[gmx-users] Fatal error in MPI_Allreduce upon REMD restart

Fri Oct 28 00:29:05 CEST 2011

I found a post on the devel list from a couple of weeks ago where a
fix is given and it appears to work for me.
The link is http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html

The fix does not appear to have been incorporated into the 4.5.5 release.

On Tue, Oct 25, 2011 at 4:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 26/10/2011 6:06 AM, Szilárd Páll wrote:
>>
>> Hi,
>>
>> Firstly, you're not using the latest version and there might have been
>> a fix for your issue in the 4.5.5 patch release.
>
> There was a bug in 4.5.5 that was not present in 4.5.4 that could have
> produced such symptoms, but it was fixed without creating a Redmine issue.
>
>> Secondly, you should check the http://redmine.gromacs.org bugtracker
>> to see what bugs have been fixed in 4.5.5 (ideally the target version
>> should tell). You can also just do a search for REMD and see what
>> matching bugs (open or closed) are in the database:
>> http://redmine.gromacs.org/search/index/gromacs?issues=1&q=REMD
>
> If the OP is right and this was with 4.5.4 and can be reproduced with 4.5.5,
> please do some testing (e.g. Do different parallel regimes produce the same
> symptoms? Can the individual replicas run in a non-REMD simulation?) and
> file a Redmine issue with your observations and a small sample case.
>
> Mark
>
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>> On Tue, Oct 25, 2011 at 8:04 PM, Ben Reynwar<ben at reynwar.net>  wrote:
>>>
>>> Hi all,
>>>
>>> I'm getting errors in MPI_Allreduce what I restart an REMD simulation.
>>>  It has occurred every time I have attempted an REMD restart.
>>> I'm posting here to check there's not something obviously wrong with
>>> the way I'm doing the restart which is causing it.
>>>
>>> I restart an REMD run using:
>>>
>>>
>>> -----------------------------------------------------------------------------------------------------------------------------------------
>>> basedir=/scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_
>>> status=${basedir}/pshsp_andva_run1_.status
>>> deffnm=${basedir}/pshsp_andva_run1_
>>> cpt=${basedir}/pshsp_andva_run0_.cpt
>>> tpr=${basedir}/pshsp_andva_run0_.tpr
>>> log=${basedir}/pshsp_andva_run1_0.log
>>> n_procs=32
>>>
>>> echo "about to check if log file exists"
>>> if [ ! -e $log ]; then
>>>    echo "RUNNING">  $status
>>>    source /usr/share/modules/init/bash
>>>    module load intel-mpi
>>>    module load intel-mkl
>>>    module load gromacs
>>>    echo "Calling mdrun"
>>>    mpirun -np 32 mdrun-mpi -maxh 24 -multi 16 -replex 1000 -s $tpr
>>> -cpi $cpt -deffnm $deffnm
>>>    retval=$?
>>>    if [ $retval != 0 ]; then
>>>        echo "ERROR">  $status
>>>        exit 1
>>>    fi
>>>    echo "FINISHED">  $status
>>> fi
>>> exit 0
>>>
>>> ------------------------------------------------------------------------------------------------------------------------------------------
>>>
>>> mdrun then gets stuck and doesn't output anything until it is
>>> terminated by the queuing system.
>>> Upon termination the following output is written to stderr.
>>>
>>> [cli_5]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x2b379c00b770, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_31]: [cli_11]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x7f489806bf60, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x7fd960002fc0, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_7]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x754400,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_9]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x757230,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_27]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x7fb3cc02a450, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_23]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x750970,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_21]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x7007b0,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_3]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x754360,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_29]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x756460,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_19]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x7f60a0066850, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_17]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x7f4bdc07b690, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_1]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x754430,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_15]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE,
>>> rbuf=0x7fc31407c830, count=16, MPI_INT, MPI_SUM, MPI_COMM
>>> _NULL) failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_25]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x6e1830,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> [cli_13]: aborting job:
>>> Fatal error in MPI_Allreduce: Invalid communicator, error stack:
>>> MPI_Allreduce(1175): MPI_Allreduce(sbuf=MPI_IN_PLACE, rbuf=0x6c2430,
>>> count=16, MPI_INT, MPI_SUM, MPI_COMM_NULL)
>>>  failed
>>> MPI_Allreduce(1051): Null communicator
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_3.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_0.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_7.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_6.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_1.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_4.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_5.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_2.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_11.tpr,
>>> VERSION 4.5.4 (sing
>>> le precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_9.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_8.tpr,
>>> VERSION 4.5.4 (singl
>>> e precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_10.tpr,
>>> VERSION 4.5.4 (sing
>>> le precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_15.tpr,
>>> VERSION 4.5.4 (sing
>>> le precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_13.tpr,
>>> VERSION 4.5.4 (sing
>>> le precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_12.tpr,
>>> VERSION 4.5.4 (sing
>>> le precision)
>>> Reading file
>>> /scr2/benreynwar/home-ben-sHSP-REMD-pshsp_andva_run1_/pshsp_andva_run0_14.tpr,
>>> VERSION 4.5.4 (sing
>>> le precision)
>>> Terminated
>>>
>>> Cheers,
>>> Ben
>>> --
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>
> --
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