Merge branch 'master' into discontinuous-galerkin

.github/workflows/build_external_lib.yml

@@ -28,13 +28,20 @@ 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 libnetcdf-dev libhdf5-dev libcgns-dev libmatio-dev libfmt-dev catch2
+        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 libnetcdf-dev libhdf5-dev libcgns-dev libmatio-dev
+
+      - name: Install Using linuxbrew
+        shell: bash -l {0}
+        run: |
+          eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
+          brew install fmt catch2
 
       - name: Run cmake
         shell: bash -l {0}
         run: |
           echo $HOME
           find /usr/include -name cgnslib.h
+          eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
           mkdir build
           cd build
           NETCDF_PATH=/usr MODERN=YES NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME} bash ../cmake-config

.github/workflows/intel-build.yml

@@ -149,13 +149,15 @@ jobs:
           mkdir build
           cd build
           source /opt/intel/oneapi/setvars.sh
-          echo "------------"
-          ls /opt/intel/oneapi/2024.0/
-          echo "------------"
-          ls /opt/intel/oneapi/2024.0/bin/
-          echo "------------"
-          export PATH=/opt/intel/oneapi/2024.0/bin/:$PATH
-          export LD_LIBRARY_PATH=/opt/intel/oneapi/2024.0/lib/:$LD_LIBRARY_PATH
+          # echo "------------"
+          # ls /opt/intel/oneapi/
+          # echo "------------"
+          # ls /opt/intel/oneapi/2024.1/
+          # echo "------------"
+          # ls /opt/intel/oneapi/2024.1/bin/
+          # echo "------------"
+          export PATH=/opt/intel/oneapi/2024.1/bin/:$PATH
+          export LD_LIBRARY_PATH=/opt/intel/oneapi/2024.1/lib/:$LD_LIBRARY_PATH
           printenv >> $GITHUB_ENV
           NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config
 

.github/workflows/spack.yml

@@ -0,0 +1,35 @@
+# This is a basic workflow to help you get started with Actions
+name: SEACAS Spack build
+
+# Controls when the action will run. Triggers the workflow on push
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+    branches:
+    - master
+
+concurrency:  
+  group: ${{ github.workflow}}-${{ github.head_ref }}  
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    steps:
+    - name: Set up Spack
+      uses: spack/setup-spack@v2
+      with:
+        ref: develop      # Spack version (examples: develop, releases/v0.21)
+        buildcache: true  # Configure oci://ghcr.io/spack/github-actions-buildcache
+        color: true       # Force color output (SPACK_COLOR=always)
+        path: spack       # Where to clone Spack
+    - run: |
+       spack external find
+       spack compiler find
+       spack spec seacas~mpi
+       spack install seacas~mpi
+       spack find
+       # spack spec seacas+mpi
+       # spack install seacas+mpi

README.md

@@ -78,6 +78,7 @@ manually as detailed in
 | KOKKOS          | YES, NO | NO  | Should Kokkos TPL be built. |
 | GNU_PARALLEL    | YES, NO | YES | Should GNU parallel script be built. |
 | FMT             | YES, NO | YES | Should Lib::FMT TPL be built. |
+| CATCH2          | YES, NO | YES | Should Catch2 be built (used for testing). |
 | H5VERSION       | V114, V110, V18 | V114 | Use HDF5-1.14.X, HDF5-1.10.X or HDF5-1.8.X |
 | H5CPP           | YES, NO | NO  | Should the HDF5 C++ library be built/installed |
 | BB              | YES, NO | NO  | Enable Burst Buffer support in PnetCDF |
@@ -230,23 +231,37 @@ add_executable(ExodusReadFor ExodusRead.f)
 target_link_libraries(ExodusReadFor PRIVATE SEACASExodus_for::all_libs)
 ```
 
-The `cmake-use-example` directory contains this sample
-`CMakeLists.txt` file and a couple C and Fortran files which provide
-an example of how to build and link a C or Fortran program with the
-Exodus library installed as part of a build of this package.
+A similar CMakeLists.txt file for using the IOSS library would be something like:
+
+```sh
+cmake_minimum_required(VERSION 3.1...3.26)
+project(IossCMakeExample VERSION 1.0 LANGUAGES CXX)
+
+#### C++ IOSS ####
+find_package(SEACASIoss CONFIG)
+add_executable(IossExample IossExample.C)
+target_link_libraries(IossExample PRIVATE SEACASIoss::all_libs)
+```
+
+The `cmake-use-example` directory contains Exodus example files in the
+`exodus` subdirectory and Ioss example files in the `ioss` subdirectory.
+These provide short examples of how to build and link a program with the 
+Exodus and/or Ioss libraries.
 
 To use this, copy the contents of the directory to your own filespace
-and modify the contents as needed.  The example provides a C
-executable and a Fortran Executable which both are linked to the
-Exodus library.
+and modify the contents as needed.  
 
 To configure and build, you would do something like:
+
 ```sh
   mkdir build; cd build
   CMAKE_PREFIX_PATH={path_to_root_of_seacas_install} cmake ..
   make
 ```
-And you would then get `ExodusWriteC` and `ExodusReadFor` compiled and linked against the Exodus library.
+
+And you would then get an executable (`ExodusWriteC` and
+`ExodusReadFor` for Exodus, `IossExample` for Ioss) compiled and linked
+against the Exodus and/or Ioss libraries.
 
 ## Required Software
 
@@ -323,7 +338,6 @@ a separate license:
 | [adler hash](https://en.wikipedia.org/wiki/Adler-32)	| `packages/seacas/libraries/suplib_c/adler.c` | [zlib](https://opensource.org/licenses/zlib) |
 | [MurmurHash](https://github.com/aappleby/smhasher) | `packages/seacas/libraries/ioss/src/Ioss_FaceGenerator.C` | public domain |
 | [json include file](http://jsoncpp.sourceforge.net) | `packages/seacas/libraries/ioss/src/visualization/` | [MIT](https://opensource.org/licenses/MIT) |
-| [terminal_color](https://github.com/matovitch/trmclr) | `packages/seacas/libraries/aprepro_lib` | [zlib](https://opensource.org/licenses/zlib) |
 | [Tessil Hash](https://github.com/Tessil/) | `packages/seacas/libraries/ioss/src/hash` |  [MIT](https://opensource.org/licenses/MIT) |
 | [pdqsort](https://github.com/orlp/pdqsort) | `packages/seacas/libraries/ioss/src` | [Zlib License](https://github.com/orlp/pdqsort/blob/master/license.txt) |
 ## Contact information

TPL/catalyst2/runcmake.sh

@@ -60,6 +60,7 @@ ${RPATH} \
 -D CATALYST_BUILD_STUB_IMPLEMENTATION:BOOL=ON \
 -D CATALYST_USE_MPI:BOOL=${MPI} \
 -D CATALYST_BUILD_TESTING:BOOL=OFF \
+-D CATALYST_WRAP_PYTHON:BOOL=OFF \
 $EXTRA_ARGS \
 ..
 

TPL/cgns/CGNS-Allow-more-liberal-version-matching.patch

@@ -0,0 +1,64 @@
+From 3c1871b84b24f14c3b5c6b99ead40c5aa2a0907e Mon Sep 17 00:00:00 2001
+From: Greg Sjaardema <[email protected]>
+Date: Fri, 5 Apr 2024 09:09:46 -0600
+Subject: [PATCH] CGNS: Allow more liberal version matching
+
+The main difference between CGNS-3.X and CGNS-4.X is the handling
+of polyhedral elements.  If the cgns file does not contain those
+elements, then the library should be able to read the file correctly.
+
+We have modified the library version from the original 4.4.X to
+be 3.99 so that files written by this version of the CGNS library
+(assuming they don't use polyhedral elements) will be readable by
+applications that are still using CGNS-3.X
+
+This is a kluge and not officially supported by the CGNS developers.
+---
+ src/cgnslib.c | 11 ++++++-----
+ src/cgnslib.h |  5 +++++
+ 2 files changed, 11 insertions(+), 5 deletions(-)
+
+diff --git a/src/cgnslib.c b/src/cgnslib.c
+index d60daf6..78bd25a 100644
+--- a/src/cgnslib.c
++++ b/src/cgnslib.c
+@@ -434,12 +434,13 @@ int cg_open(const char *filename, int mode, int *file_number)
+         /* This code allows reading version newer than the lib,
+                as long as the 1st digit of the versions are equal */
+             if ((cg->version / 1000) > (CGNSLibVersion / 1000)) {
+-                cgi_error("A more recent version of the CGNS library created the file. Therefore, the CGNS library needs updating before reading the file '%s'.",filename);
+-                return CG_ERROR;
+-            }
++	      cgi_warning("A more recent version of the CGNS library created the file. Assuming it is OK to read, but may have problems  (%d vs %d).",
++			  cg->version, CGNSLibVersion);
++            }
+             /* warn only if different in second digit */
+-            if ((cg->version / 100) > (CGNSLibVersion / 100)) {
+-                cgi_warning("The file being read is more recent that the CGNS library used");
++	    else if ((cg->version / 100) > (CGNSLibVersion / 100)) {
++	      cgi_warning("The file being read is more recent than the CGNS library used (%d vs %d).",
++			  cg->version, CGNSLibVersion);
+             }
+         }
+ #if CG_SIZEOF_SIZE == 32
+diff --git a/src/cgnslib.h b/src/cgnslib.h
+index 476c768..a4b66df 100644
+--- a/src/cgnslib.h
++++ b/src/cgnslib.h
+@@ -43,8 +43,13 @@
+ #ifndef CGNSLIB_H
+ #define CGNSLIB_H
+
++#if 0
+ #define CGNS_VERSION 4400
+ #define CGNS_DOTVERS 4.40
++#else
++#define CGNS_VERSION 3990
++#define CGNS_DOTVERS 3.99
++#endif
+
+ #define CGNS_COMPATVERSION 2540
+ #define CGNS_COMPATDOTVERS 2.54
+-- 
+2.39.3 (Apple Git-146)
+

cmake-config

@@ -544,7 +544,6 @@ ${FAODEL_SYMBOLS} \
 -D ParMETIS_ROOT:PATH=${PARMETIS_PATH} \
 -D PNetCDF_ROOT:PATH=${PNETCDF_PATH} \
 -D fmt_ROOT:PATH=${FMT_PATH} \
--D CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON \
 $EXTRA_ARGS \
 ${ACCESS}
 

cmake-use-example/CMakeLists.txt → cmake-use-example/exodus/CMakeLists.txt

@@ -16,7 +16,7 @@ add_executable(ExodusWriteC ExodusWrite.c)
 target_link_libraries(ExodusWriteC PRIVATE SEACASExodus::all_libs)
 
 
-#### FORTRAN #####
+#### FORTRAN ##### (Remove all below if only using Exodus C API)
 IF ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
   SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer -fdefault-real-8 -fdefault-integer-8 -fno-range-check")
 ELSEIF ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "XL")

cmake-use-example/ioss/CMakeLists.txt

@@ -0,0 +1,7 @@
+cmake_minimum_required(VERSION 3.1...3.26)
+project(IossCMakeExample VERSION 1.0 LANGUAGES CXX)
+
+#### C++ IOSS ####
+find_package(SEACASIoss CONFIG)
+add_executable(IossExample IossExample.C)
+target_link_libraries(IossExample PRIVATE SEACASIoss::all_libs)

cmake-use-example/ioss/IossExample.C

@@ -0,0 +1,43 @@
+#include <Ionit_Initializer.h>
+#include <Ioss_DatabaseIO.h>
+#include <Ioss_IOFactory.h>
+#include <Ioss_Region.h>
+#include <Ioss_Utils.h>
+
+#include <assert.h>
+#include <iostream>
+#include <string>
+
+int main(int argc, char *argv[]) {
+#ifdef SEACAS_HAVE_MPI
+  MPI_Init(&argc, &argv);
+  ON_BLOCK_EXIT(MPI_Finalize);
+#endif
+
+  if (argc == 1) {
+    std::cerr << "SYNTAX: " << argv[0]
+              << " '--show-config' or 'filename'\n"
+                 "        Will either show the Ioss build configuration\n"
+                 "        Or will show a summary of the data in `filename`\n";
+    std::exit(EXIT_SUCCESS);
+  }
+
+  Ioss::Init::Initializer io;
+  std::string filename = argv[1];
+  if (filename == "--show-config") {
+    std::cerr << Ioss::IOFactory::show_configuration() << "\n";
+  } else {
+    auto dbtype = Ioss::Utils::get_type_from_file(filename);
+    auto *dbi = Ioss::IOFactory::create(dbtype, filename, Ioss::READ_RESTART,
+                                        Ioss::ParallelUtils::comm_world());
+
+    if (dbi == NULL || !dbi->ok(true)) {
+      std::exit(EXIT_FAILURE);
+    }
+
+    // NOTE: 'region' owns 'dbi' pointer at this time and will close
+    // and call dbi destructor.
+    Ioss::Region region(dbi, "example_region");
+    region.output_summary(std::cerr);
+  }
+}

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.

cmake/tribits/README.DIRECTORY_CONTENTS.rst

@@ -22,9 +22,10 @@ TriBITS refactorings of TriBITS.
 
 .. _TriBITS Core:
 
-**core/**: Core TriBITS package-based architecture for CMake projects. This
-only depends on raw CMake and contains just the minimal support for building,
-testing, installing, and deployment.  Only depends on CMake and nothing else.
+**core/**: Core TriBITS test support and package-based architecture for CMake
+projects. This only depends on raw CMake and contains just the minimal support
+for building, testing, installing, and deployment.  This CMake code depends
+only on CMake and nothing else.
 
 **python_utils/**: Some basic Python utilities that are not specific to
 TriBITS but are used in TriBITS CI and testing support software.  There are
@@ -86,3 +87,49 @@ subdirectory. It supports the argument ``--components`` with values ``core``,
 * ``examples`` => (external tribits installation)
 * ``doc`` => ``core``, ``ci_support``, ``examples``
 * ``devtools_install`` => ``python_utils``
+
+
+TriBITS Core Directory Contents
+...............................
+
+The TriBITS ``core/`` directory is broken down into several subdirectories of
+its own:
+
+**core/utils**: General CMake utilities that are not specific to the TriBITS
+system and can be reused in any CMake project.
+
+**core/common**: As small set of common modules that the different TriBITS
+Core module files in different directories depend on.  These include things
+like common TriBITS constants and TriBITS CMake policies.
+
+**core/test_support**: Modules that help define CTest tests using functions
+like `tribits_add_test()`_ and `tribits_add_advanced_test()`_.  These can be
+used in CMake projects that are not full-blown TriBITS projects.
+
+**core/config_tests**: Some basic configure-time tests used by the TriBITS
+package architecture framework.
+
+**core/std_tpls**: Some ``Find<tplName>.cmake`` files for key external
+dependencies handled as TriBITS TPLs but are more central to the TriBITS
+system.  (Examples include CUDA and MPI support.)
+
+**core/installation**: A collection of ``*.cmake.in`` and related Cmake code
+supporting installations.
+
+**core/package_arch**: Modules for the full-blown TriBITS package architecture
+framework including package dependency management, multi-repository support,
+installations (including the generation of ``<Package>Config.cmake`` files),
+etc.
+
+The dependencies between these different TriBITS `core` subdirectories are:
+
+* ``core/utils`` => (external CMake)
+* ``core/common`` => ``core/utils``
+* ``core/test_support`` =>   ``core/utils``, ``core/common``
+* ``core/config_tests`` => (external CMake)
+* ``core/std_tpls`` => (external CMake)
+* ``core/installation`` <=> ``core/package_arch`` (bidirectional)
+* ``core/package_arch`` => ``core/utils``, ``core/common``,
+  ``core/test_support``, ``core/config_tests``, ``core/std_tpls``,
+  ``core/installation``
+