Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Fri, 09 Jun 2006 03:36:21 -0700 

Thanks a lot Dr. David Spoel :)
I compiled GROMACS again with CFLAGS=-g , after that i ran mdrun_mpi. It is running fine though with some warning. This time I specified the full path of mdrun_mpi binary. But now I am having one strange problem. Sometimes it runs smoothly and sometimes it does not. I am not able to pin point this problem.Actually i am running mdrun_mpi by using one wrapper script as follows: 


########################################################################################################

#!/bin/csh -f
#
#
# (c) 2004 Sun Microsystems, Inc. Use is subject to license terms.

# ---------------------------
# our name
#$ -N MPI_Job
#
# pe request
#$ -pe mpich* 2-20
#
# MPIR_HOME from submitting environment
#$ -v MPIR_HOME=/opt/mpichdefault-1.2.6
# ---------------------------

#
# needs in
#   $NSLOTS
#       the number of tasks to be used
#   $TMPDIR/machines
#       a valid machine file to be passed to mpirun

echo "Got $NSLOTS slots."

# enables $TMPDIR/rsh to catch rsh calls if available
set path=($TMPDIR $path)

$MPIR_HOME/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines
-nolocal  /to/install/gromacs/x86_64-unknown-linux-gnu/bin/mdrun_mpi -v
-s full -o full -x full -c after_full -e full -g full  >& full.job &


###################################################################################################################

Then I have to execute this script by following commands

qsub -pe mpichpar <no of nodes> -q  par.q  <file name of above script>



But the problem is: sometimes it works well and sometimes it gives me the 
following error message:


***********************************************
Cannot read /tmp/28015.1.par.q/machines.
Looked for files with extension LINUX in
directory /opt/mpichdefault-1.2.6//share .
***********************************************



It seems that there is some problem in reading machines.LINUX file, but if 
there is some problem then it should not work sometimes, as it does, so I am 
very much confused now !!!



I have also installed some other software package but they are running fine 
with same script.



I also talked with my system adminstrator he told me there is some problem 
in installing the GROMACS that why it is behaving so strangely.



Could you suggest me something about what am I doing wrong or where am I 
going wrong????



Thanks again for your kind help (Atleast now I am able to run mdrun_mpi in 
the SUN CLUSTER)


Warm regards,
Alok Jain


----- Original Message ----- 
From: "David van der Spoel" <[EMAIL PROTECTED]>

To: "Discussion list for GROMACS users" <[email protected]>
Sent: Thursday, June 08, 2006 11:11 PM
Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster



Alok wrote:

I tried ldd `which mdrun_mpi` output is :-

###########################################################################

$ldd `which mdrun_mpi`
       libnsl.so.1 => /lib64/libnsl.so.1 (0x0000002a95687000)
       libXm.so.3 => /usr/X11R6/lib64/libXm.so.3 (0x0000002a9579e000)
       libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000002a95b2e000)
       libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000002a95c8e000)
       libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000002a95d98000)
       libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000002a95eb2000)
       libXp.so.6 => /usr/X11R6/lib64/libXp.so.6 (0x0000002a95fc3000)
       libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a960cc000)
       libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x0000002a962c0000)
       libz.so.1 => /usr/lib64/libz.so.1 (0x0000002a964d9000)
       libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a965e7000)
       libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a966fc000)
       libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a96884000)
       libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000002a96ac8000)
       libdl.so.2 => /lib64/libdl.so.2 (0x0000002a96be2000)

       /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 
(0x0000002a95556000)




################################################################################## 
what can we conclude from this output ??



there is no FFT, no MPI, so these are hard linked into the program. That 
means you can not have problems with those at least.



I will try "make CFLAGS=-g install" option also....then i will come back 
to you.


Thanks a lot !

best regards,
Alok Jain







----- Original Message ----- From: "David van der Spoel" 
<[EMAIL PROTECTED]>

To: "Discussion list for GROMACS users" <[email protected]>
Sent: Thursday, June 08, 2006 8:25 PM
Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster



Alok wrote:


I tried mpirun mdrun_mpi -h but I got same error message

[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_29243:  p4_error: : 0

Thanks for your kind attention.


Apart from upgrading to FFTW3 and GROMACS 3.3.1, you could try


ldd `which mdrun` to check which libraries are being used. Maybe you are 
mixing different MPI libraries (i.e. compile with one, run with 
another).


You can also compile by
make distclean
make CFLAGS=-g install

in order to be able to debug

--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED]   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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