[gmx-users] gromacs memory usage

[Amit Choubey]

Hi Mark and Alexey,

Thank you for taking the time to write the responses. Following is the info
about the cluster

[choubey at hpc-login2 ~]$ uname -a
Linux hpc-login2 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

[choubey at hpc2000 ~]$ mpiexec --version
Version 0.82, configure options: '--host=x86_64-redhat-linux-gnu'
'--build=x86_64-redhat-linux-gnu' '--target=x86_64-redhat-linux'
'--program-prefix=' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin'
'--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share'
'--includedir=/usr/include' '--libdir=/usr/lib64'
'--libexecdir=/usr/libexec' '--localstatedir=/var'
'--sharedstatedir=/usr/com' '--mandir=/usr/share/man'
'--infodir=/usr/share/info' '--with-pbs=/usr/lib64/torque'
'--disable-p4-shmem' 'CFLAGS=-O2 -g' 'build_alias=x86_64-redhat-linux-gnu'
'host_alias=x86_64-redhat-linux-gnu' 'target_alias=x86_64-redhat-linux'

[choubey at hpc2000 ~]$ ifort --version
ifort (IFORT) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[choubey at hpc2000 ~]$ icc --version
icc (ICC) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.


Thanks for all the help.

Amit





2010/3/3 Alexey Shvetsov <alexxyum at gmail.com>

> Hi
>
> Looks like your system simply runs out of memory. So power cycling nodes
> isnt
> needed. If your cluster runs linux then it already has OOM Killer that will
> kill processes that runs out of memory. Also having swap on nodes is a good
> idea even with huge amount  of memory.
> Memory usage for mpi processes will strongly depend on mpi implentation
> because some of them are usualy caching slave process memory (like usualy
> do
> mvapich2)
>
> So can you provide info about youre cluster setup.
> OS version (including kernel version)  uname -a
> mpi version  mpirun --version or mpiexec --version
> also compiler version that was used for compiling gromacs
>
> On Четверг 04 марта 2010 03:15:53 Amit Choubey wrote:
> > Hi Roland,
> >
> > I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
> > about 154 M particles. This should be feasible according to the numbers.
> > Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core
> then
> >
> > Masternode -> (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here)
> > All other nodes 8*1.06 ~ 8.5 GB
> >
> > I am planning to try the same run on 64 nodes with 8 cores each again but
> > not until i am a little more confident. The problem is if gromacs crashes
> > due to memory it makes the nodes to hang and people have to recycle the
> > power supply.
> >
> >
> > Thank you,
> >
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com
> mailto:alexxy at gentoo.org
> mailto:alexxy at omrb.pnpi.spb.ru
>
> --
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