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authorAlbert Cheng <acheng@hdfgroup.org>2010-07-14 17:07:50 (GMT)
committerAlbert Cheng <acheng@hdfgroup.org>2010-07-14 17:07:50 (GMT)
commitaab23acc05664e1d0c066e5b6518535446a8eb89 (patch)
treede166de1cbf6486c05e07c61db2c92d8d0b69ac6 /release_docs/INSTALL_parallel
parenteea98ac8cb4743461def87f7d7d2a7d9587d5f8e (diff)
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[svn-r19070] Document update: ID 1921 change mpirun to mpiexec
Changed the use of mpirun to mpiexec which is the MPI-2 official standard. INSTALL_parallel: Also bring in previous update of Red Storm support.
Diffstat (limited to 'release_docs/INSTALL_parallel')
-rw-r--r--release_docs/INSTALL_parallel90
1 files changed, 75 insertions, 15 deletions
diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel
index e8f8bad..04643b2 100644
--- a/release_docs/INSTALL_parallel
+++ b/release_docs/INSTALL_parallel
@@ -51,17 +51,21 @@ 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>
- $ make
- $ make check
+ $ make # build the library
+ $ make check # verify the correctness
+ # Read the Details section about parallel tests.
$ make install
2.2. IBM SP
-----------
-Make sure your environment variables are set correctly to compile and execute
-a single process mpi applications for the SP machine. Unfortunately, the
-setting varies from machine to machine. E.g., the following works for the
-IBM SP machine at LLNL.
+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
@@ -104,6 +108,30 @@ 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.
@@ -115,15 +143,47 @@ not been verified.
$ cd hdf5
$ bin/yodconfigure configure
$ env RUNSERIAL="yod -sz 1" RUNPARALLEL="yod -sz 3" \
- CC="mpicc -DRED_STORM" F9X=mpif90 \
- ./configure --disable-hl --without-zlib --disable-stream-vfd \
- --enable-parallel --prefix=/project/hdf5/phdf5
+ 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 ========
+
3. Detail explanation
---------------------
@@ -169,10 +229,10 @@ For example,
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
compiler is `mpicc' and the user hasn't specified values for RUNSERIAL and
-RUNPARALLEL then configure chooses `mpirun' from the same directory as `mpicc':
+RUNPARALLEL then configure chooses `mpiexec' from the same directory as `mpicc':
- RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1
- RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=3}
+ RUNSERIAL: /usr/local/mpi/bin/mpiexec -np 1
+ RUNPARALLEL: /usr/local/mpi/bin/mpiexec -np $${NPROCS:=3}
The `$${NPROCS:=3}' will be substituted with the value of the NPROCS
environment variable at the time `make check' is run (or the value 3).
@@ -218,7 +278,7 @@ Appendix A. Sample programs
---------------------------
Here are sample MPI-IO C and Fortran programs. You may use them to run simple
tests of your MPI compilers and the parallel file system. The MPI commands
-used here are mpicc, mpif90 and mpirun. Replace them with the commands of
+used here are mpicc, mpif90 and mpiexec. Replace them with the commands of
your system.
The programs assume they run in the parallel file system. Thus they create
@@ -229,10 +289,10 @@ programs to use a different file name.
Example compiling and running:
% mpicc Sample_mpio.c -o c.out
-% mpirun -np 4 c.out
+% mpiexec -np 4 c.out
% mpif90 Sample_mpio.f90 -o f.out
-% mpirun -np 4 f.out
+% mpiexec -np 4 f.out
==> Sample_mpio.c <==