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HDF5 FAQ -- Questions About the Software

ATTRIBUTES


C++


DATASETS


DATASPACE


DATATYPES


EXTERNAL LIBRARIES


ERROR


FILE


FORTRAN


GENERAL


IDENTIFIERS


IMAGES AND PALETTES


INSTALLING/BUILDING HDF5


(For Fortran issues, see FORTRAN)

JAVA


PARALLEL HDF5


PERFORMANCE


PROPERTIES


UTILITIES


ATTRIBUTES


When would you use attributes vs. datasets for your metadata ?


When would you use compact attributes vs. compact datasets ?


C++


Does C++ support stream operators?


Does it do IO via standard library containers?


DATASETS


How do I find out what compression has been used to write a dataset?


DATASPACE


When you specify memspace and filespace for H5Dwrite and H5Dread does it mean it is allocating memory for both the dataset and memory space (ie. twice the size of dataset) ?


DATATYPES


Why was the H5T_ARRAY created ? What is it for ?


How can you tell if two datasets share their (named, committed) datatype?


How do I create a String attribute or dataset?


How do you create datasets with a time datatype (class of H5T_TIME)?


When do you use pre-defined standard vs. native datatypes?


Further Understanding Native Datatypes


Does HDF5 support a boolean datatype ?


What are the plusses and minusses of using compound datatypes ?


Does HDF5 support bitfields ?


How would you use a float pointer in a compound datatype ?


How Does the HDF5 library handle overflowing (invalid) ENUM data ?


H5Tenum_insert returns error when type has different endianness


When reading compound data from file w/different compound field name, the data is different for this field.


What is the proper way to allocate memory when reading a variable length datatype?


Is there a limit on the number of fields allowed in a compound datatype ?


Can I represent a fixed length string field of a compound datatype in memory as a struct with a "char *" pointer ?


EXTERNAL LIBRARIES


How to detect the SZIP encoder at run time


ERROR


The error report prints out full path for file name instead of file name only


How do you turn off error messages ?


FILE


How Closing a File Affects Open Objects


How can I resolve problems due to objects being left open?


FORTRAN


How do you create a dataset with a 16-bit datatype in F90 ?


How do you build HDF5 using gcc and either Intel or Lahey Fortran ?


Can you build shared Fortran libraries in HDF5 ?

Building Fortran application with Intel Fortran, get "/lib/libimf.so : warning feupdateenv is not implemented"


GENERAL


Can you delete objects in an HDF5 file ? If yes, how ?


Does HDF5 support meshes ?


How do you create files over 2GB ?


Does HDF5 support concurrent access to one or more HDF5 file(s) from multiple threads in a single process?


Does HDF5 support concurrent access to a single dataset from multiple processes?


Can you read an HDF5 file while it is being written to?


Is HDF5 multi-threaded?

    No, HDF5 is not multi-threaded.


Is HDF5 thread-safe?


Performance-wise, how does HDF5 compare to a relational database?


Why are my files sizes different, if I open an HDF5 file more than once rather than writing the data out in one call?


I'd like to access an HDF5 file without using the HDF5 library. Is this possible?


Will data manipulation routines be added to HDF5?


Given an HDF5 library, how can I determine which version of HDF5 is being used (linked)?


Given a library that calls HDF5 functions, how can I determine which version of HDF5 was used to build it?


Performance-wise, how does HDF5 compare to a relational database?


If you run an application twice on the same machine will it produce identical HDF5 files ?


Can you guarantee that a zero will not be used as a valid hid_t ?


Can you store a binary object ( Excel spreadsheet, Word document, Zip file, etc.. ) in an HDF5 file ?


IDENTIFIERS


How do you get the name of an object opened with H5Rdereference?


How do you get the path and name of a committed datatype?


IMAGES AND PALETTES


How do you store a true color image in HDF5 ?


What kind of palettes are supported?


If you have an X by Y image in Z bands how would you store that in HDF5 ?


How do you save an image made from (r,g,b) floating point values?


INSTALLING/BUILDING HDF5


Having problems building an application with pre-built libraries.


How can you determine what compiler/flags are used by an HDF5 installation?


The mtime test fails with the message 'Old modification time incorrect.', when building with an unsupported platform/compiler


Can't open shared library: ../lib...s#.0


How to build HDF5 Fortran with Intel Compilers


Building on MAC OSX, the symbols restFP and saveFP come up as undefined. Why?


Float to Conversion Tests Fail on AMD with Intel compiler. Why?


AIX Configure failure: "...config.sub: too many arguments"


AIX: HDF5 fails to build with gcc


Using Purify on HDF5 library, get uninitialized memory read error


When Building HDF5, the Object Header test, "Testing message deletion", fails.


Building on AIX 64-bit, get: ERROR: No csects or exported symbols have been saved.


JAVA


HDFView: Unsupported fileformat error opening an HDF/HDF5 file on Mac OS X


HDFView: Unsupported fileformat error opening an HDF/HDF5 file on Windows XP


Java error: can't find HDF5 file format


Data values are reversed/swapped/transposed in HDFView. Why?


The Order Returned by the Object Package for the selectedDims / selectedIndex Fields has Changed


Do you support Java 64-bit with HDF-JAVA?


What are the limitations of the HDF Java interface?


What kind of palettes are supported in HDFView?


java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path


Will you be adding a pure Java interface to HDF5?


Is parallel HDF5 supported with java?


Can HDFView handle bit-field data?


HDFView: HDF4 / HDF5 libraries are grayed out and unselectable


How do you increase the Java Virtual machine memory?


Get EXCEPTION_ACCESS_VIOLATION when more than 1024MB is allocated to the Java Virtual machine.


How to workaround error Exception - dataset too big ?


PARALLEL HDF5


What do you need to run Parallel HDF5 ?


What performance can you expect from Parallel HDF5 ?


Does HDF5 support compression with parallel HDF5 ? If not, why ?


Does Parallel HDF5 support chunking ?


Can you run Parallel HDF5 and the thread-safe feature together ? What about Parallel HDF5 and C++?


Does Parallel HDF5 support variable length datatypes ?


Problems installing Parallel HDF5 on IBM Regatta (with AIX5)


How should you write attributes in Parallel HDF5?


How to write and NOT to write compound datasets using F90 in Parallel HDF5


MPI ... failed: array services not available


How do you write data when one process doesn't have or need to write data ?


Does Parallel HDF5 support shared libraries?


How can I read/write a dataset greater than 2GB?