Mercurial > repos > iuc > package_atlas_3_10

comparison tool_dependencies.xml @ 7:86b7c19454fa draft

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author iuc
date Wed, 15 Jul 2015 10:35:14 -0400
parents 4778b172b895
children c47756a8136e
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6:4778b172b895 7:86b7c19454fa
13 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable> 13 <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
14 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> 14 <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
15 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable> 15 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
16 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable> 16 <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
17 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable> 17 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
18 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
18 </action> 19 </action>
20 <action type="shell_command"><![CDATA[
21 command -v gfortran || return 0
22 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 &&
23 BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
24 echo 'program test; end program test' > test.f90 &&
25 gfortran -o test test.f90 &&
26 LGF=`ldd test | grep libgfortran | awk '{print $3}'` &&
27 LGF_CANON=`readlink -f $LGF` &&
28 LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` &&
29 if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then
30 cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled &&
31 cp -p $LGF_CANON $BUNDLED_LGF_CANON
32 fi
33 ]]></action>
19 </actions> 34 </actions>
20 <actions architecture="x86_64" os="darwin"> 35 <actions architecture="x86_64" os="darwin">
21 <!-- NOOP: On OS X we will use Apple's vecLib --> 36 <!-- NOOP: On OS X we will use Apple's vecLib -->
22 </actions> 37 </actions>
23 <actions> 38 <actions>
26 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action> 41 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
27 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action> 42 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>
28 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action> 43 <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
29 <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action> 44 <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
30 <!-- a 64-bit architecture is assumed for compilation --> 45 <!-- a 64-bit architecture is assumed for compilation -->
31 <action type="shell_command"> 46 <action type="shell_command"><![CDATA[
32 cd ATLAS &amp;&amp; 47 cd ATLAS &&
33 mkdir ATLAS/build &amp;&amp; 48 mkdir ATLAS/build &&
34 patch -p1 &lt;/host/static_full_blas_lapack.diff &amp;&amp; 49 patch -p1 </host/static_full_blas_lapack.diff &&
35 patch -p1 &lt;/host/shared_libraries.diff &amp;&amp; 50 patch -p1 </host/shared_libraries.diff &&
36 patch -p1 &lt;/host/cpu-throttling-check.diff &amp;&amp; 51 patch -p1 </host/cpu-throttling-check.diff &&
37 cd build &amp;&amp; 52 cd build &&
38 ../configure --prefix="$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; 53 ../configure --prefix="$INSTALL_DIR" -D c -DWALL -b 64 -Fa alg '-fPIC' --with-netlib-lapack-tarfile=../../lapack-3.5.0.tgz -v 2 -t 0 -Si cputhrchk 0 &&
39 make &amp;&amp; 54 make &&
40 make install 55 make install
41 </action> 56 ]]></action>
42 <action type="set_environment"> 57 <action type="set_environment">
43 <environment_variable action="set_to" name="ATLAS_LIB_DIR">$INSTALL_DIR/lib</environment_variable> 58 <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> 59 <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> 60 <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> 61 <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>