Re: [gmx-users] running job parallel

Thank you Mark, for your valuable suggestion. Regards, Bharati On Wed, May 4, 2011 at 10:18 AM, Mark Abraham wrote: > > > On 04/05/11, *Bharati Singh * wrote: > > Hi Mark, > > Sorry for your inconvenience > As you said some kind of (dynamic) linking problem, Is it possible to > resolve it? > >

Re: [gmx-users] running job parallel

Hi lina, As you have given, Is it needed to set LD_LIBRARY_PATH ? I had loaded module for mpi and set LDFLAGS, CPPFLAGS ,at the time of installation. My cluster has LSF, I use following command to submit job- $ bsub -q -n mpirun -srun /sfs3/home/bharati/gromacs/bin/mdrun -pd -v -s Ag6A12_equi

Re: [gmx-users] running job parallel

On 04/05/11, Bharati Singh wrote: > Hi Mark, > > Sorry for your inconvenience > As you said some kind of (dynamic) linking problem, Is it possible to resolve > it? > Yes, but you will need someone who can troubleshoot what has and has not worked on your system. We do not have any relevant

Re: [gmx-users] running job parallel

Hi Mark, Sorry for your inconvenience As you said some kind of (dynamic) linking problem, Is it possible to resolve it? Thanks & Regards, Bharati On Tue, May 3, 2011 at 6:59 PM, Mark Abraham wrote: > On 3/05/2011 8:19 PM, Bharati Singh wrote: > > Mentioned method is working in another user's

Re: [gmx-users] running job parallel

On 3/05/2011 8:19 PM, Bharati Singh wrote: Mentioned method is working in another user's home directory on same machine, then I dont think the problem with linking. Please be specific... I can think of three different things you might mean by the "mentioned method", and when you've not troubl

Re: [gmx-users] running job parallel

Hi, I don't know the specific cluster you mentioned. but when I met such problems, I used to check the .log which usually gave me very helpful information. and I used to use some script to submit job, I post one as example, please set the proper one according to your cluster. more openmpi_paral

Re: [gmx-users] running job parallel

Mentioned method is working in another user's home directory on same machine, then I dont think the problem with linking. On Tue, May 3, 2011 at 3:34 PM, Mark Abraham wrote: > On 3/05/2011 7:37 PM, Bharati Singh wrote: > > Hi Team, > > Thanks for your reply. > > I had tried following method t

Re: [gmx-users] running job parallel

On 3/05/2011 7:37 PM, Bharati Singh wrote: Hi Team, Thanks for your reply. I had tried following method to install gromacs-4.0.7 - $ module load intel_all/impi/default $ ./configure --enable-mpi --with-fft=fftw2 LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/" CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/includ

Re: [gmx-users] running job parallel

Hi Team, Thanks for your reply. I had tried following method to install gromacs-4.0.7 - $ module load intel_all/impi/default $ ./configure --enable-mpi --with-fft=fftw2 LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/" CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw" F77=mpif77 --prefix=/sfs3/hom

Re: [gmx-users] running job parallel

Hi, Have you checked the error log? Please post the error log. Have you configured GROMACS using --enable-mpi? Thanks, Saikat On Tue, May 3, 2011 at 2:35 PM, Bharati Singh wrote: > Hi Team, > > I have LSF in my cluster ,I have installed gromacs-4.0.7 on Sampige. It is > working fine as a seri

[gmx-users] running job parallel

Hi Team, I have LSF in my cluster ,I have installed gromacs-4.0.7 on Sampige. It is working fine as a serial(on 1 processor) ,when I submit the job for more than one processors in queue, it gets terminated immediately.Can you suggest me something about it, please Thanks & Regards, -- Bharati Si