Error when launching svSolver (2019.01.19) from command line in Ubuntu 18.04

[Maria Nicole Antonuccio]

Dear SimVascular community,

I installed the latest release of SimVascular (2019.01.27) and the latest one of svSolver (2019.02.07) on Linux Ubuntu 18.04.1 LTS. I liked to run the "CylinderProject" tutorial using the following command line.

I have several types of errors which I am not sure are connected.

First, I launched svpre solver:
./svpre steady.svpre

Everything was fine until the line:
write_numstart 0

The errors I obtained were:
ERROR: could not open numstart.dat!
ERROR: command could not be processed.

So, I decided to create all the input files using the GUI and everything seemed to work fine (I did not have any error messages).

When I launched the svsolver with two processes (it was the same thing using more processes):
mpiexec -np 2 ./svsolver solver.inp

There were two error messages:

1)
At line 99 of file /home/davep/software/svSolver/Code/FlowSolvers/ThreeDSolver/svSolver/readnblk-varwall.f (unit = 72)
Fortran runtime error: Cannot open file 'numstart.dat': No such file or directory
---------------------------------------------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.

2)
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[4583,1],0]
Exit code: 2

I do not know if the error of the svpre solver and the one of the svsolver are linked. Am I doing something wrong?

Your help would be appreciated.

Thanks in advance,
Maria Nicole.

[David Parker]

Hi Maria,

The files needed for a svSolver job are created using the SimVascular Simulations module. In that module you set the solution parameters and then click on Create Files for Simulation button under the Simulations Create Files and Run Simulation tab.

The simulation files are stored in your project's directory under the Simulations directory in a subdirectory with the name of the simulation job (the name you typed in when creating the simulation job): numstart.dat, restart.0.1, solver.inp and <JOBNAME>.svpre.

The solver assumes that these files are in the directory the svsolver program is executed from. So you need to cd to the directory where those files are located and run the solver, for example

mpiexec -n 4 /usr/local/sv/svsolver/2019-01-19/svsolver solver.inp

Cheers,
Dave

[Maria Nicole Antonuccio]

Dear Dave,

Thank you for reply.

Following your advice, I have corrected my command line to this one: mpiexec -n 4 usr/local/sv/svsolver/2019-01-19/svsolver solver.inp

Unfortunately, the solver does not seems to run in parallel but only on 1 processor as suggested by this output:

The process ID for myrank (0) is (23876).
The number of processes is 1.
The results of this simulation that ran only on 1 processor are correct.

As this is exactly the topic of this other conversation: viewtopicPhpbb.php?f=188&t=10127&p=0&st ... a5d5e9c307 , I will then continue to reply on this other thread.

I won't add anything to this present thread.

Kind regards,

Maria Nicole.

[Maria Nicole Antonuccio]

Dear Dave,

I thank you very much for all your suggestions.

I have solved my issue by using the following command line:
mpiexec.mpich -n 4 /usr/local/sv/svsolver/2019-02-07/svsolver solver.inp

To make sure I'm using mpich from mpiexec as you suggested, I'm starting the command with "mpiexec.mpich".
The solver runs fine now.

Instead of that, I am still having problem running svSolver in parallel using the GUI and I do not understand why.

Thanks for your help.

Kind regards,

Maria Nicole

[David Parker]

Hi Maria,

You are probably having problems running from the GUI because it is not using mpiexec.mpich. You can set which MPI executable to use from the Window menu in the SimVascular toolbar and then selecting Preferences -> SimVascular Simulation.

Cheers,
Dave

[Maria Nicole Antonuccio]

Dear Dave,

I thank you for your reply and your suggestion.

I followed your instructions and I was able to run the simulation using the GUI too.

I am very grateful to you.

Kind regards,
Maria Nicole