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 <[email protected] <mailto:[email protected]>> 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> <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 <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> 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 <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> 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 <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> wrote: ----- Original Message ----- From: Sathish <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> Date: Wednesday, October 13, 2010 14:31 Subject: [gmx-users] Gromacs installation problem @ RHEL5.5 server To: [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- Regards, N. Sathishkumar, -- gmx-users mailing list [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>. 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. [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> http://folding.bmc.uu.se -- gmx-users mailing list [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>. 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 <http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================-- gmx-users mailing list [email protected]<mailto:[email protected]> 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 [email protected] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- Regards, N. Sathishkumar,
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