[gmx-users] Gromacs installation problem @ RHEL5.5 server
Sathish
sathisbioinfo at gmail.com
Thu Oct 14 04:35:33 CEST 2010
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 <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> 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>> 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>>> 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>>> wrote:
>>
>>
>>
>> ----- Original Message -----
>> From: Sathish <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>>
>>
>> > 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>
>> http://folding.bmc.uu.se
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
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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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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--
--
Regards,
N. Sathishkumar,
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