[CIG-SHORT] Pylith install error

[Brad Aagaard]

Birendra,

The differences in configuration between the compute nodes and head node 
are likely the source of the problem. You should contact the 
administrator of the cluster to resolve this problem. You may need to 
use specific settings for cross-compilation or the cluster configuration 
may simply not be setup correctly.

Regards,
Brad


On 9/11/13 10:40 AM, Birendra jha 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
>   >
>
>   _______________________________________________
>   CIG-SHORT mailing list
>   CIG-SHORT at geodynamics.org
>   http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>