Error when installing mpi4py on Ubuntu instance

Question

I'm trying to install mpi4py on my Ubuntu 18.04 instance. I have python3.6.5 installed.

First I try sudo apt-get build-dep python-mpi4py and I get:

Reading package lists... Done E: You must put some 'source' URIs in your sources.list

I then try to install simply with pip install mpi4py. I get a long error message and I include some of the most important parts below:

checking for library 'lmpe' ...
  /home/ubuntu/anaconda3/envs/tensorflow_p36/bin/mpicc -pthread -B /home/ubuntu/anaconda3/envs/tensorflow_p36/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o
  --------------------------------------------------------------------------
  The Open MPI wrapper compiler was unable to find the specified compiler
  x86_64-conda_cos6-linux-gnu-cc in your PATH.

  Note that this compiler was either specified at configure time or in
  one of several possible environment variables.
  --------------------------------------------------------------------------
  failure.

This failure occurs for most libraries. I include just one of the many, and

  warning: build_clib: command '/home/ubuntu/anaconda3/envs/tensorflow_p36/bin/mpicc' failed with exit status 1

  warning: build_clib: building optional library "vt-mpi" failed


  checking for library 'vt-hyb' ...
  /home/ubuntu/anaconda3/envs/tensorflow_p36/bin/mpicc -pthread -B /home/ubuntu/anaconda3/envs/tensorflow_p36/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o
  --------------------------------------------------------------------------
  The Open MPI wrapper compiler was unable to find the specified compiler
  x86_64-conda_cos6-linux-gnu-cc in your PATH.

  Note that this compiler was either specified at configure time or in
  one of several possible environment variables.

Running which mpcc gives:

(tensorflow_p36) ubuntu@ip-172-31-35-200:~$ which mpicc
/home/ubuntu/anaconda3/envs/tensorflow_p36/bin/mpicc

How can I add the specified compiler x86_64-conda_cos6-linux-gnu-cc to my PATH in order to resolve this error?

rrz0 · Accepted Answer · 2019-10-12 15:06:28Z

5

Simply run:

conda install -c anaconda mpi4py as shown here.

Also, a helpful comment by Lidandro Dalcin:

I guess you are missing the mpich-mpicc package, this one is a metapackage that depends in the right compiler. Why are you installing mpi4py with pip? Maybe all you need is to conda install mpi4py (available in the conda-forge channel) ?

answered Oct 12, 2019 at 15:06

rrz0

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tom · Accepted Answer · 2023-06-08 22:08:44Z

0

Or if you don't want to use conda...

sudo apt install mpi-default-dev

answered Jun 8, 2023 at 22:08

tom

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