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On 3/05/2011 7:37 PM, Bharati Singh wrote:
<blockquote
cite="mid:BANLkTi=__wNy7OD4-Z2bdA6+=wcWJg7uqQ@mail.gmail.com"
type="cite"><font face="arial">Hi Team,<br>
<br>
Thanks for your reply.<br>
<br>
I had tried following method to install gromacs-4.0.7 -<br>
<span style="text-decoration: underline;"></span><br>
$ module load intel_all/impi/default<br>
<br>
$ ./configure --enable-mpi --with-fft=fftw2
LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/"
CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw"
F77=mpif77 --prefix=/sfs3/home/bharati/gromacs<br>
<br>
$ make<br>
$ make install<br>
<br>
Following the command to submit the job in queue:<br>
<br>
bsub -q normal4c -n 4 mpirun -srun
/sfs3/home/bharati/gromacs/bin/mdrun -pd -v -s Ag6A12_equil.tpr
-o Ag6A12_equil.trr -c Ag6A12_equil.gro -e Ag6A12_equil.edr -g
Ag6A12_equil.log<br>
<br>
</font><font face="arial"><span style="text-decoration:
underline;"></span></font><font face="arial"><br>
When I submit the job for more than one processors in queue, it
gets terminated immediately without error. It is not creating
any file etc..<br>
</font></blockquote>
<br>
That set of commands should create mdrun_mpi. Why are you not using
it?<br>
<br>
If this mdrun really is the one produced by the above configuration,
the symptoms suggest some kind of (dynamic) linking problem, but we
have no way to be more specific. It's not GROMACS-related.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=__wNy7OD4-Z2bdA6+=wcWJg7uqQ@mail.gmail.com"
type="cite"><font face="arial"><br>
Thanks & Regards,</font><br>
<br>
<div class="gmail_quote">On Tue, May 3, 2011 at 2:40 PM, Saikat
Banerjee <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:banskt.saikat@gmail.com">banskt.saikat@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">Hi,<br>
<br>
Have you checked the error log? Please post the error log.<br>
<br>
Have you configured GROMACS using --enable-mpi?<br>
<br>
Thanks,<br>
Saikat<br>
<br>
<div class="gmail_quote">
<div>
<div class="h5">On Tue, May 3, 2011 at 2:35 PM, Bharati
Singh <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:bharati0307@gmail.com" target="_blank">bharati0307@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5"><font face="arial">Hi Team,<br>
<br>
I have LSF in my cluster ,I have installed
gromacs-4.0.7 on Sampige. It is working fine as a
serial(on 1 processor) ,</font><font face="arial">when
I submit the job for more than one processors in
queue, it gets terminated immediately.Can you
suggest me something about it, please<br>
<br>
Thanks & Regards,</font><br clear="all">
<br>
-- <br>
Bharati Singh<br>
System Administrator<br>
Centre for Computational Materials Science(CCMS)<br>
Jawaharlal Nehru Centre for Advanced Scientific
Research(JNCASR),<br>
Bangalore - 560 064 <br>
India.<br>
mob. : 08970898515<br>
Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
Fax : +91 80 2208 2906<br>
Email : <a moz-do-not-send="true"
href="mailto:amit@jncasr.ac.in" target="_blank">bharati_singh@jncasr.ac.in</a><br>
<br>
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<br>
<br clear="all">
<br>
-- <br>
-------------------------------------------------------------------<br>
Saikat Banerjee<br>
Integrated Ph.D student<br>
Prof B. Bagchi's group<br>
Room no. 210<br>
Solid State and Structural Chemistry Unit (SSCU)<br>
Indian Institute of Science<br>
Bangalore-560012<br>
<br>
Ph: +91-80-22933305 (lab)<br>
+91-80-23602338 (lab)<br>
+91-9980228606 (mobile)<br>
<br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
Bharati Singh<br>
System Administrator<br>
Centre for Computational Materials Science(CCMS)<br>
Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),<br>
Bangalore - 560 064 <br>
India.<br>
mob. : 08970898515<br>
Phone : +91 80 2208 2944 + Ext. 26 & 28<br>
Fax : +91 80 2208 2906<br>
Email : <a moz-do-not-send="true"
href="mailto:amit@jncasr.ac.in" target="_blank">bharati_singh@jncasr.ac.in</a><br>
<br>
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