CMB profile

examples/cmb.darwin.yaml

@@ -0,0 +1,68 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+# In the future, we'll provide better incorporation of
+# automatic environment detection.  For now, have a look
+# at the YAML files in the top-level directory and choose
+# the most *specific* file that matches your environment.
+
+extends:
+ - file: osx.yaml
+
+parameters:
+  HOST_MPICC: /usr/local/bin/mpicc
+  HOST_MPICXX: /usr/local/bin/mpic++
+  HOST_CMAKE: /usr/local/bin/cmake
+  PROLOGUE: |
+    export MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion | sed "s/\(10.[0-9]\).*/\1/"); export CXX=/usr/bin/clang++; export CC=/usr/bin/clang;
+
+# The packages list specifies all the packages that you
+# require installed.  <#> will ensure that all packages
+# and their dependencies are installed when you build this
+# profile.
+
+packages:
+  #blas and lapack are required by numpy
+  blas:
+    use: host-osx-framework-accelerate
+  lapack:
+    use: host-osx-framework-accelerate
+  cmake:
+    use: host-cmake
+  mpi:
+    use: host-mpi
+
+  libxml2:
+  png:
+  szip:
+  zlib:
+  boost:
+    toolset: clang
+    address_model: 64
+
+  #file format packages
+  hdf5:
+  netcdf4:
+  netcdf4cpp:
+
+  #now the rest
+  freetype:
+  gdal:
+  kml:
+  matplotlib:
+  molequeue:
+  numpy:
+  python:
+  qt:
+    toolset: unsupported/macx-clang
+    arch: x86_64
+  remus:
+  shiboken:
+  smtk:
+  vxl:
+  zmq:
+  launcher:
+  paraview:
+  cmb:
+
+  #not worth the time to enable
+  #ffmpeg:

examples/cmb.linux.yaml

@@ -0,0 +1,67 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+# In the future, we'll provide better incorporation of
+# automatic environment detection.  For now, have a look
+# at the YAML files in the top-level directory and choose
+# the most *specific* file that matches your environment.
+
+extends:
+ - file: linux.yaml
+
+parameters:
+  HOST_MPICC: /usr/bin/mpicc
+  HOST_MPICXX: /usr/bin/mpic++
+  HOST_MPIF77: /usr/bin/mpif77
+  HOST_MPIF90: /usr/bin/mpif90
+  HOST_MPIEXEC: /usr/bin/mpiexec
+  HOST_CMAKE: /usr/local/bin/cmake
+  PATH: |
+    /usr/local/bin:/bin:/usr/sbin:/sbin:/usr/bin:
+  PROLOGUE: |
+    export CXX=/usr/bin/g++-4.8; export CC=/usr/bin/gcc-4.8; export C_INCLUDE_PATH=/usr/include/mpi/; export CPLUS_INCLUDE_PATH=/usr/include/mpi/;
+
+# The packages list specifies all the packages that you
+# require installed.  <#> will ensure that all packages
+# and their dependencies are installed when you build this
+# profile.
+
+packages:
+  blas:
+    use: host-blas
+  cmake:
+    use: host-cmake
+  mpi:
+    use: host-mpi
+  curl:
+  szip:
+  bzip2:
+  zlib:
+  libxml2:
+  png:
+  boost:
+    toolset: gcc
+    address_model: 64
+
+  #file format packages
+  hdf5:
+  netcdf4:
+  netcdf4cpp:
+
+  #now the rest
+  freetype:
+  matplotlib:
+  numpy:
+  python:
+    host: true
+    link: shared
+  qt:
+    arch: x86_64
+  remus:
+  shiboken:
+  smtk:
+  vxl:
+  zmq:
+
+  launcher:
+  paraview:
+  cmb:

examples/paraview.darwin.yaml

@@ -0,0 +1,60 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+# In the future, we'll provide better incorporation of
+# automatic environment detection.  For now, have a look
+# at the YAML files in the top-level directory and choose
+# the most *specific* file that matches your environment.
+
+extends:
+ - file: osx.yaml
+
+parameters:
+  HOST_MPICC: /usr/local/bin/mpicc
+  HOST_MPICXX: /usr/local/bin/mpic++
+  HOST_CMAKE: /usr/local/bin/cmake
+  PROLOGUE: |
+    export MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion | sed "s/\(10.[0-9]\).*/\1/"); export CXX=/usr/bin/clang++; export CC=/usr/bin/clang;
+
+# The packages list specifies all the packages that you
+# require installed.  <#> will ensure that all packages
+# and their dependencies are installed when you build this
+# profile.
+
+packages:
+  #blas and lapack are required by numpy
+  blas:
+    use: host-osx-framework-accelerate
+  lapack:
+    use: host-osx-framework-accelerate
+  cmake:
+    use: host-cmake
+  mpi:
+    use: host-mpi
+
+  curl:
+  szip:
+  bzip2:
+  zlib:
+  libxml2:
+  png:
+  boost:
+    toolset: clang
+    address_model: 64
+
+  #file format packages
+  hdf5:
+  netcdf4:
+  netcdf4cpp:
+
+  #now the rest
+  freetype:
+  matplotlib:
+  numpy:
+  python:
+    host: true
+    link: shared
+  qt:
+    toolset: unsupported/macx-clang
+    arch: x86_64
+  launcher:
+  paraview:

examples/paraview.linux.yaml

@@ -0,0 +1,60 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+# In the future, we'll provide better incorporation of
+# automatic environment detection.  For now, have a look
+# at the YAML files in the top-level directory and choose
+# the most *specific* file that matches your environment.
+
+extends:
+ - file: linux.yaml
+
+parameters:
+  HOST_MPICC: /usr/bin/mpicc
+  HOST_MPICXX: /usr/bin/mpic++
+  HOST_MPIF77: /usr/bin/mpif77
+  HOST_MPIF90: /usr/bin/mpif90
+  HOST_MPIEXEC: /usr/bin/mpiexec
+  HOST_CMAKE: /usr/local/bin/cmake
+  PATH: |
+    /usr/local/bin:/bin:/usr/sbin:/sbin:/usr/bin:
+  PROLOGUE: |
+    export CXX=/usr/bin/g++-4.8; export CC=/usr/bin/gcc-4.8; export C_INCLUDE_PATH=/usr/include/mpi/; export CPLUS_INCLUDE_PATH=/usr/include/mpi/;
+
+# The packages list specifies all the packages that you
+# require installed.  <#> will ensure that all packages
+# and their dependencies are installed when you build this
+# profile.
+
+packages:
+  blas:
+    use: host-blas
+  cmake:
+    use: host-cmake
+  mpi:
+    use: host-mpi
+  curl:
+  szip:
+  bzip2:
+  zlib:
+  libxml2:
+  png:
+  boost:
+    toolset: gcc
+    address_model: 64
+
+  #file format packages
+  hdf5:
+  netcdf4:
+  netcdf4cpp:
+
+  #now the rest
+  freetype:
+  matplotlib:
+  numpy:
+  python:
+    host: true
+    link: shared
+  qt:
+    arch: x86_64
+  launcher:
+  paraview:

pkgs/cmb.yaml

@@ -0,0 +1,25 @@
+extends: [cmake_package]
+dependencies:
+  build: [boost, png, qt, zlib, bzip2, gdal, hdf5,
+          mpi, netcdf4, netcdf4cpp, freetype,
+          python, numpy, matplotlib, libxml2,
+          paraview, remus, vxl, kml, molequeue, smtk, zmq, {{build_with}}]
+
+sources:
+- key: git:b24225a52187a124f5f83bdb7212d363f9254519
+  url: git://public.kitware.com/CMB.git
+
+build_stages:
+- name: configure
+  mode: override
+  extra: [
+          '-DCMAKE_C_COMPILER:FILEPATH={{HOST_MPICC}}',
+          '-DCMAKE_CXX_COMPILER:FILEPATH={{HOST_MPICXX}}',
+          '-DBUILD_SHARED_LIBS:BOOL=ON',
+          '-DBUILD_TESTING:BOOL=OFF',
+          '-DKML_DIR:PATH=${KML_DIR}',
+          '-DGDAL_DIR:PATH=${GDAL_DIR}',
+          '-DParaView_DIR:PATH=${PARAVIEW_DIR}',
+          '-DMoleQueue_DIR:PATH=${MOLEQUEUE_DIR}',
+          '-DCMAKE_CXX_FLAGS:STRING="${CPPFLAGS}"',
+          ]

pkgs/molequeue/header-fix.patch

@@ -0,0 +1,9 @@
+--- a/molequeue/transport/messageidmanager_p.cpp
++++ b/molequeue/transport/messageidmanager_p.cpp
+@@ -17,6 +17,7 @@
+ #include "messageidmanager_p.h"
+
+ #include "message.h"
++#include <stdlib.h>
+
+ namespace MoleQueue {

pkgs/molequeue/molequeue.yaml

@@ -0,0 +1,26 @@
+extends: [cmake_package]
+dependencies:
+  build: [qt]
+
+sources:
+- key: git:e545ee25b4b79d5bae9e1cd0515fccb39f44d19d
+  url: git://source.openchemistry.org/molequeue.git
+
+defaults:
+  # lib/cmake/molequeue/MoleQueueConfig.cmake contains hard-coded path
+  relocatable: false
+
+build_stages:
+- name: patch
+  before: configure
+  files: [header-fix.patch]
+  handler: bash
+  bash: |
+    patch -up1 < _hashdist/header-fix.patch
+
+- name: configure
+  mode: override
+  extra: ['-DBUILD_SHARED_LIBS:BOOL=ON',
+          '-DCMAKE_BUILD_TYPE:STRING=Release',
+          '-DENABLE_TESTING:BOOL=OFF'
+          ]

pkgs/paraview/findnetcdf.patch

@@ -0,0 +1,66 @@
+--- a/VTK/CMake/FindNetCDF.cmake
++++ b/VTK/CMake/FindNetCDF.cmake
+@@ -38,17 +38,26 @@ if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
+   set (NETCDF_FIND_QUIETLY TRUE)
+ endif ()
+
++set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
++if(NETCDF_USE_DEFAULT_PATHS)
++  set(USE_DEFAULT_PATHS "")
++endif()
++
+ find_path (NETCDF_INCLUDE_DIR netcdf.h
+-  HINTS NETCDF_DIR ENV NETCDF_DIR)
++  HINTS "${NETCDF_DIR}/include")
+ mark_as_advanced (NETCDF_INCLUDE_DIR)
+ set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
+
+-find_library (NETCDF_LIBRARY NAMES netcdf)
++find_library (NETCDF_LIBRARY NAMES netcdf
++  HINTS "${NETCDF_DIR}/lib")
+ mark_as_advanced (NETCDF_LIBRARY)
++
+ set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
+
+ #start finding requested language components
+ set (NetCDF_libs "")
++set (netCDF_includes "${NETCDF_INCLUDE_DIR}")
++
+ get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
+ set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
+
+@@ -56,9 +65,15 @@ macro (NetCDF_check_interface lang header libs)
+   if (NETCDF_${lang})
+     #search starting from user modifiable cache var
+     find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
+-      HINTS "${NETCDF_INCLUDE_DIR}" NO_DEFAULT_PATH)
++      HINTS "${NETCDF_INCLUDE_DIR}"
++      HINTS "${NETCDF_${lang}_ROOT}/include"
++      ${USE_DEFAULT_PATHS})
++
+     find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
+-      HINTS "${NetCDF_lib_dirs}" NO_DEFAULT_PATH)
++      HINTS "${NetCDF_lib_dirs}"
++      HINTS "${NETCDF_${lang}_ROOT}/lib"
++      ${USE_DEFAULT_PATHS})
++
+     mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
+
+     #export to internal varS that rest of project can use directly
+@@ -67,6 +82,7 @@ macro (NetCDF_check_interface lang header libs)
+
+     if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
+       list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
++      list (APPEND netCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
+     else ()
+       set (NETCDF_HAS_INTERFACES "NO")
+       message (STATUS "Failed to find NetCDF interface for ${lang}")
+@@ -93,7 +109,7 @@ NetCDF_check_interface (F90 netcdf.mod  netcdff)
+ #export accumulated results to internal varS that rest of project can depend on
+ list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
+ set (NETCDF_LIBRARIES ${NetCDF_libs})
+-set (NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
++set (NETCDF_INCLUDE_DIRS ${netCDF_includes})
+
+ # handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
+ # all listed variables are TRUE