Merge branch 'master' into catalyst_api_2_structured_blocks

Conflicts:
	packages/seacas/libraries/ioss/src/catalyst/Iocatalyst_DatabaseIO.C

.github/workflows/build_variant.yml

@@ -28,7 +28,7 @@ jobs:
 
       - name: Install System dependencies
         shell: bash -l {0}
-        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev libboost-all-dev
 
         ###
         # Installing TPL
@@ -70,6 +70,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -84,6 +86,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -98,6 +102,8 @@ jobs:
             fortran: "NO",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -112,6 +118,8 @@ jobs:
             fortran: "NO",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -126,6 +134,8 @@ jobs:
             fortran: "NO",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -140,6 +150,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -154,6 +166,8 @@ jobs:
             fortran: "NO",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -168,6 +182,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "YES",
             extra: "",
@@ -182,6 +198,8 @@ jobs:
             fortran: "NO",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "APPLICATIONS=NO LEGACY=NO",
@@ -196,6 +214,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "YES",
             gtest: "YES",
             extra: "",
@@ -210,6 +230,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "YES",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "",
@@ -224,6 +246,8 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "NO",
             extra: "OMIT_DEPRECATED=YES",
@@ -238,18 +262,52 @@ jobs:
             fortran: "YES",
             use_kokkos: "NO",
             use_adios2: "NO",
+            use_faodel: "NO",
+            use_metis: "NO",
             use_catalyst2: "NO",
             gtest: "YES",
             extra: "MODERN=YES",
             sanitizer: "NO" # address, integer, thread, memory, undefined
           }
+        - {
+            name: "ADIOS2 enabled",
+            os: ubuntu-latest,
+            compiler: "mpi",
+            debug: "NO",
+            threadsafe: "NO",
+            fortran: "YES",
+            use_kokkos: "NO",
+            use_adios2: "YES",
+            use_faodel: "NO",
+            use_metis: "NO",
+            use_catalyst2: "NO",
+            gtest: "YES",
+            extra: "",
+            sanitizer: "NO" # address, integer, thread, memory, undefined
+          }
+        - {
+            name: "FAODEL and METIS enabled",
+            os: ubuntu-latest,
+            compiler: "mpi",
+            debug: "NO",
+            threadsafe: "NO",
+            fortran: "YES",
+            use_kokkos: "NO",
+            use_adios2: "NO",
+            use_faodel: "YES",
+            use_metis: "YES",
+            use_catalyst2: "NO",
+            gtest: "YES",
+            extra: "",
+            sanitizer: "NO" # address, integer, thread, memory, undefined
+          }
     steps:
 
       - uses: actions/checkout@v3
 
       - name: Install System dependencies
         shell: bash -l {0}
-        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev
+        run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev libboost-all-dev
 
       - name: Fetch TPL Cache
         id: cache-TPL
@@ -263,10 +321,10 @@ jobs:
         run: ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib
 
       - name: install additional TPL
-        if: ${{ matrix.config.use_kokkos == 'YES' || matrix.config.use_adios2 == 'YES' || matrix.config.gtest == 'YES' || matrix.config.use_catalyst == 'YES' }}
+        if: ${{ matrix.config.use_kokkos == 'YES' || matrix.config.use_adios2 == 'YES' || matrix.config.gtest == 'YES' || matrix.config.use_faodel == 'YES' || matrix.config.use_catalyst == 'YES' || matrix.config.use_metis == 'YES' }}
         run: |
           set -x
-          COMPILER=${{ matrix.config.compiler }} KOKKOS=${{ matrix.config.use_kokkos }} ADIOS2=${{ matrix.config.use_adios2 }} CATALYST2=${{ matrix.config.use_catalyst2 }} GNU_PARALLEL=OFF GTEST=${{ matrix.config.gtest }} INSTALL_PATH=${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh
+          COMPILER=${{ matrix.config.compiler }} KOKKOS=${{ matrix.config.use_kokkos }} ADIOS2=${{ matrix.config.use_adios2 }} CATALYST2=${{ matrix.config.use_catalyst2 }} FAODEL=${{ matrix.config.use_faodel }} METIS=${{ matrix.config.use_metis }} GNU_PARALLEL=OFF GTEST=${{ matrix.config.gtest }} INSTALL_PATH=${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh
           ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib
 
 ###

.github/workflows/cla.yml

@@ -3,33 +3,39 @@ on:
   pull_request_target:
     types: [opened,closed,synchronize]
 
+# explicitly configure permissions, in case your GITHUB_TOKEN workflow permissions are set to read-only in repository settings
+permissions:
+  actions: write
+  contents: write
+  pull-requests: write
+  statuses: write
+
 jobs:
-  CLAssistant:
+  CLAAssistant:
     runs-on: ubuntu-latest
     steps:
       - name: "CLA Assistant"
         if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target'
-        # Beta Release
-        uses: cla-assistant/[email protected]
+        uses: contributor-assistant/[email protected]
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # the below token should have repo scope and must be manually added by you in the repository's secret
-          PERSONAL_ACCESS_TOKEN : ${{ secrets.PERSONAL_ACCESS_TOKEN }}
+          # This token is required only if you have configured to store the signatures in a remote repository/organization
+          PERSONAL_ACCESS_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
         with:
           path-to-signatures: 'signatures/version1/cla.json'
           path-to-document: 'https://github.com/sandialabs/seacas/blob/master/SEACAS-CLA.md'
           # branch should not be protected
           branch: 'master'
           allowlist: user1,bot*,*@sandia.gov
 
-         #below are the optional inputs - If the optional inputs are not given, then default values will be taken
+         # the followings are the optional inputs - If the optional inputs are not given, then default values will be taken
           #remote-organization-name: enter the remote organization name where the signatures should be stored (Default is storing the signatures in the same repository)
-          #remote-repository-name:  enter the  remote repository name where the signatures should be stored (Default is storing the signatures in the same repository)
+          #remote-repository-name: enter the  remote repository name where the signatures should be stored (Default is storing the signatures in the same repository)
           #create-file-commit-message: 'For example: Creating file for storing CLA Signatures'
-          #signed-commit-message: 'For example: $contributorName has signed the CLA in #$pullRequestNo'
+          #signed-commit-message: 'For example: $contributorName has signed the CLA in $owner/$repo#$pullRequestNo'
           #custom-notsigned-prcomment: 'pull request comment with Introductory message to ask new contributors to sign'
           #custom-pr-sign-comment: 'The signature to be committed in order to sign the CLA'
           #custom-allsigned-prcomment: 'pull request comment when all contributors has signed, defaults to **CLA Assistant Lite bot** All Contributors have signed the CLA.'
           #lock-pullrequest-aftermerge: false - if you don't want this bot to automatically lock the pull request after merging (default - true)
           #use-dco-flag: true - If you are using DCO instead of CLA
-

.github/workflows/intel-build.yml

@@ -35,13 +35,12 @@ jobs:
         sudo apt-get update
     - name: install
       run: |
+        sudo apt-get install -y intel-basekit
         sudo apt-get install -y intel-oneapi-common-vars
         sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
         sudo apt-get install -y intel-oneapi-compiler-fortran
         sudo apt-get install -y intel-oneapi-mpi
         sudo apt-get install -y intel-oneapi-mpi-devel
-        sudo apt-get install -y intel-oneapi-mkl
-        sudo apt-get install -y ninja-build
 
     - name: Install System dependencies
       shell: bash -l {0}
@@ -90,13 +89,12 @@ jobs:
           sudo apt-get update
       - name: install
         run: |
+          sudo apt-get install -y intel-basekit
           sudo apt-get install -y intel-oneapi-common-vars
           sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
           sudo apt-get install -y intel-oneapi-compiler-fortran
           sudo apt-get install -y intel-oneapi-mpi
           sudo apt-get install -y intel-oneapi-mpi-devel
-          sudo apt-get install -y intel-oneapi-mkl
-          sudo apt-get install -y ninja-build
 
       - name: Install System dependencies
         shell: bash -l {0}

README.md

@@ -327,4 +327,4 @@ a separate license:
 | [pdqsort](https://github.com/orlp/pdqsort) | `packages/seacas/libraries/ioss/src` | [Zlib License](https://github.com/orlp/pdqsort/blob/master/license.txt) |
 ## Contact information
 
- Greg Sjaardema  (<[email protected]>, <[email protected]>)
+ Greg Sjaardema  (<[email protected]>, <[email protected]>)

TPL/adios2/runcmake.sh

@@ -28,11 +28,10 @@ ${RPATH} \
 -D CMAKE_INSTALL_PREFIX:PATH=${INSTALL_PATH} \
 -D CMAKE_INSTALL_LIBDIR:PATH=lib \
 -D ADIOS2_USE_MPI:BOOL=${MPI} \
+-D ADIOS2_HAVE_MPI:BOOL=${MPI} \
 -D ADIOS2_BUILD_EXAMPLES:BOOL=OFF \
--D ADIOS2_BUILD_TESTING:BOOL=OFF \
 -D INSTALL_GTEST:BOOL=OFF \
 -D ADIOS2_USE_Fortran:BOOL=OFF \
--D ADIOS_USE_Profiling=OFF \
 $EXTRA_ARGS \
 ..
 

TPL/faodel/runcmake.sh

@@ -6,14 +6,11 @@ if [ "X$ACCESS" == "X" ] ; then
   echo "ACCESS set to ${ACCESS}"
 fi
 INSTALL_PATH=${INSTALL_PATH:-${ACCESS}}
-
 . ${ACCESS}/TPL/compiler.sh
 
 if [ "X$BOOST_ROOT" == "X" ] ; then
-  BOOST_ROOT=$(cd ../../../..; pwd)
   echo "Faodel requires these Boost packages: atomic log log_setup serialization"
   echo "Please set BOOST_ROOT."
-  exit 0
 fi
 
 rm -f CMakeCache.txt
@@ -27,7 +24,7 @@ cmake ..                                 \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} \
   -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON \
   -DCMAKE_BUILD_TYPE=Release             \
-  -DBUILD_SHARED_LIBS:BOOL=OFF           \
+  -DBUILD_SHARED_LIBS:BOOL=ON            \
   -DGTEST_ROOT=${GTEST_ROOT}             \
   -DBOOST_ROOT=${BOOST_ROOT}             \
   -DFaodel_NETWORK_LIBRARY=nnti          \

TPL/netcdf/runcmake.sh

@@ -67,6 +67,8 @@ cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
          -DENABLE_MMAP:BOOL=ON \
          -DENABLE_DAP:BOOL=OFF \
          -DENABLE_V2_API:BOOL=OFF \
+	 -DENABLE_FILTER_TESTING:BOOL=OFF \
+	 -DENABLE_TESTS:BOOL=OFF \
          ${LOCAL_ZLIB} \
          ${LOCAL_SZIP} \
          ${EXTRA_DEPS} \

cmake-config

@@ -160,8 +160,8 @@ then
 
   if [ "$COMPILER" == "intel" ]
   then
-      CXX=icpx
-      CC=icx
+      CXX=icpc
+      CC=icc
       FC=ifort
       CFLAGS="-Wall -Wunused"
       CXXFLAGS="-Wall -Wextra  -Wunused"
@@ -382,6 +382,9 @@ then
 	LD_EXT="so"
     fi
 else
+# NOTE: Some systems may need `curl` added to Seacas_EXTRA_LINK_FLAGS`
+#       If you see missing symbols containing `_curl`, try adding `curl`
+#   EXTRA_LIB="-DSeacas_EXTRA_LINK_FLAGS=curl;z;dl -DSEACASExodus_ENABLE_SHARED:BOOL=OFF"
     EXTRA_LIB="-DSeacas_EXTRA_LINK_FLAGS=z;dl -DSEACASExodus_ENABLE_SHARED:BOOL=OFF"
     LD_EXT="a"
 fi

cmake/tribits/CHANGELOG.md

@@ -2,6 +2,43 @@
 ChangeLog for TriBITS
 ----------------------------------------
 
+## 2023-06-22:
+
+* **Added:** Packages are now determined to be missing if their dependencies
+  file `<packageDir>/cmake/Dependencies.cmake` is missing.  If the package
+  directory `<packageDir>` exists but the dependencies file is missing, the
+  package is determined to be missing but a warning is printed.  (This expands
+  behavior to gracefully deal with a situation where a package source
+  directory is only partially removed, such as with `git rm -r <packageDir>`,
+  but the base directory still exists.  Therefore, this allows the project to
+  gracefully configure with the package being considered missing and avoids a
+  fatal error in this case.)
+
+## 2023-06-02:
+
+* **Added/Deprecated:** External packages/TPLs can now be (and should be)
+  listed in the `[TEST|LIB]_[REQUIRED|OPTIONAL]_PACKAGES` arguments/lists in
+  the macro `tribits_package_define_dependencies()` and the
+  `[TEST|LIB]_[REQUIRED|OPTIONAL]_TPLS` arguments/lists are deprecated (but
+  with no deprecation warning yet).  This makes it easier to write
+  `<packageDir>/cmake/Dependencies.cmake` files for packages where the set of
+  internal and external upstream dependent packages is dynamic and changes
+  depending on the TriBITS project where these package are configured under.
+  (And conceptually, a downstream package should not care if an upstream
+  dependent package is pulled in as an external package or built as an
+  internal package.)
+
+## 2023-05-03:
+
+* **Added:** Added support for non-fully TriBITS-compatible external packages.
+  Now, a `<Package>Config.cmake` file need not define
+  `<UpstreamPkg>::all_libs` targets for all of its upstream dependencies.  The
+  updated macro `tribits_process_enabled_tpls()` will find any missing
+  upstream external packages/TPLs as needed (see updated documentation in the
+  section "TriBITS-Compliant External Packages" in the "TriBITS Users Guide"
+  and the section "Processing of external packages/TPLs and TriBITS-compliant
+  external packages" in the "TriBITS Maintainers Guide").
+
 ## 2023-02-24:
 
 * **Changed:** Upgraded minimum required CMake version from 3.17 to 3.23.