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 ?
On Wed, Oct 13, 2010 at 8:24 PM, Justin A. Lemkul <[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> 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]>> 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]>>> 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]>>> wrote: >> >> >> >> ----- Original Message ----- >> From: Sathish <[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]>> >> >> > 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]>> >> >> 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, >> >> >> >> >> -- >> 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, >> >> >> >> -- 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]> >> http://folding.bmc.uu.se >> >> -- 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, >> >> > -- > ======================================== > > 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 [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]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- -- Regards, N. Sathishkumar,
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