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

Vedat Durmaz durmaz at zib.de
Tue Oct 27 23:38:51 CET 2015

hi mark,

many thanks. but can you be a little more precise? the author's only 
hint regarding mpi is on this site 
"http://rashmikumari.github.io/g_mmpbsa/How-to-Run.html" and related to 
APBS. g_mmpbsa itself doesn't understand openmp/mpi afaik.

the error i'm observing is occurring pretty much before apbs is started. 
to be honest, i can't see any link to my initial question ...

Am 27.10.2015 um 22:43 schrieb Mark Abraham:
> Hi,
> I think if you check out how the g_mmpbsa author intends you to use MPI
> with the tool, your problem goes away.
> http://rashmikumari.github.io/g_mmpbsa/Usage.html
> Mark
> 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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