Problem with running SVsolver in parallel

[Dylan van der Schoot]

Hi all,

I'm trying to run svsolver in parallel on 24 cores Ubuntu 18.04 system. I use the command: mpiexec -n 24 svsolver solver.inp. Instead of running 24 processes in parallel, it runs 24 processes sequentially. Also it doesn't create the 24-procs-case directory as we would expect. Anyone knows how to solve this problem?

For our system we've installed the precompiled svSolver from: https://simtk.org/frs/?group_id=188

Thanks in advance!

Dylan

[Maria Nicole Antonuccio]

Dear Dylan and SimVascular Community,

following your post I have very similar issues. I am trying to run the `CylinderProject`tutorial with both the the last release of SimVascular and svSolver, on Windows and Linux Ubuntu 18.04.1. When I run in paralle, I can see that the number of processes-procs case folder is not created therefore, I cannot find any result files. The status bar keeps staying at 0% after a long time. When the job finished (on Linux), no result has been created.

Whit only one process the simulation runs fine.

Some screenshots are attached to illustrate my point.

Any help would be appreciated.

Thanks in advance,
Maria Nicole

[David Parker]

Hi Dylan,

What does svsolver output to the terminal you run it in? If you use mpiexec -n 24 and see

The number of processes is 1.

then there is a problem with the MPI installation on your workstation.

I've run into this problem before on Ubuntu. I believe that there is a problem with the MPI installation on your workstation. One thing to check is to make sure that the MPICH MPI implementation is installed and that the mpiexec you are using is from there.

Another potential problem is that ParaView might be messing up the MPI installation, not sure why that is happening but it happened on my workstation, I had to install ParaView not using the .deb file. Try uninstalling ParaView and see if things work.

I am adding some functionality to SimVascular to check that the MPI installation is correct, hope to have that done soon.

Cheers,
Dave

[Maria Nicole Antonuccio]

Dear Dave,

Thank you very much for your reply.

Here are some updates from my side:
1. Windows installation: When installing SimVascular with the latest svsolver version on Windows 10 it runs fine (also in parallel). I was previously using an older computer running with Windows 7.

2. Linux installation:
The command I run is the following
>> mpiexec -n 4 /usr/local/sv/svsolver/2019-01-19/svsolver solver.inp

The output I get is this one:
The process ID for myrank (0) is (23876).
The number of processes is 1.

This indicate that the simulation has ran only on 1 processor and not 4 as requested from the command line.

Following your advice, I try to check if MPICH is installed on my machine and from where it could used. I'm not quite sure about the answer here.
Correct me if I'm wrong: my mpich seems to come from mpicc package. Any idea how could I get mpich from mpiexec (anything to write in the .bashrc)?

Here are some command I typed:

>> mpi + Tab
mpic++ mpiCC mpichversion mpicxx.mpich mpiexec.hydra mpiexec.openmpi mpif77.mpich mpif90.mpich mpifort.mpich mpirun.mpich mpivars
mpicc mpicc.mpich mpicxx mpiexec mpiexec.mpich mpif77 mpif90 mpifort mpirun mpirun.openmpi

>> which mpicc.mpich
/usr/bin/mpicc.mpich

>> which mpiexec
/usr/bin/mpiexec

Thank you very much for your precious help.

Kind regards,

Maria Nicole

[David Parker]

Hi Maria,

It looks like your MPI version is good.

Do you have ParaView installed? If so uninstall it and try running the solver again.

Cheers,
Dave