[CIG-SHORT] Pylith install error
Brad Aagaard
baagaard at usgs.gov
Wed Sep 11 16:19:48 PDT 2013
Birendra,
I don't think Matt's solution of adjusting environment variables has any
hope of solving your problem. The discrepancies in versions of
libgfortran must be resolved between the head node (presumably where
openmpi was built) and the compute node. There may be another openmpi
version installed that is consistent with the compute nodes. Note that
OpenMPI versions 1.4.x and 1.6.x are the stable releases while versions
1.3.x, 1.5.x, and 1.7.x are the new feature releases that may contain
issues.
I think the problem you encountered will show up via any fortran program
built with the mpif90 compiler on the head node and trying to run it on
a compute node. If you can get that to work, check where libgfortran is
being found using "ldd MY_FORTRAN_PROGRAM". As I mentioned before, your
best bet is to work with your system admin to resolve these
discrepancies between the compute nodes and the head node.
Regards,
Brad
On 9/11/13 3:59 PM, Birendra jha wrote:
> Hi Matt
>
> I didn't modify the LD_LIBRARY_PATH after setting it through pylith's setup.sh. Because I don't know how to give the path /usr/lib of the headnode, while compiling on the compute node, which has its own /usr/lib.
>
> thanks
> Birendra
> --------------------------------------------
> On Thu, 9/12/13, Matthew Knepley <knepley at gmail.com> wrote:
>
> Subject: Re: [CIG-SHORT] Pylith install error
> To: cig-short at geodynamics.org
> Date: Thursday, September 12, 2013, 1:17 AM
>
> Did you try setting
> LD_LIBRARY_PATH?
> Matt
> On Sep 11, 2013 10:40
> AM, "Birendra jha" <bjha7333 at yahoo.com>
> wrote:
>
> Hi
>
>
>
> The configuration is such that I am installing it in my home
> directory on the head node of a cluster, but compiling on
> one of the compute nodes. I am not compiling on the head
> node because I get C compiler error during the configure
> phase.
>
>
> The headnode and the compute node have different versions of
> libgfortran (so.1 and so.3). Here are the steps I took:
>
>
>
> qrsh -l hostname=gpu-0-31 (ignore gpu in the name, I am
> not using gpu stuff)
>
> module add openmpi (I do this because there
> is no openmpi on this gpu node, only on headnode)
>
> cd /share/home/bjha/build/pylith-1.9.0/
>
> ../../src/pylith/pylith-installer-1.9.0-0/configure
> --prefix=/share/home/bjha/pylith-1.9.0
>
> source setup.sh (everything ok so
> far)
>
> make
>
> libgfortran.so.1, needed by
> /share/apps/openmpi/openmpi-1.3.3/lib/libmpi_f90.so, not
> found (try using -rpath or -rpath-link)
>
>
>
> Is it possible to add the libgfortran.so.1 path from the
> head node while compiling on the gpu node?
>
>
>
> Or, is the only option is to install openmpi (a newer
> version that goes with libgfortran.so.3) on the compute
> node? This might take a while because it depends on our
> system admin.
>
>
>
> thanks
>
> Birendra
>
>
>
> --------------------------------------------
>
> On Wed, 9/11/13, Brad Aagaard <baagaard at usgs.gov>
> wrote:
>
>
>
> Subject: Re: [CIG-SHORT] Pylith install error
>
> To: cig-short at geodynamics.org
>
> Date: Wednesday, September 11, 2013, 9:38 AM
>
>
>
> Birendra,
>
>
>
> Check to make sure than mpicc, mpicxx, and mpif90 are
>
> pointing to the
>
> correct compilers using mpicc -show, mpicxx -show, and
>
> mpif90 -show. If
>
> a consistent set of compilers and paths are being used
> for
>
> MPI and your
>
> environment, you should not get an error like this.
>
>
>
> Regards,
>
> Brad
>
>
>
>
>
>
>
> On 9/10/13 8:32 PM, Birendra jha wrote:
>
> > Hi
>
> >
>
> > I am installing pylith-1.9.0 from the installer on a
>
> different computer and I got following error during the
> make
>
> step:
>
> >
>
> > Making all in fortran
>
> > make[5]: Entering directory
>
> `/share/home/bjha/build/pylith-1.9.0/hdf5-build/fortran'
>
> > Making all in src
>
> > make[6]: Entering directory
>
> `/share/home/bjha/build/pylith-1.9.0/hdf5-build/fortran/src'
>
> > FC H5test_kind.o
>
> > FCLD H5test_kind
>
> > /usr/bin/ld: warning: libgfortran.so.1, needed by
>
> /share/apps/openmpi/openmpi-1.3.3/lib/libmpi_f90.so, not
>
> found (try using -rpath or -rpath-link)
>
> > ./H5test_kind > H5fortran_detect.f90
>
> > ./H5test_kind: error while loading shared libraries:
>
> libgfortran.so.1: cannot open shared object file: No such
>
> file or directory
>
> > make[6]: *** [H5fortran_detect.f90] Error 127
>
> > make[6]: Leaving directory
>
> `/share/home/bjha/build/pylith-1.9.0/hdf5-build/fortran/src'
>
> > make[5]: *** [all-recursive] Error 1
>
> > make[5]: Leaving directory
>
> `/share/home/bjha/build/pylith-1.9.0/hdf5-build/fortran'
>
> > make[4]: *** [all-recursive] Error 1
>
> > make[4]: Leaving directory
>
> `/share/home/bjha/build/pylith-1.9.0/hdf5-build'
>
> > make[3]: *** [hdf5] Error 2
>
> > make[3]: Leaving directory
>
> `/share/home/bjha/build/pylith-1.9.0'
>
> > make[2]: *** [installed_hdf5] Error 2
>
> > make[2]: Leaving directory
>
> `/share/home/bjha/build/pylith-1.9.0'
>
> > make[1]: *** [installed_netcdf] Error 2
>
> > make[1]: Leaving directory
>
> `/share/home/bjha/build/pylith-1.9.0'
>
> > make: *** [installed_pylith] Error 2
>
> >
>
> > I checked that the computer has libgfortran.so.1 in
>
> both /usr/lib and /usr/lib64.
>
> >
>
> > Is it a path issue?
>
> >
>
> > Thanks and regards
>
> > Birendra
>
> > _______________________________________________
>
> > CIG-SHORT mailing list
>
> > CIG-SHORT at geodynamics.org
>
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
> >
>
>
>
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