[gmx-users] error in gmx-4.0 with mpi

[David van der Spoel]

Vitaly Chaban wrote:
> Hi,
> 
> I have got a problem running a parallel version of gromacs 4.0.
> 
> 
> While running the gromacs 4.0 with mpi the following error
> permanently appears:
> 
> NNODES=4, MYRANK=1, HOSTNAME=merlin-3-9
> NNODES=4, MYRANK=0, HOSTNAME=merlin-3-9
> NNODES=4, MYRANK=2, HOSTNAME=merlin-2-24
> NNODES=4, MYRANK=3, HOSTNAME=merlin-2-24
> NODEID=0 argc=1
> NODEID=1 argc=1
> NODEID=2 argc=1
> NODEID=3 argc=1
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                    Groningen Machine for Chemical Simulation
> 
>                            :-)  VERSION 4.0_rc2  (-:
> 
> 
> Reading file topol.tpr, VERSION 3.3.3 (single precision)
> Note: tpx file_version 40, software version 58
> 
> NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
> 
> Making 1D domain decomposition 1 x 1 x 4
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> 
> WARNING: This run will generate roughly 5946 Mb of data
> 
> Dec 13 11:34:47 2008 32301 3 6.1 pServe: getMsgBuffer_() failed.
> Fatal error (code 0x94213a0f) in MPI_Scatterv():
> MPI_Scatterv(324): MPI_Scatterv(sbuf=0x8b8170, scnts=0x82b000, displs=0x82b010, MPI_BYTE, rbuf=0x8f3ce0, rcount=4680, MPI_BYTE, root=0, MPI_COMM_WORLD) failed
> MPIC_Send(50): failure
> MPIC_Wait(306): failure
> MPIDI_CH3_Progress(421): [ch3:sock] failed to connnect to remote process -1:3
> MPIDU_Sock_wait(116): connection failure (set=0,sock=4)
> ABORT - process 0
> Dec 13 11:34:52 2008 32301 4 6.1 PAM: pjl_rwait: Didn't get all TS to report status.
> Dec 13 11:34:52 2008 32301 3 6.1 PAM: pWaitRtask(): ls_rwait/pjl_rwait() failed, Communication time out.
> Dec 13 11:34:57 2008 32301 4 6.1 PAM: pjl_rwait: Didn't get all TS to report status.
> Dec 13 11:34:57 2008 32301 3 6.1 PAM: pWaitRtask(): ls_rwait/pjl_rwait() failed, Communication time out.
> Dec 13 11:34:57 2008 32301 3 6.1 pWaitAll(): NIOS is dead
> 
> I used
> grompp -np 4 to create topol.tpr
> and then
> mpirun.lsf /home/gromacs4.0-mpi/bin/mdrun
> 
> I have no problems running 1-proc gromacs.
> 
> Does anybody have ideas how to fix this?

Since you are running a prerelease version an upgrade to 4.0.2 would be 
the first step.

> 
> Thank you very much,
> Vitaly
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se