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 21:00:38 CEST 2009
Your admin compiled another version thah the one you're using. Look
closely at tle path.
/Erik
Sashank Karri skrev:
> Hi,
>
> Our cluster admin argues that gromacs was in fact compiled with
> MPI. Below is the script he used to compile gromacs. Do you see any
> errors in the script? Are there any other possible reasons why I'm
> getting this gmx_bast error?
>
> -Sashank
>
> ---------- Forwarded message ----------
> From: *Tula Paudel* <trp6 at case.edu <mailto:trp6 at case.edu>>
> Date: Thu, Jun 11, 2009 at 10:39 AM
> Subject: Re: [its-cluster-admin] Fwd: [gmx-users] gmx_blast error when
> attempting to run in parallel
> To: Sashank Karri <srk18 at case.edu <mailto:srk18 at case.edu>>
>
>
> Dear Sashank,
>
> I don't agree that it's not compliled with mpi. Here is the script, I
> used to build the gromacs. I clearly used the option --enable-mpi as
> you can see and compiled with mpicc and mpif77.
>
> #!/bin/sh
> export version=4.0.3par
> export CC=mpicc
> export CXXCPP=mpicc
> export CFLAGS="-O2"
> export F77='mpif77'
> export FFLAGS="-O2"
> export CXX=mpicc
> export CPPFLAGS="/usr/local/fftw-3.1.2/include"
> export LDFLAGS="-L/usr/local/fftw-3.1.2/lib
> -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.3.4 -L/usr/lib64 "
> export LIBS=' -lmpich -lpthread -lrt -lfftw -lm'
> cd /usr/local/src/gromacs/gromacs-${version}
> make clean
> make distclean
> ./configure --prefix=/usr/local/gromacs/gromacs-${version}
> --with-fft=fftw3 --enable-mpi
> make > make.out 2>&1
> make install
>
> 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
>
> ------------------------------------------------------------------------
>
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--
-----------------------------------------------
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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