[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 22:10:12 CET 2015

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


More information about the gromacs.org_gmx-users mailing list