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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>>     <mailto: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
>>     <mailto:gmx-users-request at gromacs.org>.
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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
>>
>> ------------------------------------------------------------------------
>>
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

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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