Issue 1214 - Implements 3D Assembly fixture and stand-in displacement tests

.github/workflows/project-date-automation.yml

@@ -0,0 +1,188 @@
+name: Automate Project Dates
+
+on:
+  issues:
+    types: [opened, edited, closed, reopened]
+  # Note: project_card is for legacy projects. For Projects V2, we need to use other triggers
+  # The workflow will run when issues/PRs change, then check if project status changed
+
+jobs:
+  update-project-dates:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get Project Item
+        id: get_item
+        uses: actions/github-script@v7
+        with:
+          script: |
+            // Get the project item details
+            const query = `
+              query($owner: String!, $repo: String!, $issueNumber: Int!) {
+                repository(owner: $owner, name: $repo) {
+                  issue(number: $issueNumber) {
+                    projectItems(first: 10) {
+                      nodes {
+                        id
+                        project {
+                          id
+                          number
+                        }
+                        fieldValues(first: 20) {
+                          nodes {
+                            ... on ProjectV2ItemFieldSingleSelectValue {
+                              name
+                              field {
+                                ... on ProjectV2SingleSelectField {
+                                  name
+                                }
+                              }
+                            }
+                            ... on ProjectV2ItemFieldDateValue {
+                              date
+                              field {
+                                ... on ProjectV2Field {
+                                  name
+                                }
+                              }
+                            }
+                          }
+                        }
+                      }
+                    }
+                  }
+                }
+              }
+            `;
+
+            const variables = {
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issueNumber: context.issue?.number || context.payload.pull_request?.number
+            };
+
+            if (!variables.issueNumber) {
+              console.log('No issue or PR number found');
+              return;
+            }
+
+            const result = await github.graphql(query, variables);
+            const projectItems = result.repository.issue.projectItems.nodes;
+
+            for (const item of projectItems) {
+              console.log(`Processing project item: ${item.id}`);
+
+              // Find status field value
+              let currentStatus = null;
+              let startDate = null;
+              let endDate = null;
+              let statusFieldId = null;
+              let startDateFieldId = null;
+              let endDateFieldId = null;
+
+              // First, get field IDs from the project
+              const projectQuery = `
+                query($projectId: ID!) {
+                  node(id: $projectId) {
+                    ... on ProjectV2 {
+                      fields(first: 20) {
+                        nodes {
+                          ... on ProjectV2Field {
+                            id
+                            name
+                          }
+                          ... on ProjectV2SingleSelectField {
+                            id
+                            name
+                          }
+                        }
+                      }
+                    }
+                  }
+                }
+              `;
+
+              const projectResult = await github.graphql(projectQuery, {
+                projectId: item.project.id
+              });
+
+              const fields = projectResult.node.fields.nodes;
+
+              // Map field names to IDs (using exact field names)
+              for (const field of fields) {
+                if (field.name.toLowerCase() === 'status') {
+                  statusFieldId = field.id;
+                } else if (field.name === 'Start Date') {
+                  startDateFieldId = field.id;
+                } else if (field.name === 'End Date') {
+                  endDateFieldId = field.id;
+                }
+              }
+
+              // Get current field values
+              for (const fieldValue of item.fieldValues.nodes) {
+                if (fieldValue.field?.name?.toLowerCase() === 'status') {
+                  currentStatus = fieldValue.name;
+                } else if (fieldValue.field?.name === 'Start Date') {
+                  startDate = fieldValue.date;
+                } else if (fieldValue.field?.name === 'End Date') {
+                  endDate = fieldValue.date;
+                }
+              }
+
+              console.log(`Current status: ${currentStatus}`);
+              console.log(`Start date: ${startDate}`);
+              console.log(`End date: ${endDate}`);
+
+              const today = new Date().toISOString().split('T')[0];
+
+              // Only update dates if they don't already exist (this prevents overwriting existing dates)
+              // Update start date if status is "In progress 🧑‍💻" and no start date exists
+              if (currentStatus === 'In progress 🧑‍💻' && !startDate && startDateFieldId) {
+                console.log('Setting start date to today');
+                await github.graphql(`
+                  mutation($projectId: ID!, $itemId: ID!, $fieldId: ID!, $value: Date!) {
+                    updateProjectV2ItemFieldValue(input: {
+                      projectId: $projectId
+                      itemId: $itemId
+                      fieldId: $fieldId
+                      value: { date: $value }
+                    }) {
+                      projectV2Item {
+                        id
+                      }
+                    }
+                  }
+                `, {
+                  projectId: item.project.id,
+                  itemId: item.id,
+                  fieldId: startDateFieldId,
+                  value: today
+                });
+              }
+
+              // Update end date if status is "Done ✅" and no end date exists
+              if (currentStatus === 'Done ✅' && !endDate && endDateFieldId) {
+                console.log('Setting end date to today');
+                await github.graphql(`
+                  mutation($projectId: ID!, $itemId: ID!, $fieldId: ID!, $value: Date!) {
+                    updateProjectV2ItemFieldValue(input: {
+                      projectId: $projectId
+                      itemId: $itemId
+                      fieldId: $fieldId
+                      value: { date: $value }
+                    }) {
+                      projectV2Item {
+                        id
+                      }
+                    }
+                  }
+                `, {
+                  projectId: item.project.id,
+                  itemId: item.id,
+                  fieldId: endDateFieldId,
+                  value: today
+                });
+              }
+            }
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.jenkins/gnu_compiler_checks.gvy

@@ -1,7 +1,7 @@
 pipeline{
     agent {
         node {
-            label 'della_rk9481'
+            label 'della-rse_specfempp'
         }
     }
     stages{
@@ -77,7 +77,7 @@ pipeline{
                                         module load ${GNU_COMPILER_MODULE}
                                         cd build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         export BUILD_DIR=build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
-                                        srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint="intel|cascade" bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest -j --output-on-failure;'
+                                        srun -N 1 -t 00:20:00 --account rse ${HOST_RUN_FLAGS} --constraint="intel|cascade" bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest -j --output-on-failure;'
                                     """
                                     echo ' Testing completed '
                                 }

.jenkins/intel_compiler_checks.gvy

@@ -1,7 +1,7 @@
 pipeline{
     agent {
         node {
-            label 'della_rk9481'
+            label 'della-rse_specfempp'
         }
     }
     stages{
@@ -78,7 +78,7 @@ pipeline{
                                         module load ${INTEL_MODULE}
                                         cd build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         export BUILD_DIR=build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
-                                        srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint="intel|cascade" bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest -j --output-on-failure;'
+                                        srun -N 1 -t 00:20:00 --account rse ${HOST_RUN_FLAGS} --constraint="intel|cascade" bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest -j --output-on-failure;'
                                     """
                                     echo ' Testing completed '
                                 }

.jenkins/nvidia_compiler_checks.gvy

@@ -1,7 +1,7 @@
 pipeline{
     agent {
         node {
-            label 'della_rk9481'
+            label 'della-rse_specfempp'
         }
     }
     stages{
@@ -92,7 +92,7 @@ pipeline{
                                         module load ${CUDA_MODULE}
                                         cd build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         export BUILD_DIR=build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
-                                        srun -N 1 -t 00:30:00 ${HOST_RUN_FLAGS} ${DEVICE_RUN_FLAGS} bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest -j 10 --output-on-failure;'
+                                        srun -N 1 -t 00:30:00 --account rse ${HOST_RUN_FLAGS} ${DEVICE_RUN_FLAGS} bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest -j 10 --output-on-failure;'
                                     """
                                     echo ' Testing completed '
                                 }

CMakeLists.txt

@@ -8,6 +8,8 @@ set(CMAKE_CXX_STANDARD 17)
 option(SPECFEM_ENABLE_ADIOS2 "Enable ADIOS2 I/O in SPECFEM++" OFF)
 option(SPECFEM_ENABLE_HDF5 "Enable HDF5 I/O in SPECFEM++" OFF)
 option(SPECFEM_ENABLE_HDF5_FORCE_INSTALL "Force install HDF5 dependency if SPECFEM_ENABLE_HDF5 is ON even if system HDF5 is found" OFF)
+option(SPECFEM_ENABLE_NPZ "Enable NPZ I/O in SPECFEM++" OFF)
+option(SPECFEM_ENABLE_ZLIB_FORCE_INSTALL "Force install ZLIB dependency even if system ZLIB is found" OFF)
 option(SPECFEM_ENABLE_VTK "Enable VTK visualization in SPECFEM++" ON)
 option(SPECFEM_ENABLE_MPI "MPI enabled" OFF)
 option(SPECFEM_BUILD_TESTS "Tests included" OFF)
@@ -103,6 +105,9 @@ include("${CMAKE_SOURCE_DIR}/cmake/boost.cmake")
 # Find HDF5
 include("${CMAKE_SOURCE_DIR}/cmake/hdf5.cmake")
 
+# Find or install NPZ library function
+include("${CMAKE_SOURCE_DIR}/cmake/npz.cmake")
+
 # Find or install ADIOS2 library function
 include("${CMAKE_SOURCE_DIR}/cmake/adios2.cmake")
 
@@ -195,10 +200,14 @@ target_link_libraries(
 
 add_library(
         io
+        # IO libraries
+        src/io/NPY/impl/npy_header.cpp
+        # SPECFEM IO
         src/io/fortranio/fortran_io.cpp
         src/io/sources/dim2/read_sources.cpp
         src/io/sources/dim3/read_sources.cpp
-        src/io/receivers.cpp
+        src/io/receivers/dim2/read_receivers.cpp
+        src/io/receivers/dim3/read_receivers.cpp
         # Fortran 2D part
         src/io/mesh/impl/fortran/dim2/mesh.cpp
         src/io/mesh/impl/fortran/dim2/read_boundaries.cpp
@@ -223,13 +232,15 @@ target_link_libraries(
         specfem::receivers
         yaml-cpp
         boost
+        $<$<BOOL:${SPECFEM_ENABLE_NPZ}>:zlib>
         $<$<BOOL:${SPECFEM_ENABLE_HDF5}>:hdf5>
         $<$<BOOL:${SPECFEM_ENABLE_ADIOS2}>:adios2>
 )
 
 target_compile_definitions(
         io
         PUBLIC
+        $<$<NOT:$<BOOL:${SPECFEM_ENABLE_NPZ}>>:-DNO_NPZ>
         $<$<NOT:$<BOOL:${SPECFEM_ENABLE_HDF5}>>:-DNO_HDF5>
         $<$<NOT:$<BOOL:${SPECFEM_ENABLE_ADIOS2}>>:-DNO_ADIOS2>
 )
@@ -245,6 +256,7 @@ add_library(
 target_link_libraries(
         enumerations
         ${BOOST_LIBS}
+        Kokkos::kokkos
 )
 
 
@@ -396,17 +408,6 @@ target_link_libraries(
 # Disable unity build for source_time_function due to KOKKOS_INLINE_FUNCTION issues
 set_target_properties(source_time_function PROPERTIES UNITY_BUILD OFF)
 
-
-add_library(coupled_interface
-        src/coupled_interface/coupled_interface.cpp
-)
-
-target_link_libraries(
-        coupled_interface
-        Kokkos::kokkos
-        assembly
-)
-
 add_library(
         kokkos_kernels
         src/kokkos_kernels/impl/compute_mass_matrix.cpp
@@ -416,9 +417,13 @@ add_library(
         src/kokkos_kernels/impl/compute_source_interaction.cpp
         src/kokkos_kernels/impl/compute_stiffness_interaction.cpp
         src/kokkos_kernels/impl/compute_material_derivatives.cpp
+        src/kokkos_kernels/impl/compute_coupling.cpp
         src/kokkos_kernels/frechet_kernels.cpp
 )
-set_target_properties(kokkos_kernels PROPERTIES UNITY_BUILD_BATCH_SIZE 4)
+set_target_properties(kokkos_kernels PROPERTIES
+        UNITY_BUILD $<NOT:$<BOOL:${__APPLE__}>>
+        UNITY_BUILD_BATCH_SIZE $<IF:$<BOOL:${__APPLE__}>,0,4>
+)
 
 target_link_libraries(
         kokkos_kernels
@@ -479,6 +484,7 @@ target_link_libraries(
         periodic_tasks
         reader
         writer
+        io
 )
 
 target_compile_definitions(
@@ -545,7 +551,6 @@ target_link_libraries(
         writer
         periodic_tasks
         reader
-        coupled_interface
         kokkos_kernels
         solver
         ${BOOST_LIBS}
@@ -580,7 +585,6 @@ target_link_libraries(
         writer
         periodic_tasks
         reader
-        coupled_interface
         kokkos_kernels
         solver
         ${BOOST_LIBS}

CMakePresets.json

@@ -104,6 +104,8 @@
         "SPECFEM_ENABLE_MPI": "OFF",
         "SPECFEM_BUILD_BENCHMARKS": "ON",
         "SPECFEM_ENABLE_ADIOS2": "ON",
+        "SPECFEM_ENABLE_NPZ": "ON",
+        "SPECFEM_ENABLE_ZLIB_FORCE_INSTALL": "ON",
         "SPECFEM_ENABLE_HDF5": "ON",
         "SPECFEM_ENABLE_HDF5_FORCE_INSTALL": "ON",
         "SPECFEM_BENCHMARKS_BUILD_DIR": "${sourceDir}/benchmarks/build/release-io"