<br /><br /><span>On 04/05/11, <b class="name">Bharati Singh </b> <bharati0307@gmail.com> wrote:</span><blockquote cite="mid:BANLkTikKF49XHtkizfT52OMYM+bYFrnsww@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi Mark,<br /><br />Sorry for your inconvenience<br />As you said some kind of (dynamic) linking problem, Is it possible to resolve it? </div></blockquote><br />Yes, but you will need someone who can troubleshoot what has and has not worked on your system. We do not have any relevant knowledge, so can't help. Using configure --disable-shared might help.<br /><br />Mark<br /><br /><blockquote cite="mid:BANLkTikKF49XHtkizfT52OMYM+bYFrnsww@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Thanks & Regards,<br />Bharati<br /><br /><br /><div class="gmail_quote">On Tue, May 3, 2011 at 6:59 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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;">
<div bgcolor="#ffffff" text="#000000"><div class="im">
On 3/05/2011 8:19 PM, Bharati Singh wrote:
<blockquote type="cite"> Mentioned method is working in another user's home
directory on same machine, then I dont think the problem with
linking.<br />
</blockquote>
<br /></div>
Please be specific... I can think of three different things you
might mean by the "mentioned method", and when you've not troubled
to address the specific points I've raised, I'm not going to be
troubled to guess what you do mean :-)<br /><font color="#888888">
<br />
Mark</font><div><div ><br/></div><div class="h5"><br />
<br />
<blockquote type="cite">
<div class="gmail_quote">On Tue, May 3, 2011 at 3:34 PM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abromeaham@anu.edu.au" target="1">Mark.Abromeaham@anu.edu.au</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;">
<div bgcolor="#ffffff" text="#000000">
<div> On 3/05/2011 7:37 PM, Bharati Singh wrote:
<blockquote 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 />
</div>
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 />
<font color="#888888"> <br />
Mark</font>
<div>
<div><br />
<br />
<blockquote 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 href="mailto:banskt.saikat@gmail.com" target="1">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>On Tue, May 3, 2011 at 2:35 PM, Bharati
Singh <span dir="ltr"><<a href="mailto:bharati0307@gmail.com" target="1">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><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 />
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28<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 />
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-- <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 href="mailto:amit@jncasr.ac.in" target="1">bharati_singh@jncasr.ac.in</a><br />
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-- <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 href="mailto:amit@jncasr.ac.in" target="1">bharati_singh@jncasr.ac.in</a><br />
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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 href="mailto:amit@jncasr.ac.in" target="1">bharati_singh@jncasr.ac.in</a><br /><br /><br /><a href="http://www.jncasr.ac.in/ccms" target="1">http://www.jncasr.ac.in/ccms</a><br />
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