diff options
| -rw-r--r-- | INSTALL | 64 | ||||
| -rw-r--r-- | INSTALL.ascired | 102 | ||||
| -rw-r--r-- | INSTALL.parallel | 28 | ||||
| -rw-r--r-- | INSTALL_Windows.txt | 239 | ||||
| -rw-r--r-- | INSTALL_parallel | 44 | ||||
| -rw-r--r-- | INSTALL_parallel.ascired | 14 | ||||
| -rw-r--r-- | README | 6 | ||||
| -rw-r--r-- | RELEASE | 80 |
8 files changed, 384 insertions, 193 deletions
@@ -1,14 +1,13 @@ -*- outline -*- -This file contains instructions for the installation of HDF5 on -Unix-like systems. Users of the Intel TFLOPS machine should see the -INSTALL.ascired for instructions. +This file contains instructions for the installation of HDF5 software. * Obtaining HDF5 The latest supported public release of HDF5 is available from - ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5 and is available in tar - format uncompressed or compressed with compress, gzip, or - bzip2. + ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5. For Unix platforms, it + is available in tar format uncompressed or compressed with + compress, gzip, or bzip2. For Microsoft Windows, it is in + ZIP format. The HDF team also makes snapshots of the source code available on a regular basis. These snapshots are unsupported (that is, @@ -63,6 +62,14 @@ INSTALL.ascired for instructions. $ make check $ make install +** TFLOPS + Users of the Intel TFLOPS machine, after reading this file, + should see the INSTALL.ascired for more instructions. + +** Windows + Users of Microsoft Windows should see the INSTALL_Windows.txt + for detailed instructions. + * HDF5 dependencies ** Zlib The HDF5 library has a predefined compression filter that uses @@ -169,11 +176,17 @@ INSTALL.ascired for instructions. $ CC=/usr/local/mpi/bin/mpicc ./configure - On Irix64 the default compiler is `cc -64'. To use an + On Irix64 the default compiler is `cc'. To use an alternate compiler specify it with the CC variable: $ CC='cc -o32' ./configure + One may also use various environment variables to change the + behavior of the compiler. E.g., to ask for -n32 ABI: + $ SGI_ABI=-n32 + $ export SGI_ABI + $ ./configure + *** Additional compilation flags If addtional flags must be passed to the compilation commands then specify those flags with the CFLAGS variable. For @@ -313,42 +326,9 @@ INSTALL.ascired for instructions. *** Parallel vs. serial library The HDF5 library can be configured to use MPI and MPI-IO for - parallelizm on a distributed multi-processor system. The easy - way to do this is to have a properly installed parallel - compiler (e.g., MPICH's mpicc or IBM's mpcc) and supply that - executable as the value of the CC environment variable: - - $ CC=mpcc ./configure - $ CC=/usr/local/mpi/bin/mpicc ./configure - - If no such wrapper script is available then you must specify - your normal C compiler along with the distribution of - MPI/MPI-IO which is to be used (values other than `mpich' will - be added at a later date): - - $ ./configure --enable-parallel=mpich - - If the MPI/MPI-IO include files and/or libraries cannot be - found by the compiler then their directories must be given as - arguments to CPPFLAGS and/or LDFLAGS: - - $ CPPFLAGS=-I/usr/local/mpi/include \ - LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ - ./configure --enable-parallel=mpich - - 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': - - RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1 - RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=2} + parallelizm on a distributed multi-processor system. Read the + file INSTALL_parallel for detailed explanations. - The `$${NPROCS:=2}' will be substituted with the value of the - NPROCS environment variable at the time `make check' is run - (or the value 2). ** Building The library, confidence tests, and programs can be build by diff --git a/INSTALL.ascired b/INSTALL.ascired index cd11de0..43dea2a 100644 --- a/INSTALL.ascired +++ b/INSTALL.ascired @@ -10,51 +10,51 @@ Sequential HDF5: The setup process for building the sequential HDF5 library for the ASCI Red machine is done by a coordination of events from sasn100 and -janus. Special effort must be made to move the compiled and linked -testers to disks local to the processors for execution. This special -effort is shown here at steps 9) and steps 10). +janus. Though janus can do compiling, it is better to build it +from sasn100 which has more complete building tools and runs faster. +It is also anti-social to tie up janus with compiling. The HDF5 building +requires the use of janus because one of steps is to execute a program +to find out the run-time characteristics of the TFLOPS machine. -The total required steps are something similar to: -FROM SASN100, - -1) uncompress hdf5-1.1.0.tar.Z +Assuming you have already unpacked the HDF5 tar-file into the +directory <hdf5>, follow the steps below: -2) tar xvf hdf5-1.1.0.tar +FROM SASN100, -3) cd ./hdf5 +1) cd <hdf5> -4) ./configure tflop +2) ./configure tflop -5) make H5detect +3) make H5detect FROM JANUS, -6) cd ./hdf5 +4) cd <hdf5> -7) make H5Tinit.c +5) make H5Tinit.c FROM SASN100, -8) make >&! comp.out & +6) make When everything is finished compiling and linking, +you can run the tests by FROM JANUS, -9) cp -r ../hdf5 /scratch +7.1) Due to a bug, you must first remove the following line from + the file test/Makefile before the next step. + RUNTEST=$(LT_RUN) +7.2) make check -10) cd /scratch/hdf5/test -11) make test >&! test.out - - -Once satisfied with the test results, as long as you -have the correct permission, +Once satisfied with the test results, you can install +the software by FROM SASN100, -12) make install +8) make install --------------- @@ -62,72 +62,46 @@ Parallel HDF5: --------------- The setup process for building the parallel version of the HDF5 library for the -ASCI Red machine is very similar to the sequential version. It is done by a -coordination of events from sasn100 and janus. Special effort must be made to -move the compiled and linked single processor testers to disks local to the -processor for execution. This special effort is shown here at steps 9) and -steps 10). Following these test, there are the edit, compile, link, and -execution of parallel tests described in steps 12) through 16). +ASCI Red machine is very similar to the sequential version. Since TFLOPS +does not support MPIO, we have prepared a shell-script file that configures +with the appropriate MPI library. - -The total required steps are something similar to: +Assuming you have already unpacked the HDF5 tar-file into the +directory <hdf5>, follow the steps below: FROM SASN100, -1) uncompress hdf5-1.1.0.tar.Z - -2) tar xvf hdf5-1.1.0.tar - -3) cd ./hdf5 +1) cd <hdf5> -4) sh INSTALL_parallel.ascired /* this is different from the sequential version */ +2) sh INSTALL_parallel.ascired /* this is different from the sequential version */ -5) make H5detect +3) make H5detect FROM JANUS, -6) cd ./hdf5 +4) cd <hdf5> -7) make H5Tinit.c +5) make H5Tinit.c FROM SASN100, -8) make >&! comp.out & +6) make When everything is finished compiling and linking, FROM JANUS, -9) cp -rp ../hdf5 /scratch - -10) cd /scratch/hdf5/test - -11) make test >&! test.out - - -Once satisfied with the single processor test results, -FROM SASN100, - -12) cd testpar - -13) go through the README file. - -14) make -f Makefile.ascired - - -When everything is finished compiling and linking, -FROM JANUS, - -15) cd ./hdf5/testpar - -16) make test -f Makefile.ascired >&! test.out +7.1) Due to a bug, you must first remove the following line from + the file test/Makefile before the next step. + RUNTEST=$(LT_RUN) +7.2) make check Once satisfied with the parallel test results, as long as you have the correct permission, FROM SASN100, -17) make install +8) make install diff --git a/INSTALL.parallel b/INSTALL.parallel deleted file mode 100644 index 278d4f3..0000000 --- a/INSTALL.parallel +++ /dev/null @@ -1,28 +0,0 @@ -This file contains instructions for the installation a version of HDF5 -that uses the parallel file I/O facilities of the MPI-IO library. A -parallel version of HDF5 can run in a serial environment as long as -the appropriate MPI-IO and MPI header files and libraries are -available. - -The parallel version of hdf5 can be build by generally following the -instructions in the INSTALL file for building a serial version and -using `mpicc' as the C compiler. This can be done by setting the CC -environment variable before invoking configure as with: - - $ CC=mpicc ./configure - -If the mpicc compiler is not available then a parallel library can -still be built as long as the appropriate header files and libraries -can be found. If these files are part of the default compiler search -paths then configuration is as simple as: - - $ ./configure --enable-parallel - -Otherwise, if the MPI and MPI-IO header files or library cannot be -found then the compiler search paths can be corrected, the files can -be moved, or configure can be told about the file locations. The -latter is done with something like: - - $ CPPFLAGS=-I/usr/local/mpi/include \ - LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ - ./configure --enable-parallel diff --git a/INSTALL_Windows.txt b/INSTALL_Windows.txt new file mode 100644 index 0000000..848ff85 --- /dev/null +++ b/INSTALL_Windows.txt @@ -0,0 +1,239 @@ +HDF5 Install Instructions for Windows NT/95/98. +------------------------------------------------------------------------- + +The instructions which follow assume that you will be using the the source +code release 'zip' file (hdf5-1_2_0.zip). + +The following sections discuss in detail installation procedures. + +Building from Source Code Release (hdf5-1_2_0.zip) +=============================================== + +STEP I: Preconditions + +To build the HDF5 and tests, it is assumed that you have done the following: + + 1. Installed MicroSoft Developer Studio, and Visual C++ 5.0 or 6.0. + + 2. Set up a directory structure to unpack the library. For + example: + c:\ (any drive) + MyHDFstuff\ (any folder name) + + 3. Copied the source distribution archive to that directory + and unpacked it using the appropriate archiver options to + create a directory hierarchy. + + Run WinZip on hdf5-1_2_0.zip (the entire source tree). + This creates a directory called 'hdf5' which + contains several files and directories. + + +STEP II: Building the Libraries and tests. + + 1. Unpack all.zip in 'hdf5'. + + 2. Invoke Microsoft Visual C++, go to "File" and select + the "Open Workspace" option. + + Then open the c:\myHDFstuff\hdf5\proj\all\all.dsw workspace. + + 3. Select "Build", then Select "Set Active Configuration". + + On Windows platform select as the active configuration + + "all -- Win32 Debug" to build debug versions of single-threaded + static libraries, and tests. + or + + "all -- Win32 Release" to build release versions of single-threaded + static libraries, and tests. + + Select "Build" and "Build all.exe" to + build the corresponding version of the HDF5 library. + + NOTE: "all" is a dummy target. You will get a link error when + "all.exe." is built : + LINK: error LNK2001: unresolved external symbol + _mainCRTStartup..... + all.exe - 2 error(s), .... + + Warning messages can be ignored. The "all.exe" is never created, + so it is OK. + + When the debug or release build is done the directories listed + below will contain the following files : + + c:\MyHDFstuff\hdf5\proj\hdf5\debug - + c:\MyHDFstuff\hdf5\proj\hdf5\release - + + hdf5.lib- the hdf5 library + + c:\MyHDFstuff\hdf5\test\"test directory"- + where test directory is one of the following: + + + big + + bittests + + chunk + + cmpd_dset + + dsets + + dtypes + + extend + + external + + fillval + + flush1 + + flush2 + + gheap + + hyperslab + + iopipe + + istore + + links + + mount (not supported in this release) + + mtime + + overhead + + ragged + + shtype + + testhdf5 + + unlink + +Each test directory contains debug and release subdirectories with the +corresponding tests. + + +STEP III: TESTING THE BUILD + + + +In a command prompt window run the test batch file which +resides in the hdf5 directory to make sure that the library +was built correctly. + +The hdf5testDBG.bat file tests the debug version of the library and +hdf5testREL.bat tests the release version of the library. + + + +STEP IV: BUILDING THE EXAMPLES + + 1. Invoke Microsoft Visual C++, go to "File" and select + the "Open Workspace" option. + Then open the c:\myHDFstuff\hdf5\examples\allexamples.dsw + workspace. + + 2. Select "Build", then Select "Set Active Configuration". + + On Windows platform select as the active configuration + "allexamples -- Win32 Debug" to build debug versions of the examples. + + or + + "allexamples -- Win32 Release" to build release versions the examples. + + Select "Build" and "Build allexamples.exe" to + build the corresponding version of the examples. + + When the debug build or release build is done there should be the + following subdirectories in C:\myHDFstuff\hdf5\examples\ + + attributetest + + chunkread + + compoundtest + + extendwritetest + + grouptest + + readtest + + selecttest + + writetest + + + + 3. Run the batch file "InstallExamples.bat" which resides in the top level directory. This file creates 2 new directories, examplesREL and examplesDEB, in the examples directory and places all the executables in it. Both the release and debug versions of the examples should be built before this step is done. The examples should be tested in these 2 new directories +due to some dependencies between the examples. + + + +STEP V: + +BUILDING AN APPLICATION USING THE HDF5 LIBRARY - SOME HELPFUL POINTERS +===================================================================== + +If you are building an application that uses the HDF5 library +the following locations will need to be specified for locating +header files and linking in the HDF libraries: + + <top-level HDF5 directory>\src + +where <top-level HDF5 directory> may be + C:\MyHDFstuff\hdf5\ + + + +MORE HELPFUL POINTERS +===================== + + +Here are some notes that may be of help if you are not familiar +with using the Visual C++ Development Environment. + +Project name and location issues: + + The files in all.zip must end up in the hdf5\ directory + installed by hdf5-1_2_0.zip + + If you must install all.dsw and all.dsp in another directory, relative + to hdf5\ , you will be asked to locate the sub-project files, + when you open the project all.dsw. + + If you want to rename all (the entire project), you will need to modify + two files all.dsw and all.dsp as text (contrary to the explicit warnings + in the files). + + You can also modify all.dsw and all.dsp as text, to allow these 2 files + to be installed in another directory. + + +Settings... details: + + If you create your own project, the necessary settings can be + read from the all.dsp file(as text), or from the Project Settings in + the Developer Studio project settings dialog. + + Project + Settings + C/C++ + Category + PreProcessor + Code Generation + Use run-time Library + These are all set to use + Single-Threaded + diff --git a/INSTALL_parallel b/INSTALL_parallel index 57ecf44..572994e 100644 --- a/INSTALL_parallel +++ b/INSTALL_parallel @@ -1,6 +1,5 @@ Installation instructions for Parallel HDF5 ------------------------------------------- - (last updated: May 21, 1999) 1. Overview ----------- @@ -79,9 +78,40 @@ make install 3. Detail explanation --------------------- -[Work in progress. Please send mail to hdfparallel@ncsa.uiuc.edu.] - - - - - +The HDF5 library can be configured to use MPI and MPI-IO for +parallelizm on a distributed multi-processor system. The easy +way to do this is to have a properly installed parallel +compiler (e.g., MPICH's mpicc or IBM's mpcc) and supply that +executable as the value of the CC environment variable: + + $ CC=mpcc ./configure + $ CC=/usr/local/mpi/bin/mpicc ./configure + +If no such wrapper script is available then you must specify +your normal C compiler along with the distribution of +MPI/MPI-IO which is to be used (values other than `mpich' will +be added at a later date): + + $ ./configure --enable-parallel=mpich + +If the MPI/MPI-IO include files and/or libraries cannot be +found by the compiler then their directories must be given as +arguments to CPPFLAGS and/or LDFLAGS: + + $ CPPFLAGS=-I/usr/local/mpi/include \ + LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ + ./configure --enable-parallel=mpich + +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': + + RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1 + RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=2} + +The `$${NPROCS:=2}' will be substituted with the value of the +NPROCS environment variable at the time `make check' is run +(or the value 2). diff --git a/INSTALL_parallel.ascired b/INSTALL_parallel.ascired index a246163..a991482 100644 --- a/INSTALL_parallel.ascired +++ b/INSTALL_parallel.ascired @@ -23,8 +23,6 @@ # The following flags are only needed when compiling/linking a user program # for execution. # -debug="-g -UH5O_DEBUG -DH5F_OPT_SEEK=0" -default_mode="$debug -DH5F_LOW_DFLT=H5F_LOW_SEC2" # Using the MPICH libary by Daniel Sands. # It contains both MPI-1 and MPI-IO functions. @@ -44,14 +42,6 @@ mpio_lib="-L$ROMIO/lib" MPI_INC="$mpi1_inc $mpio_inc" MPI_LIB="$mpi1_lib $mpio_lib" -#for version 1.1 and later -RUNSERIAL="yod -sz 1" -export RUNSERIAL -RUNPARALLEL="yod -sz 8" -export RUNPARALLEL -LIBS="-lmpich" -export LIBS - # Once these variables are set to the proper values for your installation, # you can run the configure program (i.e., ./configure tflop --enable-parallel=mpio) @@ -62,7 +52,7 @@ export LIBS # cicc and link to the MPI-IO library and the parallel version of the HDF5 # library (that was created and installed with the configure/make process). -CFLAGS="$default_mode" \ CPPFLAGS=$MPI_INC \ LDFLAGS=$MPI_LIB \ -./configure --enable-parallel --disable-shared tflop +LIBS="-lmpich" \ +./configure --enable-parallel tflop @@ -28,8 +28,10 @@ library. not a discussion list. To subscribe to a list, send mail to "majordomo@ncsa.uiuc.edu", -with "subscribe <your e-mail address> in the _body_ of the message. Messages -to be sent to the list should be sent to "<list>@ncsa.uiuc.edu". +with "subscribe <list>" in the _body_, not the Subject, of the message. +E.g., subscribe hdf5 + +Messages to be sent to the list should be sent to "<list>@ncsa.uiuc.edu". Nearly daily code snapshots are now being provided at the following URL: ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots @@ -1,4 +1,4 @@ -Release information for hdf5-1.2.0 +Release information for hdf5-1.2.0beta ------------------------------------ CHANGES SINCE VERSION 1.0.1 @@ -86,6 +86,15 @@ Persistent Pointers Parallel Support ---------------- +* Improved parallel I/O performance. + +* Supported new platforms: Cray T3E, Linux, DEC Cluster. + +* Use vendor supported version of MPIO on SGI O2K and Cray platforms. + +* Improved the algorithm that translates an HDF5 hyperslab selection + into an MPI type for better collective I/O performance. + Tools ----- @@ -94,20 +103,16 @@ Tools show file addresses for raw data, to format output more reasonably, to show object attributes, and to perform a recursive listing, -* Enhancements to h5dump similar to h5ls. - -* An hdf5 to hdf4 converter. - - - - +* Enhancements to h5dump: support new data types added since previous + versions. +* h5toh4: An hdf5 to hdf4 converter. CHANGES SINCE THE Version 1.0.0 RELEASE * [Improvement]: configure sets up the Makefile in the parallel tests - suit (testpar/) correctly. (Tested for O2K only.) + suit (testpar/) correctly. * [Bug-Fix]: Configure failed for all IRIX versions other than 6.3. It now configures correctly for all IRIX 6.x version. @@ -463,43 +468,42 @@ Ragged Arrays (alpha) H5Rwrite - write to an array H5Rread - read from an array -This release has been tested on UNIX platforms only; specifically: -Linux, FreedBSD, IRIX, Solaris & Dec UNIX. + PLATFORMS SUPPORTED + ------------------- - RELEASE INFORMATION FOR PARALLEL HDF5 - ------------------------------------- +Operating systems listed below with compiler information and MPI library, if +applicable, are systems that HDF5 1.2.0beta was tested. -* Current release supports independent access to fixed dimension datasets - only. + Compiler & libraries + Platform Information Comment + -------- ---------- -------- + + AIX 4.3.2 (IBM SP) -* The comm and info arguments of H5Cset_mpi are not used. All parallel - I/O are done via MPI_COMM_WORLD. Access_mode for H5Cset_mpi can be - H5ACC_INDEPENDENT only. + FreeBSD 3.2 gcc 2.8.1 -* This release of parallel HDF5 has been tested on IBM SP2 and SGI - Origin 2000 systems. It uses the ROMIO version of MPIO interface - for parallel I/O supports. + HP-UX 10.20 cc A.10.32.03 -* Useful URL's. - Parallel HDF webpage: "http://hdf.ncsa.uiuc.edu/Parallel_HDF/" - ROMIO webpage: "http://www.mcs.anl.gov/home/thakur/romio/" + IRIX 6.5 cc 7.2.1 -* Some to-do items for future releases - support for Intel Teraflop platform. - support for unlimited dimension datasets. - support for file access via a communicator besides MPI_COMM_WORLD. - support for collective access to datasets. - support for independent create/open of datasets. + IRIX64 6.5 (64 & n32) cc 7.30 + mpt.1.3 (SGI MPI 3.2.0.0) + Linux (SuSE and RedHat) egcs-1.1.2 configured with + --disable-hsizet + OSF1 V4.0 DEC-V5.2-033 - PLATFORMS SUPPORTED - ------------------- + SunOS 5.6 cc 4.2 no optimization + gcc 2.8.1 + + SunOS 5.5.1 gcc 2.7.2 configured with + --disable-hsizet + TFLOPS O/S 1.0.4 cicc (pgcc Rel 1.7-6i) + mpich-1.1.2 with local changes + + Unicos 2.0.4.61 (T3E) cc 6.2.1.0 + mpt.1.3 - Platform(OS) C-Compiler Fortran-Compiler - ------------ ---------- ---------------- - Sun4(Solaris 2.5) CC SC4.0 f77 SC4.0 - SGI (IRIX v6.5) CC 7.21 f77 7.21 - SGI-Origin(IRIX64 v6.4-n32) CC 7.2.1.2m f77 7.2.1.2m - SGI-Origin(IRIX64 v6.4-64) CC 7.2.1.2m f77 7.2.1.2m + Windows/NT 4.0/SP3 MSVC++ 5.0 and 6.0 |