Hi,<div><br></div><div>should we add configure errors/warning for MPI versions?</div><div><br></div><div>Problems known to me:</div><div>MVAPICH2 <1.4.1 crashes</div><div>OpenMPI <1.4.x is slow</div><div>OpenMPI 1.4.0 hangs on GCC 4.4.x on x86/x64</div>
<div><br></div><div>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 </div><div><br></div><div>Roland</div><div><br><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Da-Wei Li</b> <span dir="ltr"><<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>></span><br>Date: Wed, Aug 11, 2010 at 4:34 PM<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><br>According to our HPC manage, our MVAPICH2's version is 1.0.3.<br>
<br>
thanks for the information.<br>
<br>
dawei<br>
<div><div></div><div class="h5"><br>
On Wed, Aug 11, 2010 at 2:52 PM, Roland Schulz <<a href="mailto:roland@utk.edu">roland@utk.edu</a>> wrote:<br>
> MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1?<br>
> On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li <<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>> wrote:<br>
>><br>
>> Yes it is. Now everything is fine with openmpi instead of mvapich2.<br>
>><br>
>> dawei<br>
>><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>><br>
>> 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>
><br>
><br>
> --<br>
> ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
> 865-241-1537, ORNL PO BOX 2008 MS6309<br>
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