| Previous changeset 4:196caf0a85e9 (2013-09-20) Next changeset 6:4778b172b895 (2015-05-23) |
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tool_dependencies.xml |
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| diff -r 196caf0a85e9 -r d5b1c7875b7b tool_dependencies.xml --- a/tool_dependencies.xml Fri Sep 20 16:23:34 2013 -0400 +++ b/tool_dependencies.xml Fri Jan 23 02:24:34 2015 -0500 |
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| @@ -1,46 +1,61 @@ <tool_dependency> - <package name="atlas" version="3.10.1"> + <package name="atlas" version="3.10.2"> <install version="1.0"> - <actions> - <!-- first action is always downloading --> - <!--<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>--> - <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.1/atlas3.10.1.tar.bz2</action> - <action type="shell_command">tar -jxvf atlas3.10.1.tar.bz2</action> - <action type="download_file">http://www.netlib.org/lapack/lapack-3.4.2.tgz</action> - - <action type="shell_command"> - # try to disable cpu throttling - if hash cpufreq-selector 2>/dev/null; then - cpufreq-selector -g performance - elif hash cpupower 2>/dev/null; then - cpupower frequency-set -g performance - else - echo 'Please deactivate CPU throttling by your own, or install cpufreq-selector' - exit - fi - </action> - <action type="shell_command"> - cd ATLAS && - pwd > $INSTALL_DIR/pwd.txt && - ls -l > $INSTALL_DIR/ls.txt && - ls -l CONFIG/src/ > $INSTALL_DIR/ls2.txt && - - mkdir build && - cd build && - mkdir $INSTALL_DIR/atlas/ && - ../configure -Fa alg -fPIC --prefix=$INSTALL_DIR/atlas/ --with-netlib-lapack-tarfile=../../lapack-3.4.2.tgz && - make && make install - </action> - - <action type="set_environment"> - <environment_variable name="ATLAS_LIB_DIR" action="set_to">$INSTALL_DIR/atlas/lib</environment_variable> - <environment_variable name="ATLAS_INCLUDE_DIR" action="set_to">$INSTALL_DIR/atlas/include</environment_variable> - </action> - </actions> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/atlas/atlas-3.10.2-Linux-x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> + <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> + <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> + <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <!-- NOOP: On OS X we will use Apple's vecLib --> + </actions> + <actions> + <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action> + <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action> + <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action> + <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action> + <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action> + <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action> + <!-- a 64-bit architecture is assumed for compilation --> + <action type="shell_command"> + cd ATLAS && + mkdir ATLAS/build && + patch -p1 </host/static_full_blas_lapack.diff && + patch -p1 </host/shared_libraries.diff && + patch -p1 </host/cpu-throttling-check.diff && + cd build && + ../configure --prefix="$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 && + make && + make install + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> + <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> + <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> + <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> + <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> + </action> + </actions> + </actions_group> </install> - <readme>ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR (including libatlas.a) will be exported for later use. - 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. - Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set"). + <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. + This ATLAS build includes patches from the Debian ATLAS packages which enable additional features: + 1. Shared versions of the standard ATLAS libraries are built in addition to the static versions + 2. Full BLAS and LAPACK libraries are built, which can be found in the ATLAS_BLAS_LIB_DIR and ATLAS_LAPACK_LIB_DIR directories + 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. + On Mac OS X, this package is a dummy package - BLAS and LAPACK libraries are already provided in Apple's vecLib. </readme> </package> </tool_dependency> |