Release candidate for HTR-1.1.1

.gitattributes

@@ -0,0 +1 @@
+*.hdf filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -20,3 +20,7 @@ __pycache__
 
 src/config_schema.h
 src/*-desugared.rg
+src/version.h
+src/version.rg
+test/*.h
+test/*-desugared.rg

.gitlab-ci.yml

@@ -0,0 +1,195 @@
+###
+### Variables
+###
+
+# Global variables (will be set in every job):
+variables:
+   MAX_DIM: "4"
+   LEGION_BRANCH: "parallelizer-dcr-new"
+   HTR_DIR: "$CI_PROJECT_DIR"
+   REALM_BACKTRACE: "1"
+#  TIMELIMIT: "600"  # each test should take less than 10 minutes
+
+# Local variables (included on a case-by-case basis in each job):
+#.gcc48: &gcc48
+#  CXX: "g++-4.8"
+#.gcc49: &gcc49
+#  CXX: "g++-4.9"
+#.gcc5: &gcc5
+#  CXX: "g++-5"
+#.gcc6: &gcc6
+#  CXX: "g++-6"
+#.gcc7: &gcc7
+#  CXX: "g++-7"
+#.gcc8: &gcc8
+#  CXX: "g++-8"
+#
+#.clang35: &clang35
+#  CXX: "clang++-3.5"
+#.clang38: &clang38
+#  CXX: "clang++-3.8"
+#.clang7: &clang7
+#  CXX: "clang++-7"
+#.clang8: &clang8
+#  CXX: "clang++-8"
+#
+#.terra35: &terra35
+#  LLVM_CONFIG: "llvm-config-3.5"
+#  TERRA_DIR: "/usr/local/terra35"
+#.terra38: &terra38
+#  LLVM_CONFIG: "llvm-config-3.8"
+#  TERRA_DIR: "/usr/local/terra38"
+#.terra70: &terra70
+#  LLVM_CONFIG: "llvm-config-7"
+#  TERRA_DIR: "/usr/local/terra70"
+
+.debug: &debug
+  DEBUG: "1"
+.release: &release
+  DEBUG: "0"
+
+.openmp: &openmp
+  USE_OPENMP: "1"
+.hdf5: &hdf5
+  USE_HDF: "1"
+.llvm: &llvm
+  USE_LLVM: "1"
+.cuda: &cuda
+  USE_CUDA: "1"
+.gasnet: &gasnet
+  USE_GASNET: "1"
+
+.prof: &prof
+  USE_PROF: "1"
+
+###
+### Setup
+###
+
+# These commands will run before each job.
+before_script:
+   - |
+      if [[ "$(hostname)" = ctr-205-1.stanford.edu ]]; then
+         module load mpi/mpich-3.0-x86_64
+         export CC=mpicc
+         export CXX=mpicxx
+         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"
+         cd $HTR_DIR
+      fi
+
+   # Make sure that we are running the last version of Legion
+   - |
+      cd $LEGION_DIR/language
+      git fetch
+      LOCAL0=$(git rev-parse @)
+      git checkout $LEGION_BRANCH
+      UPSTREAM=${1:-'@{u}'}
+      LOCAL=$(git rev-parse @)
+      REMOTE=$(git rev-parse "$UPSTREAM")
+      if [ $LOCAL != $REMOTE ]; then
+         echo "Updating Legion"
+         git reset --hard $REMOTE
+         scripts/setup_env.py --llvm-version 38
+      elif [ $LOCAL != $LOCAL0 ]; then
+         echo "Building Legion on the new branch"
+         scripts/setup_env.py --llvm-version 38
+      fi
+      cd $HTR_DIR
+
+
+###
+### Tags
+###
+
+.ctr-205-1: &ctr-205-1
+   tags:
+      - centos7
+      - ctr-205-1
+
+###
+### Docker Image
+###
+
+# Each job will run in a fresh container with this image.
+#.image: &image
+#  image: stanfordlegion/gitlab-ci:ubuntu16.04 # i.e. https://hub.docker.com/r/stanfordlegion/gitlab-ci/
+
+###
+### Tests
+###
+
+# Unit tests that check the solver component by component.
+.unitTests: &unitTests
+   script:
+      - cd unitTests/configTest
+      - make
+      - ./configTest.exec
+      - cd ../..
+
+      - cd unitTests/mathUtilsTest
+      - make
+      - ./mathUtilsTest.exec
+      - cd ../..
+
+      - cd unitTests/hdfTest
+      - make
+      - ./hdfTest.exec
+      - cd ../..
+
+      - cd unitTests/mixTest
+      - make
+      - ./mixTest.exec
+      - cd ../..
+
+      - cd unitTests/geometryTest
+      - make
+      - ./geometryTest.exec
+      - cd ../..
+
+      - cd unitTests/metricTest
+      - make -j
+      - ./metricTest_Periodic.exec
+      - ./metricTest_Collocated.exec
+      - ./metricTest_Staggered.exec
+      - cd ../..
+
+      - cd unitTests/cflTest
+      - make
+      - ./cflTest.exec
+      - cd ../..
+
+      - cd unitTests/chemTest
+      - make
+      - ./chemTest.exec
+      - cd ../..
+
+      - cd unitTests/variablesTest
+      - make
+      - ./variablesTest.exec
+      - cd ../..
+
+.solverTests: &solverTests
+   script:
+      - NO_ATOMIC=1 make -j -C src/
+      - cd solverTests
+      - python ./test.py
+      - cd ../..
+
+###
+### Jobs
+###
+
+# Each item below defines a job.
+
+ctr-205-1_release_unitTests:
+   <<: [*ctr-205-1, *unitTests]
+   variables:
+      <<: [*release, *openmp, *hdf5]
+
+ctr-205-1_release_solverTests:
+   <<: [*ctr-205-1, *solverTests]
+   variables:
+      <<: [*release, *openmp, *hdf5]

CHANGES.txt

@@ -0,0 +1,11 @@
+This file lists the major changes as they appear in the master branch.
+
+Version 1.1.0 (April 23, 2020)
+   - basic test suite added to the repository
+   - timing infrastructure added to the main task of the solver
+   - NSCBC_Outflow available on the yNeg surface of the domain
+   - Added compile time flag to dump fields when a NaN appears
+   - Added compile time flag to deactivate atomic coherence mode
+   - New Sinh, SinhPlus, and SinhMinus grid stretching available to the user
+   - Less verbose input for BCs based on unions
+

README.md

@@ -40,6 +40,7 @@ Organization of the repository
    >  > [certainty.slurm](src/certainty.slurm): Submission script for Certainty (@ Stanford) (use as a template script for slurm system)  
    >  > [quartz.slurm](src/quartz.slurm): Submission script for Quartz (@ LLNL) (use as a template script for slurm system)  
    >  > [lassen.lsf](src/lassen.lsf): Submission script for Lassen (@ LLNL) (use as a template script for IBM Spectrum LSF system)  
+   >  > [galileo.slurm](src/galileo.slurm): Submission script for Galileo (@ Cineca) (use as a template script for slurm system)  
    >  > [blacklist](src/blacklist): Folder containing potential blacklists of nodes that should not be used
 
    > [scripts/](scripts/)  
@@ -52,7 +53,7 @@ Organization of the repository
    >  > [modules/](scripts/modules/): Various utility modules used by the python scripts
 
    > [testcases/](testcases/)  
-   >  > [README.md](testcases/README.md): Instructions on how to run the provided testcases
+   >  > [README.md](testcases/README.md): Instructions on how to run the provided testcases  
    >  > [SodProblem/](testcases/SodProblem/): Contains the setup and postporcessing files needed to run Sod's shock tube  
    >  > [LaxProblem/](testcases/LaxProblem/): Contains the setup and postporcessing files needed to run Lax's shock tube  
    >  > [ShuOsherProblem/](testcases/ShuOsherProblem/): Contains the setup and postporcessing files needed to run Shu-Osher's shock tube  
@@ -67,6 +68,23 @@ Organization of the repository
    >  > [MultispeciesTBL/](testcases/MultispeciesTBL/): Contains the setup and postporcessing files needed to run Multispecies hypersonic boundary layer  
    >  > [scalingTest/WS](testcases/scalingTest/WS): Contains the setup and postporcessing files needed to run the weak saling test
 
+   > [unitTests/](unitTests/)  
+   >  > [cflTest/](unitTests/cflTest/): Contains the unit test for the cfl module  
+   >  > [chemTest/](unitTests/chemTest/): Contains the unit test for the chemistry module  
+   >  > [configTest/](unitTests/configTest/): Contains the unit test for the config schema module  
+   >  > [geometryTest/](unitTests/geometryTest/): Contains the unit test for the geometry module  
+   >  > [hdfTest/](unitTests/hdfTest/): Contains the unit test for the hdf helper module  
+   >  > [mathUtilsTest/](unitTests/mathUtilsTest/): Contains the unit test for the mathUtils module  
+   >  > [metricTest/](unitTests/metricTest/): Contains the unit test for the metric module  
+   >  > [mixTest/](unitTests/mixTest/): Contains the unit test for the mixture modules  
+   >  > [variablesTest/](unitTests/variablesTest/): Contains the unit test for the variables module  
+
+   > [solverTests/](solverTests/)  
+   >  > [3DPeriodic/](solverTests/3DPeriodic/): Contains the solver test for the tri-periodic 3D testcase  
+   >  > [3DPeriodic_Air/](solverTests/3DPeriodic_Air): Contains the solver test for the tri-periodic 3D testcase with AirMix  
+   >  > [ChannelFlow/](solverTests/ChannelFlow): Contains the solver test for the bi-periodic ChannelFlow testcase  
+   >  > [BoundaryLayer/](solverTests/BoundaryLayer): Contains the solver test for a compressible boundary layer  
+
 
 Setup (generic)
 ===============
@@ -347,6 +365,8 @@ export CUDA_HOME=/usr/tce/packages/cuda/cuda-9.2.148
 export CUDA="$CUDA_HOME"
 export GPU_ARCH=volta
 
+export GROUP=???
+
 export USE_CUDA=1
 export USE_OPENMP=1
 export USE_GASNET=1
@@ -376,3 +396,59 @@ lalloc 1 scripts/setup_env.py --llvm-version 38 --terra-branch 'puc_lua_master'
 cd "$HTR_DIR"/src
 lalloc 1 -W 120 make
 ```
+
+Setup (Galileo @ Cineca)
+============================
+
+### Add to shell startup
+
+```
+# Module loads
+module load gnu
+module load openmpi/3.1.1--gnu--6.1.0
+module load cuda/9.0
+module load python
+# Build config
+export CC=gcc
+export CXX=g++
+export CONDUIT=ibv
+# Path setup
+export LEGION_DIR=???
+export HDF_ROOT="$LEGION_DIR"/language/hdf/install
+export HTR_DIR=???
+export SCRATCH=???
+# CUDA config
+export CUDA_HOME="/cineca/prod/compilers/cuda/9.0/none"
+export CUDA="$CUDA_HOME"
+export GPU_ARCH=kepler
+
+export ACCOUNT=[ACCOUNT TO BE CHARGED]
+
+export USE_CUDA=1
+export USE_OPENMP=1
+export USE_GASNET=1
+export USE_HDF=1
+export MAX_DIM=4
+
+```
+
+### Download software
+
+```
+git clone -b htr-release https://gitlab.com/mario.direnzo/legion.git "$LEGION_DIR"
+git clone https://[email protected]/mdirenzo/prometeo.git "$HTR_DIR"
+```
+
+### Install Legion
+
+```
+cd "$LEGION_DIR"/language
+scripts/setup_env.py --llvm-version 38 --terra-url 'https://github.com/StanfordLegion/terra.git' --terra-branch 'luajit2.1'
+```
+
+### Compile Prometeo
+
+```
+cd "$HTR_DIR"/src
+srun --cpus-per-task=3 --mem 30000 -p gll_usr_gpuprod -t 0:50:00 make -j &
+```