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* <[email protected] <mailto:[email protected]>>
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 <[email protected] <mailto:[email protected]>>
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 <[email protected]
<mailto:[email protected]>> 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* <[email protected] <mailto:[email protected]>>
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 <[email protected]
<mailto:[email protected]>>
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
<mailto:[email protected]>
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Please search the archive at http://www.gromacs.org/search before
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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
[email protected] http://xray.bmc.uu.se/molbiophys
_______________________________________________
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