[gmx-users] mdrun with mpich
David van der Spoel
spoel at xray.bmc.uu.se
Thu Feb 2 17:23:37 CET 2006
Pradeep Kota wrote:
> thanks for the info, Mr.David.. but when i try to compile gromacs, it
> returns an error. the following is an excerpt from the output of 'make'.
>
seems like you have two different versions of fftw3 installed, or mixed
single and double precision. Otherwise I don't know.
> /usr/local/lib/libfftw3f.a(the-planner.o) definition of
> _fftwf_the_planner in section (__TEXT,__text)
> /usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_cc in section
> (__TEXT,__cstring)
> /usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_codelet_optim
> in section (__TEXT,__cstring)
> /usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_version in
> section (__TEXT,__cstring)
> /usr/bin/libtool: internal link edit command failed
> make[4]: *** [libgmx.la <http://libgmx.la>] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
>
> i think Mr.Jack Howarth had already pointed the same thing out, sometime
> back. any suggestion!?
>
> regards,
> kota.
>
> On 2/2/06, *Pradeep Kota* < kotanmd at gmail.com
> <mailto:kotanmd at gmail.com>> wrote:
>
> Thank you for your response Mr.David. I compiled lam successfully
> without fortran support. all i wanted to know was whether it would
> make any difference to the running time of gromacs. I am curious
> because, it is well-known that fortran loops are faster than loops
> of other languages..so, i wanted to clarify ! moreover, i would want
> to know how different this is, from mpich.
> thanks for the support.
> regards,
> kota.
>
>
> On 2/2/06, *David van der Spoel* < spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> Pradeep Kota wrote:
>> Thank you for your response, itamar..but the cluster isolated
> from the
>> internet for security reasons. i dont think there is any
> chance to use
>> fink on the head node either. any other alternatives?
>> regards,
>
> compile LAM without fortran, there's a flag for it
>
>> kota.
>>
>> On 2/2/06, *Itamar Kass* < ikass at cc.huji.ac.il
> <mailto:ikass at cc.huji.ac.il>
>> <mailto: ikass at cc.huji.ac.il <mailto:ikass at cc.huji.ac.il>> >
> wrote:
>>
>> Why not using fortan?
>> install it using Fink and let lam have it.
>>
>> Itamar.
>>
>> ===========================================
>> | Itamar Kass
>> | The Alexander Silberman
>> | Institute of Life Sciences
>> | Department of Biological Chemistry
>> | The Hebrew University, Givat-Ram
>> | Jerusalem, 91904, Israel
>> | Tel: +972-(0)2-6585194
>> | Fax: +972-(0)2-6584329
>> | Email: ikass at cc.huji.ac.il <mailto:ikass at cc.huji.ac.il>
> <mailto:ikass at cc.huji.ac.il <mailto:ikass at cc.huji.ac.il>>
>> | Net:
>>
> http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> <http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html>
>> <
> http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html>
>> ============================================
>>
>> ----- Original Message -----
>> *From:* Pradeep Kota <mailto: kotanmd at gmail.com
> <mailto:kotanmd at gmail.com>>
>> *To:* Discussion list for GROMACS users
>> <mailto: gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>> *Sent:* Thursday, February 02, 2006 4:43 AM
>> *Subject:* [gmx-users] mdrun with mpich
>>
>> Dear users,
>> I have compiled gromacs on our dual core mac os x G5
>> cluster, and tried running a simulation on a 540
> residue protein
>> for 1 ns on 8 processors. i used mpich as the mpi
> environment
>> for parallelising gromacs. it worked fine, and the job
> was split
>> properly and assigned to nodes. now, the cpu usage per
> processor
>> is not more than 50% on any of the processors. and the
> total
>> running time for this was 13hrs. though output is written
>> properly onto the specified output file, mdirun doesnot
>> terminate even after running through all the steps. it
> still
>> shows two mdrun_mpi processes running on the head node,
> with a
>> 0% cpu usage. was going through gmx-users mailing list and
>> somehow figured out that mpich is not a good idea for
> running
>> gromacs. so, i wanted to switch over to lam. now when i
> complie
>> gromacs using lam, it is not able to link the libraries
>> properly. so, i tried reinstalling lam on my cluster.
> now, lam
>> keeps complaining about not being able to find a fortran
>> compiler. i should not need a fortran compiler unless
> i'm using
>> SUN or SGI for this purpose..(am i going wrong here?). what
>> flags do i need to compile lam with, in order to
> compile gromacs
>> successfully? any help is very much appreciated..
>> thanks in advance,
>> regards,
>> kota.
>>
>>
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> --
> David.
> ________________________________________________________________________
>
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> spoel at gromacs.org <mailto:spoel at gromacs.org>
> http://xray.bmc.uu.se/~spoel <http://xray.bmc.uu.se/%7Espoel>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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