[gmx-users] FW: Gromacs version 3.3

[Pradeep Kota]

for the latest versions of gromacs, it would do if u specify the number of
processors u want to run the job on, at the mpiexec level. u dont have to
repeat the same at the mdrun_mpi level. try using
usr/local/bin/mpiexec -n 4 -verbose
/usr/local/applications/bioinformatics/gromacs-3.3/bin/mdrun_mpi <other
mdrun parameters>.

hope this helps.
cheers
kota.


On 12/1/05, Wong, RYM (Richard) <R.Y.M.Wong at rl.ac.uk> wrote:
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org]On Behalf Of Florian Haberl
> Sent: 01 December 2005 10:12
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] FW: Gromacs version 3.3
>
>
> hi,
>
> On Thursday 01 December 2005 10:19, Wong, RYM (Richard) wrote:
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org
> > [mailto:gmx-users-bounces at gromacs.org]On Behalf Of David van der Spoel
> > Sent: 30 November 2005 20:01
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] FW: Gromacs version 3.3
> >
> > Wong, RYM (Richard) wrote:
> > >>Hi,
> > >>
> > >>I have installed Gromacs version 3.3 on a machine running Linux
> > >> 2.4.21-37.ELsmp.
> > >
> > >The configuration command syntax I used to compile the MPI version of
> > > Gromacs-3.3:
> >
> > What kind of machine?
> >
> > The system contains 20 dual Intel Xeon processors.
> > The version of MPI is MPICH-1.2.5..10 associated with GNU (i.e. mpicc
> > invokes gcc-3.2.3). Multiprocessors are connected together via Myrinet
> GM
> > version 2.0.8. Do you need any other information?
> >
> > >>  ./configure --prefix=/usr/local/applications/bioinformatics/gromacs-
> 3.3
> > >> --exec-prefix=/usr/local/applications/bioinformatics/gromacs-3.3
> > >> --enable-mpi --enable-shared --with-fft=fftw2 --program-suffix="_mpi"
> > >> CPPFLAGS=-I/usr/local/applications/libraries/numerical/fft/include
> > >> LDFLAGS=-L/usr/local/applications/libraries/numerical/fft/lib
> CC=mpicc
> > >>
> > >>Then executed "make"
> > >>Then executed "make install"
> > >>Then I used the command "grompp -np 2" to create the input data files
> in
> > >> the sample "water" provided by the Gromacs development team.
> > >>
> > >>When I run the command "mdrun_mpi" , I get 'segmentation fault' error.
> > >>
> > >>  Warning: main: task 0 died with signal 11 (Segmentation fault)
> > >>  Warning: main: task 1 died with signal 11 (Segmentation fault)
> >
> > Did you use mpirun?
> > Due to the security reason, we use mpiexec version 0.75 instead of using
> > mpirun directly. We are using MPICH-1.2.5..10 and Myrinet GM-2.0.8.
> > Do you need any other information?
>
> Did you use a command line like "mpiexec -np 2 /pathtomdrun/mdrun_mpi -np
> 2" ,
> you have to invoke the mpiprocess first with mpirun/ mpiexec to start
> mdrun_mpi.
>
> The command I use for executing the mdrun_mpi:
>     "/usr/local/bin/mpiexec -n 4 -verbose
> /usr/local/applications/bioinformatics/gromacs-3.3/bin/mdrun_mpi -np 4".
>
> Error messages recorded in the log file:
> ********************************************
> [1] Malloc hook test failed: the malloc provided by MPICH-GM is not used,
> it may have been overloaded by a malloc provided by another library.
>
> [0] Malloc hook test failed: the malloc provided by MPICH-GM is not used,
> it may have been overloaded by a malloc provided by another library.
>
> [2] Malloc hook test failed: the malloc provided by MPICH-GM is not used,
> it may have been overloaded by a malloc provided by another library.
>
> [3] Malloc hook test failed: the malloc provided by MPICH-GM is not used,
> it may have been overloaded by a malloc provided by another library.
>
> mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 192.168.100.5,
> killing all.
> mpiexec: Warning: main: task 0 exited with status 255.
> mpiexec: Warning: main: task 1 exited with status 255.
> mpiexec: Warning: main: task 2 exited with status 255.
> **********************************************
> Does it work without mpi, e.g. only on one cpu?
>
> Yes. The serial version of mdrun works OK.
>
> Are you using a scheduler/ queing system like maui/ torque?
> No. I create a script which contains the above command and submit it to
> PBS (portable batch system).
>
>
> >
> > Thank you
> > Richard
> > _______________________________________________
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>
>
> Greetings,
>
> Florian
> --
>
> ---------------------------------------------------------------------------------------------------
> Florian Haberl                             Universitaet Erlangen/Nuernberg
> Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
>
> Mailto: florian.haberl AT chemie.uni-erlangen.de
>
>
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