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 <[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]>
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 [email protected]
<mailto:[email protected]>.
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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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
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posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
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--
========================================
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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