MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1?<div><br><div class="gmail_quote">On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li <span dir="ltr"><<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Yes it is. Now everything is fine with openmpi instead of mvapich2.<br>
<br>
dawei<br>
<div><div></div><div class="h5"><br>
On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:<br>
><br>
><br>
> ----- Original Message -----<br>
> From: Da-Wei Li <<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>><br>
> Date: Wednesday, August 11, 2010 6:23<br>
> Subject: Re: [gmx-users] New beta release: 4.5-beta3<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
><br>
>> Hi,all<br>
>><br>
>> Unfortunately, it still crash. Here it is the output of mdrun. Both<br>
>> Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use<br>
>> mvapich2 and intel compiler.<br>
><br>
> MPICH variants are known to cause problems. Try OpenMPI.<br>
><br>
> Mark<br>
><br>
>> ***************************<br>
>> Getting Loaded...<br>
>> Reading file em.tpr, VERSION 4.5-beta3 (single precision)<br>
>> Loaded with Money<br>
>><br>
>><br>
>> Will use 9 particle-particle and 7 PME only nodes<br>
>> This is a guess, check the performance at the end of the log file<br>
>> Making 1D domain decomposition 9 x 1 x 1<br>
>><br>
>> Back Off! I just backed up em.trr to ./#em.trr.4#<br>
>><br>
>> Back Off! I just backed up em.edr to ./#em.edr.4#<br>
>><br>
>> Steepest Descents:<br>
>> Tolerance (Fmax) = 1.00000e+03<br>
>> Number of steps<br>
>> = 50000<br>
>> rank 9 in job 1 hpc-8-6.local_58777 caused<br>
>> collective abort of all ranks<br>
>> exit status of rank 9: killed by signal 9<br>
>><br>
>> *******************************<br>
>><br>
>> dawei<br>
>><br>
>> On Tue, Aug 10, 2010 at 3:24 PM, Rossen Apostolov<br>
>> <<a href="mailto:rossen.apostolov@cbr.su.se">rossen.apostolov@cbr.su.se</a>> wrote:<br>
>> ><br>
>> > New beta release of gromacs is available for testing:<br>
>> > <a href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz" target="_blank">ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz</a>.<br>
>> ><br>
>> > Many bugs have been fixed in this release, mainly double<br>
>> precision support<br>
>> > with icc compilers, SSE2. Have a look at the release note on<br>
>> the website for<br>
>> > more details. There are still some issues on Windows platofrms<br>
>> that will be<br>
>> > resolved before the final release.<br>
>> ><br>
>> > Please try it out and see if it works as expected! Hopefully<br>
>> there won't be<br>
>> > many more betas :))<br>
>> ><br>
>> > Rossen<br>
>> > --<br>
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> --<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
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