wiki:InstallHdf5

This is required by the continuous test pack. Chaste has been developed using HDF5 version 1.6, although using 1.8 is also possible (see below).

NB: You can now get PETSc to download and install HDF5 as part of its installation process; in this case you do not need a separate HDF5 install, and can ignore this page.

Download the source from ftp://ftp.hdfgroup.org/HDF5/prev-releases/hdf5-1.6.6/src/hdf5-1.6.6.tar.gz

tar -zxf hdf5-1.6.6.tar.gz 
cd hdf5-1.6.6
export CC=mpicc 
./configure --enable-parallel --prefix=${HOME}/hdf5
make
cd test
make check
cd ../testpar
make check
cd ..
make install

The include & lib paths will need to be added to your hostconfig script, and you need to link with the hdf5 library (and possibly the z library too). See chastebob.py for an example.

An optional java viewer for HDF5 files can be found at ftp://ftp.hdfgroup.org/HDF5/hdf-java/hdfview/hdfview_install_linux_novm.bin The h5dump utility will also give a view of an HDF5 file:

[chaste@userpc44 hdf5]$ ~/hdf5/bin/h5dump test.h5 
HDF5 "test.h5" {
GROUP "/" {
   DATASET "IntArray" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SIMPLE { ( 14, 5 ) / ( 14, 5 ) }
      DATA {
      (0,0): 0, 1, 2, 3, 4,
      (1,0): 10, 11, 12, 13, 14,
      (2,0): 100, 101, 102, 103, 104,
      (3,0): 110, 111, 112, 113, 114,
      (4,0): 200, 201, 202, 203, 204,
      (5,0): 210, 211, 212, 213, 214,
      (6,0): 300, 301, 302, 303, 304,
      (7,0): 310, 311, 312, 313, 314,
      (8,0): 400, 401, 402, 403, 404,
      (9,0): 410, 411, 412, 413, 414,
      (10,0): 500, 501, 502, 503, 504,
      (11,0): 510, 511, 512, 513, 514,
      (12,0): 600, 601, 602, 603, 604,
      (13,0): 610, 611, 612, 613, 614
      }
   }
}
}

HDF5 1.8

As of r6872, Chaste is also compatible with version 1.8 of HDF5. The change to the Chaste source code required to achieve compatibility is minor, and can be applied to previous releases manually or using the attached patch (attachment:hdf5-1.8.patch).

Last modified 8 years ago Last modified on Jun 1, 2012, 9:06:51 AM

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