OK!!!<br>now it works.<br>I installed a kernel-image smp (for my kernel 2.6)<br>and now with "-c 2" it works!!!<br>I've two processes running at nearly 100%, and the simulation time is reduced at 50%!<br>But now i don't understand why before (one week ago without smp it worked....) mah....
<br>I thank all you very much<br><br>regards<br>Beniamino<br><br><div><span class="gmail_quote">2006/6/4, Yang Ye <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
So, the kernel you used from Debian could be a non-SMP one. Change<br>another in the boot screen if there is.<br>\<br>Yang Ye<br><br>David van der Spoel wrote:<br>> Beniamino Sciacca wrote:<br>>> with "-c 2" I've two processes, each one running at nearly 50%.
<br>>> with "-c 4" I've four processes, each one running at nearly 25%<br>>> with "-c 1" I've only one process wich runs at nearly 99%<br>>> I tried also with mdrun_Nmpi (compiled without enabling mpi), and it
<br>>> runs at nearly 99%.<br>>> Is it possible that the software sees only one core?<br>><br>> I think your OS only sees one processor.<br>> if Linux try:<br>> cat /proc/cpuinfo<br>><br>><br>
>><br>>> Beniamino<br>>><br>>> Yang Ye ha scritto:<br>>><br>>>> Use top to check, you shall have two processes running at nearly<br>>>> 100% with "-c 2"<br>>>>
<br>>>> Yang Ye<br>>>><br>>>> Beniamino Sciacca wrote:<br>>>><br>>>>> I've just tried "mpirun -c 2 mdrun..." (34 h/ns).<br>>>>> It works, but the problem is the same... the simulation time....
<br>>>>> In fact I also tried "mpirun -c 1 mdrun" (32 h/ns) and "mpirun -c<br>>>>> 4 mdrun" (34 h/ns), but the simulation time remain the same!<br>>>>><br>>>>>
<br>>>>> Yang Ye ha scritto:<br>>>>><br>>>>>> Beniamino Sciacca wrote:<br>>>>>><br>>>>>>> I never used mprun -np 2, and I had not problem. Before I didn't
<br>>>>>>> use "mprun -np 2", now I don't use "mprun -np 2" but simulation<br>>>>>>> time now is twice. It has changed from a day to the other.<br>>>>>>> However I've just tried, like you suggested, to use " -np 2" (in
<br>>>>>>> grompp and in mdrun) but I obtain an error:<br>>>>>>> -------------------------------------------<br>>>>>>> "Program mdrun_d, VERSION 3.3.1<br>>>>>>> Source code file:
init.c, line: 69<br>>>>>>><br>>>>>>> Fatal error:<br>>>>>>> run input file DNA8_mdEq.tpr was made for 2 nodes,<br>>>>>>> while mdrun_d expected it to be for 1 nodes.
<br>>>>>>> "<br>>>>>>> -------------------------------------------<br>>>>>>> In fact I've only one node.<br>>>>>><br>>>>>> Try David's mpirun -c 2 mdrun
<br>>>>>><br>>>>>>><br>>>>>>> Laptop should be running in top speed, I never modified the<br>>>>>>> configuration of energy profile.<br>>>>>>> Beniamino
<br>>>>>>><br>>>>>>><br>>>>>>> 2006/6/3, Yang Ye <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a><br>>>>>>> <mailto:
<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a>>>:<br>>>>>>><br>>>>>>> First, make sure that you used mdrun -np 2.<br>>>>>>> Second, check your energy profile. Is your laptop running in top
<br>>>>>>> speed?<br>>>>>>> or does it have sleep time?<br>>>>>>><br>>>>>>> Yang Ye<br>>>>>>><br>>>>>>> Beniamino Sciacca wrote:
<br>>>>>>> > I don't understand what you talking about...<br>>>>>>> > I didn't write any hostfile.... I'm not in a cluster. I<br>>>>>>> only use my<br>>>>>>> > notebook with the two cores.
<br>>>>>>> > In fact I type "lamboot" without -v.......<br>>>>>>> ><br>>>>>>> > Beniamino<br>>>>>>> ><br>>>>>>> > Mark Abraham ha scritto:
<br>>>>>>> >> Did your default LAM hostfile configuration (or whatever<br>>>>>>> it is)<br>>>>>>> >> change from 2 processors to one?<br>>>>>>> >>
<br>>>>>>> >> Mark<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<br>>>>>>> the www<br>>>>>>> >> interface or send it to
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<br>>>>>>> <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>>>>>>> > 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<br>>>>>>> the www<br>>>>>>> > 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
<br>>>>>>> <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>>>>>>> ><br>>>>>>><br>>>>>>> --
<br>>>>>>> /Regards,/<br>>>>>>> Yang Ye<br>>>>>>> /Computational Biology Lab<br>>>>>>> School of Biological Sciences<br>>>>>>> Nanyang Technological University
<br>>>>>>> Singapore<br>>>>>>> Tel: 6316-2884<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
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<br>>>>>>><br>>>>>>> ------------------------------------------------------------------------<br>>>>>>><br>>>>>>><br>>>>>>> _______________________________________________
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</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 www<br>>>>> interface or send it to
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</a><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 www<br>>>> interface or send it to
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