superbenji@beniamino:~$ cat /proc/cpuinfo<br>processor : 0<br>vendor_id : GenuineIntel<br>cpu family : 6<br>model : 14<br>model name : Genuine Intel(R) CPU T2400 @ 1.83GHz<br>stepping : 8
<br>cpu MHz : 1829.111<br>cache size : 2048 KB<br>fdiv_bug : no<br>hlt_bug : no<br>f00f_bug : no<br>coma_bug : no<br>fpu : yes<br>fpu_exception : yes<br>cpuid level : 10
<br>wp : yes<br>flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pni monitor vmx est tm2 xtpr<br>bogomips : 3662.13
<br><br>that's all.<br>bogomips is twice cpu frquency.... it seems that OS sees two cpu.... isn't it?<br><br><br><div><span class="gmail_quote">2006/6/4, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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 100%<br>>> 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 4
<br>>>> 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 only<br>>>>>> 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 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 <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>>>>>> > 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<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 <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>
>>>>> 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
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.<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>>>>>
<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 <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>>>> 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 <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>>><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 <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>> 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
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</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://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list
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</a><br></blockquote></div><br>