Recently I installed gromacs4.5.1 without mpi support on my workstation with 8 cores using cmake and make -j 8, make install commands ( as suggested on installation instructions).
Now when I do mdrun it automatically utilizes all the cores and runs much faster than earlier version (4.0.7) , which was not using all cores. I am also surprised , how can mdrun runs on 8 cores without explicitly specifying no. of cores? Its good that mdrun is using all cores, but there may be situations when I dont want mdrun to use all cores. Can I anyone suggest how to control that? thanks sikandar On Wed, Oct 13, 2010 at 10:35 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 14/10/2010 1:35 PM, Sathish wrote: > > > Thanks for clarifying my doubts. I have started to run demo its working. > I have checked processor speed its says only one cpu is running for that > program (pdb2gmx). my server configuration (RHEL 5.5) is 2 processor with 6 > core, totally 24 processor. I have set "export NCPU=24" while installing > gromacs. Could you tell me how to run gromacs with all processor ? > > > The only thing that parallelizes is mdrun. Nothing much else runs for long > enough for it to be worth it. Either MPI or thread-based parallelism can > work. Search the website and/or tutorial material for more details. > > > Mark > > > > On Wed, Oct 13, 2010 at 8:24 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> >> >> Sathish wrote: >> >>> Dear Mark, >>> >>> wow its working. Thank you lot.. As per installation instruction gromacs >>> installed successfully and demo also working. >>> Then i have downloaded test set "gmxtest-4.0.4.tgz". While running i got >>> error message like this, >>> >>> [r...@xxx gmxtest]# ./gmxtest.pl <http://gmxtest.pl> all >>> >>> FAILED. Check files in angles1 >>> FAILED. Check files in angles125 >>> FAILED. Check files in bham >>> FAILED. Check files in bonds1 >>> FAILED. Check files in bonds125 >>> FAILED. Check files in dih1 >>> FAILED. Check files in dih125 >>> FAILED. Check files in g96angles1 >>> FAILED. Check files in g96angles125 >>> FAILED. Check files in g96bonds1 >>> FAILED. Check files in g96bonds125 >>> FAILED. Check files in imp1 >>> FAILED. Check files in imp36 >>> FAILED. Check files in morse >>> FAILED. Check files in rb1 >>> FAILED. Check files in rb125 >>> 16 out of 16 simple tests FAILED >>> FAILED. Check files in acetonitrilRF >>> FAILED. Check files in aminoacids >>> FAILED. Check files in argon >>> FAILED. Check files in butane >>> FAILED. Check files in dec+water >>> FAILED. Check files in ethyleenglycol >>> FAILED. Check files in fe_test >>> FAILED. Check files in field >>> FAILED. Check files in nacl >>> FAILED. Check files in sw >>> FAILED. Check files in tip4p >>> FAILED. Check files in tip4pflex >>> FAILED. Check files in urea >>> FAILED. Check files in water >>> 14 out of 14 complex tests FAILED >>> FAILED. Check files in kernel020 >>> FAILED. Check files in kernel120 >>> FAILED. Check files in kernel121 >>> FAILED. Check files in kernel122 >>> FAILED. Check files in kernel123 >>> FAILED. Check files in kernel124 >>> FAILED. Check files in kernel220 >>> FAILED. Check files in kernel221 >>> FAILED. Check files in kernel222 >>> FAILED. Check files in kernel223 >>> FAILED. Check files in kernel224 >>> FAILED. Check files in kernel320 >>> FAILED. Check files in kernel321 >>> FAILED. Check files in kernel322 >>> FAILED. Check files in kernel323 >>> FAILED. Check files in kernel324 >>> 16 out of 63 kernel tests FAILED >>> Error not all 45 pdb2gmx tests have been done successfully >>> Only 9 energies in the log file >>> [r...@xxx gmxtest]# >>> Could you explain what is exact problem and how to solve it? >>> >>> >> 1. The test set is not very robust, so failures are not necessarily >> indicative of any actual problem. >> 2. You're using the 4.0.4 test set with version 4.5.1, so some failures >> are probably due to new command line options, etc. (especially in the case >> of pdb2gmx) being necessary but not invoked. >> >> As it stands, there is no effective way to test the validity of a Gromacs >> installation. >> >> -Justin >> >> >>> On Wed, Oct 13, 2010 at 6:15 PM, David van der Spoel < >>> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote: >>> >>> On 2010-10-13 10.54, Sathish wrote: >>> >>> Dear Mark, >>> >>> I have one more doubt. How to run "luck". If i run luck >>> anywhere its says command not found.. >>> my installed and binary directory cant find luck program. how to >>> do? >>> without checking luck shall i start to run demo? >>> >>> Instructions are outdated. The program is now called g_luck >>> >>> >>> >>> On Wed, Oct 13, 2010 at 3:19 PM, Mark Abraham >>> <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> >>> <mailto:mark.abra...@anu.edu.au >>> <mailto:mark.abra...@anu.edu.au>>> wrote: >>> >>> On 13/10/2010 5:01 PM, Mark Abraham wrote: >>> >>> On 13/10/2010 4:55 PM, Sathish wrote: >>> >>> Dear Mark, >>> Thanks for your reply. In my server gromacs >>> installed at >>> "local/gromacs". I have checked out point 8 as you >>> mentioned. >>> It was working with this "source >>> /local/gromacs/bin/GMXRC" command. >>> >>> >>> That's all you need to do, in every shell from which you >>> want to >>> use GROMACS. Or, put that command in your shell login >>> scripts >>> (Google for details). >>> >>> and also tried , entered "local/gromacs/bin" path and >>> calling to >>> GMXRC but it shows error >>> >>> [r...@xxx bin]# GMXRC >>> /local/gromacs/bin/GMXRC: line 35: return: can only >>> `return' from >>> a function >>> or >>> sourced script >>> /local/gromacs/bin/GMXRC: line 44: CSH:: command not >>> found >>> /local/gromacs/bin/GMXRC.csh: line 8: syntax error near >>> unexpected token `setenv ' >>> /local/gromacs/bin/GMXRC.csh: line 8: `if (! >>> $?LD_LIBRARY_PATH) >>> setenv >>> LD_LIBRAR >>> Y_PATH ""' >>> [r...@xxx bin]# >>> >>> This doesn't work, and shouldn't. >>> >>> And the only thing you should be doing as root are "make >>> install" >>> and "make links" (if you want the latter). Otherwise you'll >>> trash >>> your system before you know what you've done. >>> >>> Mark >>> >>> >>> kindly help me to fix this problem and luck is not >>> working. >>> >>> It should, if the "source" command worked. >>> >>> Mark >>> >>> >>> >>> >>> >>> On Wed, Oct 13, 2010 at 12:57 PM, Mark Abraham >>> <mark.abra...@anu.edu.au >>> <mailto:mark.abra...@anu.edu.au> >>> <mailto:mark.abra...@anu.edu.au >>> <mailto:mark.abra...@anu.edu.au>>> wrote: >>> >>> >>> >>> ----- Original Message ----- >>> From: Sathish <sathisbioi...@gmail.com >>> <mailto:sathisbioi...@gmail.com> >>> <mailto:sathisbioi...@gmail.com >>> <mailto:sathisbioi...@gmail.com>>> >>> Date: Wednesday, October 13, 2010 14:31 >>> Subject: [gmx-users] Gromacs installation problem >>> @ RHEL5.5 >>> server >>> To: gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> <mailto:gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org>> >>> >>> > Dear all, >>> > I have compiled and installed gromacs 4.5.1 on >>> RHEL5.5 >>> server. I have also installed openmpi-1.2.8, >>> fftw-3.2.2 and >>> gsl-1.11. After gromacs 4.5.1 installation did >>> make tests and >>> make links. Finally got message "GROMACS is >>> installed under >>> /root/software" and "binary executable installed >>> /usr/local/bin". Utill this am not getting any >>> errors. >>> > Then i was tried to calling "luck" but get >>> "command not >>> found".I have searched the forum it says binary >>> executable >>> not in your path. >>> > Am installing first time and need to know PATH >>> is right >>> which i given? Could anybody help me to solve >>> this problem? >>> > Advance thanks.. >>> >>> Check out point 8 of >>> >>> http://www.gromacs.org/Downloads/Installation_Instructions >>> >>> 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://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before >>> posting! >>> Please don't post (un)subscribe requests to the >>> list. Use the >>> www interface or send it to >>> gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org> >>> <mailto:gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>>. >>> >>> Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- >>> -- >>> Regards, >>> N. Sathishkumar, >>> >>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >>> >>> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org> >>> <mailto:gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- >>> -- >>> Regards, >>> N. Sathishkumar, >>> >>> >>> >>> -- David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >>> http://folding.bmc.uu.se >>> >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> -- >>> -- >>> Regards, >>> N. Sathishkumar, >>> >>> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > -- > Regards, > N. Sathishkumar, > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
