Commit 41511462 authored by gsell's avatar gsell

repo migration

parents
* text=auto !eol
/AUTHORS -text
/COPYRIGHT -text
/ChangeLog -text
/GNUmakefile.orig -text
/Makefile.am -text
/Makefile.orig -text
/NEWS -text
/README -text
/autogen.sh -text
/config.guess -text
/config.h.in -text
/config.sub -text
/configure.ac -text
/depcomp -text
doc/2006-Berkeley-Visit/BethelSAP_1page-4.doc -text
doc/2006-Berkeley-Visit/H5Part.ppt -text
doc/2006-Berkeley-Visit/H5xxx.ppt -text
doc/2006-Berkeley-Visit/H5xxxVisIt.fig -text
doc/2006-Berkeley-Visit/SAP-Combined-v6.doc -text
doc/2006-Berkeley-Visit/aqpsi2006mar22.pdf -text
doc/2006-Berkeley-Visit/hdf.ps -text
doc/Building.html -text
doc/BuildingHDF5.html -text
doc/Downloading.html -text
doc/Doxyfile -text
doc/H5PartExpress.html -text
doc/H5PartIDL.html -text
doc/H5PartParaview.html -text
doc/H5PartTools.html -text
doc/H5PartVisIt.html -text
doc/H5PartVisIt/cloud_visit.png -text
doc/H5PartVisIt/cloud_visit.s.png -text
doc/H5PartVisIt/cloud_visit_2D.png -text
doc/H5PartVisIt/cloud_visit_2D.s.png -text
doc/H5PartVisIt/visit_query1.png -text
doc/H5PartVisIt/visit_query1.s.png -text
doc/H5tools/H5tools.htm -text
doc/H5tools/H5tools_files/snapshot1.jpg -text
doc/H5xxx/H5xxx.tex -text
doc/H5xxx/JAC2003.cls -text
doc/H5xxx/makefile -text
doc/InternalLayout.html -text
doc/ReferencePages/H5PartF_8c.html -text
doc/ReferencePages/H5Part_8c.html -text
doc/ReferencePages/H5Part_8h-source.html -text
doc/ReferencePages/H5Part_8h.html -text
doc/ReferencePages/annotated.html -text
doc/ReferencePages/doxygen.css -text
doc/ReferencePages/doxygen.png -text
doc/ReferencePages/files.html -text
doc/ReferencePages/functions.html -text
doc/ReferencePages/functions_vars.html -text
doc/ReferencePages/globals.html -text
doc/ReferencePages/globals_defs.html -text
doc/ReferencePages/globals_func.html -text
doc/ReferencePages/globals_type.html -text
doc/ReferencePages/index.html -text
doc/ReferencePages/structH5IO__getname__t-members.html -text
doc/ReferencePages/structH5IO__getname__t.html -text
doc/ReferencePages/structH5PartFile-members.html -text
doc/ReferencePages/structH5PartFile.html -text
doc/UsingC.html -text
doc/UsingF.html -text
doc/collision_6.png -text
doc/collision_6.s.png -text
doc/h5part.html -text
doc/hdf5.pdf -text
doc/layout.png -text
/install-sh -text
/license.txt -text
/missing -text
/rules.make -text
src/H5Block.c -text
src/H5Block.h -text
src/H5BlockErrors.h -text
src/H5BlockF90.inc -text
src/H5BlockPrivate.h -text
src/H5BlockTypes.h -text
src/H5Part++.cc -text
src/H5Part++.hh -text
src/H5Part.c -text
src/H5Part.cc -text
src/H5Part.h -text
src/H5Part.hh -text
src/H5PartErrors.h -text
src/H5PartF.c -text
src/H5PartF90.inc -text
src/H5PartPrivate.h -text
src/H5PartTypes.h -text
src/H5Units.h -text
src/Makefile.am -text
src/TestUnderscore.f -text
src/TestUnderscoreC.c -text
src/addToDoxygenMainPage.h -text
test/Bench.c -text
test/H5BlockParallelTest1.c -text
test/H5BlockReadParallel1.c -text
test/H5BlockTest1.c -text
test/H5BlockWrite1.c -text
test/H5ParallelTest.cc -text
test/H5PartAndreasTest.cc -text
test/H5PartTest.cc -text
test/H5PartTestParallel.cc -text
test/H5ecloudExample.cc -text
test/H5test.cc -text
test/H5testF.f -text
test/H5testFpar.f -text
test/Makefile.am -text
tools/Makefile.am -text
tools/README -text
tools/h5pAttrib.cc -text
tools/h5pToGNUplot.cc -text
tools/h5pToGNUplot.py -text
visit_plugins/databases/H5Part/.depend -text
visit_plugins/databases/H5Part/Makefile -text
visit_plugins/databases/H5Part/README.txt -text
visit_plugins/databases/H5Part/avth5partFileFormat.C -text
visit_plugins/databases/H5Part/avth5partFileFormat.h -text
visit_plugins/databases/H5Part/h5part.xml -text
visit_plugins/databases/H5Part/h5partCommonPluginInfo.C -text
visit_plugins/databases/H5Part/h5partEnginePluginInfo.C -text
visit_plugins/databases/H5Part/h5partMDServerPluginInfo.C -text
visit_plugins/databases/H5Part/h5partPluginInfo.C -text
visit_plugins/databases/H5Part/h5partPluginInfo.h -text
visit_plugins/operators/BinnerFilter/.depend -text
visit_plugins/operators/BinnerFilter/Binner.xml -text
visit_plugins/operators/BinnerFilter/BinnerCommonPluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerEnginePluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerFilter.C -text
visit_plugins/operators/BinnerFilter/BinnerFilter.h -text
visit_plugins/operators/BinnerFilter/BinnerFilter.java -text
visit_plugins/operators/BinnerFilter/BinnerGUIPluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerMakefile -text
visit_plugins/operators/BinnerFilter/BinnerPluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerPluginInfo.h -text
visit_plugins/operators/BinnerFilter/BinnerScriptingPluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerViewerPluginInfo.C -text
visit_plugins/operators/BinnerFilter/Binnerreplace.txt -text
visit_plugins/operators/BinnerFilter/Makefile -text
visit_plugins/operators/BinnerFilter/PyBinner.C -text
visit_plugins/operators/BinnerFilter/PyBinner.h -text
visit_plugins/operators/BinnerFilter/QvisBinnerWindow.C -text
visit_plugins/operators/BinnerFilter/QvisBinnerWindow.h -text
visit_plugins/operators/BinnerFilter/avtBinnerFilter.C -text
visit_plugins/operators/BinnerFilter/avtBinnerFilter.h -text
visit_plugins/operators/BinnerFilter/icon.xpm -text
visit_plugins/operators/RandomSample/.depend -text
visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.C -text
visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.h -text
visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.java -text
visit_plugins/operators/RandomSample/H5PartRandomSampleCommonPluginInfo.C -text
visit_plugins/operators/RandomSample/H5PartRandomSampleEnginePluginInfo.C -text
visit_plugins/operators/RandomSample/H5PartRandomSampleGUIPluginInfo.C -text
visit_plugins/operators/RandomSample/H5PartRandomSamplePluginInfo.C -text
visit_plugins/operators/RandomSample/H5PartRandomSamplePluginInfo.h -text
visit_plugins/operators/RandomSample/H5PartRandomSampleScriptingPluginInfo.C -text
visit_plugins/operators/RandomSample/H5PartRandomSampleViewerPluginInfo.C -text
visit_plugins/operators/RandomSample/Makefile -text
visit_plugins/operators/RandomSample/PyH5PartRandomSampleAttributes.C -text
visit_plugins/operators/RandomSample/PyH5PartRandomSampleAttributes.h -text
visit_plugins/operators/RandomSample/QvisH5PartRandomSampleWindow.C -text
visit_plugins/operators/RandomSample/QvisH5PartRandomSampleWindow.h -text
visit_plugins/operators/RandomSample/RandomSample.xml -text
visit_plugins/operators/RandomSample/avtH5PartRandomSampleFilter.C -text
visit_plugins/operators/RandomSample/avtH5PartRandomSampleFilter.h -text
visit_plugins/operators/RandomSample/icon.xpm -text
Andreas Adelmann (PSI)
Achim Gsell (PSI)
Benedikt Oswald (PSI)
Wes Bethel (NERSC/LBNL)
John Shalf (NERSC/LBNL)
Cristina Siegerist (NERSC/LBNL)
Please use h5part@lists.psi.ch for communicaion.
*** Copyright Notice ***
H5Part Copyright (c) 2006, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and the Paul Scherrer Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
# for host specific options
HOST := $(shell hostname)
# for processor-specific options
ifeq ($(UNAME), Linux)
PROC := $(shell uname -p)
endif
CXX = c++
CC = cc
H5HOME = /usr/local/hdf5
CFLAGS = -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# MacOS-X Serial
ifeq ($(UNAME), Darwin)
ifeq ($(PARALLEL), yes)
CXX = g++
CC = mpicc
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
else
CXX = c++
CC = cc
F90 = xlf
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# SGI MIPS/Irix
ifeq ($(UNAME), IRIX64)
CXX = CC
CC = cc
F90 = f90
ifeq ($(PARALLEL), yes)
H5HOME = $(HDF5_DIR)
CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
else
H5HOME = /usr/local
CFLAGS = -O3 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# AIX/SP-2 Parallel/serial : Seaborg
ifeq ($(UNAME), AIX)
ifeq ($(PARALLEL), yes) # parallel
CXX = mpCC_r
CC = mpxlc_r
# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
# /usr/common/usg/hdf5/1.4.4/parallel
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -q64 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
else # serial
CXX = xlC
CC = xlc
H5HOME = /usr/common/usg/hdf5/1.4.4/serial
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
endif
endif
# Linux
ifeq ($(UNAME), Linux)
# if this machine is NERSC/Davinci Altix system
ifeq ($(PROC), ia64)
CC = icc
CXX = icc
ifeq ($(PARALLEL), yes)
# IA64 Linux Parallel
ifeq ($(HOST), davinci)
H5HOME = $(HDF5_PAR)
MPILIB = -lmpi
else
H5HOME = /usr/local
HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
HDF5_PAR_INCLUDE = -I$(H5HOME)/include
MPIHOME = /usr/local
MPILIB = -lmpich
endif # HOST
CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE)
LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
else # IA64 Linux Serial
CFLAGS = -O3 $(HDF5_INCLUDE)
LDFLAGS = $(HDF5_LIB) -lm
endif # PARALLEL
# else this is standard IA32 linux
else
ifeq ($(PARALLEL), yes)
# Linux Parallel
CC = gcc
CXX = g++
H5HOME = /usr/local
MPIHOME = /usr/local
CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
else # Linux Serial
CXX = g++
CC = gcc
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif # !PARALLEL
endif # PROC!ia64
endif # !Linux
ifeq ($(PARALLEL), yes) #parallel
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
endif
else
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o
endif
endif
include rules.make
# Trial by Antino Kim
# Top level Makefile.am
SUBDIRS = \
src \
test \
tools
MAINTAINERCLEANFILES = \
config.h \
config.log \
config.status \
stamp-h.in \
stamp-h1
# This is a very rudimentary multiarchitecture makefile
# You need to uncomment the default block of make variables you need
# Some key things to watch for are the following defines
# -DREGRESSIONTEST : enables a main(){} inside of
# the H5Part.cc file that does simple regression testing.
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
# enable this. Otherwise, you get only the serial
# implementation of the library.
# MacOS-X Serial
#CXX = c++
#CC = cc
#F90 = xlf
#H5HOME = /usr/local
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# AIX/SP-2 Parallel : Seaborg
#CXX = mpCC_r
#CC = mpcc_r
#F90 = mpxlf
#H5HOME = /usr/common/usg/hdf5/1.4.4/parallel
#H4HOME = /usr/common/usg/hdf/default
#OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
#CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
# Linux Serial
#CXX = g++
#CC = gcc
#F90 = g77 # or could be pgif90
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Jacquard
CC = mpicc
CXX = mpicxx
F90 = mpif90
H5HOME = /usr/common/usg/hdf5/1.6.3/parallel
CFLAGS = -O2 -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Parallel
#CC = gcc
#CXX = g++
#F90 = g77
#H5HOME = /usr/local
# /usr/common/usg/hdf5/1.6.3/parallel
#MPIHOME = /usr/local
#CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
all: H5PartTest H5PartTest.o H5Part.o
parallel: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest # parallel regression tests
fortran: H5PartF.o # fortran bindings
include rules.make
Error Handling
--------------
Now all functions, in which an error could occure, are returning a
value. This value is either a 64bit integer or a pointer.
A negative 64bit integer as result indicates an error. Values >= 0
indicates successfull execution. This is similiar to the convention
used in UNIX system calls, but we do not return -1 but the error
number (which is always negative).
For functions returning a pointer the NULL-pointer is used to indicate
an error. You can call the function H5PartGetErrno() to get the error
number. For the time being there is no strerror(3) or perror(3)
equivalent.
API Changes
-----------
There are several changes in the API of H5Part. The biggest change is
a side-effect of the implementation of strict error handling. The
impact to the existing C/C++ code is very small. But now you *can*
and *should* implement some kind of error handling. The simplest
error handling is to set an error handler which aborts the program as
soon as an error occured.
The next "biggest" change is the use of H5Part types instead of "long
long" and "double". The replacement of "long long" is "h5part_int64_t"
and for "double" "h5part_float64_t". This change has now effect in
Fortran.
In some functions the argument type changed from "int" to
"h5part_int64_t". Since on most systems "int" is a 32bit integer,
calls to these functions must be adapted to the new API. In C/C++ the
compiler will complain about it. But in Fortran you will *not* get an
error message.So, you must check your Fortran code carefully.
Changes in detail (not listed are functions where only the return
type changed from any to "h5part_int64_t"):
New API Changes to old API
h5part_int64_t void
H5PartSetNumParticles (
H5PartFile *f,
h5part_int64_t nparticles long long
);
h5part_int64_t int
H5PartWriteDataFloat64 (
H5PartFile *f,
char *name,
h5part_float64_t *dta double
);
h5part_int64_t int
H5PartWriteDataInt64 (
H5PartFile *f,
char *name,
h5part_int64_t *dta long long
);
h5part_int64_t void
H5PartSetStep (
H5PartFile *f,
h5part_int64_t step int
);
h5part_int64_t void
H5PartSetView (
H5PartFile *f,
h5part_int64_t start, long long
h5part_int64_t end long long
);
h5part_int64_t int
H5PartGetView (
H5PartFile *f,
h5part_int64_t *start, long long
h5part_int64_t *end long long
);
h5part_int64_t int
H5PartReadDataFloat64 (
H5PartFile *f,
char *name,
h5part_float64_t *dta double
);
h5part_int64_t int
H5PartReadDataInt64 (
H5PartFile *f,
char *name,
h5part_int64_t *dta long long
);
h5part_int64_t void
H5PartReadParticleStep (
H5PartFile *f,
h5part_int64_t step, int
h5part_float64_t *x, double
h5part_float64_t *y, double
h5part_float64_t *z, double
h5part_float64_t *px, double
h5part_float64_t *py, double
h5part_float64_t *pz, double
h5part_int64_t *id long long
);
New functions:
h5part_int64_t
H5PartSetVerbosityLevel (
unsigned int
);
h5part_int64_t
H5PartSetErrorHandler (
h5part_error_handler handler
);
h5part_int64_t
H5PartGetErrno (
void
);
h5part_int64_t
H5PartDefaultErrorHandler (
const char *funcname,
const h5part_int64_t eno,
const char *fmt,
...
);
h5part_int64_t
H5PartAbortErrorHandler (
const char *funcname,
const h5part_int64_t eno,
const char *fmt,
...
);
Removed functions:
int
H5PartFileIsValid (
H5PartFile *f
);
==============================================================================
README file for H5Part configure
==============================================================================
+ 0. HDF5 library
-----------------
Make sure you have a working version of the HDF5 library in your computer. If you plan
to use parallel I/O you need to use a parallel HDF5 version. If you don't have the
library download the sources from http://hdf.ncsa.uiuc.edu/HDF5/
+ 1. Quick start (If you feel lucky...)
----------------------------------------
For many platforms, where compilers are installed in the "default" location
and all the environment variables are set correctly, it should be sufficient
to type:
./configure [OPTIONS] && make [install]
to have the libraries and test program compiled.
==============================================================================
+ 2. configure line options
----------------------------
(1) Enable options
--enable-fortran
--enable-parallel
--enable-tools
--enable-python
--enable-64 (only for AIX and Irix)
(2) Setting compilers related variables manually
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
Compiler environment variables:
CC C compiler command
CXX C++ compiler command
FC Fortran compiler command
(3) Setting prefix for installation manually
--prefix=PREFIX install files in PREFIX
For more information, type:
./configure --help
==============================================================================
+ 3. Platform specific settings for compiling libraries & test programs
------------------------------------------------------------------------
Building
make : builds the libraries and test programs
make install: builds and installs
make clean : removes extraneous object files
make distclean : returns configuration to unconfigured state
As tested on hosts:
(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
---------------------------------------------------
FIRST THING FIRST!! Type:
module load intel
to have the proper compilers set up for use.
module load hdf5_par
[NOTE: module load hdf5 does not work at this moment.
Possible installation error of HDF5 on Davinci.]
Brief profile:
CC = icc
CXX = icc
FC = ifort
MPICC = icc
MPICXX = icc
MPIFC = ifort
If default doesn't work, try:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
mpirun 2 H5testFpar
mpirun 2 H5PartTestP