Hi,<br><br> 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?<br><br>-Sashank<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Tula Paudel</b> <span dir="ltr"><<a href="mailto:trp6@case.edu">trp6@case.edu</a>></span><br>
Date: Thu, Jun 11, 2009 at 10:39 AM<br>Subject: Re: [its-cluster-admin] Fwd: [gmx-users] gmx_blast error when attempting to run in parallel<br>To: Sashank Karri <<a href="mailto:srk18@case.edu">srk18@case.edu</a>><br>
<br><br>Dear Sashank, <br><br>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. <br>
<br>#!/bin/sh<br>export version=4.0.3par<br>export CC=mpicc<br>export CXXCPP=mpicc<br>export CFLAGS="-O2"<br>export F77='mpif77'<br>export FFLAGS="-O2"<br>export CXX=mpicc<br>export CPPFLAGS="/usr/local/fftw-3.1.2/include"<br>
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 "<br>export LIBS=' -lmpich -lpthread -lrt -lfftw -lm'<br>cd /usr/local/src/gromacs/gromacs-${version}<br>
make clean<br>make distclean<br>./configure --prefix=/usr/local/gromacs/gromacs-${version} --with-fft=fftw3 --enable-mpi<br>make > make.out 2>&1<br>make install<br><br>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. <br>
<br>Thanks. <br>Tula<div><div></div><div class="h5"><br> <br><br><br><br><div class="gmail_quote">On Thu, Jun 11, 2009 at 10:29 AM, Sashank Karri <span dir="ltr"><<a href="mailto:srk18@case.edu" target="_blank">srk18@case.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Tula,<br><br>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.<br>
<br>Thanks,<br><br>Sashank<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Justin A. Lemkul</b> <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
Date: Thu, Jun 11, 2009 at 8:24 AM<br>Subject: Re: [gmx-users] gmx_blast error when attempting to run in parallel<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div>
<br>
<br><br><div><br>
<br>
Sashank Karri wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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. <br>
Back Off! I just backed up md.log to ./#md.log.5#<br>
Reading file ionsol_minim96-1.tpr, VERSION 4.0.3 (single precision)<br>
<br>
------------------------------<br>
-------------------------<br>
Program mdrun, VERSION 4.0.3<br>
Source code file: network.c, line: 357<br>
<br>
Routine should not have been called:<br>
gmx_bast<br>
-------------------------------------------------------<br>
<br>
"I'll Match Your DNA" (Red Hot Chili Peppers).<br>
<br>
Here is my job that I'm submitting to the cluster.<br>
<br>
#PBS -N ionsol_karri<br>
#PBS -l walltime=24:00:00<br>
#PBS -l nodes=4:ppn=4:quad<br>
#PBS -j oe<br>
<br>
module load mpich<br>
module load gromacs-4.0.3<br>
cd /home/srk18/newplcre/<br>
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<br>
<br>
</blockquote>
<br></div></div>
Is your mdrun truly MPI-enabled? Typically the configure script advises you to append _mpi to the parallel version.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div>
When discussing the installation of gromacs earlier with the cluster admin, he sent the following message:<br>
<br>
>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.<br>
<br>
Do you folks have any idea as to how to fix the above error?<br>
<br>
Thanks,<br>
Sashank Karri<br>
<br>
<br></div></div><div>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote></div><br><br clear="all"><br></div></div><font color="#888888">-- <br>Tula R Paudel Ph.D <br>10900 Euclid Ave <br>Rockfeller 104A / Crawford 403<br>Cleveland OH-44106<br>@216 368 4035, 216 368 0395<br>
</font></div><br>