Problem
I'm trying to use mpi4py on a cluster. Because of other dependencies I have to use gnu, not intel. However, there are both compiler versions on the cluster and I don't manage to force mpi4py to install with the gnu compilers.
Questions
How can I make mpi4py work with gnu instead of intel?
Why is mpi4py installed with intel even though I unloaded all intel modules?
Why is mpi4py installed with intel despite me specifying
env MPICC?
Failed Attempts
I first tried to unload the intel modules and load a gnu openmpi module, such that I get:
me@cluster:~$ module purge
me@cluster:~$ module load python
me@cluster:~$ source .virtualenvs/py36env/bin/activate
(py36env) me@cluster:~$ module load openmpi/gcc/9.1/4.0.1
(py36env) me@cluster:~$ module list
Currently Loaded Modulefiles:
1) python/3.6 2) openmpi/gcc/9.1/4.0.1
(py36env) me@cluster:~$ which mpicc
/usr/local/Cluster-Apps/openmpi/gnu/4.0.1-gcc-9.1/bin/mpicc
(py36env) me@cluster:~$ mpicc --version
gcc (GCC) 9.1.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(py36env) me@cluster:~$ which mpirun
/usr/local/Cluster-Apps/openmpi/gnu/4.0.1-gcc-9.1/bin/mpirun
(py36env) me@cluster:~$ mpirun --version
mpirun (Open MPI) 4.0.1
Report bugs to http://www.open-mpi.org/community/help/
However, when I pip install mpi4py it uses the intel compilers despite my efforts to unload them:
(py36env) me@cluster:~$ pip install mpi4py
Collecting mpi4py
Installing collected packages: mpi4py
Successfully installed mpi4py-3.0.2
(py36env) me@cluster:~$ python -c "import mpi4py; print(mpi4py.get_config())"
{'mpicc': '/usr/local/Cluster-Apps/intel/2017.4/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicc',
'mpicxx': '/usr/local/Cluster-Apps/intel/2017.4/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx',
'mpifort': '/usr/local/Cluster-Apps/intel/2017.4/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif90',
'mpif90': '/usr/local/Cluster-Apps/intel/2017.4/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif90',
'mpif77': '/usr/local/Cluster-Apps/intel/2017.4/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif77'}
I get the same result even when I try to specify the mpi environment with
$ env MPICC=/usr/local/Cluster-Apps/openmpi/gnu/4.0.1-gcc-9.1/bin/mpicc pip install mpi4py
as suggested in the Note at https://mpi4py.readthedocs.io/en/stable/install.html#using-pip-or-easy-install.
Errors
As pointed out in the comments to "mpiexec and python mpi4py gives rank 0 and size 1", having mpi4py being built against a different MPI implementation than the used mpirun results in errors:
(py36env) me@login-e-11:~$ mpirun -n 5 python -m mpi4py.bench helloworld
Hello, World! I am process 0 of 1 on login-e-11.
Hello, World! I am process 0 of 1 on login-e-11.
Hello, World! I am process 0 of 1 on login-e-11.
Hello, World! I am process 0 of 1 on login-e-11.
Hello, World! I am process 0 of 1 on login-e-11.
This should actually be (see https://mpi4py.readthedocs.io/en/stable/install.html#testing):
$ mpirun -n 5 python -m mpi4py.bench helloworld
Hello, World! I am process 0 of 5 on localhost.
Hello, World! I am process 1 of 5 on localhost.
Hello, World! I am process 2 of 5 on localhost.
Hello, World! I am process 3 of 5 on localhost.
Hello, World! I am process 4 of 5 on localhost.
