[gmx-users] Re: gmx-users Digest, Vol 56, Issue 44

[David van der Spoel]

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