243
Finding curand from System
	named  libcurand.so.10.1.1.243
Finding nvvm from System
	named  libnvvm.so.3.3.0
Finding libdevice from System
	searching for compute_20...	ok
	searching for compute_30...	ok
	searching for compute_35...	ok
	searching for compute_50...	ok

__ROC Information__
ROC available                                 : False
Error initialising ROC due to                 : No ROC toolchains found.
No HSA Agents found, encountered exception when searching:
Error at driver init: 
NUMBA_HSA_DRIVER /opt/rocm/lib/libhsa-runtime64.so is not a valid file path.  Note it must be a filepath of the .so/.dll/.dylib or the driver:

__SVML Information__
SVML state, config.USING_SVML                 : False
SVML library found and loaded                 : False
llvmlite using SVML patched LLVM              : True
SVML operational                              : False

__Threading Layer Information__
TBB Threading layer available                 : True
OpenMP Threading layer available              : False
+--> Disabled due to                          : Unknown import problem.
Workqueue Threading layer available           : True

__Numba Environment Variable Information__
None set.

__Conda Information__
ERROR: The install method you used for conda--probably either `pip install conda`
or `easy_install conda`--is not compatible with using conda as an application.
If your intention is to install conda as a standalone application, currently
supported install methods include the Anaconda installer and the miniconda
installer.  You can download the miniconda installer from
https://conda.io/miniconda.html.

Conda not present/not working.
Error was Command '['conda', 'info', '--json']' returned non-zero exit status 1.

--------------------------------------------------------------------------------
If requested, please copy and paste the information between
the dashed (----) lines, or from a given specific section as
appropriate.

=============================================================
IMPORTANT: Please ensure that you are happy with sharing the
contents of the information present, any information that you
wish to keep private you should remove before sharing.
=============================================================

[seibert]

The one difference I can see here is that while @stuartarchibald is installing icc_rt and numba with pip, he's still doing it inside a conda environment, instead of virtualenv. (They aren't that different in disk layout, but set different environment variables.) Maybe our SVML environment detection code is accidentally making a conda-specific assumptions?

[stuartarchibald]

This indeed might be a path thing. If you do (on the command line, in your virtual env with numba+icc_rt in it):

python -c 'from llvmlite import binding; binding.load_library_permanently("libsvml.so")'

does it raise an exception?

[sogoogos]

Yes, it gave the following.

$ python -c 'from llvmlite import binding; binding.load_library_permanently("libsvml.so")'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/sogo/work/python-virtualenvs/rmine-py3/lib/python3.6/site-packages/llvmlite/binding/dylib.py", line 30, in load_library_permanently
    raise RuntimeError(str(outerr))
RuntimeError: libsvml.so: cannot open shared object file: No such file or directory

[stuartarchibald]

@sogoogos thanks, I guess the next question is... where does pip put that file and where is it in relation to something known, like python or site-packages?

[sogoogos]

Looks like libsvml.so is in lib

find . -name 'libsvml*'
./work/python-virtualenvs/rmine-py3/lib/libsvml.so

[jampekka]

I got the same problem on Debian Sid, and it turned out the problem was that the pip doesn't run ldconfig. After installing icc_rt globally (sudo pip3 install icc_rt), loading the libsvml.so fails with the always confusing "No such file or directory", but this is because the linker can't find the libintlc.so.5 required by libsvml.so even though it is in /usr/local/lib

TD:DR: sudo pip3 install icc_rt; sudo ldconfig

Don't know how this applies to virtualenvs or per-user installations.

[esc]

@jampekka thanks for posting this workaround, from what you are suggesting, this might be an issue with the icc_rt wheel.

[MyraBaba]

Hi ,
@stuartarchibald
is there any solution for this issue ? I saw the mentioned .so in the .venv lib dir , but still not loading both binding or numba