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

Hi, As written on the website, g_mmpbsa does not directly support MPI. g_mmpbsa does not include any code concerning OpenMP and MPI. However, We have tried to interface MPI and OpenMP functionality of APBS by some mechanism. One may use g_mmpbsa with MPI by following: (1) allocate number of

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

after several days of trial and error, i was told only today that our HPC indeed has one cluster/queue (40 core nodes SMP) that does not require the use of aprun/mprun. so, after having compiled all the tools again on that cluster, i am finally able to execute many processes per node.

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

Ok. I misunderstood your intention to be to run a single calculation with three MPI domains sharing its work. To simply get three independent non-MPI calculations you could indeed use your approach. It sounds like you ran into some behaviour where only one of the three calculations got the stdin,

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

hi again, 3 answers are hidden somewhere below .. Am 28.10.2015 um 15:45 schrieb Mark Abraham: Hi, On Wed, Oct 28, 2015 at 3:19 PM Vedat Durmaz wrote: Am 27.10.2015 um 23:57 schrieb Mark Abraham: Hi, On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz wrote:

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

Am 27.10.2015 um 23:57 schrieb Mark Abraham: Hi, On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz 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;

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

Hi, On Wed, Oct 28, 2015 at 3:19 PM Vedat Durmaz wrote: > > > Am 27.10.2015 um 23:57 schrieb Mark Abraham: > > Hi, > > > > > > On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz wrote: > > > >> hi mark, > >> > >> many thanks. but can you be a little more precise? the

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

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 wrote: > hi guys, > > I'm struggling with the use of diverse

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

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

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

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

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

Hi, On Tue, Oct 27, 2015 at 11:39 PM Vedat Durmaz 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