Error cannot compile mpi programs check your configuration - Исправление ошибок и поиск оптимальных решений проблем

it’s my first post here so apologies if my style is wrong!

I’ve been trying to install mpi4py (as SU2 requires it for parallel processing) on Ubuntu 16.04 using python 3.6. I downloaded mpi4py and tried to build from source as I would like to use the OpenMPI libraries I had configured, and tried the following:

sudo python setup.py build --mpicc=/opt/openmpi/openmpi-2.1.0/bin/mpicc

However, it ultimately fails with «error: Cannot link MPI programs. Check your configuration!!!»

Looking at the SU2 and mpi4py documentation, they recommend using pip instead. I also tried this:

sudo pip install mpi4py

and env MPICC=/opt/openmpi/openmpi-2.1.0/bin/mpicc pip install mpi4py but they also gave the same error.

I have saved both outputs — please see the link for the attachments. It seems to pick up on a lot of the files from my NVIDIA CUDA installation, though I’m not sure why.

I’m a beginner at at compiling programs so I’d appreciate it if anyone could shed any light on this? Thanks.

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Hi, I’m trying to build mpi4py using my install of openmpi but python setup.py keeps failing.

I have built openmpi in my opt directory (/opt/openmpi/openmpi-2.1.0) and I am running Ubuntu 16.04.

I edited the mpi.cfg file to add my paths and include directory for my install and executed:

python setup.py build --mpi=openmpi

However, I am getting the following error:

running build
running build_src
running build_py
running build_clib
MPI configuration: [openmpi] from 'mpi.cfg'
MPI C compiler:    /opt/openmpi/openmpi-2.1.0/bin/mpicc
MPI C++ compiler:  /opt/openmpi/openmpi-2.1.0/bin/mpicxx
running build_ext
MPI configuration: [openmpi] from 'mpi.cfg'
MPI C compiler:    /opt/openmpi/openmpi-2.1.0/bin/mpicc
MPI C++ compiler:  /opt/openmpi/openmpi-2.1.0/bin/mpicxx
checking for MPI compile and link ...
/opt/openmpi/openmpi-2.1.0/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -I/opt/openmpi/openmpi-2.1.0/include -c _configtest.c -o _configtest.o
/opt/openmpi/openmpi-2.1.0/bin/mpicc: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no version information available (required by /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20)
success!
removing: _configtest.c _configtest.o
/opt/openmpi/openmpi-2.1.0/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -I/opt/openmpi/openmpi-2.1.0/include -c _configtest.c -o _configtest.o
/opt/openmpi/openmpi-2.1.0/bin/mpicc: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no version information available (required by /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20)
/opt/openmpi/openmpi-2.1.0/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-2.7 -L/opt/openmpi/openmpi-2.1.0/lib -Wl,-R/opt/openmpi/openmpi-2.1.0/lib -o _configtest
/opt/openmpi/openmpi-2.1.0/bin/mpicc: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no version information available (required by /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20)
/opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined reference to `clGetPlatformInfo@OPENCL_1.0'
/opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined reference to `clGetPlatformIDs@OPENCL_1.0'
/opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined reference to `clGetDeviceInfo@OPENCL_1.0'
/opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined reference to `clGetDeviceIDs@OPENCL_1.0'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!

It seems to be picking up some paths to my NVIDIA CUDA installation, though I am unsure of the reason why.

Can anyone point out if I set some options wrongly or not installed openmpi correctly? (Sorry, I’m a bit new to this). Thanks in advance.

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У меня есть код Python, размещенный в gitlab. Недавно я добавил использование для обработки параллельных запусков с MPI. У меня есть набор тестов, который запускается системой gitlab CI. Однако он терпит неудачу, как только пытается установить пакет mpi4py.

Я использую образ python 3.7. Файл .gitlab-ci.yml:

image: python:3.7

test:
  stage: test
  script:
    - pip install -r requirements.txt
    - python setup.py build
    - python setup.py install
    - pytest --junitxml=report.xml -v tests/short.py
  artifacts:
    when: always
    paths:
      - report.xml
    reports:
      junit: report.xml

Сбой происходит, когда после установки пакета mpi4py в соответствии с запросом в файле requirements.txt процесс сборки завершается с ошибкой с сообщением:

 gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include/python3.7m -c _configtest.c -o _configtest.o
      _configtest.c:2:10: fatal error: mpi.h: No such file or directory
          2 | #include <mpi.h>
            |          ^~~~~~~
      compilation terminated.
      failure.
      removing: _configtest.c _configtest.o
      error: Cannot compile MPI programs. Check your configuration!!!
      [end of output]

Я полагаю, что библиотека mpi C отсутствует? Как мне его установить?

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