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[svn-r23470] update INSTALL_parallel with build instructions for Hopper.

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Mohamad Chaarawi 2013-03-27 17:06:16 -05:00
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release_docs/INSTALL_parallel
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@ -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
---------------------