Fwd: [its-cluster-admin] Fwd: [gmx-users] gmx_blast error when attempting to run in parallel
Erik Marklund
erikm at xray.bmc.uu.se
Thu Jun 11 21:20:08 CEST 2009
Justin A. Lemkul skrev:
>
>
> 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"
Indeed.
>
>>> ./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.
>
I disagree. One should always sift through the configure-/make-output,
obviously (and therefore a tee would be better than the redirection
above), but I find scripting is superior to manual compilation. It makes
it easy to see exactly what options and stuff you used and to alter when
needed. Plus, I can just copy the script when compiling with a slightly
different setup or with another version of gromacs.
/Erik
> -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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>>> <mailto:gmx-users 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 <http://vt.edu> | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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