Merge pull request #468 from PrincetonUniversity/devel

v0.3.0

Author: lsawade

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,28 +4,32 @@ about: Create a report to help us improve
 title: ''
 labels: ''
 assignees: ''
-
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+## Expected behavior
+A clear and concise description of what you expected to happen.
+
+## Actual (buggy) behavior
+A clear and concise description of what is happening instead.
 
-**To Reproduce**
+## Screenshots
+
+If applicable, add screenshots to help explain your problem.
+
+## Setup information:
 
 - Installation instructions:
 ```
-      Please paste the cmake configuration command here
+Please paste the cmake configuration command here
 ```
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+## Machine information:
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+[please complete the following information:]
 
-**Machine information (please complete the following information):**
  - OS: [e.g. Redhat]
  - GPU available: [e.g. Yes (NVIDIA A100)]
 
-**Additional context**
+## Additional context
+
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -7,11 +7,16 @@ assignees: ''
 
 ---
 
-**Is your feature request related to a problem? Please describe.**
+## Is your feature request related to a problem?
 A clear and concise description of what the problem is.
 
-**Describe the solution you'd like**
+## Describe the solution you'd like
+
 A clear and concise description of what you want to happen.
 
-**Additional context**
+## Additional context
+
 Add any other context or screenshots about the feature request here.
+
+If this feature request helps with an existing issue, please link the issue here.
+E.g. #<issue number>

.github/pull_request_template.md

@@ -1,18 +1,18 @@
-# Description
+## Description
 
-Please describe the changes/features in this pull request. 
+Please describe the changes/features in this pull request.
 
-# Issue Number
+## Issue Number
 
 If there is an issue created for these changes, link it here
 
-# Checklist
+## Checklist
 
-Please make sure to check developer documentation on specfem docs. 
+Please make sure to check developer documentation on specfem docs.
 
-[] I ran the code through pre-commit to check style
-[] My code passes all the integration tests
-[] I have added sufficient unittests to test my changes
-[] I have added/updated documentation for the changes I am proposing
-[] I have updated CMakeLists to ensure my code builds
-[] My code builds across all platforms 
+- [ ] I ran the code through pre-commit to check style
+- [ ] My code passes all the integration tests
+- [ ] I have added sufficient unittests to test my changes
+- [ ] I have added/updated documentation for the changes I am proposing
+- [ ] I have updated CMakeLists to ensure my code builds
+- [ ] My code builds across all platforms

.gitignore

@@ -8,6 +8,7 @@ firebase*.yml
 *.out
 debug.sh
 output.log
+output.txt
 results/
 timing.sh
 examples/*/*_config.yaml

.jenkins/gnu_compiler_checks.gvy

@@ -25,7 +25,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 1 -c 10'
                     }
                 }
                 stages {
@@ -66,10 +66,10 @@ pipeline{
                                 steps {
                                     echo "Building ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} with ${GNU_COMPILER_NAME}"
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${GNU_COMPILER_MODULE}
-                                        cmake3 -S . -B build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -DBUILD_TESTS=ON
-                                        cmake3 --build build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}
+                                        cmake3 -S . -B build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -DBUILD_TESTS=ON -D BUILD_EXAMPLES=OFF
+                                        cmake3 --build build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
                                     """
                                     echo ' Build completed '
                                 }
@@ -78,9 +78,9 @@ pipeline{
                                 steps {
                                     echo ' Testing '
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${GNU_COMPILER_MODULE}
-                                        cd build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}/tests/unit-tests
+                                        cd build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint=skylake bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'
                                     """
                                     echo ' Testing completed '
@@ -90,7 +90,7 @@ pipeline{
                         post {
                             always {
                                 echo ' Cleaning '
-                                sh "rm -rf build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}"
+                                sh "rm -rf build_cpu_${GNU_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}"
                             }
                         }
                     }

.jenkins/intel_compiler_checks.gvy

@@ -21,7 +21,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON -DKokkos_ENABLE_ATOMICS_BYPASS=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 1 -c 10'
                     }
                     axis{
                         name 'SIMD'
@@ -65,12 +65,12 @@ pipeline{
                                 steps {
                                     echo "Building ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} with ${INTEL_COMPILER_NAME}"
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${INTEL_MODULE}
                                         export CC=icx
                                         export CXX=icpx
-                                        cmake3 -S . -B build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON
-                                        cmake3 --build build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}
+                                        cmake3 -S . -B build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON -D BUILD_EXAMPLES=OFF
+                                        cmake3 --build build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
                                     """
                                     echo ' Build completed '
                                 }
@@ -79,9 +79,9 @@ pipeline{
                                 steps {
                                     echo ' Testing '
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${INTEL_MODULE}
-                                        cd build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}/tests/unit-tests
+                                        cd build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} --constraint=skylake bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'
                                     """
                                     echo ' Testing completed '
@@ -91,7 +91,7 @@ pipeline{
                         post {
                             always {
                                 echo ' Cleaning '
-                                sh "rm -rf build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}"
+                                sh "rm -rf build_cpu_${INTEL_COMPILER_NAME}_${CMAKE_HOST_NAME}_${SIMD_NAME}_${env.BUILD_TAG}"
                             }
                         }
                     }

.jenkins/nvidia_compiler_checks.gvy

@@ -21,7 +21,7 @@ pipeline{
                     }
                     axis{
                         name 'HostSpace'
-                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON;-n 10'
+                        values 'SERIAL;-DKokkos_ENABLE_SERIAL=ON;-n 1', 'OPENMP;-DKokkos_ENABLE_OPENMP=ON; -n 1 -c 10'
                     }
                     axis{
                         name 'DeviceSpace'
@@ -81,10 +81,10 @@ pipeline{
                                 steps {
                                     echo "Building ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} with ${CUDA_COMPILER_NAME}"
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${CUDA_MODULE}
-                                        cmake3 -S . -B build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON
-                                        cmake3 --build build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}
+                                        cmake3 -S . -B build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG} -DCMAKE_BUILD_TYPE=Release ${CMAKE_HOST_FLAGS} ${CMAKE_DEVICE_FLAGS} ${SIMD_FLAGS} -D BUILD_TESTS=ON -D BUILD_EXAMPLES=OFF
+                                        cmake3 --build build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}
                                     """
                                     echo ' Build completed '
                                 }
@@ -93,9 +93,9 @@ pipeline{
                                 steps {
                                     echo ' Testing '
                                     sh """
-                                        module load boost/1.73.0
+                                        module load boost/1.85.0
                                         module load ${CUDA_MODULE}
-                                        cd build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}/tests/unit-tests
+                                        cd build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}/tests/unit-tests
                                         srun -N 1 -t 00:20:00 ${HOST_RUN_FLAGS} ${DEVICE_RUN_FLAGS} bash -c 'export OMP_PROC_BIND=spread; export OMP_THREADS=places; ctest --verbose;'
                                     """
                                     echo ' Testing completed '
@@ -105,7 +105,7 @@ pipeline{
                         post {
                             always {
                                 echo ' Cleaning '
-                                sh "rm -rf build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.GIT_COMMIT}"
+                                sh "rm -rf build_cuda_${CUDA_COMPILER_NAME}_${CMAKE_HOST_NAME}_${CMAKE_DEVICE_NAME}_${SIMD_NAME}_${env.BUILD_TAG}"
                             }
                         }
                     }

.pre-commit-config.yaml

@@ -11,13 +11,13 @@ repos:
       - id: requirements-txt-fixer
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v14.0.5"
+    rev: "v15.0.6"
     hooks:
       - id: clang-format
         types_or: [c++]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.9.1
     hooks:
       # Run the linter.
       - id: ruff