path: root/release_docs/RELEASE.txt

HDF5 version 1.10.1-pre0 currently under development
================================================================================


INTRODUCTION

This document describes the differences between HDF5-1.10.0-patch1 and
HDF5 1.10.1, and contains information on the platforms tested and known problems in HDF5-1.10.1.
For more details check the HISTORY*.txt files in the HDF5 source.


Links to HDF5 1.10.1 source code, documentation, and additional materials can be found on The HDF5 web page at:

     https://support.hdfgroup.org/HDF5/

The HDF5 1.10.1 release can be obtained from:

     https://support.hdfgroup.org/HDF5/release/obtain5110.html

User documentation for the snapshot can be accessed directly at this location:

     https://support.hdfgroup.org/HDF5/doc1.10/

New features in the HDF5-1.10.x release series, including brief general
descriptions of some new and modified APIs, are described in the "What's New
in 1.10.1?" document:

     https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew1101.html

All new and modified APIs are listed in detail in the "HDF5 Software Changes
from Release to Release" document, in the section "Release 1.8.19 (current
release) versus Release 1.10.1

     https://support.hdfgroup.org/HDF5/doc1.10/ADGuide/Changes.html

If you have any questions or comments, please send them to the HDF Help Desk:

    help@hdfgroup.org


CONTENTS

- New Features
- Support for new platforms and languages
- Bug Fixes since HDF5-1.10.0-patch1
- Supported Platforms
- Tested Configuration Features Summary
- More Tested Platforms
- Known Problems


New Features
============

    Configuration:
    -------------
    - CMake minimum is now 3.2.2.
      (ADB 2017/01/10)

    - Tools folder is separated into source and test folders. This
      allows autotools to skip the make command and just execute
      the make check command.
      (HDFFV-9719 ADB 2016/10/27)

    Library:
    --------
    -

    Parallel Library:
    -----------------
    -

    Fortran Library:
    ----------------
    -

    C++ Library:
    ------------
    - New wrappers for C APIs:
        (HDFFV-10004, HDFFV-10139, HDFFV-10145 - PRs #209, #232, #310, #334, #348)

        // Sets/Gets the strategy and the threshold value that the library will
        // will employ in managing file space.
        FileCreatPropList::setFileSpaceStrategy - H5Pset_file_space_strategy
        FileCreatPropList::getFileSpaceStrategy - H5Pget_file_space_strategy

        // Sets/Gets the file space page size for paged aggregation.
        FileCreatPropList::setFileSpacePagesize - H5Pset_file_space_page_size
        FileCreatPropList::getFileSpacePagesize - H5Pget_file_space_page_size

        // Checks if the given ID is valid.
        IdComponent::isValid - H5Iis_valid

        // Sets/Gets the number of soft or user-defined links that can be
        // traversed before a failure occurs.
        LinkAccPropList::setNumLinks - H5Pset_nlinks
        LinkAccPropList::getNumLinks - H5Pget_nlinks

        // Returns a copy of the creation property list of a datatype.
        DataType::getCreatePlist - H5Tget_create_plist

        // Opens/Closes an object within a group or a file, regardless object type
        Group::getObjId - H5Oopen
        Group::closeObjId - H5Oclose

        // Maps elements of a virtual dataset to elements of the source dataset.
        DSetCreatPropList::setVirtual - H5Pset_virtual

        // Gets general information about this file.
        H5File::getFileInfo - H5Fget_info2

        // Returns the number of members in a type.
        IdComponent::getNumMembers - H5Inmembers

        // Determines if an element type exists.
        IdComponent::typeExists - H5Itype_exists

        // Determines if an object exists.
        H5Location::exists - H5Lexists.

        // Returns the header version of an HDF5 object.
        H5Object::objVersion - H5Oget_info for version
      -BMR, 2017/03/20

    - New exception: ObjHeaderIException for H5O interface.
      (HDFFV-10145 - PR #334) -BMR, 2017/03/15

    - New class LinkAccPropList for link access property list, to be used by
      wrappers of H5Lexists. (HDFFV-10145 - PR #232) -BMR, 2017/01/04

    - New constructors to open datatypes in ArrayType, CompType, DataType,
      EnumType, FloatType, IntType, StrType, and VarLenType.
      (HDFFV-10056 - PR #209) -BMR, 2016/12/26

    - New member functions
        DSetCreatPropList::setNbit() to setup N-bit compression for a dataset.
        (HDFFV-8623 patch 7) -BMR, 2016/04/25

        ArrayType::getArrayNDims() const
        ArrayType::getArrayDims() const
        both to replace the non-const versions. (HDFFV-9725) -BMR, 2016/04/25


    Tools:
    ------
     -

    High-Level APIs:
    ---------------

    C Packet Table API
    ------------------
     -

    Internal header file
    --------------------
    -

    Documentation
    -------------

Support for new platforms, languages and compilers.
=======================================
    -

Bug Fixes since HDF5-1.10.0-patch1 release
==================================

    Library
    -------
    - Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY
      (PR 201 ADB 2016/12/12)

    Configuration
    -------------
    - Configuration will check for the strtoll and strtoull functions
      before using alternatives
      (PR 340 ADB 2017/03/17)

    - CMake uses a Windows pdb directory variable if available and
      will generate both static and shared pdb files.
      (HDFFV-9875 ADB 2017/02/06)

    - CMake now builds shared versions of tools.
      (HDFFV-10123 ADB 2017/02/01)

    Performance
    -------------
      -

    Fortran
    --------
    -

    Tools
    -----
    - h5diff correctly ignores strpad in comparing strings.
      (HDFFV-10128 ADB 2017/03/03)

    - h5repack now correctly parses the command line filter options.
      (HDFFV-10046 ADB 2017/01/24)

    High-Level APIs:
    ------
    -

    Fortran High-Level APIs:
    ------
    -

    Documentation
    -------------


    F90 APIs
    --------
    -


    C++ APIs
    --------
    - Due to the change in the C API, the overloaded functions of
      PropList::setProperty now need const for some arguments.  They are
      planned for deprecation and are replaced by new versions with proper
      consts. (PR #344) -BMR, 2017/03/17

    - The problem where a user-defined function cannot access both, attribute
      and dataset, using only one argument is now fixed.
      (HDFFV-9920 - PR #45) -BMR, 2016/10/11

    - The high-level API Packet Table (PT) did not write data correctly when
      the datatype is a compound type that has string type as one of the
      members.  This problem started in 1.8.15, after the fix of HDFFV-9042
      was applied, which caused the Packet Table to use native type to access
      the data.  It should be up to the application to specify whether the
      buffer to be read into memory is in the machine's native architecture.
      Thus, the PT is fixed to not use native type but to make a copy of the
      user's provided datatype during creation or the packet table's datatype
      during opening.  If an application wishes to use native type to read the
      data, then the application will request that.  However, the Packet Table
      doesn't provide a way to specify memory datatype in this release.  This
      feature will be available in future releases, HDFFV-10023.
      (HDFFV-9758 - PRs #93 and #108) -BMR, 2016/10/27

    - The obsolete macros, H5_NO_NAMESPACE and H5_NO_STD, are removed.
      (HDFFV-9532 - PR #92) -BMR, 2016/10/23

    - In-memory array information, ArrayType::rank and
      ArrayType::dimensions, were removed. This is an implementation
      detail and should not affect applications. (HDFFV-9725) -BMR, 2016/04/25


    Testing
    -------
    -

Supported Platforms
===================

    Linux 2.6.32-573.18.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
                                  IBM XL C/C++ V13.1
                                  IBM XL Fortran V15.1

    Linux 3.10.0-327.10.1.el7   GNU C (gcc), Fortran (gfortran), C++ (g++)
    #1 SMP x86_64 GNU/Linux       compilers:
    (kituo/moohan)                  Version 4.8.5 20150623 (Red Hat 4.8.5-4)
                                    Version 4.9.3, Version 5.2.0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 15.0.3.187 Build 20150407
                                  MPICH 3.1.4 compiled with GCC 4.9.3

    SunOS 5.11 32- and 64-bit     Sun C 5.12 SunOS_sparc
    (emu)                         Sun Fortran 95 8.6 SunOS_sparc
                                  Sun C++ 5.12 SunOS_sparc

    Windows 7                     Visual Studio 2012 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2015 w/ Intel Fortran 16 (cmake)
                                  Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
                                  (cmake and autotools)

    Windows 7 x64                 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
                                  Visual Studio 2015 w/ Intel Fortran 16 (cmake)
                                  Visual Studio 2015 w/ Intel Parallel Studio 2017 (cmake)

    Windows 10                    Visual Studio 2015 w/ Intel Fortran 16 (cmake)

    Windows 10 x64                Visual Studio 2015 w/ Intel Fortran 16 (cmake)

    Mac OS X Mt. Lion 10.8.5      Apple clang/clang++ version 5.1 from Xcode 5.1
    64-bit                        gfortran GNU Fortran (GCC) 4.8.2
    (swallow/kite)                Intel icc/icpc/ifort version 15.0.3

    Mac OS X Mavericks 10.9.5     Apple clang/clang++ version 6.0 from Xcode 6.2
    64-bit                        gfortran GNU Fortran (GCC) 4.9.2
    (wren/quail)                  Intel icc/icpc/ifort version 15.0.3

    Mac OS X Yosemite 10.10.5     Apple clang/clang++ version 6.1 from Xcode 7.0
    64-bit                        gfortran GNU Fortran (GCC) 4.9.2
    (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 15.0.3

    Mac OS X El Capitan 10.11.6   Apple clang/clang++ version 7.3.0 from Xcode 7.3
    64-bit                        gfortran GNU Fortran (GCC) 5.2.0
    (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 16.0.2


Tested Configuration Features Summary
=====================================

    In the tables below
          y   = tested
          n   = not tested in this release
          C   = Cluster
          W   = Workstation
          x   = not working in this release
          dna = does not apply
          ( ) = footnote appears below second table
          <blank> = testing incomplete on this feature or platform

Platform                              C         F90/   F90      C++  zlib  SZIP
                                      parallel  F2003  parallel
Solaris2.11 32-bit                      n        y/y    n        y    y     y
Solaris2.11 64-bit                      n        y/n    n        y    y     y
Windows 7                               y        y/y    n        y    y     y
Windows 7 x64                           y        y/y    y        y    y     y
Windows 7 Cygwin                        n        y/n    n        y    y     y
Windows 7 x64 Cygwin                    n        y/n    n        y    y     y
Windows 10                              y        y/y    n        y    y     y
Windows 10 x64                          y        y/y    n        y    y     y
Mac OS X Mountain Lion 10.8.5 64-bit    n        y/y    n        y    y     y
Mac OS X Mavericks 10.9.5 64-bit        n        y/y    n        y    y     y
Mac OS X Yosemite 10.10.5 64-bit        n        y/y    n        y    y     y
Mac OS X El Capitan 10.11.6 64-bit      n        y/y    n        y    y     y
CentOS 7.2 Linux 2.6.32 x86_64 PGI      n        y/y    n        y    y     y
CentOS 7.2 Linux 2.6.32 x86_64 GNU      y        y/y    y        y    y     y
CentOS 7.2 Linux 2.6.32 x86_64 Intel    n        y/y    n        y    y     y
Linux 2.6.32-573.18.1.el6.ppc64         n        y/y    n        y    y     y


Platform                                 Shared  Shared    Shared    Thread-
                                         C libs  F90 libs  C++ libs  safe
Solaris2.11 32-bit                         y       y         y         y
Solaris2.11 64-bit                         y       y         y         y
Windows 7                                  y       y         y         y
Windows 7 x64                              y       y         y         y
Windows 7 Cygwin                           n       n         n         y
Windows 7 x64 Cygwin                       n       n         n         y
Windows 10                                 y       y         y         y
Windows 10 x64                             y       y         y         y
Mac OS X Mountain Lion 10.8.5 64-bit       y       n         y         y
Mac OS X Mavericks 10.9.5 64-bit           y       n         y         y
Mac OS X Yosemite 10.10.5 64-bit           y       n         y         y
Mac OS X El Capitan 10.11.6 64-bit         y       n         y         y
CentOS 7.2 Linux 2.6.32 x86_64 PGI         y       y         y         n
CentOS 7.2 Linux 2.6.32 x86_64 GNU         y       y         y         y
CentOS 7.2 Linux 2.6.32 x86_64 Intel       y       y         y         n
Linux 2.6.32-573.18.1.el6.ppc64            y       y         y         n

Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.


More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.

    Linux 2.6.32-573.22.1.el6    GNU C (gcc), Fortran (gfortran), C++ (g++)
    #1 SMP x86_64 GNU/Linux       compilers:
    (mayll/platypus)                 Version 4.4.7 20120313
                                     Version 4.8.4
                                  PGI C, Fortran, C++ for 64-bit target on
                                  x86-64;
                                      Version 16.10-0
                                  Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                  compilers:
                                     Version 15.0.3.187 (Build 20150407)
                                  MPICH 3.1.4 compiled with GCC 4.9.3

    Linux 2.6.32-573.18.1.el6.ppc64  MPICH mpich 3.1.4 compiled with
    #1 SMP ppc64 GNU/Linux           IBM XL C/C++ for Linux, V13.1
    (ostrich)                        and IBM XL Fortran for Linux, V15.1

    Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
                                  gcc, g++ (Debian 4.9.2-10) 4.9.2
                                  GNU Fortran (Debian 4.9.2-10) 4.9.2
                                  (cmake and autotools)

    Fedora 24  4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
                                  gcc, g++ (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
                                  GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
                                  (cmake and autotools)

    Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
                                  gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609
                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 20160609
                                  (cmake and autotools)


Known Problems
==============
* "make check" fails on CYGWIN when building shared lib files is enabled.  The
   default on Cygwin has been changed to disable shared.  It can be enabled with
   the --enable-shared configure option but is likely to fail "make check"
   with GCC compilers. (LK -2015/04/16)

* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
  catches some undefined behavior in the alignment algorithm of the macro DETECT_I
  in H5detect.c (Issue 8147).  Since the algorithm is trying to detect the alignment
  of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
  H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
  the library. (SLU - 2013/10/16)

* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp.  It
  complains with this message:
      "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.

  The reason is that __func__ is a predefined identifier in C99 standard.  The
  HDF5 C library uses it in H5private.h.  The test ttypes.cpp includes
  H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h).  Sun's 5.9
  C++ compiler doesn't support __func__, thus fails to compile the C++ test.
  But 5.11 C++ compiler does.  To check whether your Sun C++ compiler knows this
  identifier, try to compile the following simple C++ program:
      #include<stdio.h>

      int main(void)
      {
          printf("%s\n", __func__);
          return 0;
      }
  (SLU - 2012/11/5)

* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
  native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
  ports (and probably gcc releases after that).
  (QAK - 2012/10/19)

* The data conversion test dt_arith.c has failures (segmentation fault) from
  "long double" to other datatypes during hard conversion when the library
  is built with the default GCC 4.2.1 on Mac Lion system.  It only happens
  with optimization (-O3, -O2, and -O1).  Some newer versions of GCC do not
  have this problem.  Users should disable optimization or try newer version
  of GCC. (Issue 8017. SLU - 2012/6/12)

* The data conversion test dt_arith.c fails in "long double" to integer
  conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library
  is built with optimization -O3 or -O2.  The older GCC (4.5) or newer kernal
  (3.2.2 on Fedora) doesn't have the problem.  Users should lower down the
  optimization level (-O1 or -O0) by defining CFLAGS in the command line of
  "configure" like:

      CFLAGS=-O1 ./configure

  It will overwrite the library's default optimization level. (Issue 7829.
  SLU - 2012/2/7)

* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10)

* While working on the 1.8.6 release of HDF5, a bug was discovered that can
  occur when reading from a dataset in parallel shortly after it has been
  written to collectively. The issue was exposed by a new test in the parallel
  HDF5 test suite, but had existed before that. We believe the problem lies with
  certain MPI implementations and/or filesystems.

  We have provided a pure MPI test program, as well as a standalone HDF5
  program, that can be used to determine if this is an issue on your system.
  They should be run across multiple nodes with a varying number of processes.
  These programs can be found at:
  http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/

* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
  it treats "exit(134) the same as if process 0 had received an abort signal.
  This is fixed and will be available in the next release. AKC - 2009/11/3

* The PathScale MPI implementation, accessing a Panasas file system, would
  cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
  existing. This is due to the MPI_File_open() call failing if the amode has
  the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11

* Parallel tests failed with 16 processes with data inconsistency at testphdf5
  / dataset_readAll. Parallel tests also failed with 32 and 64 processes with
  collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
  with MPI IO. (CMC - 2009/04/28)

* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
  tests failed with MPI-IO file locking message. AKC - 2007/6/25.
* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use
  -mp -O1 compilation flags to build the libraries. Higher level of optimization
  causes failures in several HDF5 library tests.
* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
  shared libraries (tested for 1.8.0-beta2)
* For SNL, Red Storm: only paralle HDF5 is supported.  The serial tests pass
  and the parallel tests also pass with lots of non-fatal error messages.
* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test
* configuring with --enable-debug=all produces compiler errors on most
  platforms.  Users who want to run HDF5 in debug mode should use
  --enable-debug rather than --enable-debug=all to enable debugging
  information on most modules.
* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
  double to (unsigned) long long and from (unsigned)long long to long double.
* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3
  optimization flag.
* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to
  HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard
  for floating-point data.
* On Cray X1, a lone colon on the command line of h5dump --xml (as in
  the testh5dumpxml.sh script) is misinterpereted by the operating system
  and causes an error.
* On mpich 1.2.5 and 1.2.6, we found that if more than two processes
  contribute no IO and the application asks to do IO with collective, we found
  that when using 4 processors, a simple collective write will be hung
  sometimes. This can be verified with t_mpi test under testpar.
* The dataset created or rewritten with the v1.6.3 library or after can't
  be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is
  enabled.  There was a bug in the calculating code of the Fletcher32
  checksum in the library before v1.6.3.  The checksum value wasn't consistent
  between big-endian and little-endian systems.  This bug was fixed in
  Release 1.6.3.  However, after fixing the bug, the checksum value is no
  longer the same as before on little-endian system.  The library release
  after 1.6.4 can still read the dataset created or rewritten with the library
  of v1.6.2 or before.  SLU - 2005/6/30
* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron
  processor, there's a bug in the compiler for optimization(-O2).  The library
  failed in several tests but all related to multi driver.  The problem has
  been reported to the vendor.
* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
  messages like "INFO: 0031-XXX ...".  This is from the command poe.
  Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
  and run the tests again.
  The tests may fail with messages like "The socket name is already
  in use".  HDF5 does not use sockets (except for stream-VFD).  This is
  due to problems of the poe command trying to set up the debug socket.
  Check if there are many old /tmp/s.pedb.* staying around.  These are
  sockets used by the poe command and left behind due to failed commands.
  Ask your system administrator to clean them out.  Lastly, request IBM
  to provide a mean to run poe without the debug socket.

* The C++ library's tests fails when compiling with PGI C++ compiler.  The
  workaround until the problem is correctly handled is to use the
  flag "--instantiate=local" prior to the configure and build steps, as:
        setenv CXX "pgCC --instantiate=local"  for pgCC 5.02 and higher


* The stream-vfd test uses ip port 10007 for testing. If another
  application is already using that port address, the test will hang
  indefinitely and has to be terminated by the kill command. To try the
  test again, change the port address in test/stream_test.c to one not
  being used in the host.

* The --enable-static-exec configure flag will only statically link libraries
  if the static version of that library is present. If only the shared version
  of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
  for example, only have shared versions), the flag should still result in a
  successful compilation, but note that the installed executables will not be
  fully static. Thus, the only guarantee on these systems is that the
  executable is statically linked with just the HDF5 library.

* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
  compilation. The ANSI version of the compiler complains about not being
  able to handle the `long long' datatype with the warning:

        warning: ANSI C does not support `long long'

  This warning is innocuous and can be safely ignored.

* Certain platforms give false negatives when testing h5ls:
    - Cray J90 and Cray T90IEEE give errors during testing when displaying
      some floating-point values. These are benign differences due to
      the different precision in the values displayed and h5ls appears to
      be dumping floating-point numbers correctly.

* Not all platforms behave correctly with szip's shared libraries. Szip is
  disabled in these cases, and a message is relayed at configure time. Static
  libraries should be working on all systems that support szip, and should be
  used when shared libraries are unavailable. There is also a configure error
  on Altix machines that incorrectly reports when a version of szip without
  an encoder is being used.

* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library,
  compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90
  complaining about exit subroutine. Comment out the line
  IF (total_error .ne. 0) CALL exit (total_error)

* Information about building with PGI and Intel compilers is available in
  INSTALL file sections 5.7 and 5.8

* On at least one system, (SDSC DataStar), the scheduler (in this case
  LoadLeveler) sends job status updates to standard error when you run
  any executable that was compiled with the parallel compilers.

  This causes problems when running "make check" on parallel builds, as
  many of the tool tests function by saving the output from test runs,
  and comparing it to an exemplar.

  The best solution is to reconfigure the target system so it no longer
  inserts the extra text.  However, this may not be practical.

  In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
  the configure and build.  This will cause "make check" to continue after
  detecting errors in the tool tests.  However, in the case of SDSC DataStar,
  it also leaves you with some 150 "failed" tests to examine by hand.

  A second solution is to write a script to run serial tests and filter
  out the text added by the scheduler.  A sample script used on SDSC
  DataStar is given below, but you will probably have to customize it
  for your installation.

  Observe that the basic idea is to insert the script as the first item
  on the command line which executes the the test.  The script then
  executes the test and filters out the offending text before passing
  it on.

        #!/bin/csh

        set STDOUT_FILE=~/bin/serial_filter.stdout
        set STDERR_FILE=~/bin/serial_filter.stderr

        rm -f $STDOUT_FILE $STDERR_FILE

        ($* > $STDOUT_FILE) >& $STDERR_FILE

  set RETURN_VALUE=$status

        cat $STDOUT_FILE

        tail +3 $STDERR_FILE

  exit $RETURN_VALUE

  You get the HDF make files and test scipts to execute your filter script
  by setting the environment variable "RUNSERIAL" to the full path of the
  script prior to running configure for parallel builds.  Remember to
  "unsetenv RUNSERIAL" before running configure for a serial build.

  Note that the RUNSERIAL environment variable exists so that we can
  can prefix serial runs as necessary on the target system.  On DataStar,
  no prefix is necessary.  However on an MPICH system, the prefix might
  have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
  get the serial tests to run at all.

  In such cases, you will have to include the regular prefix in your
  filter script.

* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
  is turn on. The value of the reference in the destination attriubte is
  wrong. This H5Ocopy problem will affect h5copy tool