Thank you for your response, itamar..but the cluster isolated from the
internet for security reasons. i dont think there is any chance to use
fink on the head node either. any other alternatives?<br>regards,<br>kota.<br><br>
<div><span class="gmail_quote">On 2/2/06, <b class="gmail_sendername">Itamar Kass</b> <<a href="mailto:ikass@cc.huji.ac.il" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">ikass@cc.huji.ac.il</a>
> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><font face="Arial" size="2">Why not using fortan?</font></div>
<div><font face="Arial" size="2">install it using Fink and let lam have
it.</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font face="Arial" size="2"> Itamar.</font></div>
<div> </div>
<div>===========================================<br>| Itamar Kass<br>| The
Alexander Silberman<br>| Institute of Life Sciences<br>| Department of
Biological Chemistry<br>| The Hebrew University, Givat-Ram<br>| Jerusalem,
91904, Israel<br>| Tel: +972-(0)2-6585194<br>| Fax: +972-(0)2-6584329<br>|
Email: <a href="mailto:ikass@cc.huji.ac.il" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">ikass@cc.huji.ac.il</a><br>| Net: <a href="http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html</a><br>============================================</div>
<blockquote style="border-left: 2px solid rgb(0, 0, 0); padding-right: 0px; padding-left: 5px; margin-left: 5px; margin-right: 0px;"><div><span>
<div style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: ;">----- Original Message ----- </div>
<div style="background: rgb(228, 228, 228) none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial; font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: ;">
<b>From:</b>
<a title="kotanmd@gmail.com" href="mailto:kotanmd@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">Pradeep Kota</a>
</div>
<div style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: ;"><b>To:</b> <a title="gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
Discussion list for GROMACS users</a>
</div>
<div style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: ;"><b>Sent:</b> Thursday, February 02, 2006 4:43
AM</div>
<div style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: ;"><b>Subject:</b> [gmx-users] mdrun with
mpich</div>
<div><br></div>Dear users,<br> I have compiled gromacs on
our dual core mac os x G5 cluster, and tried running a simulation on a 540
residue protein for 1 ns on 8 processors. i used mpich as the mpi environment
for parallelising gromacs. it worked fine, and the job was split properly and
assigned to nodes. now, the cpu usage per processor is not more than 50% on
any of the processors. and the total running time for this was 13hrs. though
output is written properly onto the specified output file, mdirun doesnot
terminate even after running through all the steps. it still shows two
mdrun_mpi processes running on the head node, with a 0% cpu usage. was going
through gmx-users mailing list and somehow figured out that mpich is not a
good idea for running gromacs. so, i wanted to switch over to lam. now when i
complie gromacs using lam, it is not able to link the libraries properly. so,
i tried reinstalling lam on my cluster. now, lam keeps complaining about not
being able to find a fortran compiler. i should not need a fortran compiler
unless i'm using SUN or SGI for this purpose..(am i going wrong here?). what
flags do i need to compile lam with, in order to compile gromacs successfully?
any help is very much appreciated..<br>thanks in
advance,<br>regards,<br>kota.<br>
</span></div><p>
</p><hr>
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