[gmx-users] Running GROMACS in parallel

[Carsten Kutzner]

Hi Anna,

I suspect that you somehow mixed LAM and MPICH. In the logfile it says
that the program is aborted due to a "p4_error" which is an mpich
error message. Probably the included mdrun was not compiled with LAM,
so you have to recompile with LAM or use mpich's mpirun.

Carsten


Anna Marabotti wrote:
> Hi folks,
> I'd need an help to run GROMACS in parallel on a cluster with x86_64
> architecture, with BioBrew 4.1.2-1 roll (GROMACS is one of the programs
> included in the package). After launching lamboot (with no problems) on 5
> nodes of this machine (with names lilligridgiga,lilligridgiga2/3/4/5), with
> 2 CPUs each, I'm trying to do the speptide tutorial running the final full
> MD in parallel. Therefore, I used the grompp -np 10 program (all other
> settings left as in the tutorial), and after that I made several attempts to
> launch mdrun. Here a brief resume of all my trials and of error messages
> received:
> 
> 1) as indicated in the section "Running GROMACS in parallel" of the manual:
> $ mpirun -p
> lilligridgiga,lilligridgiga2,lilligridgiga3,lilligridgiga4,lilligridgiga5 2
> mdrun -v -s full etc (if I understand well, this should mean that mdrun is
> made on nodes lilligridgigax, 2 processes on each)
> ERROR MESSAGE: mpirun (locate_aschema): 2: No such file or directory
> 
> 2) as suggested in a previous post in gmx-user archive:
> $ mpirun C mdrun -v -s full etc (as in the tutorial) -g flog >& full.job &
> ERROR MESSAGES:
>>From file flog.log: Fatal error: run input file full.tpr was made for 10
> nodes, while mdrun expected it to be for 1 nodes.
>>From file full.job: It seems that [at least] one of the processes that was
> started with mpirun did not invoke MPI_INIT before quitting (it is possible
> that more than one process did not invoke MPI_INIT -- mpirun was only
> notified of the first one, which was on node n0). mpirun can *only* be used
> with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE).
> You can use the "lamexec" program to run non-MPI programs over the lambooted
> nodes.
> 
> 3) as suggested in another previous post in gmx-user archive:
> $ mpirun -np 10 mdrun -v -s full etc (as in the tutorial) -g flog1 >&
> full1.job &
> ERROR MESSAGE: 
>>From file flog1.log :Fatal error: run input file full.tpr was made for 10
> nodes, while mdrun expected it to be for 1 nodes.
> File full1.job was saved in multiple copies as #full1.job.1# and therefore I
> am not able to see its content
> 
> 4) as suggested in another previous post in gmx-user archive:
> $ mpirun -np 10 mdrun -np 10 -v -s full etc (as in the tutorial) -g flog2 >&
> full2.job &
> ERROR MESSAGE:
> same as in 2)
> 
> 5) Last trial, following error messages:
> $ lamexec -np 10 -mdrun -np 10 -v -s full etc (as in the tutorial) -g flog3
>> & full3.job &
> ERROR MESSAGE:
>>From flog3.log file: no error messages
>>From file full3.job: Fatal error: run input file full.tpr was made for 10
> nodes, while mdrun expected it to be for 1 nodes.
> 
> I really don't understand why mdrun is not working on 10 processors. As you
> see I've always checked the gmx-user archive trying to find something that
> could help me, but I didn't. Could anybody give me a suggestion? To be clear
> at best, I'm attaching here flog.log file and full.job (transformed in
> full.txt) file.
> Many thanks and regards
> Anna
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratorio di Bioinformatica e Biologia Computazionale
> Istituto di Scienze dell'Alimentazione, CNR
> Via Roma 52 A/C
> 83100 Avellino (Italy)
> Tel: +39 0825 299651
> Fax: +39 0825 299813
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> Web page: http://bioinformatica.isa.cnr.it/anna.htm
> ____________________________________________________
> "If you think you are too small to make a difference, try sleeping with a
> mosquito"
> 

> 
> Halting program mdrun
> 
> gcq#302: "The Candlelight Was Just Right" (Beastie Boys)
> 
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
>     p4_error: latest msg from perror: No such file or directory
> p0_5520:  p4_error: : -1
> 
> 
> 
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-- 
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne