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 <dur...@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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