CMake updates; flush with upstream

.github/workflows/docs.yml

@@ -35,7 +35,11 @@ jobs:
         - name: build code
           run: |
             mkdir -p build
-            cmake -DSINGULARITY_BUILD_PYTHON=ON -DSINGULARITY_USE_HDF5=OFF -DSINGULARITY_USE_FORTRAN=OFF -B build .
+            cmake -DSINGULARITY_BUILD_PYTHON=ON \
+                  -DSINGULARITY_USE_SPINER=ON \
+                  -DSINGULARITY_USE_SPINER_WITH_HDF5=OFF \
+                  -DSINGULARITY_FORCE_SUBMODULE_MODE=ON \
+                  -B build .
             cmake --build build
             sudo cmake --install build
         - name: build docs

.github/workflows/tests.yml

@@ -30,14 +30,16 @@ jobs:
             cd bin
             mkdir -p ${HOME}/install
             cmake -DCMAKE_INSTALL_PREFIX=${HOME}/install \
+                  -DSINGULARITY_USE_SPINER=ON \
                   -DSINGULARITY_BUILD_TESTS=ON \
                   -DSINGULARITY_BUILD_EXAMPLES=ON \
                   -DSINGULARITY_BUILD_PYTHON=ON \
-                  -DSINGULARITY_USE_HDF5=ON \
                   -DSINGULARITY_TEST_SESAME=OFF \
-                  -DSINGULARITY_TEST_PYTHON=ON \
-                  -DSINGULARITY_TEST_STELLAR_COLLAPSE=ON \
+                  -DSINGULARITY_FORCE_SUBMODULE_MODE=ON \
                   ..
+                  #-DSINGULARITY_TEST_PYTHON=ON \
+                  #-DSINGULARITY_TEST_STELLAR_COLLAPSE=ON \
+                  #..
             make
             make install
             make test

.github/workflows/tests_minimal.yml

@@ -28,13 +28,10 @@ jobs:
             cd bin
             mkdir -p ${HOME}/install
             cmake -DCMAKE_INSTALL_PREFIX=${HOME}/install \
+                  -DSINGULARITY_USE_SPINER=ON \
+                  -DSINGULARITY_USE_SPINER_WITH_HDF5=OFF \
                   -DSINGULARITY_BUILD_TESTS=ON \
-                  -DSINGULARITY_BUILD_PYTHON=OFF \
-                  -DSINGULARITY_USE_HDF5=OFF \
-                  -DSINGULARITY_BUILD_CLOSURE=OFF \
-                  -DSINGULARITY_TEST_SESAME=OFF \
-                  -DSINGULARITY_TEST_PYTHON=OFF \
-                  -DSINGULARITY_TEST_STELLAR_COLLAPSE=OFF \
+                  -DSINGULARITY_FORCE_SUBMODULE_MODE=ON \
                   ..
             make
             make install

.gitignore

@@ -10,4 +10,5 @@ spack-build-*
 spack-configure-*
 ._*
 *.sublime*
+CMakeUserPresets.json
 

.gitlab-ci.yml

@@ -10,7 +10,7 @@ variables:
   SINGULARITY_EOS_GCC_VERSION: "9.3.0"
   SINGULARITY_EOS_OPENMPI_VERSION: "4.1.3"
   SINGULARITY_EOS_CUDA_VERSION: "11.6.0"
-  SINGULARITY_EOS_SPACK_SPEC: "singularity-eos@main+mpi+python+tests%gcc@${SINGULARITY_EOS_GCC_VERSION} ^openmpi@${SINGULARITY_EOS_OPENMPI_VERSION}"
+  SINGULARITY_EOS_SPACK_SPEC: "singularity-eos@main+mpi+hdf5+python+tests%gcc@${SINGULARITY_EOS_GCC_VERSION} ^openmpi@${SINGULARITY_EOS_OPENMPI_VERSION}"
   COLOR_CYAN: '\033[1;36m'
   COLOR_PLAIN: '\033[0m'
   # set to different spack upstream for testing
@@ -51,7 +51,7 @@ before_script:
 
 .gpu: &gpu
   SINGULARITY_USE_CUDA: "true"
-  SINGULARITY_EOS_SPACK_SPEC: "singularity-eos@main+mpi+tests+cuda+kokkos cuda_arch=70 +kokkos-kernels%gcc@${SINGULARITY_EOS_GCC_VERSION} ^cuda@${SINGULARITY_EOS_CUDA_VERSION} ^openmpi@${SINGULARITY_EOS_OPENMPI_VERSION}"
+  SINGULARITY_EOS_SPACK_SPEC: "singularity-eos@main+mpi+tests+cuda+kokkos+hdf5 cuda_arch=70 +kokkos-kernels%gcc@${SINGULARITY_EOS_GCC_VERSION} ^cuda@${SINGULARITY_EOS_CUDA_VERSION} ^openmpi@${SINGULARITY_EOS_OPENMPI_VERSION}"
 
 .fort: &fort
   SINGULARITY_USE_FORTRAN: "true"
@@ -103,8 +103,8 @@ before_script:
       then
         echo -e "\e[0Ksection_start:`date +%s`:spack_build[collapsed=true]\r\e[0K${COLOR_CYAN}Building via Spack${COLOR_PLAIN}"
         mkdir -p spack_build_env
-        spack env create -d spack_build_env
-        spack env activate -d spack_build_env
+        spack env create spack_build_env
+        spack env activate spack_build_env
         spack repo add spack-repo
         spack config add upstreams:default:install_tree:${SINGULARITY_EOS_SPACK_DIR}/opt/spack/
         spack dev-build -j $(nproc) ${SINGULARITY_EOS_SPACK_SPEC}
@@ -113,8 +113,8 @@ before_script:
       fi
     - echo -e "\e[0Ksection_start:`date +%s`:spack_env[collapsed=true]\r\e[0K${COLOR_CYAN}Creating Spack environment${COLOR_PLAIN}"
     - mkdir -p spack_env
-    - spack env create -d spack_env
-    - spack env activate -d spack_env
+    - spack env create spack_env
+    - spack env activate spack_env
     - spack repo add spack-repo
     - spack config add upstreams:default:install_tree:${SINGULARITY_EOS_SPACK_DIR}/opt/spack/
     - spack spec -I ${SINGULARITY_EOS_SPACK_SPEC}
@@ -133,7 +133,8 @@ before_script:
     - |
       cmake -DCMAKE_INSTALL_PREFIX=${CI_PROJECT_DIR}/install ${SINGULARITY_CMAKE_CXX_COMPILER_FLAG} \
             -DSINGULARITY_USE_EOSPAC=ON \
-            -DSINGULARITY_USE_HDF5=ON \
+            -DSINGULARITY_USE_SPINER=ON \
+            -DSINGULARITY_USE_SPINER_WITH_HDF5=ON \
             -DSINGULARITY_BUILD_SESAME2SPINER=ON \
             -DSINGULARITY_BUILD_STELLARCOLLAPSE2SPINER=ON \
             -DSINGULARITY_BUILD_PYTHON=${SINGULARITY_BUILD_PYTHON:-OFF} \

.gitmodules

@@ -3,7 +3,7 @@
 	url = https://gitlab.com/libeigen/eigen.git
 [submodule "utils/spiner"]
 	path = utils/spiner
-	url = ../spiner.git
+  url = https://github.com/lanl/spiner
 [submodule "utils/variant"]
 	path = utils/variant
 	url = https://github.com/mpark/variant.git
@@ -12,4 +12,7 @@
 	url = https://github.com/kokkos/kokkos.git
 [submodule "utils/ports-of-call"]
 	path = utils/ports-of-call
-	url = ../ports-of-call.git
+	url = https://github.com/lanl/ports-of-call.git
+[submodule "utils/kokkos-kernels"]
+	path = utils/kokkos-kernels
+	url = https://github.com/kokkos/kokkos-kernels.git