Fwd: [its-cluster-admin] Fwd: [gmx-users] gmx_blast error when attempting to run in parallel
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 11 21:08:14 CEST 2009
Erik Marklund wrote:
> Your admin compiled another version thah the one you're using. Look
> closely at tle path.
>
> /Erik
<snip>
>> export CPPFLAGS="/usr/local/fftw-3.1.2/include"
In addition, this is not correct. It should read:
export CPPFLAGS="-I/usr/local/fftw-3.1.2/include"
>> ./configure --prefix=/usr/local/gromacs/gromacs-${version}
>> --with-fft=fftw3 --enable-mpi
>> make > make.out 2>&1
>> make install
I don't know if this makes any difference or not (probably not), but if you just
want the mdrun executable, the commands should be "make mdrun" and "make
install-mdrun"
For diagnostic purposes, it may be more useful to run the installation manually,
instead of with a script. That way, if there are warnings along the way
(configure should have complained about the CPPFLAGS...), then you will see them
instead of going on auto-pilot.
-Justin
>>
>> The name of executable should not really matter. Any way I will try to
>> build new version later today or tomorrow. You can give a try
>> yourself. If you are succeded or I make progress let me know. Also
>> could you please sene me some of your simple test files.
>>
>> Thanks.
>> Tula
>>
>>
>>
>>
>>
>> On Thu, Jun 11, 2009 at 10:29 AM, Sashank Karri <srk18 at case.edu
>> <mailto:srk18 at case.edu>> wrote:
>>
>> Hi Tula,
>>
>> I received two e-mails informing me that gromacs was not compiled
>> with MPI. Here is the second, more informative e-mail. Could you
>> possibly try compiling gromacs-4.0.5 this time? I'm around
>> Fridays with nothing to do now, if you want someone with a little
>> bit of gromacs experience around while you're working on it.
>>
>> Thanks,
>>
>> Sashank
>>
>> ---------- Forwarded message ----------
>> From: *Justin A. Lemkul* <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> Date: Thu, Jun 11, 2009 at 8:24 AM
>> Subject: Re: [gmx-users] gmx_blast error when attempting to run in
>> parallel
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>
>>
>>
>>
>>
>>
>> Sashank Karri wrote:
>>
>> Hi, I'm running gromacs-4.0.3 on a cluster. I am testing
>> gromacs on it. We are currently getting this error when I run
>> with 4 nodes with one dedicated to PME calculations.
>> Back Off! I just backed up md.log to ./#md.log.5#
>> Reading file ionsol_minim96-1.tpr, VERSION 4.0.3 (single
>> precision)
>>
>> ------------------------------
>> -------------------------
>> Program mdrun, VERSION 4.0.3
>> Source code file: network.c, line: 357
>>
>> Routine should not have been called:
>> gmx_bast
>> -------------------------------------------------------
>>
>> "I'll Match Your DNA" (Red Hot Chili Peppers).
>>
>> Here is my job that I'm submitting to the cluster.
>>
>> #PBS -N ionsol_karri
>> #PBS -l walltime=24:00:00
>> #PBS -l nodes=4:ppn=4:quad
>> #PBS -j oe
>>
>> module load mpich
>> module load gromacs-4.0.3
>> cd /home/srk18/newplcre/
>> mpirun -nodes 4 /usr/local/gromacs/gromacs-4.0.3/bin/mdrun
>> -npme 1 -s ionsol_minim96-1.tpr -o finminim96_traj.trr -x
>> finminim96_traj.xtc -c final_minim.g96 -e enermin_fin.edr -cpo
>> state96.cpt
>>
>>
>> Is your mdrun truly MPI-enabled? Typically the configure script
>> advises you to append _mpi to the parallel version.
>>
>> Also, upgrade to the newest version of Gromacs, 4.0.5, and try
>> again. That way, if it is a bug, then changes can be made to the
>> newest version, and not one that is five months old.
>>
>> -Justin
>>
>> When discussing the installation of gromacs earlier with the
>> cluster admin, he sent the following message:
>>
>> >I remember I seeing your error (not the present error) while
>> I tried to make the dynamic version of the GROMACS. So I used
>> the --enable-static while building parallel version of the
>> GROMACS. That build the executable and most of the inbuilt
>> test were successful. If you think we need dynamic build let
>> me know, I might have to struggle a bit. Also It would be good
>> if you share information you have regarding building.
>>
>> Do you folks have any idea as to how to fix the above error?
>>
>> Thanks,
>> Sashank Karri
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>> Tula R Paudel Ph.D
>> 10900 Euclid Ave
>> Rockfeller 104A / Crawford 403
>> Cleveland OH-44106
>> @216 368 4035, 216 368 0395
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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>> Please search the archive at http://www.gromacs.org/search before
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>> interface or send it to gmx-users-request at gromacs.org.
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>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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