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Diffstat (limited to 'release_docs/INSTALL_parallel')
| -rw-r--r-- | release_docs/INSTALL_parallel | 174 |
1 files changed, 5 insertions, 169 deletions
diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index 2624b3b..e4c540c 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -49,54 +49,15 @@ more detailed explanations. ---------------------------- HDF5 knows several parallel compilers: mpicc, hcc, mpcc, mpcc_r. To build parallel HDF5 with one of the above, just set CC as it and configure. -The "--enable-parallel" is optional in this case. - $ CC=/usr/local/mpi/bin/mpicc ./configure --prefix=<install-directory> + $ CC=/usr/local/mpi/bin/mpicc ./configure --enable-parallel --prefix=<install-directory> $ make # build the library $ make check # verify the correctness # Read the Details section about parallel tests. $ make install -2.2. IBM SP ------------ -During the build stage, the H5detect is compiled and executed to generate -the source file H5Tinit.c which is compiled as part of the HDF5 library. In -parallel mode, make sure your environment variables are set correctly to -execute a single process mpi application. Otherwise, multiple processes -attempt to write to the same H5Tinit.c file, resulting in a scrambled -source file. Unfortunately, the setting varies from machine to machine. -E.g., the following works for the IBM SP machine at LLNL. - - setenv MP_PROCS 1 - setenv MP_NODES 1 - setenv MP_LABELIO no - setenv MP_RMPOOL 0 - setenv LLNL_COMPILE_SINGLE_THREADED TRUE # for LLNL site only - -The shared library configuration is problematic. So, only static library -is supported. - -Then do the following steps: - - $ ./configure --disable-shared --prefix=<install-directory> - $ make # build the library - $ make check # verify the correctness - # Read the Details section about parallel tests. - $ make install - -We also suggest that you add "-qxlf90=autodealloc" to FCFLAGS when building -parallel with fortran enabled. This can be done by invoking: - - setenv FCFLAGS -qxlf90=autodealloc # 32 bit build -or - setenv FCFLAGS "-q64 -qxlf90=autodealloc" # 64 bit build - -prior to running configure. Recall that the "-q64" is necessary for 64 -bit builds. - - -2.3. Linux 2.4 and greater +2.2. Linux 2.4 and greater -------------------------- Be sure that your installation of MPICH was configured with the following configuration command-line option: @@ -107,89 +68,9 @@ This allows for >2GB sized files on Linux systems and is only available with Linux kernels 2.4 and greater. -2.4. Red Storm (Cray XT3) (for v1.8 and later) -------------------------- -Both serial and parallel HDF5 are supported in Red Storm. - -2.4.1 Building serial HDF5 for Red Storm ------------------------------------------- -The following steps are for building the serial HDF5 for the Red Storm -compute nodes. They would probably work for other Cray XT3 systems but have -not been verified. - -# Assume you already have a copy of HDF5 source code in directory `hdf5' and -# want to install the binary in directory `/project/hdf5/hdf5'. - -$ cd hdf5 -$ bin/yodconfigure configure -$ env RUNSERIAL="yod -sz 1" \ - CC=cc FC=ftn CXX=CC \ - ./configure --prefix=/project/hdf5/hdf5 -$ make -$ make check - -# if all is well, install the binary. -$ make install - -2.4.2 Building parallel HDF5 for Red Storm ------------------------------------------- -The following steps are for building the Parallel HDF5 for the Red Storm -compute nodes. They would probably work for other Cray XT3 systems but have -not been verified. - -# Assume you already have a copy of HDF5 source code in directory `hdf5' and -# want to install the binary in directory `/project/hdf5/phdf5'. You also -# have done the proper setup to have mpicc and mpif90 as the compiler commands. - -$ cd hdf5 -$ bin/yodconfigure configure -$ env RUNSERIAL="yod -sz 1" RUNPARALLEL="yod -sz 3" \ - CC=cc FC=ftn \ - ./configure --enable-parallel --prefix=/project/hdf5/phdf5 -$ make -$ make check - -# if all is well, install the binary. -$ make install - -2.4.3 Red Storm known problems ------------------------------- -For Red Storm, a Cray XT3 system, the yod command sometimes gives the -message, "yod allocation delayed for node recovery". This interferes with -test suites that do not expect seeing this message. To bypass this problem, -I launch the executables with a command shell script called "myyod" which -consists of the following lines. (You should set $RUNSERIAL and $RUNPARALLEL -to use myyod instead of yod.) -==== myyod ======= -#!/bin/sh -# sleep 2 seconds to allow time for the node recovery else it pops the -# message, -# yod allocation delayed for node recovery -sleep 2 -yod $* -==== end of myyod ======= - -For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on -the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is -expected to fail and exit with a non-zero code but the yod command does -not propagate the exit code of the executables. Yod always returns 0 if it -can launch the executable. The test suite shell expects a non-zero for -this particular test, therefore it concludes the test has failed when it -receives 0 from yod. To bypass this problem for now, change the following -lines in the tools/h5ls/testh5ls.sh. -======== Original ========= -# The following combination of arguments is expected to return an error message -# and return value 1 -TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 -======== Skip the test ========= -echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 -======== end of bypass ======== - -2.5. Hopper (Cray XE6) (for v1.8 and later) +2.3. Hopper (Cray XE6) (for v1.8 and later) ------------------------- -2.5.1 Building HDF5 for Hopper ------------------------------------------- The following steps are for building HDF5 for the Hopper compute nodes. They would probably work for other Cray systems but have not been verified. @@ -226,43 +107,6 @@ The build will be in build-hdf5/hdf5/ (or whatever you specify in --prefix). To compile other HDF5 applications use the wrappers created by the build (build-hdf5/hdf5/bin/h5pcc or h5fc) -2.5.2 Hopper known issues ------------------------------- -Issue 1: -Sometimes when building the library with make, you might get this problem: - -LD_LIBRARY_PATH="$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>). - -Issue 2: -* When building using the Cray compilers on Cray machines, HDF5 - configure mistakenly thinks the compiler is an intel compiler and - sets the -std=c99 flag which breaks configure on Cray. To build HDF5 - properly on a Cray machine, please consult with the instructions in - INSTALL_parallel for building on Hopper. - (MSC - 2013/04/26 - HDFFV-8429) - -Issue 3: -* On hopper, the build failed when RUNSERIAL and RUNPARALLEL are set - to aprun -np X, because the H5lib_settings.c file was not generated - properly. Not setting those environment variables works, because - configure was able to automatically detect that it's a Cray system - and used the proper launch commands when necessary. - (MSC - 2012/04/18) - 3. Detail explanation --------------------- @@ -293,16 +137,8 @@ a properly installed parallel compiler (e.g., MPICH's mpicc or IBM's mpcc_r) and supply the compiler name as the value of the CC environment variable. For examples, - $ CC=mpcc_r ./configure - $ CC=/usr/local/mpi/bin/mpicc ./configure - -If no such a compiler command is available then you must use your normal -C compiler along with the location(s) of MPI/MPI-IO files to be used. -For example, - - $ CPPFLAGS=-I/usr/local/mpi/include \ - LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ - ./configure --enable-parallel=mpich + $ CC=mpcc_r ./configure --enable-parallel + $ CC=/usr/local/mpi/bin/mpicc ./configure --enable-parallel If a parallel library is being built then configure attempts to determine how to run a parallel application on one processor and on many processors. If the |