Merge remote-tracking branch 'ssh/master'

base/cmake_package.py

@@ -34,6 +34,9 @@ def configure(ctx, stage_args):
     else:
         conf_lines.append('-DCMAKE_BUILD_TYPE:STRING=Release')
 
+    if ctx.parameters['platform'] == 'Darwin':
+        conf_lines.append('-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=""')
+
     #cmake needs to be given all the dependency dirs as prefix paths
     #so that we search the hashdist directories before the system directories
     #CMake doesn't use the CPPFLAGS implicitly to find libraries

base/setuptools_package.yaml

@@ -22,6 +22,7 @@ build_stages:
   handler: bash
   bash: |
     ${PYTHON} -c 'import setuptools; __file__="setup.py"; exec(open(__file__).read())' \
+       ${SETUPTOOLS_PACKAGE_EXTRA_OPTIONS} \
        install \
        --prefix=. --root=${ARTIFACT} \
        --single-version-externally-managed

examples/hd_base.Darwin.yaml

@@ -0,0 +1,41 @@
+# This profile builds with the default clang compiler on Mac OS X 10.10
+# Yosemite. In particular it builds gcc (g++, gcc, gfortran). This profile can
+# then be used as a base for building the rest of Hashstack.
+
+extends:
+ - file: config.yaml
+
+parameters:
+  platform: Darwin
+  fortran: false
+  PATH: /usr/bin:/bin:/usr/sbin:/sbin
+  PROLOGUE: |
+    export MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion | sed -E "s/([0-9]+\.[0-9]+).*/\1/")
+
+packages:
+
+  launcher:
+  blas:
+    use: host-osx-framework-accelerate
+  lapack:
+    use: host-osx-framework-accelerate
+  mpi:
+    use: mpich
+  python:
+    link: shared
+  swig:
+    build_with: |
+      perl
+  ipython:
+  nose:
+  numpy:
+  sphinx:
+  sympy:
+  gmp:
+  matplotlib:
+  doxygen:
+  breathe:
+  gcc:
+  git:
+  perl:
+  pyliblzma:

examples/proteus.Darwin.yaml

@@ -44,6 +44,7 @@ packages:
     debug: false
   petsc4py:
     with_conf: true
+  pillow:
   pytables:
   sphinx:
   superlu:

examples/proteus.linux2.yaml

@@ -43,6 +43,7 @@ packages:
     debug: false
   petsc4py:
     with_conf: true
+  pillow:
   pytables:
   sphinx:
   superlu:

pkgs/Tempita.yaml

@@ -0,0 +1,9 @@
+extends: [setuptools_package]
+
+dependencies:
+  build: []
+  run: []
+
+sources:
+ - key: tar.gz:ha4sxnyiueasqqm7ox5jcifg2lencnyb
+   url: https://pypi.python.org/packages/source/T/Tempita/Tempita-0.5.3dev.tar.gz

pkgs/ansible.yaml

@@ -5,5 +5,5 @@ dependencies:
   run: [paramiko, jinja2, yaml]
 
 sources:
-- key: tar.gz:2n6ajm5lz2nqg2tmqmi7zszwbrolypwi
-  url: https://pypi.python.org/packages/source/a/ansible/ansible-1.8.4.tar.gz
+- key: tar.gz:wimt7wneaynlmjh2m4yrpfsbtj2z3ydl
+  url: https://pypi.python.org/packages/source/a/ansible/ansible-1.9.0.1.tar.gz

pkgs/backports-ssl_match_hostname.yaml

@@ -0,0 +1,5 @@
+extends: [setuptools_package]
+
+sources:
+- key: tar.gz:a5aq475qtkvxxwxv4ymn4zwd3lee4lr5
+  url: https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/backports.ssl_match_hostname-3.4.0.2.tar.gz

pkgs/bddc.yaml

@@ -3,18 +3,42 @@ dependencies:
   build: [mpi, lapack, mumps, blopex, parmetis, scalapack]
 
 sources:
-- url: https://github.com/certik/bddc.git
-  key: git:3d6cfa120682be5925861c022bd3a3f2c5d77940
+- key: git:acd093697417f49ec856b69e2d8b442e5adbbe85
+  url: https://github.com/certik/bddc.git
+
+defaults:
+  # Build in Debug mode (debug symbols, bounds checks, ...)
+  debug: false
 
 build_stages:
 
+- when: debug
+  name: debug-flags
+  after: prologue
+  before: make-configure
+  handler: bash
+  bash: |
+    FFLAGS="-g -C -Wall -fbounds-check"
+    CFLAGS="-g -Wall"
+
+- when: not debug
+  name: debug-flags
+  after: prologue
+  before: make-configure
+  handler: bash
+  bash: |
+    FFLAGS="-C -Wall -O3 -march=native -ffast-math -funroll-loops"
+    CFLAGS="-Wall -O3 -march=native -ffast-math -funroll-loops"
+
 - name: make-configure
   after: prologue
   handler: bash
   bash: |
     cp make.inc.example make.inc
     make \
         BDDCML_ROOT=$ARTIFACT \
+        BDDCML_MPFFLAGS="$FFLAGS" \
+        BDDCML_MPCFLAGS="$CFLAGS" \
         BDDCML_INCPARMETIS=-I$PARMETIS_DIR/include \
         BDDCML_LIBPARMETIS="-L$PARMETIS_DIR/lib -Wl,-rpath=${PARMETIS_DIR}/lib -lparmetis" \
         BDDCML_INCMETIS= \
@@ -27,7 +51,9 @@ build_stages:
         BDDCML_LIBSCALAPACK="-L$SCALAPACK_DIR/lib -Wl,-rpath=${SCALAPACK_DIR}/lib -lscalapack" \
         BDDCML_LIBLAPACK="-L$LAPACK_DIR/lib -Wl,-rpath=${LAPACK_DIR}/lib -llapack" \
         BDDCML_LIBBLAS="-lblas" \
-        BDDCML_LIBBLACS=
-    mkdir -p $ARTIFACT/bin
+        BDDCML_LIBBLACS= \
+        -j 1 # The BDDC's makefile system doesn't work in parallel
+    mkdir -p $ARTIFACT/bin $ARTIFACT/include
+    cp src/bddcml_interface_fortran.mod $ARTIFACT/include/
     cd examples
     cp bddcml_global bddcml_local poisson_on_cube $ARTIFACT/bin/

pkgs/boost/boost.yaml

@@ -91,7 +91,7 @@ build_stages:
   after: bjam
   handler: bash
   bash: |
-    for lib in ${ARTIFACT}/lib/*.so; do
+    for lib in ${ARTIFACT}/lib/*.so.*; do
         ${PATCHELF} --set-rpath ${ARTIFACT}/lib:${BZIP2_DIR}/lib:${ZLIB_DIR}/lib ${lib}
     done
 

pkgs/buildbot.yaml

@@ -1,8 +1,8 @@
 extends: [distutils_package]
 
 dependencies:
-  build: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil, setuptools]
-  run: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil]
+  build: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil, Tempita, decorator, MarkupSafe, zope-interface, setuptools]
+  run: [SQLAlchemy, SQLAlchemy-Migrate, jinja2, Twisted, sqlite, python-dateutil, Tempita, decorator, MarkupSafe, zope-interface]
 
 sources:
 - key: zip:tsyafdgdsontllm5ujazrcbcnysx3o2g

pkgs/cmake.yaml

@@ -1,12 +1,36 @@
 extends: [autotools_package]
 
+dependencies:
+  build: [zlib, bzip2, curl, openssl, libidn, expat]
+
 sources:
-- key: tar.gz:kcrzjtzo7wnjfxkbctv6fgmurgmezzxg
-  url: http://www.cmake.org/files/v3.2/cmake-3.2.0-rc1.tar.gz
+- key: tar.gz:vxuu43rwaodxivs7flwyqzsbkrbuit5x
+  url: http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz
 
 build_stages:
+- when: platform == 'Darwin'
+  name: fix_deployment_target
+  after: prologue
+  before: configure
+  handler: bash
+  bash: |
+    unset MACOSX_DEPLOYMENT_TARGET
+
 - name: configure
-  extra: ['--parallel=${HASHDIST_CPU_COUNT}']
+  extra: ['--parallel=${HASHDIST_CPU_COUNT}',
+          '--system-bzip2',
+          '--system-curl',
+          '--system-expat',
+          #'--system-jsoncpp',
+          #'--system-libarchive',
+          '--system-zlib',
+          '--',
+          '-DCMAKE_PREFIX_PATH=${CURL_DIR}/lib;${ZLIB_DIR}/lib;${BZIP2_DIR}/lib;${EXPAT_DIR}/lib',
+          '-DCURL_INCLUDE_DIR=${CURL_DIR}/include',
+          '-DZLIB_INCLUDE_DIR=${ZLIB_DIR}/include',
+          '-DBZIP2_INCLUDE_DIR=${BZIP2_DIR}/include',
+          '-DEXPAT_INCLUDE_DIR=${EXPAT_DIR}/include',
+          ]
 
 when_build_dependency:
 - set: CMAKE

pkgs/coffeescript.yaml

@@ -0,0 +1,20 @@
+extends: [base_package]
+dependencies:
+  build: [node]
+
+defaults:
+  relocatable: false
+
+sources:
+- key: tar.gz:uwx36n3nhdu7dwxtwp46sffv3t3orhtw
+  url: https://github.com/jashkenas/coffeescript/archive/1.9.1.tar.gz
+
+build_stages:
+-  name: install
+   mode: replace
+   handler: bash
+   after: prologue
+   bash: |
+     "$NODE_DIR"/bin/npm --proxy 127.0.0.1:2 --production --global \
+         --prefix="$ARTIFACT" install .
+

pkgs/cryptography.yaml

@@ -1,7 +1,7 @@
 extends: [setuptools_package]
 
 dependencies:
-  build: [six, cffi, cryptography-vectors, openssl, pytest]
+  build: [six, cffi, cryptography-vectors, openssl, pytest, pycparser]
   run: []
 
 sources:

pkgs/decorator.yaml

@@ -0,0 +1,9 @@
+extends: [setuptools_package]
+
+dependencies:
+  build: []
+  run: []
+
+sources:
+ - key: tar.gz:omqaalhgdxvgvisk3skf3hlyggzwnfkt
+   url: https://pypi.python.org/packages/source/d/decorator/decorator-3.4.2.tar.gz

pkgs/doxygen.yaml

@@ -1,7 +1,7 @@
 extends: [autotools_package]
 
 dependencies:
-  build: [bison]
+  build: [bison, flex]
 
 sources:
 - url: https://github.com/doxygen/doxygen.git

pkgs/gcc/gcc.yaml

@@ -22,6 +22,16 @@ build_stages:
       patch -up1 < _hashdist/rpath.patch
       sed -i "s|@@ARTIFACT@@|${ARTIFACT}|g" gcc/config/i386/gnu-user.h gcc/config/i386/gnu-user64.h
 
+  - when: platform == 'Darwin'
+    name: fix_object_h
+    before: configure
+    handler: bash
+    bash: |
+      if [ -f /usr/include/dispatch/object.h ]; then
+        mkdir -p "$ARTIFACT/include/dispatch"
+        sed 's+typedef void (\^dispatch_block_t)(void)+typedef void* dispatch_block_t+' /usr/include/dispatch/object.h > "$ARTIFACT/include/dispatch/object.h"
+      fi
+
   - name: link_lib64_to_lib
     after: install
     handler: bash

pkgs/gdb.yaml

@@ -1,13 +1,21 @@
 extends: [autotools_package]
 
 dependencies:
-  build: [python, expat, xz, ncurses, libiconv, zlib, {{build_with}}]
+  build: [python, expat, xz, ncurses, libiconv, zlib, readline, {{build_with}}]
 
 sources:
-- key: tar.bz2:bw6veycan4nqy4h46at4msefe75n3ygn
-  url: http://ftp.gnu.org/gnu/gdb/gdb-7.7.1.tar.bz2
+- key: tar.xz:tmyvmunbmuuppl4mpwbii2m7wdewlxzr
+  url: https://ftp.gnu.org/gnu/gdb/gdb-7.9.tar.xz
+
+defaults:
+  # lib/libbfd.a contains hard-coded path
+  relocatable: false
 
 build_stages:
+  - name: configure
+    global_flags: true
+    extra: ['--with-system-readline']
+
   - name: fail_on_osx
     before: prologue
     mode: replace

pkgs/genshi.yaml

@@ -0,0 +1,9 @@
+extends: [setuptools_package]
+
+dependencies:
+  build: []
+  run: []
+
+sources:
+-  key: zip:ptgbosdhel3aawcwn3pqmd6iy2xqvqkv
+   url: https://pypi.python.org/packages/source/G/Genshi/Genshi-0.7.zip

pkgs/geos.yaml

@@ -3,3 +3,7 @@ extends: [autotools_package]
 sources:
   - url: http://download.osgeo.org/geos/geos-3.4.2.tar.bz2
     key: tar.bz2:cxul7x36feehvfl3k2wfipvjvabscsa4
+
+when_build_dependency:
+  - prepend_path: PATH
+    value: '${ARTIFACT}/bin'

pkgs/git.yaml

@@ -4,12 +4,13 @@ dependencies:
   build: [curl, pcre, openssl, libiconv, gettext, expat, zlib, perl]
 
 sources:
-- key: tar.gz:xix6qfhhbgs5b4bu5pucba74477o2cez
-  url: http://www.kernel.org/pub/software/scm/git/git-2.3.0.tar.gz
+- key: tar.gz:2wghm2ua3bvf4gcgybghiymotc76yfmh
+  url: https://www.kernel.org/pub/software/scm/git/git-2.4.0.tar.gz
 
 defaults:
   # /bin/git contains hard-coded path
   relocatable: false
+  disable_crypto: false
 
 build_stages:
 
@@ -19,6 +20,13 @@ build_stages:
   bash: |
     export PERL_PATH="/usr/bin/env perl"
 
+- when: platform == 'Darwin' and disable_crypto
+  name: fix_crypto_compile_failure
+  before: configure
+  handler: bash
+  bash: |
+    export NO_APPLE_COMMON_CRYPTO=1
+
 - name: configure
   mode: override
   extra: ['--with-libpcre=${PCRE_DIR}', '--with-zlib=${ZLIB_DIR}', '--with-iconv=${LIBICONV_DIR}', '--with-expat=${EXPAT_DIR}', '--with-curl=${CURL_DIR}']

pkgs/glm.yaml

@@ -0,0 +1,7 @@
+extends: [cmake_package]
+dependencies:
+  build: []
+
+sources:
+- key: zip:crsrwvvrb6tibasenlfpniirnvllov6i
+  url: http://downloads.sourceforge.net/project/ogl-math/glm-0.9.6.3/glm-0.9.6.3.zip