update uberenv and related configs (#1164)

* wip: update uberenv and related configs

* add missing file

* update to use ub with fix

* fix editor undermine

* recipe woes, try newer spack (bleeding edge)

* avoid system hdf5

* fix for mult externals

* build the world

* no more python 2 :-( back to spack v0.21.0 release

* fix for more complex specs

* try python view path fix

* updates

* path fix

* spack build mpi is sad

* typo

* fix

* one bite at a time

* docker recipe fix

* python path fix needed for standalone

* ...

* docker use spack env file (spack built mpi does not work)

* ub env use external lapack

* yaml vs cyrus

* docs updates

* more docs updates

* fix config

* side quest to get docs working

* upate

* different strategy

* add new cfg

* heal rtd settings

* updates

* update uberenv

* fix ci test python path loc

* more path adj

* more fun

.readthedocs.yaml

@@ -18,3 +18,4 @@ sphinx:
 python:
   install:
     - requirements: src/docs/sphinx/requirements.txt
+

.uberenv_config.json

@@ -5,24 +5,12 @@
 "spack_build_mode" : "uberenv-pkg",
 "spack_configs_path": "scripts/uberenv_configs/spack_configs",
 "spack_packages_path": "scripts/uberenv_configs/packages",
+"spack_skip_externals": "true",
 "spack_url": "https://github.com/spack/spack",
-"spack_commit": "6983d520fa64d8c7343dcc627197b0e6c621d1a6",
-"spack_activate" : {"py-numpy" : ["+python"], 
-                    "py-sphinx": ["+python","+doc"],
-                    "py-docutils": ["+python","+doc"],
-                    "py-pygments": ["+python","+doc"],
-                    "py-babel": ["+python","+doc"],
-                    "py-jinja2": ["+python","+doc"],
-                    "py-packaging": ["+python","+doc"],
-                    "py-snowballstemmer": ["+python","+doc"],
-                    "py-imagesize": ["+python","+doc"],
-                    "py-sphinxcontrib-htmlhelp": ["+python","+doc"],
-                    "py-sphinxcontrib-serializinghtml": ["+python","+doc"],
-                    "py-sphinxcontrib-applehelp": ["+python","+doc"],
-                    "py-sphinxcontrib-devhelp": ["+python","+doc"],
-                    "py-sphinxcontrib-qthelp": ["+python","+doc"],
-                    "py-alabaster": ["+python","+doc"],
-                    "py-requests": ["+python","+doc"],
-                    "py-mpi4py" : ["+python", "+mpi"],
-                    "py-sphinx-rtd-theme": ["+python","+doc"] }
+"spack_commit": "6812713cf470b473a607f0de0e8e1cf53f804fb7",
+"spack_host_config_patches":
+ {
+   "PYTHON_EXECUTABLE": "spack_view/bin/python3",
+   "SPHINX_EXECUTABLE": "spack_view/bin/sphinx-build"
+ }
 }

azure-pipelines.yml

@@ -79,40 +79,11 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: OFF
           ENABLE_PYTHON: OFF
-          ENABLE_PYTHON2: OFF
           CMAKE_VERSION: 3.14.2
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
 
-        ub_18_shared_py27_cmake_3_14:
-          containerImage: ${{ variables.ubuntu_18_tag }}
-          COMPILER_CC: gcc
-          COMPILER_CXX: g++
-          COMPILER_FC: gfortran
-          COMPILER_SPEC: gcc
-          FORCE_COMPILERS: OFF
-          BUILD_SHARED_LIBS: ON
-          CMAKE_BUILD_TYPE: Debug
-          ENABLE_COVERAGE: ON
-          ENABLE_MPI: ON
-          ENABLE_DOCS: OFF
-          ENABLE_RELAY_WEBSERVER: ON
-          ENABLE_OPENMP: ON
-          ENABLE_HDF5: ON
-          ENABLE_HDF5_COMPAT: ON
-          HDF5_SPEC: "hdf5~mpi"
-          ENABLE_SILO: ON
-          ENABLE_ADIOS: OFF
-          ENABLE_PYTHON: ON
-          ENABLE_PARMETIS: ON
-          ENABLE_PYTHON2: ON
-          PYTHON2_CONSTRAINTS: " ^[email protected] ^[email protected]"
-          PYTHON_VERSION: 2.7.18
-          CMAKE_VERSION: 3.14.2
-          BLT_CXX_STD: c++11
-          BLT_ENABLE_FIND_MPI: ON
-
-        ub_18_static_py27_cmake_3_14:
+        ub_18_static_py37_cmake_3_14:
           containerImage: ${{ variables.ubuntu_18_tag }}
           COMPILER_CC: gcc
           COMPILER_CXX: g++
@@ -133,9 +104,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: ON
-          PYTHON2_CONSTRAINTS: " ^[email protected] ^[email protected]"
-          PYTHON_VERSION: 2.7.18
+          PYTHON_VERSION: 3.7.16
           CMAKE_VERSION: 3.14.2
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -161,8 +130,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.7.6
+          PYTHON_VERSION: 3.7.16
           CMAKE_VERSION: 3.14.2
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -188,8 +156,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.8.8
+          PYTHON_VERSION: 3.8.16
           CMAKE_VERSION: 3.21.1
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -215,8 +182,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.8.8
+          PYTHON_VERSION: 3.8.16
           CMAKE_VERSION: 3.21.1
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -244,8 +210,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.8.8
+          PYTHON_VERSION: 3.8.16
           CMAKE_VERSION: 3.20.0
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -273,8 +238,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.10.6
+          PYTHON_VERSION: 3.10.10
           CMAKE_VERSION: 3.24.2
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -302,8 +266,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.10.6
+          PYTHON_VERSION: 3.10.10
           CMAKE_VERSION: 3.26.0
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -332,7 +295,6 @@ stages:
         #   ENABLE_ADIOS: OFF
         #   ENABLE_PARMETIS: ON
         #   ENABLE_PYTHON: ON
-        #   ENABLE_PYTHON2: OFF
         #   PYTHON_VERSION: 3.11.2
         #   CMAKE_VERSION: 3.26.0
         #   BLT_CXX_STD: c++11
@@ -383,8 +345,7 @@ stages:
           ENABLE_ADIOS: OFF
           ENABLE_PARMETIS: ON
           ENABLE_PYTHON: ON
-          ENABLE_PYTHON2: OFF
-          PYTHON_VERSION: 3.8.8
+          PYTHON_VERSION: 3.8.16
           CMAKE_VERSION: 3.21.1
           BLT_CXX_STD: c++11
           BLT_ENABLE_FIND_MPI: ON
@@ -443,7 +404,6 @@ stages:
            export SPACK_SPEC="${SPACK_SPEC} ^cmake@${CMAKE_VERSION}"
            # python constraints
            if [ $ENABLE_PYTHON = 'ON' ]; then export SPACK_SPEC="${SPACK_SPEC} ^python@${PYTHON_VERSION}"; fi
-           if [ $ENABLE_PYTHON2 = 'ON' ]; then export SPACK_SPEC="${SPACK_SPEC} ${PYTHON2_CONSTRAINTS}"; fi
            # hdf5 constraints
            if [ $ENABLE_HDF5 = 'ON' ]; then export SPACK_SPEC="${SPACK_SPEC} ^${HDF5_SPEC}"; fi
            # silo constraints
@@ -452,7 +412,7 @@ stages:
            echo "SPACK SPEC:"
            echo $SPACK_SPEC
            # run uber to build tpls
-           python3 scripts/uberenv/uberenv.py -k --spack-allow-deprecated --spec "${SPACK_SPEC}" --spack-config-dir=scripts/uberenv_configs/spack_configs/configs/alpinedav/ubuntu_18.04_devel/
+           python3 scripts/uberenv/uberenv.py -k --spec "${SPACK_SPEC}" --spack-env-file=scripts/uberenv_configs/spack_configs/envs/alpinedav-ubuntu_18.04_devel/spack.yaml
         displayName: 'Spack Build Tpls'
 
       - script: |
@@ -467,25 +427,22 @@ stages:
            # capture current path
            export ROOT_DIR=`pwd`
            # find spack generated host config file
-           export HOST_CONFIG=`ls ${ROOT_DIR}/uberenv_libs/*.cmake`
+           export HOST_CONFIG=`ls ${ROOT_DIR}/uberenv_libs/*-patch.cmake`
            echo $HOST_CONFIG
            # find spack installed cmake
            export CMAKE_BIN_DIR=`ls -d ${ROOT_DIR}/uberenv_libs/spack/opt/spack/*/*/cmake*/bin`
            export PATH=${CMAKE_BIN_DIR}:$PATH
            echo $PATH
            which cmake
            cmake --version
-           # prepare build dir
-           mkdir build
-           cd build
            # setup cmake options
            export CMAKE_OPTS="-C ${HOST_CONFIG}"
            export CMAKE_OPTS="${CMAKE_OPTS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}"
            export CMAKE_OPTS="${CMAKE_OPTS} -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}"
            export CMAKE_OPTS="${CMAKE_OPTS} -DENABLE_COVERAGE=${ENABLE_COVERAGE}"
            export CMAKE_OPTS="${CMAKE_OPTS} -DBLT_CXX_STD=${BLT_CXX_STD}"
            export CMAKE_OPTS="${CMAKE_OPTS} -DENABLE_FIND_MPI=${BLT_ENABLE_FIND_MPI}"
-           export CMAKE_OPTS="${CMAKE_OPTS} -DCMAKE_INSTALL_PREFIX=../install"
+           export CMAKE_OPTS="${CMAKE_OPTS} -DCMAKE_INSTALL_PREFIX=${ROOT_DIR}/install"
            # this is now getting set to the uberenv-pkg loc by spack, ignore for ci
            export CMAKE_OPTS="${CMAKE_OPTS} -DPYTHON_MODULE_INSTALL_PREFIX=IGNORE"
            if [ $FORCE_COMPILERS = 'ON' ]; then export CMAKE_OPTS="${CMAKE_OPTS} -DCMAKE_C_COMPILER=${COMPILER_CC}"; fi
@@ -495,7 +452,7 @@ stages:
            # configure
            echo "CMAKE OPTIONS:"
            echo ${CMAKE_OPTS}
-           cmake ${CMAKE_OPTS} ../src
+           cmake ${CMAKE_OPTS} -B build -S src
         displayName: 'Configure with CMake'
 
       - script: |
@@ -648,13 +605,20 @@ stages:
           ls -l
           # find spack installed cmake
           export ROOT_DIR=`pwd`
-          export CMAKE_BIN_DIR=`ls -d ${ROOT_DIR}/uberenv_libs/spack/opt/spack/*/*/cmake*/bin`
+          export CMAKE_BIN_DIR=`ls -d ${ROOT_DIR}/uberenv_libs/spack/opt/spack/*/*/cmake*/bin/`
           export PATH=${CMAKE_BIN_DIR}:$PATH
           echo $PATH
-          # find spack installed python
-          export PYTHON_EXE=`ls -d ${ROOT_DIR}/uberenv_libs/spack/opt/spack/*/*/python*/bin/python`
+          # find spack installed python (use spack view dir)
+          export PYTHON_EXE=`ls ${ROOT_DIR}/uberenv_libs/spack_view/bin/python3` 
           # add conduit module to python path
           export PYTHONPATH=${ROOT_DIR}/install/python-modules/
+          # NOTE:
+          #  also add spack's python view dir to python path env var
+          #  this wasn't needed with older spack. 
+          #  I think embedded linking logic is resolving symlinks and therefore
+          #  not using view layout that wires up dependent python modules
+          py_site_pkgs_dir=`ls -d ${ROOT_DIR}/uberenv_libs/spack_view/lib/python*/site-packages`
+          export PYTHONPATH=${PYTHONPATH}:${py_site_pkgs_dir}
           echo $PYTHONPATH
           # CI LD_LIB FIX
           # NOTE: