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| -rw-r--r-- | release_docs/INSTALL_parallel | 45 |
1 files changed, 19 insertions, 26 deletions
diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index 28068f1..2624b3b 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -191,7 +191,7 @@ echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 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 +nodes. They would probably work for other Cray systems but have not been verified. Obtain a copy from the HDF ftp server: @@ -199,39 +199,32 @@ 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 +The entire build process should be done on a MOM node in an interactive allocation and on a file system accessible by all compute nodes. +Request an interactive allocation with qsub: +qsub -I -q debug -l mppwidth=8 -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/ +- create a build directory build-hdf5: + mkdir build-hdf5; cd build-hdf5/ -save the PBS script into your HDF5 build directory. The PBS script -should contain (besides the PBS node allocation requests)the -following: +- configure HDF5: + RUNSERIAL="aprun -q -n 1" RUNPARALLEL="aprun -q -n 6" FC=ftn CC=cc /path/to/source/configure --enable-fortran --enable-parallel --disable-shared --------------------------------------------------------------- -cd $PBS_O_WORKDIR + RUNSERIAL and RUNPARALLEL tells the library how it should launch programs that are part of the build procedure. -##set RUNSERIAL and RUNPARALLEL like this in the PBS script: -export RUNPARALLEL="aprun -n 6" -export RUNSERIAL="aprun -n 1" +- Compile HDF5: + gmake -##execute make check: -make check --------------------------------------------------------------- +- Check HDF5 + gmake check + +- Install HDF5 + gmake install + +The build will be in build-hdf5/hdf5/ (or whatever you specify in --prefix). +To compile other HDF5 applications use the wrappers created by the build (build-hdf5/hdf5/bin/h5pcc or h5fc) -Once the job runs and all is well, install the binary: -$ make install 2.5.2 Hopper known issues ------------------------------ |