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

[Vitaly Chaban]

David, Mark,

Thank you!

I will compile the latest version instead. Am I true starting the run
via:

grompp -np 4
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?