[gmx-users] Gromacs installation problem @ RHEL5.5 server
Sikandar Mashayak
symashayak at gmail.com
Thu Oct 14 05:49:00 CEST 2010
Recently I installed gromacs4.5.1 without mpi support on my workstation with
8 cores using cmake and make -j 8, make install commands ( as suggested on
installation instructions).
Now when I do mdrun it automatically utilizes all the cores and runs much
faster than earlier version (4.0.7) , which was not using all cores.
I am also surprised , how can mdrun runs on 8 cores without explicitly
specifying no. of cores? Its good that mdrun is using all cores, but there
may be situations when I dont want mdrun to use all cores. Can I anyone
suggest how to control that?
thanks
sikandar
On Wed, Oct 13, 2010 at 10:35 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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> 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
>>>
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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,
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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