Release candidate for HTR-1.4.1

stanfordhpccenter · Aug 7, 2022 · 328f842 · 328f842
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commit 328f842
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -5,7 +5,7 @@
 # Global variables (will be set in every job):
 variables:
    MAX_DIM: "3"
-   LEGION_COMMIT: "e1ce6c67f58a0e6b70023c31d202eebc88efa265"
+   LEGION_COMMIT: "36851ec77ea6a317ba72a730e3df2e0bb0a0d586"
    HTR_DIR: "$CI_PROJECT_DIR"
    REALM_BACKTRACE: "1"
 #  TIMELIMIT: "600"  # each test should take less than 10 minutes
@@ -44,23 +44,31 @@ variables:
 #  TERRA_DIR: "/usr/local/terra70"
 
 .debug: &debug
-  DEBUG: "1"
+   DEBUG: "1"
 .release: &release
-  DEBUG: "0"
+   DEBUG: "0"
 
 .openmp: &openmp
-  USE_OPENMP: "1"
+   USE_OPENMP: "1"
 .hdf5: &hdf5
-  USE_HDF: "1"
+   USE_HDF: "1"
 .llvm: &llvm
-  USE_LLVM: "1"
+   USE_LLVM: "1"
 .cuda: &cuda
-  USE_CUDA: "1"
+   USE_CUDA: "1"
 .gasnet: &gasnet
-  USE_GASNET: "1"
+   USE_GASNET: "1"
 
 .prof: &prof
-  USE_PROF: "1"
+   USE_PROF: "1"
+
+###
+### Optional execution modes
+###
+
+.rpn2: &rpn2
+   RANKS: "2"
+   RANKS_PER_NODE: "2"
 
 ###
 ### Optional modules
@@ -79,25 +87,27 @@ variables:
 # These commands will run before each job.
 before_script:
    - |
-      if [[ "$(hostname)" = ctr-205-1.stanford.edu ]]; then
-         module load mpi/mpich-3.0-x86_64
+      if [[ "$(hostname)" == ctr-205-1.stanford.edu ]]; then
          export CC=gcc
          export CXX=g++
-         export LEGION_DIR=/home/gitlab-runner/legion
-         export HDF_ROOT=$LEGION_DIR/language/hdf/install
-         export USE_GASNET=0
-         export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$LEGION_DIR/bindings/regent:$LEGION_DIR/language/hdf/install/lib"
+         export LEGION_DEP_PREFIX_DIR=/home/gitlab-runner/legion/language
+         if [[ $DEBUG == 1 ]]; then
+            export LEGION_DIR=/home/gitlab-runner/legion-debug
+         else
+            export LEGION_DIR=/home/gitlab-runner/legion
+         fi
+         export HDF_ROOT=$LEGION_DEP_PREFIX_DIR/hdf/install
+         export CONDUIT="mpi"
+         export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$LEGION_DIR/bindings/regent:$HDF_ROOT/lib"
+
+         # Make sure that we are running the last version of Legion
+         cd $LEGION_DIR/language
+         git fetch
+         git checkout $LEGION_COMMIT
+         scripts/setup_env.py --llvm-version 90 --prefix $LEGION_DEP_PREFIX_DIR
          cd $HTR_DIR
       fi
 
-   # Make sure that we are running the last version of Legion
-   - |
-      cd $LEGION_DIR/language
-      git fetch
-      git checkout $LEGION_COMMIT
-      scripts/setup_env.py --llvm-version 90
-      cd $HTR_DIR
-
 ###
 ### Tags
 ###
@@ -115,6 +125,22 @@ before_script:
 #.image: &image
 #  image: stanfordlegion/gitlab-ci:ubuntu16.04 # i.e. https://hub.docker.com/r/stanfordlegion/gitlab-ci/
 
+###
+### Test rules
+###
+
+# rules for which jobs will run
+.test_rules: &test_rules
+   rules:
+      # commits only run a short suite of jobs
+      - if: '$CI_PIPELINE_SOURCE == "push" && $IS_SHORT_JOB != "1"'
+        when: never
+      # if none of the above exclusions apply, run the job
+      - when: always
+
+.short: &short
+   IS_SHORT_JOB: "1"
+
 ###
 ### Tests
 ###
@@ -135,6 +161,7 @@ before_script:
       - python3 solverTests/3DPeriodic/test.py
       - python3 solverTests/RecycleBoundary/test.py
       - python3 solverTests/ShockTube/test.py
+      - python3 solverTests/PlanarJet/test.py
       - python3 solverTests/VortexAdvection2D/test.py
 
 
@@ -145,32 +172,47 @@ before_script:
 # Each item below defines a job.
 
 ctr-205-1_release_unitTests:
-   <<: [*ctr-205-1, *unitTests]
+   <<: [*ctr-205-1, *unitTests, *test_rules]
    variables:
-      <<: [*release, *openmp, *hdf5, *noelectricSolver]
+      <<: [*release, *openmp, *hdf5, *noelectricSolver, *short]
 
 ctr-205-1_release_solverTests:
-   <<: [*ctr-205-1, *solverTests]
+   <<: [*ctr-205-1, *solverTests, *test_rules]
    variables:
-      <<: [*release, *openmp, *hdf5, *noelectricSolver]
+      <<: [*release, *openmp, *hdf5, *noelectricSolver, *short]
+
+ctr-205-1_release_solverTests_rpn2:
+   <<: [*ctr-205-1, *solverTests, *test_rules]
+   variables:
+      <<: [*release, *openmp, *hdf5, *noelectricSolver, *rpn2]
 
 ctr-205-1_debug_unitTests:
-   <<: [*ctr-205-1, *unitTests]
+   <<: [*ctr-205-1, *unitTests, *test_rules]
    variables:
       <<: [*debug, *openmp, *hdf5, *noelectricSolver]
 
 ctr-205-1_debug_quickSolverTests:
-   <<: [*ctr-205-1, *quickSolverTests]
+   <<: [*ctr-205-1, *quickSolverTests, *test_rules]
    variables:
       <<: [*debug, *openmp, *hdf5, *noelectricSolver]
 
+ctr-205-1_debug_quickSolverTests_rpn2:
+   <<: [*ctr-205-1, *quickSolverTests, *test_rules]
+   variables:
+      <<: [*debug, *openmp, *hdf5, *noelectricSolver, *rpn2]
+
 ctr-205-1_release_electricSolver_unitTests:
-   <<: [*ctr-205-1, *unitTests]
+   <<: [*ctr-205-1, *unitTests, *test_rules]
    variables:
-      <<: [*release, *openmp, *hdf5, *electricSolver]
+      <<: [*release, *openmp, *hdf5, *electricSolver, *short]
 
 ctr-205-1_release_electricSolver_solverTests:
-   <<: [*ctr-205-1, *solverTests]
+   <<: [*ctr-205-1, *solverTests, *test_rules]
+   variables:
+      <<: [*release, *openmp, *hdf5, *electricSolver, *short]
+
+ctr-205-1_debug_electricSolver_unitTests:
+   <<: [*ctr-205-1, *unitTests, *test_rules]
    variables:
       <<: [*release, *openmp, *hdf5, *electricSolver]
 
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "solverTests/referenceData"]
+	path = solverTests/referenceData
+	url = https://gitlab.com/mario.direnzo/htr-referencedata.git
+   branch = master
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,5 +1,29 @@
 This file lists the major changes as they appear in the master branch.
 
+Version 1.4.1 (August 1, 2022)
+   - Minor bug fixes and performance improvements
+
+Version 1.4.0 (July 1, 2022)
+   - NSCBC (Inflow/Outflow) are now available for xNeg/xPos/yNeg/yPos/zNeg/zPos
+   - new NSCBC FarField added to the solver
+   - unitTest suite is now compatible with CUDA
+   - solverTest suite is now compatible with GPUs
+   - laser energy kernel based on Wang et al., JFM (2020) implemented, with accompanying test case
+   - boundary buffer zones based on Freund, AIAA (1997)
+   - one-dimensional planar flame for calculating flame speed added to test cases
+   - low-priority samples that use only CPUs can be passed using the -lp argument
+   - 26 species (including ions) chemical scheme (Di Renzo & Cuenot (2022) CnF 244) added to the solver with the name CH4_26SpIonsMix
+   - several improvements in precision of task privileges
+   - new implementation of constant TKE forcing for proposed in Bassenne et al., POF (2016)
+   - TENO added as option for Euler flux reconstruction
+   - less intrusive flux limiter to avoid negative species partial densities
+   - fixed compatibility with macOS
+   - UCSD mechanism for H2 combustion added to the solver (Saxena & Williams (2006) CnF 145)
+   - ability to repartition on different number of nodes the simulation data upon restart
+   - new python module to read and write the restart files
+   - new grid parameter section in the input file
+   - new grid IO
+
 Version 1.3.0 (February 28, 2021)
    - normalization of the multicomponent mixture
    - NSCBCInflow is now available for yLeft BC

diff --git a/Makefile.in b/Makefile.in
@@ -9,6 +9,9 @@ endif
 # OS-specific options
 ifeq ($(shell uname),Darwin)
   DYNLINK_PATH := DYLD_LIBRARY_PATH
+  C_FLAGS    += -DDARWIN
+  CXX_FLAGS  += -DDARWIN
+  NVCC_FLAGS += -DDARWIN
 else
   DYNLINK_PATH := LD_LIBRARY_PATH
 endif
@@ -36,20 +39,17 @@ CUFFT_LIBNAME ?= cufft
 # C and CUDA compilers options:
 # - Warnings
 C_FLAGS    += -Wall -Werror -fno-strict-aliasing
-CXX_FLAGS  += -Wall -Werror
-# - define standard
-CXX_FLAGS  += -std=c++11
-NVCC_FLAGS += -std=c++11
+CXX_FLAGS  += -Wall -Werror -Wno-return-type-c-linkage
 # - Include paths
-C_FLAGS    += -I$(LEGION_DIR)/runtime -I$(LEGION_DIR)/bindings/regent -I$(HTR_DIR)/src -I$(HTR_DIR)/src/Mixtures -I$(HTR_DIR)/src/Utils -I. -I$(HTR_DIR)/src/Poisson -I.
-CXX_FLAGS  += -I$(LEGION_DIR)/runtime -I$(LEGION_DIR)/bindings/regent -I$(HTR_DIR)/src -I$(HTR_DIR)/src/Mixtures -I$(HTR_DIR)/src/Utils -I. -I$(HTR_DIR)/src/Poisson -I.
-NVCC_FLAGS += -I$(LEGION_DIR)/runtime -I$(LEGION_DIR)/bindings/regent -I$(HTR_DIR)/src -I$(HTR_DIR)/src/Mixtures -I$(HTR_DIR)/src/Utils -I. -I$(HTR_DIR)/src/Poisson -I.
+C_FLAGS    += -I$(LEGION_DIR)/runtime -I$(LEGION_DIR)/bindings/regent -I$(HTR_DIR)/src -I$(HTR_DIR)/src/Mixtures -I$(HTR_DIR)/src/Utils -I$(HTR_DIR)/src/Poisson -I.
+CXX_FLAGS  += -I$(LEGION_DIR)/runtime -I$(LEGION_DIR)/bindings/regent -I$(HTR_DIR)/src -I$(HTR_DIR)/src/Mixtures -I$(HTR_DIR)/src/Utils -I$(HTR_DIR)/src/Poisson -I.
+NVCC_FLAGS += -I$(LEGION_DIR)/runtime -I$(LEGION_DIR)/bindings/regent -I$(HTR_DIR)/src -I$(HTR_DIR)/src/Mixtures -I$(HTR_DIR)/src/Utils -I$(HTR_DIR)/src/Poisson -I.
 
 # Regent options
 export TERRA_PATH := ?.rg;$(HTR_DIR)/src/?.rg;$(HTR_DIR)/src/Mixtures/?.rg;$(HTR_DIR)/src/Utils/?.rg;$(HTR_DIR)/src/Poisson/?.rg
 export INCLUDE_PATH := .;$(HTR_DIR)/src;$(HTR_DIR)/src/Mixtures;$(HTR_DIR)/src/Utils;$(HTR_DIR)/src/Poisson
 REGENT := $(LEGION_DIR)/language/regent.py
-REGENT_FLAGS := -fflow 0 -finner 1 -foffline 1
+REGENT_FLAGS += -fflow 0 -finner 1 -foffline 1
 
 # Link flags
 LINK_FLAGS += -L$(LEGION_DIR)/bindings/regent -lregent
@@ -94,7 +94,8 @@ endif
 # If DEBUG mode is active
 ######################################################
 ifeq ($(DEBUG), 1)
-   REGENT_FLAGS += -g -fbounds-checks 1
+   REGENT_OPTS  += -g
+   REGENT_FLAGS += -fbounds-checks 1
    C_FLAGS    += -g -O0 -DLEGION_BOUNDS_CHECKS -DLEGION_PRIVILEGE_CHECKS
    CXX_FLAGS  += -g -O0 -DLEGION_BOUNDS_CHECKS -DLEGION_PRIVILEGE_CHECKS
    NVCC_FLAGS += -g -O0 -DLEGION_BOUNDS_CHECKS -DLEGION_PRIVILEGE_CHECKS -G