[gmx-users] error: Cannot compile and link MPI code with mpicc

[Mark Abraham]

On 01/02/10 20:19, Sarath Kumar wrote:
>
>
>     Message: 2
>     Date: Mon, 1 Feb 2010 12:31:32 +0530
>     From: Chandan Choudhury <iitdckc at gmail.com <mailto:iitdckc at gmail.com>>
>     Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>             mpicc
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
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>     <4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3 at mail.gmail.com
>     <mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3 at mail.gmail.com>>
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>
>     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.

None of this will help if the MPI environment is not configured, e.g. a 
hostfile set up. Chandan needs to get a test MPI program to run before 
there is evidence any of this discussion belongs on the GROMACS mailing 
last.

Mark