[gmx-users] GROMACS with MPICH on Sun Cluster

[David van der Spoel]

Alok wrote:
> I tried ldd `which mdrun_mpi` output is :-
> 
> ###########################################################################
> 
> $ldd `which mdrun_mpi`
>        libnsl.so.1 => /lib64/libnsl.so.1 (0x0000002a95687000)
>        libXm.so.3 => /usr/X11R6/lib64/libXm.so.3 (0x0000002a9579e000)
>        libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000002a95b2e000)
>        libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000002a95c8e000)
>        libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000002a95d98000)
>        libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000002a95eb2000)
>        libXp.so.6 => /usr/X11R6/lib64/libXp.so.6 (0x0000002a95fc3000)
>        libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a960cc000)
>        libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x0000002a962c0000)
>        libz.so.1 => /usr/lib64/libz.so.1 (0x0000002a964d9000)
>        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a965e7000)
>        libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a966fc000)
>        libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a96884000)
>        libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000002a96ac8000)
>        libdl.so.2 => /lib64/libdl.so.2 (0x0000002a96be2000)
>        /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 
> (0x0000002a95556000)
> 
> 
> ################################################################################## 
> 
> 
> what can we conclude from this output ??

there is no FFT, no MPI, so these are hard linked into the program. That 
means you can not have problems with those at least.
> 
> I will try "make CFLAGS=-g install" option also....then i will come back 
> to you.
> 
> Thanks a lot !
> 
> best regards,
> Alok Jain
> 
> 
> 
> 
> 
> 
> ----- Original Message ----- From: "David van der Spoel" 
> <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Thursday, June 08, 2006 8:25 PM
> Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster
> 
> 
>> Alok wrote:
>>
>>> I tried mpirun mdrun_mpi -h but I got same error message
>>>
>>> [0] MPI Abort by user Aborting program !
>>> [0] Aborting program!
>>> p0_29243:  p4_error: : 0
>>>
>>> Thanks for your kind attention.
>>>
>> Apart from upgrading to FFTW3 and GROMACS 3.3.1, you could try
>>
>> ldd `which mdrun` to check which libraries are being used. Maybe you 
>> are mixing different MPI libraries (i.e. compile with one, run with 
>> another).
>>
>> You can also compile by
>> make distclean
>> make CFLAGS=-g install
>>
>> in order to be able to debug
>>
>> -- 
>> 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://folding.bmc.uu.se
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++