Stable/proteus

.travis.yml

@@ -48,7 +48,7 @@ before_install:
       sudo apt-get install cmake libopenmpi-dev python-dev libblas-dev liblapack-dev wget libboost-program-options1.48-dev libboost-filesystem1.48-dev libboost-serialization1.48-dev libboost-thread1.48-dev libboost-iostreams1.48-dev libboost-math1.48-dev libboost-timer1.48-dev libboost-chrono1.48-dev;
     fi
 install:
-  - git clone https://github.com/hashdist/hashdist
+  - git clone https://github.com/hashdist/hashdist -b cekees/add_bld_mirrors
   - export PATH=`pwd`/hashdist/bin:$PATH
 script:
   - cp tests/$TEST_PROFILE $TEST_PROFILE

adh-stack.yaml

@@ -0,0 +1,33 @@
+# 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: debian.yaml
+
+# 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:
+  cmake:
+  openssl:
+    use: host-openssl
+  python:
+    host: false
+    link: shared
+    build_with: |
+      bzip2, sqlite, openssl
+  blas:
+    use: openblas
+  lapack:
+    use: openblas-lapack
+  mpi:
+    use: mpich
+  parmetis:
+  sympy:
+  adh:

base/base_package.yaml

@@ -44,6 +44,12 @@ post_process:
       - "check-ignore=.*\\.pyc\\$"
       - "check-ignore=.*\\.pyo\\$"
 
+  - name: insert_location
+    when: relocatable !=  True
+    after: [default]
+    hit:
+      - insert-location
+
 profile_links:
   - when: platform == 'Cygwin'
     name: copy_dlls

base/cmake_package.py

@@ -33,8 +33,11 @@ def configure(ctx, stage_args):
     if stage_args['debug']:
         conf_lines.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
     else:
-        conf_lines.append('-DCMAKE_BUILD_TYPE:STRING=Release')
-
+       if stage_args['relwithdebinfo']:
+          conf_lines.append('-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo')
+       else:
+          conf_lines.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+
     if stage_args.get('empty_osx_deployment_target', False):
         conf_lines.append('-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=""')
 

base/cmake_package.yaml

@@ -15,6 +15,7 @@ build_stages:
   - name: configure
     after: setup_builddir
     debug: {{debug}}
+    relwithdebinfo: {{relwithdebinfo}}
 
   - name: make
     after: configure

cygwin.yaml

@@ -8,6 +8,7 @@ parameters:
   HOST_MPIF77: /usr/bin/mpif77
   HOST_MPIF90: /usr/bin/mpif90
   HOST_MPIEXEC: /usr/bin/mpiexec
+  HOST_JASPER_DIR: /usr
   HOST_CMAKE: /usr/bin/cmake
   HOST_PYTHON: /usr/bin/python
   HOST_PKG_CONFIG_EXECUTABLE: /usr/bin/pkgconfig

examples/adh-stack.yaml

@@ -0,0 +1,33 @@
+# 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: debian.yaml
+
+# 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:
+  cmake:
+  openssl:
+    use: host-openssl
+  python:
+    host: false
+    link: shared
+    build_with: |
+      bzip2, sqlite, openssl
+  blas:
+    use: openblas
+  lapack:
+    use: openblas-lapack
+  mpi:
+    use: mpich
+  parmetis:
+  sympy:
+  adh:

examples/proteus.Cygwin.yaml

@@ -32,7 +32,9 @@ packages:
   mpi4py:
   nose:
   hdf5:
-  ipython:
+  pygments:
+  tornado:
+  pyzmq:
   matplotlib:
   petsc:
     build_with: |

examples/proteus.Darwin.yaml → examples/proteus.darwin.yaml

@@ -5,13 +5,14 @@
 # at the YAML files in the top-level directory and choose
 # the most *specific* file that matches your environment.
 
+parameters:
+  airgap: True
+
 extends:
-- file: osx.yaml
+- file: osx_clt.yaml
 
-parameters:
-  fortran: true
 
-# The packages list specifies all the packages that you 
+# 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.
@@ -20,45 +21,66 @@ packages:
 
   launcher:
   cmake:
+  openjpeg:
+    version: '2.1'
   python:
     host: false
+    link: shared
     build_with: |
 
   blas:
     use: host-osx-framework-accelerate
+  lapack:
+    use: host-osx-framework-accelerate
   daetk:
   mpi:
-    use: mpich
+    use: openmpi
   mpi4py:
   nose:
   hdf5:
+  pygments:
+  tornado:
+  pyzmq:
+  parmetis:
   ipython:
   matplotlib:
   petsc:
+    version: 3.7.5
     build_with: |
-      parmetis      
+      parmetis, cmake, suitesparse
     download: |
       superlu, superlu_dist
     coptflags: -O2
     link: shared
     debug: false
+    disable_fortran: true
   petsc4py:
+    version: 3.7.0
     with_conf: true
   pillow:
   pytables:
+  scorec:
   sphinx:
-  superlu:
+  #superlu:
   sympy:
   tetgen:
   triangle:
   memory_profiler:
   ipdb:
   pip:
+  pexpect:
   doxygen:
-  scipy:
   netcdf4:
-  netcdf4f:
   netcdf4cpp:
   python-netcdf4:
   h5py:
   ode:
+  openblas:
+  jupyter:
+  functools:
+    use: host-functools
+  yaml:
+  pytest:
+  pytest-xdist:
+  boost:
+    toolset: darwin

examples/proteus.garnet.gnu.yaml

@@ -1,5 +1,4 @@
 # 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
@@ -15,6 +14,7 @@ extends:
 
 parameters:
   machine: CrayXE6
+  HOST_MATLAB: '/usr/local/applic/matlab/R2012b/bin/matlab'
   HOST_MPICC: cc
   HOST_MPICXX: CC
   HOST_MPIF77: ftn
@@ -23,27 +23,31 @@ parameters:
   PATH: |
     /usr/bin:/bin:/usr/sbin:/sbin
   PROLOGUE: |
-    source /opt/modules/default/init/bash; export MODULEPATH=/opt/cray/gem/modulefiles:/opt/cray/xt-asyncpe/default/modulefiles:/opt/modulefiles:/opt/cray/modulefiles:/cm/local/modulefiles:/cm/shared/modulefiles:/usr/local/modulefiles/COTS:/usr/local/modulefiles/unsupported; export MODULESHOME=/opt/modules/3.2.6.7; export MODULE_VERSION=3.2.6.7; export MODULE_VERSION_STACK=3.2.6.7; echo "unloading modules"; module unload PrgEnv-pgi; echo "loading modules"; module load PrgEnv-gnu/4.2.34; module load cray-mpich/6.0.0; module unload cray-libsci; module load acml/5.3.1; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
+    unset RCLOCAL_PRGENV; source /etc/bash.bashrc; source  /etc/bash.bashrc.local; module swap PrgEnv-cray PrgEnv-gnu; module load cray-mpich; module list; echo "setting default compilers"; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran; export F90=gfortran; export CPP=cpp;
   DYNAMIC_EXE_LINKER_FLAGS: -dynamic
 
 packages:
   launcher:
   cmake:
   python:
     host: false
+    link: shared
     build_with: |
       openssl,bzip2,sqlite
+    link: shared
   blas:
-    use: host-acml-blas
+    use: host-libsci-blas
   lapack:
-    use: host-acml-lapack
+    use: host-libsci-lapack
   daetk:
   mpi:
     use: host-mpi
   mpi4py:
   nose:
   hdf5:
-  ipython:
+  pygments:
+  tornado:
+  pyzmq:
   matplotlib:
   parmetis:
     without_check: true
@@ -64,12 +68,51 @@ packages:
   tetgen:
   triangle:
   memory_profiler:
-  scipy:
+#  boost:
+#    toolset: gcc
+#    address_model: 64
+#    build_with: |
+#      python
+#
+#  cgal:
+#  pycgal:
+  netcdf4:
   netcdf4f:
   python-netcdf4:
-  ipdb:
-  pip:
+  vapory:
+  jasper:
+  grib_api:
+  pyproj:
+  pygrib:
+  #adh:
+  #  link: shared  
+  stwave:  
+  scipy:
+#  ipython:
+#    sources:
+#      - key: git:68f6519cdfd23581ed7358fa1941ae1bbd76e5b3
+#        url: https://github.com/ellisonbg/ipython.git
+#
   h5py:
+  pydap:
+#  leafletwidget: 
+#    sources:
+#      - key: git:f9147c5b13a69b80bc28d3574f7ba6b2c576aed2
+#        url: https://github.com/erdc-cm/leafletwidget.git
+  geojson:
+  rdp:
+#  ipython-widgetmode:
+#  ipython-d3plot:
+#  ipython-gridwidget:
+#  shapely:
+#  rtree:
+#  matlab:
+#    use: host-matlab
+#  pymatbridge:
   ode:
+#  ipdb:
+  pip:
+  pexpect:
+  ipdb:
  # vtk:
  # pyvtk:

examples/proteus.linux2-scorec.yaml

@@ -0,0 +1,65 @@
+# 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: debian.yaml
+
+# 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:
+
+  launcher:
+  cmake:
+    use: host-cmake
+  python:
+    host: false
+    link: shared
+    build_with: |
+      bzip2, sqlite
+  blas:
+    use: host-blas
+  daetk:
+  mpi:
+    use: host-mpi
+  mpi4py:
+  nose:
+  hdf5:
+  ipython:
+  matplotlib:
+  petsc:
+    build_with: |
+      parmetis
+    download: |
+      hypre, blacs, scalapack, superlu, superlu_dist
+    coptflags: -O2
+    link: shared
+    debug: true
+  petsc4py:
+    with_conf: true
+  pytables:
+  scorec:
+  simmetrix:
+  sphinx:
+  superlu:
+  sympy:
+  tetgen:
+  triangle:
+  zoltan:
+    build_with: |
+      parmetis
+
+parameters:
+  HOST_MPI_DIR: /usr/local/mpich3/3.1.2-thread-multiple
+  HOST_CMAKE: /usr/local/cmake/latest/bin/cmake
+  HOST_SIMMETRIX_LIB: /net/common/meshSim/9.0-140816/lib/x64_rhel5_gcc41
+  HOST_SIMMETRIX_INCLUDE: /net/common/meshSim/9.0-140816/include
+  HOST_PYTHON: python
+  HOST_PKG_CONFIG_EXECUTABLE: pkg-config
+  PATH: /usr/bin:/bin:/usr/local/mpich3/3.1.2-thread-multiple/bin/