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[svn-r26746] install_parallel updates.

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Mohamad Chaarawi 2015-04-07 10:50:40 -05:00
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release_docs/INSTALL_parallel
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@ -107,89 +107,9 @@ 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 $*
==== end of myyod =======
For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on
the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is
expected to fail and exit with a non-zero code but the yod command does
not propagate the exit code of the executables. Yod always returns 0 if it
can launch the executable. The test suite shell expects a non-zero for
this particular test, therefore it concludes the test has failed when it
receives 0 from yod. To bypass this problem for now, change the following
lines in the tools/h5ls/testh5ls.sh.
======== Original =========
# The following combination of arguments is expected to return an error message
# and return value 1
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Skip the test =========
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== end of bypass ========
2.5. Hopper (Cray XE6) (for v1.8 and later)
2.4. Hopper (Cray XE6) (for v1.8 and later)
-------------------------
2.5.1 Building HDF5 for Hopper
------------------------------------------
The following steps are for building HDF5 for the Hopper compute
nodes. They would probably work for other Cray systems but have
not been verified.
@ -226,43 +146,6 @@ The build will be in build-hdf5/hdf5/ (or whatever you specify in --prefix).
To compile other HDF5 applications use the wrappers created by the build (build-hdf5/hdf5/bin/h5pcc or h5fc)
2.5.2 Hopper known issues
------------------------------
Issue 1:
Sometimes when building the library with make, you might get this problem:
LD_LIBRARY_PATH="$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
---------------------