-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Beniamino,
No, you should see a line: processor : 1 together with its full description. Your output means your system sees a single processor. Looks like a hardware problem, then. HTH, Miguel En/na Beniamino Sciacca ha escrit: > [EMAIL PROTECTED]:~$ cat /proc/cpuinfo > processor : 0 > vendor_id : GenuineIntel > cpu family : 6 > model : 14 > model name : Genuine Intel(R) CPU T2400 @ 1.83GHz > stepping : 8 > cpu MHz : 1829.111 > cache size : 2048 KB > fdiv_bug : no > hlt_bug : no > f00f_bug : no > coma_bug : no > fpu : yes > fpu_exception : yes > cpuid level : 10 > wp : yes > 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 > bogomips : 3662.13 > > that's all. > bogomips is twice cpu frquency.... it seems that OS sees two cpu.... > isn't it? > > > 2006/6/4, David van der Spoel <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>: > > Beniamino Sciacca wrote: > > with "-c 2" I've two processes, each one running at nearly 50%. > > with "-c 4" I've four processes, each one running at nearly 25% > > with "-c 1" I've only one process wich runs at nearly 99% > > I tried also with mdrun_Nmpi (compiled without enabling mpi), and it > > runs at nearly 99%. > > Is it possible that the software sees only one core? > > I think your OS only sees one processor. > if Linux try: > cat /proc/cpuinfo > > > > > > Beniamino > > > > Yang Ye ha scritto: > > > >> Use top to check, you shall have two processes running at nearly 100% > >> with "-c 2" > >> > >> Yang Ye > >> > >> Beniamino Sciacca wrote: > >> > >>> I've just tried "mpirun -c 2 mdrun..." (34 h/ns). > >>> It works, but the problem is the same... the simulation time.... > >>> In fact I also tried "mpirun -c 1 mdrun" (32 h/ns) and "mpirun > -c 4 > >>> mdrun" (34 h/ns), but the simulation time remain the same! > >>> > >>> > >>> Yang Ye ha scritto: > >>> > >>>> Beniamino Sciacca wrote: > >>>> > >>>>> I never used mprun -np 2, and I had not problem. Before I didn't > >>>>> use "mprun -np 2", now I don't use "mprun -np 2" but simulation > >>>>> time now is twice. It has changed from a day to the other. > >>>>> However I've just tried, like you suggested, to use " -np 2" (in > >>>>> grompp and in mdrun) but I obtain an error: > >>>>> ------------------------------------------- > >>>>> "Program mdrun_d, VERSION 3.3.1 > >>>>> Source code file: init.c, line: 69 > >>>>> > >>>>> Fatal error: > >>>>> run input file DNA8_mdEq.tpr was made for 2 nodes, > >>>>> while mdrun_d expected it to be for 1 nodes. > >>>>> " > >>>>> ------------------------------------------- > >>>>> In fact I've only one node. > >>>> > >>>> Try David's mpirun -c 2 mdrun > >>>> > >>>>> > >>>>> Laptop should be running in top speed, I never modified the > >>>>> configuration of energy profile. > >>>>> Beniamino > >>>>> > >>>>> > >>>>> 2006/6/3, Yang Ye <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > >>>>> <mailto: [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>>: > >>>>> > >>>>> First, make sure that you used mdrun -np 2. > >>>>> Second, check your energy profile. Is your laptop running > in top > >>>>> speed? > >>>>> or does it have sleep time? > >>>>> > >>>>> Yang Ye > >>>>> > >>>>> Beniamino Sciacca wrote: > >>>>> > I don't understand what you talking about... > >>>>> > I didn't write any hostfile.... I'm not in a cluster. I only > >>>>> use my > >>>>> > notebook with the two cores. > >>>>> > In fact I type "lamboot" without -v....... > >>>>> > > >>>>> > Beniamino > >>>>> > > >>>>> > Mark Abraham ha scritto: > >>>>> >> Did your default LAM hostfile configuration (or > whatever it is) > >>>>> >> change from 2 processors to one? > >>>>> >> > >>>>> >> Mark > >>>>> >> _______________________________________________ > >>>>> >> gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >>>>> <mailto: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> > >>>>> >> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>> >> Please don't post (un)subscribe requests to the list. Use > >>>>> the www > >>>>> >> interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > >>>>> <mailto:[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>. > >>>>> >> Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > >>>>> <http://www.gromacs.org/mailing_lists/users.php> > >>>>> >> > >>>>> > _______________________________________________ > >>>>> > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >>>>> <mailto: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> > >>>>> > http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>> > Please don't post (un)subscribe requests to the list. > Use the > >>>>> www > >>>>> > interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > >>>>> <mailto: [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>. > >>>>> > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > >>>>> > > >>>>> > >>>>> -- > >>>>> /Regards,/ > >>>>> Yang Ye > >>>>> /Computational Biology Lab > >>>>> School of Biological Sciences > >>>>> Nanyang Technological University > >>>>> Singapore > >>>>> Tel: 6316-2884 > >>>>> / > >>>>> > >>>>> _______________________________________________ > >>>>> gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >>>>> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>>> Please don't post (un)subscribe requests to the list. Use the > >>>>> www interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > >>>>> <mailto: [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>. > >>>>> Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > >>>>> > >>>>> > >>>>> > ------------------------------------------------------------------------ > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users > <http://www.gromacs.org/mailman/listinfo/gmx-users> > >>>>> Please don't post (un)subscribe requests to the list. Use the www > >>>>> interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> . > >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >>>> http://www.gromacs.org/mailman/listinfo/gmx-users > >>>> Please don't post (un)subscribe requests to the list. Use the www > >>>> interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>>> > >>> _______________________________________________ > >>> gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > <http://www.gromacs.org/mailman/listinfo/gmx-users> > >>> Please don't post (un)subscribe requests to the list. Use the www > >>> interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >>> > >> > >> > >> > >> _______________________________________________ > >> gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > >> http://www.gromacs.org/mailman/listinfo/gmx-users > <http://www.gromacs.org/mailman/listinfo/gmx-users> > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >> > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > <http://www.gromacs.org/mailing_lists/users.php> > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > <http://www.gromacs.org/mailing_lists/users.php> > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: [EMAIL PROTECTED] - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFEguFmF6oOrDvhbQIRAmBvAJ4s6eRv9CyjmNwkY5IbQZU0xiImJQCgnDuz UTMxbS23SV52J3Fd3yfDUbA= =FL5e -----END PGP SIGNATURE----- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
