Thank you for your response Mr.David. I compiled lam successfully
without fortran support. all i wanted to know was whether it would make
any difference to the running time of gromacs. I am curious because, it
is well-known that fortran loops are faster than loops of other
languages..so, i wanted to clarify ! moreover, i would want to know how
different this is, from mpich. <br>
thanks for the support.<br>
regards,<br>
kota.<br><br><div><span class="gmail_quote">On 2/2/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
Pradeep Kota wrote:<br>> Thank you for your response, itamar..but the cluster isolated from the<br>> internet for security reasons. i dont think there is any chance to use<br>> fink on the head node either. any other alternatives?
<br>> regards,<br><br>compile LAM without fortran, there's a flag for it<br><br>> kota.<br>><br>> On 2/2/06, *Itamar Kass* <<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a><br>> <mailto:<a href="mailto:ikass@cc.huji.ac.il">
ikass@cc.huji.ac.il</a>> > wrote:<br>><br>> Why not using fortan?<br>> install it using Fink and let lam have it.<br>><br>> Itamar.<br>><br>> ===========================================
<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">ikass@cc.huji.ac.il</a> <mailto:<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il
</a>><br>> | Net:<br>> <a href="http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html">http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html</a><br>> <<a href="http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html">
http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html</a>><br>> ============================================<br>><br>> ----- Original Message -----<br>> *From:* Pradeep Kota <mailto:
<a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com</a>><br>> *To:* Discussion list for GROMACS users<br>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Thursday, February 02, 2006 4:43 AM
<br>> *Subject:* [gmx-users] mdrun with mpich<br>><br>> Dear users,<br>>
I have compiled gromacs on our dual core mac os x G5<br>> cluster, and tried running a simulation on a 540 residue protein<br>> for 1 ns on 8 processors. i used mpich as the mpi environment<br>> for parallelising gromacs. it worked fine, and the job was split
<br>> properly and assigned to nodes. now, the cpu usage per processor<br>> is not more than 50% on any of the processors. and the total<br>> running time for this was 13hrs. though output is written
<br>> properly onto the specified output file, mdirun doesnot<br>> terminate even after running through all the steps. it still<br>> shows two mdrun_mpi processes running on the head node, with a
<br>> 0% cpu usage. was going through gmx-users mailing list and<br>> somehow figured out that mpich is not a good idea for running<br>> gromacs. so, i wanted to switch over to lam. now when i complie
<br>> gromacs using lam, it is not able to link the libraries<br>> properly. so, i tried reinstalling lam on my cluster. now, lam<br>> keeps complaining about not being able to find a fortran
<br>> compiler. i should not need a fortran compiler unless i'm using<br>> SUN or SGI for this purpose..(am i going wrong here?). what<br>> flags do i need to compile lam with, in order to compile gromacs
<br>> successfully? any help is very much appreciated..<br>> thanks in advance,<br>> regards,<br>> kota.<br>><br>> ------------------------------------------------------------------------
<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a>><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the
<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>><br>> _______________________________________________
<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a><br>> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><br>> <<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>><br>><br>><br>><br>> ------------------------------------------------------------------------
<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________
<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>