Conda recipes

README.md

@@ -38,3 +38,51 @@ You can now for example run the IPython Notebook as follows:
 ```
 ./default/bin/ipython notebook
 ```
+
+### Conda Python in Hashstack (experimental)
+
+The recipe for Python supports a conda based version of Python. Using
+a conda based version of Python allows using conda to install packages
+in the profile while in develop mode.
+
+
+#### Specifying the conda installation to use
+
+When using conda python, supply the path for the conda installation to
+use using the "conda_prefix" parameter. This should be the place where
+conda (anaconda or miniconda) was installed. The conda executable to use
+will be <conda-prefix>/bin/conda.
+
+
+#### Using the conda version of Python
+
+In your profile file use, use "conda: true" in the python package:
+
+```
+packages:
+  python:
+    conda: true
+	pyver: '2.7'
+```
+
+The pyver will be used to select which version of python to install
+(as would without conda). Supported versions for conda are 2.7, 3.3,
+3.4, 3.5 and 3.6.
+
+
+#### Installing conda packages inside your profile (in develop mode)
+
+Just use conda install with the '-p' parameter pointing to the profile
+in question.
+
+Bear in mind that conda automatically handles dependencies, and that
+conda might not be aware of software installed in your profile that
+has not been installed by conda.
+
+For example, to install NumPy into a profile linked as "default":
+
+```
+conda install -p default numpy
+```
+
+

base/conda_package.py

@@ -0,0 +1,15 @@
+from hashdist import build_stage
+import pprint
+@build_stage()
+def conda_install(ctx, stage_args):
+    """
+    Generates conda install line
+
+    Example::
+
+        - name: conda-install
+          pkgspec: the spec to use for conda
+    """
+    conda_path = ctx.parameters["conda_prefix"]
+    cmd_line = '%s/bin/conda install -y -q --copy -p "${ARTIFACT}" %s' %(conda_path, stage_args['pkgspec'])
+    return [cmd_line] 

base/conda_package.yaml

@@ -0,0 +1,10 @@
+# use a conda package
+
+extends: [ base_package ]
+
+dependencies:
+  build: [ conda ]
+
+build_stages:
+  - name: conda_install
+    after: prologue

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/conda-python.osx.yaml

@@ -0,0 +1,16 @@
+# This profile file controls your <#> (HashDist) build environment.
+
+
+extends:
+- file: osx.yaml
+
+
+parameters:
+# Specify the conda path to use. This should be the path to the conda script without
+# bin/conda
+  conda_prefix: /Users/FooBar/anaconda
+
+packages:
+  python:
+    conda: true
+    pyver: '2.7'

examples/proteus.garnet.gnu.yaml

@@ -98,7 +98,7 @@ packages:
 #  leafletwidget: 
 #    sources:
 #      - key: git:f9147c5b13a69b80bc28d3574f7ba6b2c576aed2
-#        url: https://github.com/erdc-cm/leafletwidget.git
+#        url: https://github.com/erdc/leafletwidget.git
   geojson:
   rdp:
 #  ipython-widgetmode:

pkgs/adh/adh.yaml

@@ -1,13 +1,20 @@
 extends: [cmake_package]
 
 dependencies:
-  build: [python,mpi,parmetis,umfpack3]
+  build: [python,mpi,parmetis,lapack,blas]
 
 sources:
-- url: https://github.com/cekees/adh.git
-  key: git:ab5024c569e8bac972d706a3d354e43cce319ac3
+- url: git@public.git.erdc.dren.mil:adh/adh.git
+  key: git:01f9fba7f6f95b77be3560cce8bfaa87f174431e
 
 build_stages:
+- name: fix_link
+  files:
+    - fix_link.patch
+  before: configure
+  handler: bash
+  bash: |
+    patch -p1 < _hashdist/fix_link.patch
 
 - name: setup_builddir
   after: prologue
@@ -29,7 +36,7 @@ build_stages:
     '-DPARMETIS_INCLUDE_DIR:PATH=${PARMETIS_DIR}/include',
     '-DPARMETIS_LIBRARY:FILEPATH=${PARMETIS_DIR}/lib/libparmetis.dylib',
     '-DMETIS_LIBRARY=${PARMETIS_DIR}/lib/libmetis.dylib',
-    '-DPACKAGE_UMFPACK:BOOL=True',
+    '-DPACKAGE_UMFPACK:BOOL=False',
     '-DUMFPACK_INCLUDE_DIR:PATH=${UMFPACK_INCLUDE}',
     '-DUMFPACK_VERSION:STRING=3',
     '-DUMFPACK_INT_SIZE:STRING=32',
@@ -42,14 +49,52 @@ build_stages:
   extra: [
     '-DCMAKE_C_COMPILER:FILEPATH=${MPICC}',
     '-DCMAKE_CXX_COMPILER:FILEPATH=${MPICXX}',
+    '-DCMAKE_INSTALL_PREFIX:PATH=${ARTIFACT}',
+    '-DCMAKE_VERBOSE_MAKEFILE:BOOL=True',
+    '-DCMAKE_EXE_LINKER_FLAGS:STRING="-L${PARMETIS_DIR}/lib -Wl,-rpath=${PARMETIS_DIR}/lib -L${OPENBLAS_DIR}/lib -lm -Wl,-rpath=${OPENBLAS_DIR}/lib"',
+    '-DUSE_MPI:BOOL=ON',
+    '-DPACKAGE_MPI:BOOL=ON',
+    '-DUSE_BLAS:BOOL=ON',
+    '-DUSE_LAPACK:BOOL=ON',
+    '-DBLAS_openblas_LIBRARY:FILEPATH=${OPENBLAS_DIR}/lib/libopenblas.so',
+    '-DUSE_PARMETIS:BOOL=ON',
+    '-DPACKAGE_PARMETIS:BOOL=ON',
+    '-DPARMETIS_INCLUDE_DIR:PATH=${PARMETIS_DIR}/include',
+    '-DPARMETIS_LIBRARY:FILEPATH=${PARMETIS_DIR}/lib/libparmetis.so',
+    '-DMETIS_LIBRARY=${PARMETIS_DIR}/lib/libmetis.so',
+    '-DUSE_SUPER_LIBRARY:BOOL=False',
+    '-DPACKAGE_UMFPACK:BOOL=False',
+    '-DUMFPACK_INCLUDE_DIR:PATH=${UMFPACK_INCLUDE}',
+    '-DUMFPACK_VERSION:STRING=3',
+    '-DUMFPACK_INT_SIZE:STRING=32',
+    '-DUMFPACK_LIBRARY:FILEPATH=${UMFPACK_LIBRARY}'
+    ]
+
+- when: machine == 'CrayXE6'
+  name: configure
+  mode: override
+  extra: [
+    '-DCMAKE_C_COMPILER:FILEPATH=${MPICC}',
+    '-DCMAKE_C_FLAGS:STRING="-fPIC"',
+    '-DCMAKE_C_FLAGS_DEBUG:STRING="-g -fPIC"',
+    '-DCMAKE_C_FLAGS_OPT:STRING="-03 -fPIC"',
+    '-DCMAKE_C_FLAGS_RELEASE:STRING="-O3 -fPIC"',
+    '-DCMAKE_CXX_COMPILER:FILEPATH=${MPICXX}',
+    '-DCMAKE_CXX_FLAGS:STRING="-fPIC"',
+    '-DCMAKE_CXX_FLAGS_DEBUG:STRING="-g -fPIC"',
+    '-DCMAKE_CXX_FLAGS_RELEASE:STRING="-O3 -fPIC"',
     '-DCMAKE_Fortran_COMPILER:FILEPATH=${MPIF90}',
+    '-DCMAKE_Fortran_FLAGS:STRING="-fPIC"',
+    '-DCMAKE_Fortran_FLAGS_DEBUG:STRING="-g -fPIC"',
+    '-DCMAKE_Fortran_FLAGS_RELEASE:STRING="-O3 -fPIC"',
     '-DCMAKE_INSTALL_PREFIX:PATH=${ARTIFACT}',
+    '-DCMAKE_EXE_LINKER_FLAGS:STRING="-static"',
     '-DPACKAGE_MPI:BOOL=True',
     '-DPACKAGE_PARMETIS:BOOL=True',
     '-DPARMETIS_INCLUDE_DIR:PATH=${PARMETIS_DIR}/include',
     '-DPARMETIS_LIBRARY:FILEPATH=${PARMETIS_DIR}/lib/libparmetis.so',
     '-DMETIS_LIBRARY=${PARMETIS_DIR}/lib/libmetis.so',
-    '-DPACKAGE_UMFPACK:BOOL=True',
+    '-DPACKAGE_UMFPACK:BOOL=False',
     '-DUMFPACK_INCLUDE_DIR:PATH=${UMFPACK_INCLUDE}',
     '-DUMFPACK_VERSION:STRING=3',
     '-DUMFPACK_INT_SIZE:STRING=32',
@@ -67,7 +112,7 @@ build_stages:
     '-DCMAKE_INSTALL_PREFIX:PATH=${ARTIFACT}',
     '-DPACKAGE_MPI:BOOL=True',
     '-DPACKAGE_PARMETIS:BOOL=False',
-    '-DPACKAGE_UMFPACK:BOOL=True',
+    '-DPACKAGE_UMFPACK:BOOL=False',
     '-DUMFPACK_INCLUDE_DIR:PATH=${UMFPACK_INCLUDE}',
     '-DUMFPACK_VERSION:STRING=3',
     '-DUMFPACK_INT_SIZE:STRING=32',