[gmx-users] Fftw and gromac build

[Krewson, Tom]

Thanks Erik,

When I put your command in: mpirun -np 9 mdrun_mpi
I got the expected:
NNODES=3, MYRANK=0, HOSTNAME=rockscluster.rscc.cc.tn.us
NNODES=3, MYRANK=1, HOSTNAME=compute-0-4.local
NNODES=3, MYRANK=2, HOSTNAME=compute-0-5.local
NODEID=1 argc=1
NODEID=0 argc=1
NODEID=2 argc=1

Here is the problem I believe:
Fatal error: run input file topol.tpr was made for 1 nodes,
             while mdrun_mpi expected it to be for 3 nodes.

I did not know the tpr file dependant on the number of nodes it was
created on.....Ugh.

Thanks Avell for the excellent spec files.




-----Original Message-----
From: Erik Lindahl [mailto:lindahl at sbc.su.se] 
Sent: Wednesday, May 04, 2005 4:41 PM
To: Krewson, Tom
Cc: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fftw and gromac build 


Hi,

Sounds normal. You cannot initialize the MPI environment unless the  
virtual parallel computer has been initialized with lamboot.

Are you starting mdrun as

mpirun -np 9 mdrun_mpi ... <other args>


The extra -np command to mdrun_mpi is usually not necessary - all  
modern MPI implementations provide it to the program automatically if  
you have given it to mpirun.


Cheers,

Erik


On May 4, 2005, at 10:21 PM, Krewson, Tom wrote:

> Hi,
> Thanks. My mistake for not including that I was able to build the RPM 
> and run it.....but mdrun_mpi only runs on a single node at a time.
> If I
> ssh compute-0-0, I can run mdrun_mpi no problem. If I don't lamboot,
> mdrun_mpi complains there is no lam running. When I do run  
> mdrun_mpi -np
> 9 the number of output says:
> NNODES=1, MYRANK=0, even though   "-np int 9  Number of nodes, must be
> the same as used for" is given for the np value. Is there any way to
> trace mdrun or fftw to see where the parallel job is failing? BTW
> running mprun -np 9 mpipi works fine across all nodes.
>
>
>
> -----Original Message-----
> From: Erik Lindahl [mailto:lindahl at sbc.su.se]
> Sent: Wednesday, May 04, 2005 1:41 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Fftw and gromac build
>
>
> Hi,
>
>
> On May 4, 2005, at 5:27 PM, Krewson, Tom wrote:
>
>
>> I have still not been able to get gromacs to work in parallel. I 
>> believe that when I link against using the spec file below that 
>> Gromacs
>> cannot
>> find the lib and include files from fftw.
>> I keep getting the message below over and over again but it finally
>> goes
>> through.
>>
>>
>> libtool: link: warning: library `/usr/lib/libsrfftw_mpi.la' was
>> moved.
>> libtool: link: warning: library `/usr/lib/libsfftw_mpi.la' was moved.
>> libtool: link: warning: library `/usr/lib/libsrfftw.la' was moved.
>> libtool: link: warning: library `/usr/lib/libsfftw.la' was moved.
>> libtool: link: warning: library `/usr/lib/libsrfftw_mpi.la' was  
>> moved.
>> libtool: link: warning: library `/usr/lib/libsfftw_mpi.la' was moved.
>> libtool: link: warning: library `/usr/lib/libsrfftw.la' was moved.
>> libtool: link: warning: library `/usr/lib/libsfftw.la' was moved.
>>
>>
>
> This is just a note that the fftw library files are currently in a 
> different place from the original build location. You can safely 
> ignore it.
>
>
>
>>
>>
>> I have set the CPPFLAGS (-I/opt/lam/gnu/include) and LDFLAGS
>> (-L/opt/lam/gnu/lib) to point to the lam libraries and fftw seems to 
>> go without a problem. But I don't know where the lib and include 
>> files are
>> for fftw for the CPPFLAGS and LDFLAGS. Am I anywhere near home  
>> base or
>> just way off here?
>>
>
> On linux it's usually in /usr/local/lib or /usr/lib, which should be 
> searched automatically. Judging from the warnings above, it seems as 
> if they were found.
>
> Do you get an error message at the end of the rpmbuild stage? If not, 
> check if you have the rpm files in a subdirectory (i forgot the name, 
> but it's somewhere under rpm in the current one).
>
> Cheers,
>
> Erik
>
>
>
>
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