libatlas, libblas components; added scikit-learn+scipy to erp5

component/libatlas/buildout.cfg

+[buildout]
+parts =
+  libatlas
+
+
+[skip-throttle-check.patch]
+recipe = hexagonit.recipe.download
+md5sum = 17c8471d67c99fac80ace05273ce0817
+url = ${:_profile_base_location_}/${:filename}
+filename = ${:_buildout_section_name_}
+download-only = true
+
+
+[atlas-download]
+recipe = hexagonit.recipe.download
+version = 3.10.1
+filename = atlas${:version}.tar.bz2
+url = http://downloads.sourceforge.net/project/math-atlas/Stable/${:version}/${:filename}
+md5sum = 78753e869231cc1417a92eebaa076718
+download-only = true
+mode = 0644
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+
+
+[lapack-download]
+recipe = hexagonit.recipe.download
+version = 3.5.0
+filename = lapack-${:version}.tgz
+url = http://www.netlib.org/lapack/${:filename}
+md5sum = b1d3e3e425b2e44a06760ff173104bdf
+download-only = true
+mode = 0644
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+
+
+
+[libatlas]
+recipe = cp.recipe.cmd
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+lapack_version = 3.5.0
+install_cmd =
+  set -e
+  mkdir -p ${:location}__compile__
+  cd ${:location}__compile__
+  export SRCdir=`pwd`/ATLAS
+  export BLDdir=`pwd`/build
+  tar xfj ${atlas-download:location}/${atlas-download:filename}
+  cd $SRCdir
+  # http://stackoverflow.com/questions/14592401/atlas-install-really-need-to-get-past-cpu-throttle-check
+  # http://sourceforge.net/p/math-atlas/support-requests/886/
+  patch -p1 <${skip-throttle-check.patch:location}/${skip-throttle-check.patch:filename}
+  mkdir -p $BLDdir
+  cd $BLDdir
+  export F77LIB=${gcc-fortran:location}/lib64/libgfortran.so.3
+  export LD_PRELOAD=$F77LIB
+  $SRCdir/configure -b 64 \
+        --prefix=${:location} \
+        --with-netlib-lapack-tarfile=${lapack-download:location}/${lapack-download:filename} \
+        -C acg ${gcc-fortran:location}/bin/gcc \
+        -C if ${gcc-fortran:location}/bin/gfortran \
+        --shared
+
+  #-Ss f77lib `${gcc-fortran:location}/bin/gfortran --print-file-name=libgfortran.so` \
+
+  make build    # tune & build lib
+  make check    # sanity check correct answer
+#  make ptcheck  # sanity check parallel
+  make time     # check if lib is fast
+  make install  # copy libs to install dir 
+

component/libatlas/skip-throttle-check.patch

+diff --git a/CONFIG/src/probe_arch.c b/CONFIG/src/probe_arch.c
+index 75edef9..f440bf6 100644
+--- a/CONFIG/src/probe_arch.c
++++ b/CONFIG/src/probe_arch.c
+@@ -238,8 +238,7 @@ int main(int nargs, char **args)
+       printf("CPU MHZ=%d\n",
+              ProbeOneInt(OS, asmd, targ, "-m", "CPU MHZ=", &sure));
+    if (flags & Pthrottle)
+-      printf("CPU THROTTLE=%d\n",
+-             ProbeOneInt(OS, asmd, targ, "-t", "CPU THROTTLE=", &sure));
++      printf("CPU THROTTLE=0\n");
+    if (flags & P64)
+    {
+       if (asmd == gas_x86_64)

component/libblas/buildout.cfg

+[buildout]
+parts =
+  libblas
+
+
+[libblas]
+recipe = cp.recipe.cmd
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+gfortran=${gcc-fortran:location}/bin/gfortran
+gcc=${gcc-fortran:location}/bin/gcc
+install_cmd =
+  set -e
+  mkdir -p ${:location}__compile__
+  cd ${:location}__compile__
+  wget -nc http://www.netlib.org/blas/blas.tgz
+  tar xzf blas.tgz
+  cd BLAS
+  ${:gfortran} -O3 -std=legacy -m64 -fno-second-underscore -fPIC -c *.f
+  ar r libfblas.a *.o
+  ranlib libfblas.a
+  ${:gcc} -shared -Wl,-soname,libf77blas.so.3 -o libf77blas.so.3.0.0 *.o -lc
+  # rm -rf *.o
+  mkdir -p ${:location}
+  mv libfblas.a ${:location}/
+  cp libf77blas.so.3.0.0 ${:location}/
+  cd ${:location}
+  ln -sf libf77blas.so.3.0.0 libf77blas.so.3.0
+  ln -sf libf77blas.so.3.0 libf77blas.so.3
+

component/numpy/buildout.cfg

+[buildout]
+
+extends =
+  ../git/buildout.cfg
+  ../gcc/buildout.cfg
+  ../libatlas/buildout.cfg
+  ../libblas/buildout.cfg
+
+
+[scipy-repository.git]
+recipe = slapos.recipe.build:gitclone
+repository = https://github.com/mmariani/scipy.git
+# bumped version number to ensure we're using the freshly compiled egg
+branch = 0.13.3001
+git-executable = ${git:location}/bin/git
+
+[scikit-learn-repository.git]
+recipe = slapos.recipe.build:gitclone
+repository = https://github.com/scikit-learn/scikit-learn.git
+branch = master
+git-executable = ${git:location}/bin/git
+
+
+[build-venv]
+dependency = ${prerequired-eggs:recipe}
+recipe = cp.recipe.cmd
+location = ${buildout:parts-directory}/${:_buildout_section_name_}
+install_cmd =
+  if [ -d ${:location} ]; then
+    exit
+  fi
+  mkdir -p ${:location}
+  cd ${:location}
+  unset PYTHONPATH
+  export PATH="${gcc-fortran:location}/bin:$PATH"
+  export LD_PRELOAD="${gcc-fortran:location}/lib64/libgfortran.so.3 ${libblas:location}/libf77blas.so.3"
+  export ATLAS=${libatlas:location}/lib/libsatlas.so
+  export BLAS=${libblas:location}/lib/libfblas.a
+  export LAPACK=${libatlas:location}/lib/liblapack.a
+  ${python2.7-virtualenv:executable} ${:location}
+  . ${:location}/bin/activate
+  ${:location}/bin/pip install numpy
+  ${:location}/bin/pip install Tempita
+  export PYTHONPATH=${buildout:eggs-directory}/numpy-${versions:numpy}-py2.7-linux-x86_64.egg
+  cd ${scipy-repository.git:location}
+  python setupegg.py bdist_egg
+  cd ${scikit-learn-repository.git:location}
+  python setup.py bdist_egg
+update_cmd = ${:install_cmd}
+
+
+[prerequired-eggs]
+recipe = zc.recipe.egg
+eggs =
+  slapos.cookbook
+  numpy
+
+
+[numpy-eggs]
+dependencies = ${build-venv:recipe}
+recipe = zc.recipe.egg
+find-links =
+    ${scipy-repository.git:location}/dist
+    ${scikit-learn-repository.git:location}/dist
+eggs =
+  numpy
+  scipy
+  scikit-learn
+interpreter = python-numpy
+
+
+[versions]
+numpy = 1.8.1
+scipy = 0.13.3001
+scikit-learn = 0.16-git
+

component/numpy/software.cfg

+# A minimal software release to test the numpy component (depends on gfortran).
+
+[buildout]
+extends = 
+  ../../stack/slapos.cfg
+  ../../component/numpy/buildout.cfg
+
+parts =
+  numpy-eggs
+
+[versions]
+numpy = 1.8.1
+scipy = 0.13.3001
+scikit-learn = 0.16-git
+

stack/erp5/buildout.cfg

@@ -66,6 +66,7 @@ extends =
   ../../component/aspell/buildout.cfg
   ../../component/cloudooo/buildout.cfg
   ../../component/jsl/buildout.cfg
+  ../../component/numpy/buildout.cfg
 
 parts =
   rdiff-backup
@@ -430,6 +431,7 @@ ZODB3-patch-binary = ${patch:location}/bin/patch
 [eggs]
 recipe = zc.recipe.egg
 eggs =
+  ${numpy-eggs:eggs}
   ${mysql-python:egg}
   ${lxml-python:egg}
   ${pil-python:egg}
@@ -581,7 +583,7 @@ setuptools = 2.2
 huBarcode = 0.63
 
 # Known version with works
-numpy = 1.6.2
+numpy = 1.8.1
 
 # test_UserManagerInterfaces in testERP5Security fails with 1.10.0.
 Products.PluggableAuthService = 1.9.0