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.abra...@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<b...@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 >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
