R: [BioBrew Users] all parallel capable?

[Anna Marabotti]

Dear Glen,
when the commands "grompp" and "mdrun" are to be used in GROMACS, there is
an option (-np) for, respectively, generating the status file for n nodes
and indicating the number of nodes to be used for calculations. When I used
the option -np and launched these commands, I retrieved the error message
"Fatal error: GROMACS compiled without MPI support - can't do parallel
runs".
On the cluster I'm using, the installation for BioBrew was made following
the default indications.It includes Rocks 4.1 and Biobrew roll 4.1.2-1 and
Intel (all for the architecture x86_64). The default mpi are installed
(mpich and lam). We did not add any other thing, supposing that BioBrew
installation comprises all things that are needed to run in parallel. Are we
true or should we install some other mpi?

Anna


-----Messaggio originale-----
Da: Glen Otero [mailto:glen at callident.com] 
Inviato: lunedì 11 settembre 2006 7.33
A: BioBrew Users
Cc: Anna Marabotti
Oggetto: Re: [BioBrew Users] all parallel capable?

Anna-

It's possible that you're trying to run gromacs with an mpich that it  
wasn't built with. Which mpi are you trying to use? Can you send me  
the command you are using to try and run gromacs in parallel? If you  
send me the data, configuration, and commands you would like run, I  
can give it a try on a cluster over here.

Glen

On Sep 6, 2006, at 8:14 AM, Anna Marabotti wrote:

> Dear Glen,
> I'm joining the discussion about parallelism. I have Rocks 4.1  
> installed on
> a cluster with x86_64 architecture, with BioBrew 4.1.2-1 roll. At  
> present,
> I'm testing GROMACS, which should be able to run in parallel, but  
> although I
> tried to use it with 2 nodes, it only works on the frontend. When I  
> tried to
> force GROMACS to run in parallel, it gave me the following message:  
> "Fatal
> error: GROMACS compiled without MPI support - can't do parallel  
> runs". Is
> this a problem of installation or something else went wrong? Could you
> please help me?
> Thank you 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"
>
> _______________________________________________
> BioBrew-Users mailing list
> BioBrew-Users at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biobrew-users
>