Opened 2 weeks ago

Closed 38 hours ago

#2266 closed help (answered)

prebuild Jules.exe from one suite used in another suite on CEDA JASMIN; HDF/NETCDF

Reported by: pmcguire Owned by: um_support
Priority: normal Component: JULES
Keywords: rebuild, Jules, rose suite, CEDA Jasmin, HDF, NETCDF Cc:
Platform: Other UM Version: <select version>

Description

I have checked out rose suite u-ap631, and this runs properly with the pre-existing Jules.exe prebuild on Monsoon. My task is to get this suite working on CEDA Jasmin.

On CEDA Jasmin, I have successfully run the suite u-ai833. As part of its work, this suite produces a Jules.exe executable in a subsubdirectory of cylc-run. I am trying to use this executable as the pre-build for u-ap631 on Jules. But when I do this, I get a run-time error after a while.

The run-time error is:
in the file CEDA-JASMIN:/home/users/pmcguire/cylc-run/u-ap631/log/job/1/main_2006/01/job.err:
/home/users/pmcguire/cylc-run/u-ai843gren/share/fcm_make/build/bin/jules.exe: symbol lookup error: /apps/libs/netCDF/intel14/4.3.2/lib/libnetcdf.so.7: undefined symbol: H5Pset_fapl_mpio

I have tried several things to fix this. I tried looking at the ldd output and nm output for the shared libraries and executable, as well as the versions of the netcdf and hdf libraries on Monsoon and CEDA Jasmin. I am trying now (without success so far) to compile a serial nompi version of Jules with the u-ai843 suite.

Change History (5)

comment:1 Changed 8 days ago by willie

Hi Patrick,

You could try

module show cray-hdf5

This will list paths to libraries that you may need to include in the compilation process.

Regards
Willie

comment:2 Changed 6 days ago by willie

  • Component changed from Rose/Cylc to JULES

comment:3 Changed 2 days ago by pmcguire

I am already doing a "module load parallel-netcdf/intel" in the suite. I did a "module show parallel-netcdf/intel",
and it says: [pmcguire@jasmin-sci1 r6483_spdm_slope]$ module show parallel-netcdf/intel


/apps/modulefiles/parallel-netcdf/intel/20141122:

module-whatis adds parallel-enabled netcdf stack (version built with Intel compiler) to your environment variables
module add libPHDF5/intel/14.0/1.8.12
module add libpnetcdf/intel/14.0/1.5.0
module add netcdf/intel/14.0/4.3.2
module add netcdff/intel/14.0/4.2
module add intel/fce/14.0.2.144
module add intel/cce/14.0.2.144


These paths are already set in my PATH, as well.

comment:4 Changed 2 days ago by pmcguire

I was able to make a different suite that replaces the need for using a prebuilt Jules. This suite completely works on CEDA Jasmin. It is suite number u-aq202. So even though the above issue is unresolved, it is not so important to me anymore.

comment:5 Changed 38 hours ago by willie

  • Resolution set to answered
  • Status changed from new to closed
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