[gmx-users] multiple processes of a gromacs tool requiring user action at runtime on one Cray XC30 node using aprun

Mark Abraham mark.j.abraham at gmail.com
Tue Oct 27 22:44:05 CET 2015


I think if you check out how the g_mmpbsa author intends you to use MPI
with the tool, your problem goes away.


On Tue, Oct 27, 2015 at 10:10 PM Vedat Durmaz <durmaz at zib.de> wrote:

> hi guys,
> I'm struggling with the use of diverse gromacs commands on a Cray XC30
> system. actually, it's about the external tool g_mmpbsa which requires
> user action during runtime. i get similar errors with other Gromacs
> tools, e.g., make_ndx, though, i know that it doesn't make sense to use
> more than one core for make_ndx. however, g_mmpsa (or rather apbs used
> by g_mmpbsa) is supposed to be capable of multiple cores using openmp.
> so, as long as i assign all of the 24 cores of a computing node to one
> process through
> aprun -n 1 ../run_mmpbsa.sh
> everthing works fine. user input is accepted either interactively, by
> using the echo command, or through a here construction (""... << EOF ...
> EOF). however, as soon as I try to split the 24 cores of a node to
> multiple processes (more than one) using for instance
> aprun -n 3 -N 3 -cc 0-7:8-15:16-23 ../run_mmpbsa.sh
> (and OMP_NUM_THREADS=8), there is neither an occasion to feed with user
> input in the interactive mode nor it is recognized through echo/here in
> the script. instead, i get the error
>  >> Source code file: .../gromacs-4.6.7/src/gmxlib/index.c, line: 1192
>  >> Fatal error:
>  >> Cannot read from input
> where, according to the source code, "scanf" malfunctions. when i use,
> for comparison purposes, make_ndx that i would like to feed with "q" i
> observe a similar error:
>  >>Source code file: .../gromacs-4.6.7/src/tools/gmx_make_ndx.c, line: 1219
>  >>Fatal error:
>  >>Error reading user input
> here, it's "fgets" which is malfunctioning.
> does anyone have an idea what this could be caused by? what do i need to
> consider/change in order to be able to start more than process on one
> computing node?
> thanks in advance
> vedat
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