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

[Mark Abraham]

Hi,


On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz <durmaz at zib.de> wrote:

> 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 ...
>

It has the sentence "Although g_mmpbsa does not support mpirun..." aprun is
a form of mpirun, so I assumed you knew that what you were trying was
actually something that could work, which would therefore have to be with
the APBS back end. The point of what it says there is that you don't run
g_mmpbsa with aprun, you tell it how to run APBS with aprun. This just
avoids the problem entirely because your redirected/interactive input goes
to a single g_mmpbsa as normal, which then launches APBS with MPI support.

Tool authors need to actively write code to be useful with MPI, so unless
you know what you are doing is supposed to work with MPI because they say
it works, don't try.

Mark


>
> 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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