Sorry for the multiple emails but everytime I tried to send the mail I obtained a message like this:
"The message's content type was not explicitly allowed. Please send your messages as plain text only. See http://www.gromacs.org/Support/Mailing_Lists" So I tried as long as no message has been replied to me. Concerning the bug fixes, I did the following steps git clone git://git.gromacs.org/gromacs.git gromacs-4.5.5-patches cd gromacs-4.5.5-patches git checkout --track -b release-4-5-patches origin/release-4-5-patches git pull ./bootstrap ./configure --prefix=/ibpc/etna/oteri/PKG/gromacs/4.5.5/patched --without-x --enable-mpi --program-suffix=_mpi --enable-all-static CFLAGS="-I/ibpc/etna/oteri/PKG/openmpi/1.4.5/include -I/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/include" "LDFLAGS=-L/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/lib -L/ibpc/etna/oteri/PKG/openmpi/1.4.5/lib" LIBSUFFIX=_mpi make mdrun make install-mdrun 2012/7/19 Mark Abraham <mark.abra...@anu.edu.au>: > On 19/07/2012 12:32 AM, francesco oteri wrote: >> >> Dear gromacs users, >> I am trying to run a replica exchange simulation using the files you find >> in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz >> >> The 4 replicas have been generated, as following: >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp >> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp >> >> The simulation was started with command, using gromacs 4.5.5 with the >> latest bug fix: > > > Which bug fix? How did you apply it? > > Mark > > >> mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out1 >> >> giving the following error: >> >> [etna:10799] *** An error occurred in MPI_comm_size >> [etna:10799] *** on communicator MPI_COMM_WORLD >> [etna:10799] *** MPI_ERR_COMM: invalid communicator >> [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) >> -------------------------------------------------------------------------- >> mpirun has exited due to process rank 0 with PID 10796 on >> node etna exiting without calling "finalize". This may >> have caused other processes in the application to be >> terminated by signals sent by mpirun (as reported here). >> -------------------------------------------------------------------------- >> [etna:10795] 3 more processes have sent help message >> help-mpi-errors.txt / mpi_errors_are_fatal >> [etna:10795] Set MCA parameter "orte_base_help_aggregate" to 0 to see >> all help / error messages >> >> >> The nice thing is that the same error doesn't appear either if I use >> the 4.5.5 without applying tha patches!!! >> >> mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out2 >> >> or the bug fixed with multiple processors per replica: >> >> mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out3 >> >> Since I have to use more then 4 replicas, I need to run 1cpu/replica. >> >> Has someone any idea of the probem? >> >> Francesco > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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