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Diffstat (limited to 'release_docs')
| -rw-r--r-- | release_docs/INSTALL_parallel | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index eacaf68..03b3ecf 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -186,6 +186,73 @@ TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== end of bypass ======== +2.5. Hopper (Cray XE6) (for v1.8 and later) +------------------------- + +2.5.1 Building HDF5 for Hopper +------------------------------------------ +The following steps are for building HDF5 for the Hopper compute +nodes. They would probably work for other Cray XE6 systems but have +not been verified. + +Obtain a copy from the HDF ftp server: +http://www.hdfgroup.org/ftp/HDF5/current/src/ +(link might change, so always double check the HDF group website). + +$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-x.x.x.tar.gz + +unpack the tarball + +$ cd hdf5-x.x.x/ +$ CC=cc FC=ftn ./configure \ +--prefix=/project/hdf5/hdf5 --enable-parallel --enable-fortran \ +--disable-shared --disable-production +$ make + +Run make check. make check should be run on the compute nodes, not the +front end nodes. So using a PBS batch script, allocate 4 or more +cores. Always consult with the machine's website on how to create PBS +scripts and allocate nodes for your job. For Hopper, all the +information can be found on: +http://www.nersc.gov/systems/hopper-cray-xe6/ + +save the PBS script into your HDF5 build directory. The PBS script +should contain (besides the PBS node allocation requests)the +following: + +-------------------------------------------------------------- +cd $PBS_O_WORKDIR + +##set RUNSERIAL and RUNPARALLEL like this in the PBS script: +export RUNPARALLEL="aprun -n 6" +export RUNSERIAL="aprun -n 1" + +##execute make check: +make check +-------------------------------------------------------------- + +Once the job runs and all is well, install the binary: +$ make install + +2.5.2 Hopper known issues +------------------------------ +Sometimes when building the library with make, you might get this problem: + +LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ +sed -e 's/-L/:/g' -e 's/ +//g'`" \ +./H5make_libsettings > H5lib_settings.c +|| \ +(test $HDF5_Make_Ignore && echo "*** Error ignored") +|| \ +(rm -f H5lib_settings.c ; exit 1) +/bin/sh: line 4: 9644 Segmentation fault +LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | sed -e 's/-L/:/g' -e 's/ +//g'`" ./H5make_libsettings > H5lib_settings.c + +If that happens, you are probable running with make -j <x>. In that +case, you need to cleanup everything and start again as detailed above +but use serial make (do not use -j <x>). 3. Detail explanation --------------------- |