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comparison tool_dependencies.xml @ 1:37ff27ea37ed draft

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author iuc
date Sat, 14 Feb 2015 22:28:18 -0500
parents 597c0e54eded
children b36c9ee883e9
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0:597c0e54eded 1:37ff27ea37ed
1 <tool_dependency> 1 <tool_dependency>
2 <package name="atlas" version="3.10.1"> 2 <package name="atlas" version="3.10.2">
3 <install version="1.0"> 3 <install version="1.0">
4 <actions> 4 <actions_group>
5 <!-- first action is always downloading --> 5 <actions architecture="x86_64" os="linux">
6 <!--<action type="download_by_url" target_filename="ATLAS.tar.bz2">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2</action>--> 6 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/atlas/atlas-3.10.2-Linux-x86_64.tar.gz</action>
7 <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2</action> 7 <action type="move_directory_files">
8 <action type="shell_command">tar xfvj atlas3.10.1.tar.bz2</action> 8 <source_directory>.</source_directory>
9 <action type="download_file">http://www.netlib.org/lapack/lapack-3.4.2.tgz</action> 9 <destination_directory>$INSTALL_DIR</destination_directory>
10 10 </action>
11 <action type="shell_command"> 11 <action type="set_environment">
12 # try to disable cpu throttling 12 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
13 if hash cpufreq-selector 2>/dev/null; then 13 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
14 cpufreq-selector -g performance 14 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
15 elif hash cpupower 2>/dev/null; then 15 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
16 cpupower frequency-set -g performance 16 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
17 else 17 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
18 echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' 18 </action>
19 exit 19 </actions>
20 fi 20 <actions architecture="x86_64" os="darwin">
21 </action> 21 <!-- NOOP: On OS X we will use Apple's vecLib -->
22 <action type="shell_command"> 22 </actions>
23 cd ATLAS &amp;&amp; 23 <actions>
24 mkdir build &amp;&amp; 24 <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action>
25 cd build &amp;&amp; 25 <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action>
26 mkdir $INSTALL_DIR/atlas/ &amp;&amp; 26 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
27 ../configure -Fa alg -fPIC --prefix=$INSTALL_DIR/atlas/ --with-netlib-lapack-tarfile=../../lapack-3.4.2.tgz 27 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>
28 </action> 28 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
29 <action type="shell_command">cd ./ATLAS/build &amp;&amp; make </action> 29 <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
30 <action type="shell_command">cd ./ATLAS/build &amp;&amp; make install</action> 30 <!-- a 64-bit architecture is assumed for compilation -->
31 31 <action type="shell_command">
32 <action type="set_environment"> 32 cd ATLAS &amp;&amp;
33 <environment_variable name="ATLAS_LIB_DIR" action="set_to">$INSTALL_DIR/atlas/lib</environment_variable> 33 mkdir ATLAS/build &amp;&amp;
34 <environment_variable name="ATLAS_INCLUDE_DIR" action="set_to">$INSTALL_DIR/atlas/include</environment_variable> 34 patch -p1 &lt;/host/static_full_blas_lapack.diff &amp;&amp;
35 </action> 35 patch -p1 &lt;/host/shared_libraries.diff &amp;&amp;
36 </actions> 36 patch -p1 &lt;/host/cpu-throttling-check.diff &amp;&amp;
37 cd build &amp;&amp;
38 ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 &amp;&amp;
39 make &amp;&amp;
40 make install
41 </action>
42 <action type="set_environment">
43 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable>
44 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
45 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
46 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
47 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
48 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
49 </action>
50 </actions>
51 </actions_group>
37 </install> 52 </install>
38 <readme>ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR (including libatlas.a) will be exported for later use. 53 <readme>Compiling ATLAS requires a C and Fortran compiler (typically gcc and gfortran). The base ATLAS installation path can be is exported as ATLAS_ROOT_PATH, libraries as ATLAS_LIB_DIR, and headers as ATLAS_INCLUDE_DIR.
39 During ATLAS library compilation, ATLAS performs code efficiency checks. These checks can only provide optimal results, if "frequency scaling" is disabled on the CPU, and no other load-intense processes are running. 54 This ATLAS build includes patches from the Debian ATLAS packages which enable additional features:
40 Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set"). 55 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions
56 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories
57 This package also includes a bundled libgfortran and export LD_LIBRARY_PATH=$ATLAS_LIB_DIR so that any dependent packages which link to ATLAS will be able to resolve all necessary libraries at runtime.
58 On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib.
41 </readme> 59 </readme>
42 </package> 60 </package>
43 </tool_dependency> 61 </tool_dependency>