[MITgcm-support] RES: Doubts to compilation and running the model MITgcm

Wed Jul 2 18:07:46 EDT 2014

Hi Paulo,

This type of error message:
> error while loading shared libraries: libifort.so.5: cannot open shared object file: No such file or directory
is generally related to LD_LIBRARY_PATH being not set correctly.
And with some (old, mpich-1) version of MPI, I found some cases where
I had to add in my ".tcshrc":
> setenv LD_LIBRARY_PATH {the path of ifort shared libs}
in order to use mpirun on several procs (the export/setenv in the
current session was not enough).

Now in your case, when you tried to run one of the standard verification 
experiment (i.e., not coupled), compiled with "genmake2 -mpi -of {the same optfile}
with the same version of MPI (and same mpirun) on more than 1 proc, 
I would have expected the same error.

Since I saw in the screen shot you sent (BTW, a plain text attachment instead
of a png file would have been easier to cut and paste):
> make[1]: 'mitgcmuv' is up to date.
I am tempted to ask confirmation that you clean-up everything 
(left from a previous attempt ; "./run_cpl_test 0") and proceed with 
the same environment setting as when you successfully tested the other 
experiments with MPI.

Cheers,
Jean-Michel

On Wed, Jul 02, 2014 at 04:13:53PM -0300, C0388991 (Paulo Ricardo) wrote:
> Hi Dear Jean-Michel,
> 
> Same problem. I'm proceed with the 3 steps, every experiment compile and run all fine. But this one, has the same error. I tried with ifort+mpi and gfortran, compile ok, but when i try run, shows the error (in attachments). So, some light for me?
> 
> 
> At.,
> 
> Paulo Ricardo
> Instituto Tecnológico Vale / Vale Institue of Technology
> Desenvolvimento Sustentável / Sustainable Development
> Tecnologia da Informação / Information Technology
> Boa Ventura da Silva, 955  - Nazaré 66055-090 Belém PA Brazil
> Tel: 55 (91) 3213 5430 Carrier: 865 5430 / (91) 9234 3845
> c0388991 at vale.com (Paulo Ricardo)
> ________________________________________
> De: Jean-Michel Campin [jmc at ocean.mit.edu]
> Enviado: terça-feira, 1 de julho de 2014 23:41
> Para: mitgcm-support at mitgcm.org
> Assunto: Re: [MITgcm-support] Doubts to compilation and running the model MITgcm
> 
> Hi Paulo,
> 
> I would recommand to proceed by steps:
> 
> 1) check that you can compile and run one (or several) of the
>  simple verification experiments (any of those that contains
>  a results/output.txt file, except cpl_aim+ocn; might give it
>  a try with aim.5l_cs/ and global_ocean.cs32x15/ which you can
>  view as uncoupled version of the coupled set-up).
>  You can start without using MPI, just on one proc (all the verification
>  experiment are small enough), and check that your optfile is working well.
>  BTW, if you want to use intel compiler, you might want to start from
>  the default (amd64) ifort optfile: linux_amd64_ifort11
> 
> 2) check that you are able to compile and run with MPI ;
>  this might requires other settings, e.g., with linux_amd64_ifort11,
>  as written in the top comments of linux_amd64_ifort11 optfile:
> # ==> DON'T FORGET to set environment variable MPI_INC_DIR to the include
> #     directory of your MPI implementation
> 
> 3) when you are confident that the 2 steps above work well,
>  you can try to compile and run the coupled set-up "cpl_aim+ocn";
>  Because the way to run, with MPI, different executables is highly
>  dependent on the type of MPI implementation, you might need to modify the
>  little script "run_cpl_test" (it is provided more as an example
>  of the diversity of mpirun command line options rather than a
>  solid script, which is hard to set-up given the reason above).
> 
> Cheers,
> Jean-Michel
> 
> On Tue, Jul 01, 2014 at 10:02:40AM -0300, C0388991 (Paulo Ricardo) wrote:
> >
> > Hi,
> >
> > My name is Paulo, i'm from Brazil and i'm a systems analyst of a Institute of Research (ITV). We have one researcher trying to use this model, and i don't found a list of softwares to compile this, do you have a list? I'm using the compiler "ifort" with openMPI, and i installed "netcdf" in our Cluster. I guess that i get it right way. I'm attaching the files that i'm using. I'm trying compile the "/verification/cpl_aim+ocn/".
> >
> > I'm using that steps:
> >
> > editing my output file = ../../tools/build_options/linux_amd64_gfortran-luis2 (in attachments).
> >
> > compilation: ./run_cpl_test 1 -of ../../tools/build_options/linux_amd64_gfortran-luis2
> >
> > and running: cd /build_cpl
> >                      ./mitgcmuv
> >
> > And i have the error: ./mitgcmuv: error while loading shared libraries: libifport.so.5: cannot open shared object file: No such file or directory
> >
> > I've tried to put the export the library: LD_LIBRARY_PATH=/opt/intel/composer_xe_2013.1.117/compiler/lib/intel64
> >                                                           export LD_LIBRARY_PATH
> >
> > and when i run again, show a new error: ./mitgcmuv: symbol lookup error: ./mitgcmuv: undefined symbol: mpi_init_ (in attachments)
> >
> >
> > How could you help me? Where i'm wrong?
> >
> >
> >
> >
> > At.,
> >
> > Paulo Ricardo
> > Instituto Tecnológico Vale / Vale Institue of Technology
> > Desenvolvimento Sustentável / Sustainable Development
> > Tecnologia da Informação / Information Technology
> > Boa Ventura da Silva, 955  - Nazaré 66055-090 Belém PA Brazil
> > Tel: 55 (91) 3213 5430 Carrier: 865 5430 / (91) 9234 3845
> > c0388991 at vale.com (Paulo Ricardo)
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> 
> 
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