repo migration

.gitattributes

+* 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
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+doc/ReferencePages/doxygen.png -text
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+doc/UsingC.html -text
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+doc/collision_6.png -text
+doc/collision_6.s.png -text
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+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
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+test/Bench.c -text
+test/H5BlockParallelTest1.c -text
+test/H5BlockReadParallel1.c -text
+test/H5BlockTest1.c -text
+test/H5BlockWrite1.c -text
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+test/H5test.cc -text
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+tools/h5pAttrib.cc -text
+tools/h5pToGNUplot.cc -text
+tools/h5pToGNUplot.py -text
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+visit_plugins/operators/RandomSample/.depend -text
+visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.C -text
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AUTHORS

+
+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

+*** 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.

GNUmakefile.orig

+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

Makefile.am

+# Trial by Antino Kim
+# Top level Makefile.am
+
+SUBDIRS = \
+	src \
+	test \
+	tools
+
+MAINTAINERCLEANFILES = \
+	config.h \
+	config.log \
+	config.status \
+	stamp-h.in \
+	stamp-h1

Makefile.orig

+
+# 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
+

NEWS

+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

+==============================================================================
+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
+