Message: 2 > Date: Mon, 1 Feb 2010 12:31:32 +0530 > From: Chandan Choudhury <iitd...@gmail.com> > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with > mpicc > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks. > I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc > file, and could compile the mpi version of gromacs. > The next thing is I got the error on executing mdrun_mpi -h > Following is the output. Kindly help. > > corsica:/usr/local/gromacs/bin # mdrun_mpi -h > [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file > runtime/orte_init_stage1.c at line 182 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_rml_base_select failed > --> Returned value -13 instead of ORTE_SUCCESS > > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init_stage1 failed > --> Returned "Not found" (-13) instead of "Success" (0) > -------------------------------------------------------------------------- > *** An error occurred in MPI_Init > *** before MPI was initialized > *** MPI_ERRORS_ARE_FATAL (goodbye) > [corsica:17130] Abort before MPI_INIT completed successfully; not able to > guarantee that all other processes were killed! > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > >
U will be getting error s like this as the MPI failed. When u run mdrun with MPI. If u use this CPPFLAGS, and i also had a problem. When i used this option, after that i was unable to revert back it to the original state also. So the better option update the gcc, c++ compilers, If u have doubt in this, remove gromacs, All MPi. then do yum install -y *openmpi* --It will automatically install the missing libraries in dependencies. and then download fftw ---latest the install fftw with ./configure --enable-threads --enable-mpi the gromacs ./configure --enable-threads --enable-mpi this will surely work, because in order gromacs work with MPI. U should compile fftw with MPI as above. -- B. Sarath Kumar, B.tech.
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