[gmx-developers] Configure warning for MPI version, was: [gmx-users] New beta release: 4.5-beta3

[Roland Schulz]

Hi,

should we add configure errors/warning for MPI versions?

Problems known to me:
MVAPICH2 <1.4.1 crashes
OpenMPI <1.4.x is slow
OpenMPI 1.4.0 hangs on GCC 4.4.x on x86/x64

Thus I would suggest we give an error for MVAPICH2 <1.4.1 and OpenMPI 1.4.0
and a warning for OpenMPI <1.4.x

Roland

---------- Forwarded message ----------
From: Da-Wei Li <lidawei at gmail.com>
Date: Wed, Aug 11, 2010 at 4:34 PM
Subject: Re: [gmx-users] New beta release: 4.5-beta3
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


According to our HPC manage, our MVAPICH2's version is 1.0.3.

thanks for the information.

dawei

On Wed, Aug 11, 2010 at 2:52 PM, Roland Schulz <roland at utk.edu> wrote:
> MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1?
> On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li <lidawei at gmail.com> wrote:
>>
>> Yes it is. Now everything is fine with openmpi instead of mvapich2.
>>
>> dawei
>>
>> On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham <mark.abraham at anu.edu.au>
>> wrote:
>> >
>> >
>> > ----- Original Message -----
>> > From: Da-Wei Li <lidawei at gmail.com>
>> > Date: Wednesday, August 11, 2010 6:23
>> > Subject: Re: [gmx-users] New beta release: 4.5-beta3
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >
>> >> Hi,all
>> >>
>> >> Unfortunately, it still crash. Here it is the output of mdrun. Both
>> >> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use
>> >> mvapich2 and intel compiler.
>> >
>> > MPICH variants are known to cause problems. Try OpenMPI.
>> >
>> > Mark
>> >
>> >> ***************************
>> >> Getting Loaded...
>> >> Reading file em.tpr, VERSION 4.5-beta3 (single precision)
>> >> Loaded with Money
>> >>
>> >>
>> >> Will use 9 particle-particle and 7 PME only nodes
>> >> This is a guess, check the performance at the end of the log file
>> >> Making 1D domain decomposition 9 x 1 x 1
>> >>
>> >> Back Off! I just backed up em.trr to ./#em.trr.4#
>> >>
>> >> Back Off! I just backed up em.edr to ./#em.edr.4#
>> >>
>> >> Steepest Descents:
>> >>    Tolerance (Fmax)   =  1.00000e+03
>> >>    Number of steps
>> >> =        50000
>> >> rank 9 in job 1  hpc-8-6.local_58777   caused
>> >> collective abort of all ranks
>> >>   exit status of rank 9: killed by signal 9
>> >>
>> >> *******************************
>> >>
>> >> dawei
>> >>
>> >> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov
>> >> <rossen.apostolov at cbr.su.se> wrote:
>> >> >
>> >> > New beta release of gromacs is available for testing:
>> >> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz.
>> >> >
>> >> > Many bugs have been fixed in this release, mainly double
>> >> precision support
>> >> > with icc compilers, SSE2. Have a look at the release note on
>> >> the website for
>> >> > more details. There are still some issues on Windows platofrms
>> >> that will be
>> >> > resolved before the final release.
>> >> >
>> >> > Please try it out and see if it works as expected! Hopefully
>> >> there won't be
>> >> > many more betas :))
>> >> >
>> >> > Rossen
>> >> > --
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>
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