Issue setting up Maker for MPI on cluster

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Issue setting up Maker for MPI on cluster

Zoe Clarke
Hello!

I am having a bit of trouble running Maker on a compute cluster with MPI. I am using the Compute Canada cluster which actually had Maker installed with openmpi, but I don't think it was installed quite properly as Maker crashes after 6 hours. I then decided to install Maker using a mpich that was available on the cluster but ran into an error. I figured this error may have been due to mpich not being set up with the shared libraries, so I installed a new version of mpich and configured Maker following instructions on this thread: http://gmod.827538.n3.nabble.com/WARNING-Multiple-MAKER-processes-td4040133.html

After following the instructions on this thread exactly, I am running into the exact same errors that I previously ran into with mpich, which are permission errors pasted below. I'm thinking I might have to modify some permissions somewhere, but I'm not sure where - do you know why this process is failing? I am testing Maker using the command /home/zocla/mpich3/bin/mpiexec -n 3 maker --help and getting the error below.

Thanks so much for your help!
Zoe

Argument "2.53_01" isn't numeric in numeric ge (>=) at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/forks.pm line 1570.
Argument "2.53_01" isn't numeric in numeric ge (>=) at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/forks.pm line 1570.
Argument "2.53_01" isn't numeric in numeric ge (>=) at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/forks.pm line 1570.
Can't create Inline validation file /scratch/zocla/maker_mympich/maker/perl/lib/auto/Parallel/Application/MPI/MPI.inl: Permission denied at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=cedar1.cedar.computecanada.ca
 at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
Parallel::Application::MPI::_bind("/home/zocla/mpich3/bin/mpicc", "/home/zocla/mpich3/include", "/scratch/zocla/maker_mympich/maker/bin/../perl", "") called at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
Parallel::Application::MPI::_load() called at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
Parallel::Application::MPI::MPI_Init() called at /scratch/zocla/maker_mympich/maker/bin//maker line 265
--> rank=NA, hostname=cedar1.cedar.computecanada.ca
Can't create Inline validation file /scratch/zocla/maker_mympich/maker/perl/lib/auto/Parallel/Application/MPI/MPI.inl: Permission denied at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=cedar1.cedar.computecanada.ca
 at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
Parallel::Application::MPI::_bind("/home/zocla/mpich3/bin/mpicc", "/home/zocla/mpich3/include", "/scratch/zocla/maker_mympich/maker/bin/../perl", "") called at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
Parallel::Application::MPI::_load() called at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
Parallel::Application::MPI::MPI_Init() called at /scratch/zocla/maker_mympich/maker/bin//maker line 265
--> rank=NA, hostname=cedar1.cedar.computecanada.ca
Can't create Inline validation file /scratch/zocla/maker_mympich/maker/perl/lib/auto/Parallel/Application/MPI/MPI.inl: Permission denied at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
--> rank=NA, hostname=cedar1.cedar.computecanada.ca
 at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
Parallel::Application::MPI::_bind("/home/zocla/mpich3/bin/mpicc", "/home/zocla/mpich3/include", "/scratch/zocla/maker_mympich/maker/bin/../perl", "") called at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
Parallel::Application::MPI::_load() called at /scratch/zocla/maker_mympich/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
Parallel::Application::MPI::MPI_Init() called at /scratch/zocla/maker_mympich/maker/bin//maker line 265
--> rank=NA, hostname=cedar1.cedar.computecanada.ca

=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 13
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

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