Merge branch 'nag-workflow' into 'develop'

Add support for the NAG Fortran compiler v6.2 See merge request mhm/mhm!32
pallavhydro · Apr 24, 2020 · bc17636 · bc17636
2 parents 3792d3f + eaeede3
commit bc17636
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Showing 5 changed files with 110 additions and 6 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -26,6 +26,19 @@ show-env-vars:
   script:
     - echo -e "${SEP}\n${S00}$(date)\n${SEP}\n${S01}\n${S02}\n${S03}\n${S04}\n${SEP}\n${S05}${GIT_CLONE_PATH}\n${S06}\n${SEP}"
 
+cmake-nag62:
+  stage: cmake
+  variables:
+    GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_PATH/$CI_COMMIT_REF_NAME/$CI_JOB_NAME
+  script:
+    - source moduleLoadScripts/eve.nag62
+    - source CI-scripts/compile
+    - source CI-scripts/compile_debug
+  artifacts:
+    paths:
+    - mhm
+    - mhm_debug
+
 cmake-gcc73:
   stage: cmake
   variables:
@@ -116,6 +129,27 @@ cmake-intel18MPI:
     - mhm_mpi
     - mhm_mpi_debug
 
+valgrind-nag62:
+  when: always
+  stage: valgrind
+  variables:
+    GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_PATH/$CI_COMMIT_REF_NAME/$CI_JOB_NAME
+  needs:
+    - job: cmake-nag62
+      artifacts: true
+  script:
+    - source moduleLoadScripts/eve.nag62
+    - module load Anaconda3
+    - source activate /global/apps/mhm_checks/mhm_env
+    - valgrind --version
+    - valgrind --tool=memcheck --leak-check=full --show-leak-kinds=all --track-origins=yes --verbose ./mhm_debug
+    # execute mem-use check
+    - valgrind --tool=massif --stacks=yes --time-unit=i --massif-out-file=massif.out.0 ./mhm_debug
+    - ms_print massif.out.0
+  artifacts:
+    paths:
+    - massif.out.0
+
 valgrind-gcc73:
   when: always
   stage: valgrind
@@ -179,6 +213,41 @@ valgrind-intel18:
     paths:
     - massif.out.0
 
+check-nag62:
+  when: always
+  stage: test
+  variables:
+    GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_PATH/$CI_COMMIT_REF_NAME/$CI_JOB_NAME
+  needs:
+    - job: cmake-nag62
+      artifacts: true
+  script:
+    - source moduleLoadScripts/eve.nag62
+    - source CI-scripts/pre_check
+    - python -u run_mhm_checks.py -l logs -e ../mhm
+  artifacts:
+    when: always
+    paths:
+    - check/logs/
+
+check-nag62DEBUG:
+  when: always
+  stage: test
+  variables:
+    GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_PATH/$CI_COMMIT_REF_NAME/$CI_JOB_NAME
+  needs:
+    - job: cmake-nag62
+      artifacts: true
+  script:
+    - source moduleLoadScripts/eve.nag62
+    - source CI-scripts/pre_check
+    # skip cases with optimization due to overflow in the random-number-generator (NAG uses -ieee=stop in DEBUG)
+    - python -u run_mhm_checks.py -l logs -e ../mhm_debug -s case_03 case_06 case_07 case_08 case_11
+  artifacts:
+    when: always
+    paths:
+    - check/logs/
+
 check-gcc73:
   when: always
   stage: test

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -97,6 +97,13 @@ function(cpp_definitions defName defCMakeName value cacheString)
 	endif()
 endfunction()
 
+# add pre-processor -fpp for NAG
+CHECK_Fortran_COMPILER_FLAG("-fpp" FPP_FLAG)
+# if the flag exists, we add it to the compilation flags
+if (FPP_FLAG)
+	set(ADDITIONAL_GCC_FLAGS "-fpp")
+endif()
+
 # Add definitions. These should later be set via the cache line file and only
 # have a default value here. These part only concerns user build definitions like MRM2MHM
 #add_definitions(-DMRM2MHM=.true.)
@@ -131,6 +138,11 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
 	set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -warn all -g -debug -traceback -fp-stack-check -O0 -debug -check all")
 	set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -O3 -qoverride-limits")
 endif()
+if(CMAKE_Fortran_COMPILER_ID MATCHES "NAG")
+	set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -colour -unsharedf95 -ideclient")
+	set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -g -nan -O0 -C=all -strict95 -ieee=stop")
+	set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -O4 -ieee=full")
+endif()
 message(STATUS "the following debug flags will be used: ${CMAKE_Fortran_FLAGS_DEBUG}")
 # Usually that works fine, except, one is on a module system and tries to execute the executable
 # in the end without having the modules loaded. A workaround is provided using the variable

diff --git a/check/README.md b/check/README.md
@@ -8,7 +8,7 @@ A summary for all cases is given at the end.
 
 ## Usage
 
-    python run_mhm_checks.py [-h] [-e EXE [EXE ...]] [-v] [-l LOG_PATH] [-m MPI_NOP] [-t OPENMP_THREADS]
+    python run_mhm_checks.py [-h] [-e EXE [EXE ...]] [-v] [-l LOG_PATH] [-m MPI_NOP] [-t OPENMP_THREADS] [-s [SKIP [SKIP ...]]]
 
 Run the mhm check cases with a given mhm executable.
 
@@ -26,6 +26,8 @@ Run the mhm check cases with a given mhm executable.
     -t OPENMP_THREADS, --threads OPENMP_THREADS
                           Number of threads for openMP. No mpi allowed!
                           (default: 0)
+    -s [SKIP [SKIP ...]], --skip [SKIP [SKIP ...]]
+                          skip cases (case_01 case_03 ..) (default: [])
 
 ## Examples
 Run mhm from parent directory in verbosity mode with mpi on 4 processes:

diff --git a/check/run_mhm_checks.py b/check/run_mhm_checks.py
@@ -77,6 +77,7 @@
 MHM_EXE = ["../mhm"]
 # case 5 and 7 don't work with MPI. case 4 has a bug working with ifort+debug
 SKIP_CASES_MPI = ["case_04", "case_05", "case_07"]
+SKIP = []
 
 
 # ARGUMENT PARSER #############################################################
@@ -144,13 +145,23 @@ def parse_args():
         dest="openmp_threads",
         help="Number of threads for openMP. No mpi allowed! (default: 0)",
     )
+    parser.add_argument(
+        "-s",
+        "--skip",
+        action="store",
+        nargs="*",
+        default=SKIP,
+        dest="skip",
+        help="skip cases (case_01 case_03 ..) (default: {})".format(SKIP),
+    )
     args = parser.parse_args()
     return (
         args.exe,
         args.verbose,
         args.log_path,
         args.mpi_nop,
         args.openmp_threads,
+        args.skip,
     )
 
 
@@ -448,9 +459,10 @@ def run_model(
     child.expect(pexpect.EOF)
     if sys.platform != "win32":
         child.close()
-    # close the output stream
+        exitstatus = child.exitstatus
+    else:
+        exitstatus = child.wait()
     out.close()
-    exitstatus = child.exitstatus
     exit_ok = exitstatus == 0
     # check the last 4 lines of the log-file for "mHM: Finished!"
     with open(log) as log_f:
@@ -471,7 +483,7 @@ def run_model(
 
 if __name__ == "__main__":
     # get args
-    exe_list, print_log, log_path, mpi_nop, openmp_threads = parse_args()
+    exe_list, print_log, log_path, mpi_nop, openmp_threads, skip = parse_args()
     # checking path
     cases_path = os.path.dirname(os.path.realpath(__file__))
     # get all cases folders (in the cases_path)
@@ -483,6 +495,9 @@ def run_model(
     final_result = True
     final_exe_results = {}
     exe_case_results = {}
+    # skip some cases for mpi
+    if int(mpi_nop) > 0:
+        skip += SKIP_CASES_MPI
     # iterate of all mhm exe-s given
     for exe in exe_list:
         # dict for checking results
@@ -505,8 +520,8 @@ def run_model(
         for case in cases:
             # base name of the case
             case_base = os.path.basename(case)
-            # skip some cases for mpi
-            if int(mpi_nop) > 0 and case_base in SKIP_CASES_MPI:
+            # skip some cases
+            if case_base in skip:
                 print(sep_text("skip case: " + case_base, sep_n=60, tab_n=1))
                 continue
             print(sep_text("checking case: " + case_base, sep_n=60, tab_n=1))

diff --git a/moduleLoadScripts/eve.nag62 b/moduleLoadScripts/eve.nag62
@@ -0,0 +1,6 @@
+module purge
+module load NAGfor
+module load netcdf-fortran
+module load CMake
+export FC=nagfor
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH":/usr/lib64"