simtk.org

Hi,

I am wondering where can I set the correct setting for the number of processors to use for the svsolver which I want to run from the command line (with provided solver.inp and .svpre files). The option is available in the SimVascular UI but I cannot find any documentation as to where it fits in any of the files svsolver gets its settings from.

Thanks and best regards,
Rok

Hi Rok,

If you want to run simulation from the command line, follow the steps as below:
1. Launch a terminal
2. Go to the directory where you have all the required files, such as solver.inp, restart.0.1, geombc.dat.1, bct,dat, numstart.dat, etc.
3. Run "mpiexec -np [numver of processor] [solver path]/svsolver"

You can find info about where the solvers are installed in your computer at
http://simvascular.github.io/docsInstallation.html

Thanks,
SimVascular Development Team

Hi Hongzhi,

thanks, I just went through the svsolver source file and I saw that it performs the MPI_Comm_size command (and others) to detect the size and rank of the process, to detect how it was ran through MPI.

I was already executing the command "mpiexec -np 8 svsolver" but every process seemed to get the rank of 0, so I just noticed that I have the same problem as another user: viewtopicPhpbb.php?f=188&t=7857&p=0&start=0&view=

So 8 processes are started, but they are all "full" processes as it seems the MPI size and rank are not correctly determined.


I am on OSX Sierra and I manually installed the latest OpenMPI (following these instructions: https://wiki.helsinki.fi/display/HUGG/O ... n+Mac+OS+X).

Do you have any idea what might be causing this issue?

Thanks and best regards,
Rok

To use solvers from the command line, the only required is to install svSolver from simtk. You don't need to install any other pakckages, such as Open MPI. Also svSolver uses mpich (which is already included in svSolver), NOT OpenMPI.
In your case the installer is svSolver-2017-06-19-MacOSX-64bit.pkg
After installation, follow the instructions I mentioned before.
Since you are using Mac, you need to run
"/usr/local/sv/svsolver/[yyyy-mm-dd]/bin/mpiexec -np [numver of processor] /usr/local/sv/svsolver/[yyyy-mm-dd]/svsolver" . This command provides full path for mpiexec and svsolver.

Thanks,
SimVascular Development Team

Thanks very much! Using the provided mpiexec, I was able to get it running properly.

Best regards,
Rok