[gmx-users] Gromacs installation problem @ RHEL5.5 server
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Oct 14 05:35:00 CEST 2010
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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,
>
> [root at 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
> [root at 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
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at 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.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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
>
> [root at 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 ""'
> [root at 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.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
> <mailto:mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>>
> <mailto:mark.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>>> wrote:
>
>
>
> ----- Original Message -----
> From: Sathish <sathisbioinfo at gmail.com
> <mailto:sathisbioinfo at gmail.com>
> <mailto:sathisbioinfo at gmail.com <mailto:sathisbioinfo at gmail.com>>
> <mailto:sathisbioinfo at gmail.com <mailto:sathisbioinfo at gmail.com>
> <mailto:sathisbioinfo at gmail.com
> <mailto:sathisbioinfo at gmail.com>>>>
> Date: Wednesday, October 13, 2010 14:31
> Subject: [gmx-users] Gromacs
> installation problem
> @ RHEL5.5
> server
> To: gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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
> --
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> --
> --
> Regards,
> N. Sathishkumar,
>
>
>
>
> --
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>
> --
> --
> 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.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
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>
>
> --
> --
> 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
>
> ========================================
>
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>
>
> --
> --
> Regards,
> N. Sathishkumar,
>
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