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HDF5-1.6.0 Known Problems

HDFView Problem with Mac OS X and JDK 1.4

 Due to a bug in JDK 1.4 on Mac OS X, the HDFView tool cannot be run by clicking on it from the desktop. The Java virtual machine in JDK 1.4 cannot obtain the environment variable, DYLD_LIBRARY_PATH, from the system. Therefore, HDFView cannot find the HDF5 library. This problem does not occur with JDK 1.3.

To work around this problem you can run HDFView from a command line prompt, by going to the directory where it is located and typing: 

    open -a <absolute path to HDFView exectuable>
You can also use Mac's 'explorer' to get to the location of the HDFView executable, and then click on it.

Data Corruption Problem in HDF5-1.6.0

There is a data corruption problem with using H5Gunlink. It can be reproduced by creating two datasets, closing one, then unlinking the other. The dataset that was closed will have 0's written to it when it should not. Two workarounds that have helped users are:
  1. Call H5Fflush just before you unlink the dataset.
  2. Move the H5Dclose call to be AFTER the H5Gunlink call.

Data Corruption Problem in HDF5

There is a data corruption problem in HDF5-1.6.0 and previous releases which affects users who use the H5Pset_istore_k and H5Pget_istore_k functions to control B-trees for indexing chunked datasets. This feature has been disabled in the HDF5-1.4.5-post8 snapshot, and fixed in the HDF5-1.6.0-post* and development (HDF5-1.7*) snapshots. The fix required a slight change to the HDF5 format.

See the HDF5 snapshots directory at: 

   ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots/

Detailed Information:

The HDF5 library provides APIs to control B-trees for indexing chunked datasets. The non-default 'K' value can be set up during file creation time and retrieved from the file creation property list by using the H5Pset_istore_k and H5Pget_istore_k functions.

The HDF5 library (1.6.0 release and any earlier releases) has the following problem:

When a non-default indexed storage B-tree internal 'K' value is set, the chunked datasets created in the file use the user's 'K' value. The data can be accessed correctly until the file is closed. After the file is closed, the non-default 'K' value is lost, since it is not stored in the file. This may cause data corruption for the chunked datasets with the non-default 'K' value.

In HDF5-1.4.5-post8, the H5Pset_istore_k() function will not allow the default 'K' value to be changed, so no error is generated. In the HDF5-1.6.0-post* and HDF5-1.7* snapshots, the library properly stores and uses the user-defined 'K' value.

If your application uses non-default 'K' values for chunked datasets, we strongly recommend that you move to the next appropriate version of the library.

H5Dwrite failure when using a combination of chunking and point selection

This patch fixes a problem with using chunked datasets with point selection: 
   ftp://ftp.hdfgroup.org/HDF5/current/src/patches/

Download ptchunkpatch.tar.gz

Problem with variable-length datatypes and chunked datasets

This patch corrects an error with variable-length datatypes and chunked datasets which caused H5Dwrite to fail sometimes. 
   ftp://ftp.hdfgroup.org/HDF5/current/src/patches/

Download the file H5D.c.

The "configure --enable-hdf5v1_4" fails when using C++

This switch was not meant to be used with C++. It only works for C.

HDF5-1.6.0, RedHat Linux 8.0, Intel Fortran 7.1 IA32

You must include -lgcc_s to the LIBS definition in the Makefile in the ./hdf5-1.6.0/fortran/test directory, to get the Fortran tests to compile. This also needs to be added to the source.

Using gcc 2.96 with Parallel HDF5

Parallel HDF5 fails if built with gcc 2.96. Gcc version 3.2.* should be used with Parallel HDF5.

"make install" Fails on Some Platforms

On some platforms, "make install" fails with the following messages: 
+ make install
          ../bin/mkdirs /include
../bin/mkdirs: test: 0403-004 Specify a parameter with this command.
mkdir: 0653-357 Cannot access directory /.
This his been encountered on HP-UX, OSF1, and AIX, and is due to a new gmake feature introduced in HDF5-1.6.0 that is not recognized by some make commands. There are three solutions:
  1. Run "make distclean" or reload the source. Then make the following change: 
        cd config
    edit commence.in
       look for the following line and remove the '?'.
           prefix?=@prefix@
    Build the library again by "configure ...; make ; make install".

  2. If you would rather not recompile, try the following: 
       a) Try "make prefix=... install";
   b) If a) fails, try "make -e prefix=... install";
   c) If b) also fails, walk down the hdf5 build tree and edit
      every Makefile by removing '?' from the following line
          prefix?=....
       then try "make install" again.
  3. If you have access to the "gmake" command, try 2a) above with the gmake command.

H5T_BKG_TEMP support was removed in 5-1.6.0

Support for H5T_BKG_TEMP was inadvertently removed. We put support for this back into HDF5. The changed files can be obtained from: 
   ftp://ftp.hdfgroup.org/HDF5/current/src/patches/

Download the file BKGpatch.tar.gz.

"libtool: link: warning: `AC_LIBTOOL_DLOPEN'. Assuming no dlopen support"

This warning may occur when building on Linux. It can be ignored.

Known Problems At Release Time

This information can be found in the Release Notes for 5-1.6.0 file.

- - Last modified:May 22nd 2007