Differences

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--- hdf5-software [2015/06/08 09:36] – [HDF5] aorth
+++ hdf5-software [2017/09/28 10:35] (current) – [Installation] aorth
@@ Line 2: / Line 2: @@
 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
-==== v1.8.14 ====
+===== Information =====
-  * Version: 1.8.14
+  * Version: 1.8.19
   * Added: December, 2014
+  * Updated: September, 2017
   * Link: http://www.hdfgroup.org/HDF5/
-=== Usage ===
+===== Usage =====
-  * Show all available versions of hdf5<code>module avail hdf5</code>
+See versions of hdf5 which are available:
-  * Load hdf5 module: <code>module load hdf5/1.8.14</code>
+<code>$ module avail hdf5</code>
-=== Installation ===
+Load a particular version:
-  * Download src tarball, its already compiled so just copy /export/apps<code>
-wget "http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-centos6-x86_64-gcc447/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared.tar.gz" - O hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared.tar.gz
-cd hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared
-sudo mkdir -p /export/apps/hdf5/1.8.14/
-sudo chown -R joguya:joguya /export/apps/hdf5/1.8.14/
-cp -r * /export/apps/hdf5/1.8.14/
-sudo chown -R root:root /export/apps/hdf5/1.8.14/</code>
-  * hdf5 module file<code>
+<code>$ module load hdf5/1.8.19</code>
-#%Module1.0
-#####################################################################
-##
-## HDF5 Modulefile
-## by James Oguya, <j.oguya@cgiar.org>
-## January, 2015
-##
-set appname         hdf5
+List contents of an archive:
-set version         1.8.14
-set prefix          /export/apps/${appname}/${version}
-set exec_prefix     ${prefix}/bin
-set datarootdir     ${prefix}/share
-set url             "http://www.hdfgroup.org/HDF5/"
-set msg             "HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.\nOfficial Site: $url\n"
-module-whatis $msg
+<code>$ h5dump -n file_s1_p0.bas.h5</code>
-proc ModulesHelp { } {
+Print referenced datasets:
-    puts stderr "$msg"
-}
-conflict            hdf5
+<code>$ h5dump -d /MultiPart/Parts file_s1_p0.bas.h5</code>
-prepend-path        PATH            ${exec_prefix}
+===== Installation =====
-prepend-path        MANPATH         ${datarootdir}
+Notes from the sysadmin during installation:
-prepend-path        LD_LIBRARY_PATH ${prefix}/lib
-# load dependencies
+<code>$ cd /tmp
-if { ![is-loaded openmpi/1.8.2] } {
+$ wget https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.19.tar.gz
-    module load openmpi/1.8.2
+$ tar xf hdf5-1.8.19.tar.gz
-}
+$ cd hdf5-1.8.19
-</code>
+$ scl enable devtoolset-4 bash
+$ ./configure --prefix=/export/apps/hdf5/1.8.19 --enable-production --enable-cxx
-  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=module</code>
+$ make
+$ make check
+$ sudo mkdir -p /export/apps/hdf5/1.8.19
+$ sudo chown aorth /export/apps/hdf5/1.8.19
+$ make install
+$ sudo chown -R root /export/apps/hdf5/1.8.19</code>
+Note that the ''--enable-cxx'' option to configure is important as it enables the installation of the C++ header files that other programs can use to compile against.