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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 28 01:09:50 CEST 2011 

On 28/10/2011 9:29 AM, Ben Reynwar wrote:
> 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.

Yes, this is the bug in 4.5.5 to which I referred. Your original post 
didn't state a GROMACS version, but your output suggested 4.5.4, else 
I'd have told you this was the bug... instead everyone wasted some time :)

Mark

>
> 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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>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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