Add GitLab CI pipeline. (#500)

* Add GitLab CI configuration.
* Small CMake changes for gitlab integration 
* Added CMake/coreneuron-config.cmake.in for passing options to NEURON

Author: olupton

.gitlab-ci.yml

@@ -0,0 +1,59 @@
+include:
+  - project: hpc/gitlab-pipelines
+    file:
+      - spack-build-components.gitlab-ci.yml
+      - github-project-pipelines.gitlab-ci.yml
+
+stages:
+    - .pre
+    - build
+    - test
+    - build_neuron
+    - test_neuron
+
+# Set up Spack
+spack_setup:
+  extends: .spack_setup_ccache
+
+.spack_intel:
+  variables:
+    SPACK_PACKAGE_COMPILER: intel
+.spack_coreneuron:
+  variables:
+    SPACK_PACKAGE: coreneuron
+    SPACK_PACKAGE_SPEC: +debug+tests~legacy-unit
+.spack_neuron:
+  variables:
+    SPACK_PACKAGE: neuron
+    SPACK_PACKAGE_REF: '' # Take the default branch
+    SPACK_PACKAGE_SPEC: +coreneuron+debug+tests~legacy-unit
+
+# CoreNEURON will be checked out for us by default
+build:coreneuron:intel:
+  extends:
+    - .spack_build
+    - .spack_coreneuron
+    - .spack_intel
+
+test:coreneuron:intel:
+  extends:
+    - .ctest
+  needs: ["build:coreneuron:intel"]
+
+build:neuron:intel:
+  stage: build_neuron
+  extends:
+    - .spack_build
+    - .spack_neuron
+    - .spack_intel
+  needs: ["build:coreneuron:intel"]
+
+test:neuron:intel:
+  stage: test_neuron
+  before_script:
+    - !reference [.ctest, before_script]
+    # Wipe Slurm environment to try and keep mpiexec happy.
+    - unset $(env|awk -F= '/^SLURM_/ {if (match($1, "_(ACCOUNT|PARTITION)$")==0) print $1}')
+  extends:
+    - .ctest
+  needs: ["build:neuron:intel"]

CMake/coreneuron-config.cmake CMake/coreneuron-config.cmake.inCMake/coreneuron-config.cmake renamed to CMake/coreneuron-config.cmake.in

@@ -8,6 +8,10 @@
 
 get_filename_component(CONFIG_PATH "${CMAKE_CURRENT_LIST_FILE}" PATH)
 
+set(CORENRN_ENABLE_GPU @CORENRN_ENABLE_GPU@)
+set(CORENRN_ENABLE_NMODL @CORENRN_ENABLE_NMODL@)
+set(CORENRN_ENABLE_REPORTING @CORENRN_ENABLE_REPORTING@)
+
 find_path(CORENEURON_INCLUDE_DIR "coreneuron/coreneuron.h" HINTS "${CONFIG_PATH}/../../include")
 find_path(
   CORENEURON_LIB_DIR

CMakeLists.txt

@@ -316,7 +316,8 @@ endif()
 # =============================================================================
 # Install cmake modules
 # =============================================================================
-install(FILES CMake/coreneuron-config.cmake DESTINATION share/cmake)
+configure_file(CMake/coreneuron-config.cmake.in CMake/coreneuron-config.cmake @ONLY)
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/CMake/coreneuron-config.cmake" DESTINATION share/cmake)
 install(EXPORT coreneuron DESTINATION share/cmake)
 
 if(NOT CORENEURON_AS_SUBPROJECT)

coreneuron/CMakeLists.txt

@@ -58,23 +58,23 @@ set(NMODL_UNITS_FILE "${CMAKE_BINARY_DIR}/share/mod2c/nrnunits.lib")
 file(GLOB builtin_modfiles
      "${CORENEURON_PROJECT_SOURCE_DIR}/coreneuron/mechanism/mech/modfile/*.mod")
 # get the corresponding list of paths to the modfiles in the build directory
-set(builtin_modfile_in_build_dir)
+set(builtin_modfiles_in_build_dir)
 foreach(builtin_modfile ${builtin_modfiles})
   get_filename_component(builtin_modfile_name "${builtin_modfile}" NAME)
-  list(APPEND builtin_modfile_in_build_dir
+  list(APPEND builtin_modfiles_in_build_dir
        "${CMAKE_BINARY_DIR}/share/modfile/${builtin_modfile_name}")
 endforeach()
 file(MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/share/modfile")
 # set up a build rule that ensures the modfiles in the build directory are updated if their
 # counterparts in the source directory are touched
 add_custom_command(
-  OUTPUT ${builtin_modfile_in_build_dir}
+  OUTPUT ${builtin_modfiles_in_build_dir}
   DEPENDS ${builtin_modfiles}
   COMMAND ${CMAKE_COMMAND} -E copy_if_different ${builtin_modfiles}
           "${CMAKE_BINARY_DIR}/share/modfile")
-add_custom_target(copy-builtin-modfiles ALL DEPENDS ${builtin_modfile_in_build_dir})
+add_custom_target(copy-builtin-modfiles ALL DEPENDS ${builtin_modfiles_in_build_dir})
 set(CORENEURON_BUILTIN_MODFILES
-    "${builtin_modfile_in_build_dir}"
+    "${builtin_modfiles_in_build_dir}"
     CACHE STRING "List of builtin modfiles that nrnivmodl-core implicitly depends on" FORCE)
 
 # =============================================================================

tests/integration/CMakeLists.txt

@@ -79,12 +79,14 @@ file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/ring/out.dat.ref"
 # Configure test scripts
 foreach(args_line ${TEST_CASES_WITH_ARGS})
   string(REPLACE "!" ";" string_line ${args_line})
+  set(test_num_processors 1)
   if(MPI_FOUND)
     # serial test run without srun or mpiexec
     if(args_line MATCHES "ring_serial.*")
       string(REPLACE ";" " " SRUN_PREFIX "")
     else()
-      string(REPLACE ";" " " SRUN_PREFIX "${TEST_MPI_EXEC_BIN};-n;2")
+      set(test_num_processors 2)
+      string(REPLACE ";" " " SRUN_PREFIX "${TEST_MPI_EXEC_BIN};-n;${test_num_processors}")
     endif()
   endif()
   list(GET string_line 0 TEST_NAME)
@@ -95,12 +97,15 @@ foreach(args_line ${TEST_CASES_WITH_ARGS})
     NAME ${TEST_NAME}_TEST
     COMMAND "/bin/sh" ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}/integration_test.sh
     WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}")
+  set_tests_properties(${TEST_NAME}_TEST PROPERTIES PROCESSORS ${test_num_processors})
 endforeach()
 
 foreach(args_line ${NEGATIVE_TEST_CASES})
   string(REPLACE "!" ";" string_line ${args_line})
+  set(test_num_processors 1)
   if(MPI_FOUND)
-    string(REPLACE ";" " " SRUN_PREFIX "${TEST_MPI_EXEC_BIN};-n;2")
+    set(test_num_processors 2)
+    string(REPLACE ";" " " SRUN_PREFIX "${TEST_MPI_EXEC_BIN};-n;${test_num_processors}")
   endif()
   list(GET string_line 0 TEST_NAME)
   list(GET string_line 1 TEST_ARGS)
@@ -110,6 +115,7 @@ foreach(args_line ${NEGATIVE_TEST_CASES})
     NAME ${TEST_NAME}_TEST
     COMMAND "/bin/sh" ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}/negative_integration_test.sh
     WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}")
+  set_tests_properties(${TEST_NAME}_TEST PROPERTIES PROCESSORS ${test_num_processors})
 endforeach()
 
 if(CORENRN_ENABLE_REPORTING)