[gmx-users] Gromacs installation problem @ RHEL5.5 server

Sathish sathisbioinfo at gmail.com
Wed Oct 13 12:54:07 CEST 2010 

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 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?



On Wed, Oct 13, 2010 at 6:15 PM, David van der Spoel
<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>> 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>> wrote:
>>>>
>>>>
>>>>
>>>>        ----- Original Message -----
>>>>        From: Sathish <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>
>>>>
>>>>        > 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 at gromacs.org
>>>>        <mailto:gmx-users at 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-request at gromacs.org
>>>>        <mailto:gmx-users-request at gromacs.org>.
>>>>
>>>>        Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>>
>>>>
>>>>
>>>>    --
>>>>    --
>>>>    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    http://folding.bmc.uu.se
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-- 
-- 
Regards,
N. Sathishkumar,
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