Thanks Dr.David. I could compile gromacs successfully. But when i run
an md simulation on four processors, it returns the following error.<br>
<br>
<br>
[0] MPI Abort by user Aborting program !<br>
[0] Aborting program!<br>
p4_error: latest msg from perror: No such file or directory<br>
p0_2057: p4_error: : -1<br>
-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 3.3<br>
Source code file: futil.c, line: 308<br>
<br>
File input/output error:<br>
md.log<br>
-------------------------------------------------------<br>
<br>
Thanx for Using GROMACS - Have a Nice Day<br>
<br>
Halting program mdrun_mpi<br>
<br>
gcq#1768121632: Thanx for Using GROMACS - Have a Nice Day<br>
<br>
[0] MPI Abort by user Aborting program !<br>
[0] Aborting program!<br>
p4_error: latest msg from perror: No such file or directory<br>
-----------------------------------------------------------------------------<br>
It seems that [at least] one of the processes that was started with<br>
mpirun did not invoke MPI_INIT before quitting (it is possible that<br>
more than one process did not invoke MPI_INIT -- mpirun was only<br>
notified of the first one, which was on node n8952p0_<br>
058: p4_error: : -1<br>
mpirun can *only* be used with MPI programs (i.e., programs that<br>
invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program<br>
to run non-MPI programs over the lambooted nodes.<br>
-----------------------------------------------------------------------------<br>
<br>
<br>
i had lambooted all the nodes properly and it did not have any problems
at that stage. and as it said, i tried using lamexec too. still no
luck. i tried using other switches with mpirun too..couldnt quite
figure out what the error could be.<br>
<br>
thanks in anticipation,<br>
kota.<br><br><div><span class="gmail_quote">On 2/2/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Pradeep Kota wrote:<br>> thanks for the info, Mr.David.. but when i try to compile gromacs, it<br>> returns an error. the following is an excerpt from the output of 'make'.<br>><br>seems like you have two different versions of fftw3 installed, or mixed
<br>single and double precision. Otherwise I don't know.<br><br><br><br>> /usr/local/lib/libfftw3f.a(the-planner.o) definition of<br>> _fftwf_the_planner in section (__TEXT,__text)<br>> /usr/local/lib/libfftw3f.a(
version.o) definition of _fftwf_cc in section<br>> (__TEXT,__cstring)<br>> /usr/local/lib/libfftw3f.a(version.o) definition of _fftwf_codelet_optim<br>> in section (__TEXT,__cstring)<br>> /usr/local/lib/libfftw3f.a(
version.o) definition of _fftwf_version in<br>> section (__TEXT,__cstring)<br>> /usr/bin/libtool: internal link edit command failed<br>> make[4]: *** [<a href="http://libgmx.la">libgmx.la</a> <<a href="http://libgmx.la">
http://libgmx.la</a>>] Error 1<br>> make[3]: *** [all-recursive] Error 1<br>> make[2]: *** [all-recursive] Error 1<br>> make[1]: *** [all] Error 2<br>> make: *** [all-recursive] Error 1<br>><br>> i think
Mr.Jack Howarth had already pointed the same thing out, sometime<br>> back. any suggestion!?<br>><br>> regards,<br>> kota.<br>><br>> On 2/2/06, *Pradeep Kota* < <a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com
</a><br>> <mailto:<a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com</a>>> wrote:<br>><br>> Thank you for your response Mr.David. I compiled lam successfully<br>> without fortran support. all i wanted to know was whether it would
<br>> make any difference to the running time of gromacs. I am curious<br>> because, it is well-known that fortran loops are faster than loops<br>> of other languages..so, i wanted to clarify ! moreover, i would want
<br>> to know how different this is, from mpich.<br>> thanks for the support.<br>> regards,<br>> kota.<br>><br>><br>> On 2/2/06, *David van der Spoel* < <a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Pradeep Kota wrote:<br>>> Thank you for your response, itamar..but the cluster isolated
<br>> from the<br>>> internet for security reasons. i dont think there is any<br>> chance to use<br>>> fink on the head node either. any other alternatives?<br>>> regards,<br>>
<br>> compile LAM without fortran, there's a flag for it<br>><br>>> kota.<br>>><br>>> On 2/2/06, *Itamar Kass* < <a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a><br>> <mailto:
<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a>><br>>> <mailto: <a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a> <mailto:<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a>
>> ><br>> wrote:<br>>><br>>> Why not using fortan?<br>>> install it using Fink and let lam have it.<br>>><br>>> Itamar.<br>>><br>>> ===========================================
<br>>> | Itamar Kass<br>>> | The Alexander Silberman<br>>> | Institute of Life Sciences<br>>> | Department of Biological Chemistry<br>>> | The Hebrew University, Givat-Ram
<br>>> | Jerusalem, 91904, Israel<br>>> | Tel: +972-(0)2-6585194<br>>> | Fax: +972-(0)2-6584329<br>>> | Email: <a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a> <mailto:
<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a>><br>> <mailto:<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a> <mailto:<a href="mailto:ikass@cc.huji.ac.il">ikass@cc.huji.ac.il</a>
>><br>>> | Net:<br>>><br>> <a href="http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html">http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html</a><br>> <
<a href="http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html">http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html</a>><br>>> <<br>> <a href="http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html">
http://www.ls.huji.ac.il/%7Emembranelab/itamar/itamar_homepage.html</a>><br>>> ============================================<br>>><br>>> ----- Original Message -----<br>>> *From:* Pradeep Kota <mailto:
<a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com</a><br>> <mailto:<a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com</a>>><br>>> *To:* Discussion list for GROMACS users<br>>> <mailto:
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>>> *Sent:* Thursday, February 02, 2006 4:43 AM
<br>>> *Subject:* [gmx-users] mdrun with mpich<br>>><br>>> Dear users,<br>>>
I have compiled gromacs on our dual core mac os x G5<br>>> cluster, and tried running a simulation on a 540<br>> residue protein<br>>> for 1 ns on 8 processors. i used mpich as the mpi
<br>> environment<br>>> for parallelising gromacs. it worked fine, and the job<br>> was split<br>>> properly and assigned to nodes. now, the cpu usage per<br>> processor
<br>>> is not more than 50% on any of the processors. and the<br>> total<br>>> running time for this was 13hrs. though output is written<br>>> properly onto the specified output file, mdirun doesnot
<br>>> terminate even after running through all the steps. it<br>> still<br>>> shows two mdrun_mpi processes running on the head node,<br>> with a<br>>> 0% cpu usage. was going through gmx-users mailing list and
<br>>> somehow figured out that mpich is not a good idea for<br>> running<br>>> gromacs. so, i wanted to switch over to lam. now when i<br>> complie<br>>> gromacs using lam, it is not able to link the libraries
<br>>> properly. so, i tried reinstalling lam on my cluster.<br>> now, lam<br>>> keeps complaining about not being able to find a fortran<br>>> compiler. i should not need a fortran compiler unless
<br>> i'm using<br>>> SUN or SGI for this purpose..(am i going wrong here?). what<br>>> flags do i need to compile lam with, in order to<br>> compile gromacs<br>>> successfully? any help is very much appreciated..
<br>>> thanks in advance,<br>>> regards,<br>>> kota.<br>>><br>>><br>> ------------------------------------------------------------------------<br>><br>>>
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</a><br>><br>><br>> --<br>> David.<br>> ________________________________________________________________________<br>><br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>>
Husargatan 3, Box
596, 75124
Uppsala, Sweden<br>>
phone: 46 18 471
4205 fax: 46
18 511 755<br>> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
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