Merge pull request #201 from LLNL/bugfix/hdf5-lib

hdf5 lib issue

.github/workflows/test-tpls.yml

@@ -0,0 +1,37 @@
+name: Test external build.
+
+on:
+  pull_request:
+    paths:
+      - .uberenv_config.json
+      - scripts/spack/**
+      - scripts/devtools/**
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: llnl/spheral
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - name: Log into registry ${{ env.REGISTRY }}
+      if: github.event_name != 'pull_request'
+      uses: docker/login-action@v2
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: build env image
+      run: docker build --target spheral-build-env-local --tag spheral-build-env .
+
+    - name: build spheral image
+      run: docker build --target spheral --tag ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest --network none .
+

RELEASE_NOTES.md

@@ -10,20 +10,20 @@ This release contains ...
 Notable changes include:
 
   * New features/ API changes:
-    * New Discrete Element Model (DEM) physics package with linear-damped spring approach
+    * New Discrete Element Model (DEM) physics package with linear-damped spring approach.
     * Adding a CUDA smoke test that can be called from the Spheral python API.
     * NVCC / CUDA 11 gitlab-ci jobs.
     * ATS default filters for non-MPI, debug and CUDA builds are injected into spheral-atstest script.
-    * Latest Develop docker containers hosted on ghcr.io/llnl/spheral:latest
+    * Latest Develop docker containers hosted on ghcr.io/llnl/spheral:latest.
     * External / offline builds are tested through github actions.
-    * New polyhedral gravity solver
-    * Improved DEM timestep choice, so that points that do not overlap do not overly constrain the timestep
-    * Point potential gravity solver can now have non-unit metrics
-    * Pair-max damage algorithm now decouples points in different NodeLists or with different fragmentIDs
-    * Added direct support for FacetedVolumes to FileIO interface
-    * ANEOS now allows shallow copies to be made
-    * Polyhedron contain method can now optionally use Axom methods to test for containment
-    * Adding user specified functions for shear modulus and yield strength as a function of damage    
+    * New polyhedral gravity solver.
+    * Improved DEM timestep choice, so that points that do not overlap do not overly constrain the timestep.
+    * Point potential gravity solver can now have non-unit metrics.
+    * Pair-max damage algorithm now decouples points in different NodeLists or with different fragmentIDs.
+    * Added direct support for FacetedVolumes to FileIO interface.
+    * ANEOS now allows shallow copies to be made.
+    * Polyhedron contain method can now optionally use Axom methods to test for containment.
+    * Adding user specified functions for shear modulus and yield strength as a function of damage.
 
   * Build changes / improvements:
     * The C++ library interface is compiled into a single Spheral_CXX library. 
@@ -32,19 +32,20 @@ Notable changes include:
     * Eigen bumped to 3.4.0 for NVCC compatiblity.
     * C++ flag suppression is gaurded with build time CMake generators to only apply to C++ compilers.
     * Python runtime libraries are now managed through Spack / tpl-manager.
-    * Added ENABLE_NAN_EXCEPTIONS (default OFF) Cmake flag to raise an exception when a NAN occurs (Gnu only)
-    * Byte-compiling python installed in virtual spheral environment
-    * Invoking spheral no longer byte-compiles Python imported in a spheral script
+    * Added ENABLE_NAN_EXCEPTIONS (default OFF) Cmake flag to raise an exception when a NAN occurs (Gnu only).
+    * Byte-compiling python installed in virtual spheral environment.
+    * Invoking spheral no longer byte-compiles Python imported in a spheral script.
+    * HDF5 links as a shared library. Static lib usage can be forced with ENABLE_STATIC_TPL.
 
   * Bug Fixes / improvements:
     * spheral-atstest scripts always point to locally installed ATS instance.
     * gitlab-ci report-results script for analyzing ATS CI runs.
     * Support for offline Spheral builds (provided TPLs are installed).
-    * Fixes for restarting without regenerating the original node positions in the Python script
-    * Protected from division by zero in DEM when points coincide
-    * Corrected support for minimum pressure (intact and damaged) with porous materials
-    * Removed term driving damaged material to the reference density in solid hydros
-    * Added verbose flag to EquationOfState::specificThermalEnergyForPressure so users can see how the iterative search proceeds
+    * Fixes for restarting without regenerating the original node positions in the Python script.
+    * Protected from division by zero in DEM when points coincide.
+    * Corrected support for minimum pressure (intact and damaged) with porous materials.
+    * Removed term driving damaged material to the reference density in solid hydros.
+    * Added verbose flag to EquationOfState::specificThermalEnergyForPressure so users can see how the iterative search proceeds.
 
 Version v2022.06.1 -- Release date 2022-06-24
 =============================================

cmake/spheral/SpheralAddLibs.cmake

@@ -113,7 +113,7 @@ function(spheral_add_cxx_library
 
   # Set the r-path of the C++ lib such that it is independent of the build dir when installed
   set_target_properties(Spheral_${package_name} PROPERTIES
-                        INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib"
+                        INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${hdf5_DIR}/lib"
                         )
 endfunction()
 
@@ -161,7 +161,7 @@ function(spheral_add_pybind11_library package_name)
 
   # Set the r-path of the C++ lib such that it is independent of the build dir when installed
   set_target_properties(${MODULE_NAME} PROPERTIES
-                        INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${python_DIR}/lib"
+    INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${python_DIR}/lib;${hdf5_DIR}/lib"
                         )
 
 endfunction()

cmake/tpl/hdf5.cmake

@@ -1 +1,5 @@
-set(${lib_name}_libs libhdf5.a libhdf5_hl.a)
+set(${lib_name}_libs libhdf5.so libhdf5_hl.so)
+
+if(ENABLE_STATIC_TPL)
+  string(REPLACE ".so" ".a;" ${lib_name}_libs ${${lib_name}_libs})
+endif()

docs/build_guide/include/appendecies/cmake_config.rst.inc

@@ -83,6 +83,9 @@ In this section we list the CMake variables that can be tweaked for a Spheral bu
 ``<TPL-Name-Here>_DIR``
   Directory of previously built TPL.
 
+``ENABLE_STATIC_TPL`` (On, *Off*)
+  Link static libraries instead of shared for HDF5 and Conduit.
+
 ``ENABLE_OPENMP`` (*On*, Off)
   Support for OpenMP.
 

scripts/devtools/tpl-manager.py

@@ -35,6 +35,9 @@ def parse_args():
   parser.add_argument('--upstream-dir', type=str, default=default_upstream_dir,
       help='Dir of upstream spack installation.')
 
+  parser.add_argument('--no-upstream', action="store_true",
+      help='Do not use an upstream spack instance.')
+
   parser.add_argument('--spack-url', type=str, default="",
       help='URL of spack to use.')
 
@@ -96,7 +99,7 @@ def build_deps(args):
     spack_config_dir_opt="--spack-config-dir={0}".format(os.path.join(project_dir, "scripts/spack/configs/x86_64"))
 
   spack_upstream_opt=""
-  if os.path.isdir(args.upstream_dir):
+  if os.path.isdir(args.upstream_dir) and not args.no_upstream:
     spack_upstream_opt="--upstream {0}".format(args.upstream_dir)
 
   uberenv_spack_url_opt=""

scripts/spack/packages/spheral/package.py

@@ -7,7 +7,7 @@
 import socket
 import os
 
-class Spheral(CachedCMakePackage, CudaPackage, PythonPackage):
+class Spheral(CachedCMakePackage, CudaPackage):
     """Spheral++ provides a steerable parallel environment for performing coupled hydrodynamical and gravitational numerical simulations."""
 
     homepage = "https://spheral.readthedocs.io/"
@@ -44,14 +44,14 @@ class Spheral(CachedCMakePackage, CudaPackage, PythonPackage):
     depends_on('m-aneos')
     depends_on('py-polyclipper')
     depends_on('[email protected]', type='build')
-    depends_on('[email protected] ~shared ~mpi +hl', type='build', when='~mpi')
-    depends_on('[email protected] ~shared +mpi +hl', type='build', when='+mpi')
+    depends_on('[email protected] ~mpi +hl', type='build', when='~mpi')
+    depends_on('[email protected] +mpi +hl', type='build', when='+mpi')
 
     depends_on('[email protected] +hdf5', type='build')
 
     # Zlib fix has been merged into conduit, using develop until next release.
-    depends_on('[email protected] +shared +mpi +hdf5 -test', type='build', when='+mpi')
-    depends_on('[email protected] +shared ~mpi +hdf5 -test', type='build', when='~mpi')
+    depends_on('[email protected] +shared +mpi +hdf5 -test ~parmetis', type='build', when='+mpi')
+    depends_on('[email protected] +shared ~mpi +hdf5 -test ~parmetis', type='build', when='~mpi')
 
     depends_on('[email protected] ~shared +mpi +hdf5 -lua -examples -python -fortran -umpire -raja', type='build', when='+mpi')
     depends_on('[email protected] ~shared ~mpi +hdf5 -lua -examples -python -fortran -umpire -raja', type='build', when='~mpi')