Merge branch 'dev' into adjust_blocks_sysboundaries_setup

Author: markusbattarbee

.github/workflows/github-ci.yml

@@ -15,7 +15,7 @@ jobs:
     # (to be used in any subsequent compilation and run jobs on said image)
     runs-on: ubuntu-latest
     container: ursg/vlasiator_ci:20230220_1
-    
+
     steps:
       - name: Setup libraries dir
         run: |
@@ -25,26 +25,20 @@ jobs:
           cd library-build
       - name: Build phiprof
         run: |
-          git clone https://github.com/fmihpc/phiprof/ 
+          git clone https://github.com/fmihpc/phiprof/
           cd phiprof/src
           make -j 4 CCC=mpic++
           cp ../include/* $GITHUB_WORKSPACE/libraries/include
           cp ../lib/* $GITHUB_WORKSPACE/libraries/lib
           cd ../..
       - name: Build VLSV
         run: |
-          git clone https://github.com/fmihpc/vlsv.git  
+          git clone https://github.com/fmihpc/vlsv.git
           cd vlsv
           make
           cp libvlsv.a $GITHUB_WORKSPACE/libraries/lib
           cp *.h $GITHUB_WORKSPACE/libraries/include
           cd ..
-      - name: Download vectorclass
-        run: | 
-          git clone https://github.com/vectorclass/version1
-          git clone https://github.com/vectorclass/add-on
-          cp add-on/vector3d/vector3d.h version1/
-          cp version1/*.h $GITHUB_WORKSPACE/libraries/include
       - name: Build papi
         run: |
           git clone https://github.com/icl-utk-edu/papi
@@ -83,7 +77,7 @@ jobs:
     steps:
       - name: Submit library job
         run: |
-          srun --interactive -p arriesgado-jammy -J vlasiator-libs --pty -t 01:00:00 bash -lc 'module load openmpi; cp ~/vlasiator/build_libraries.sh .; ./build_libraries.sh arriesgado'
+          srun --interactive -p arriesgado-jammy -J vlasiator-libs -n 1 -c 4 --pty -t 01:00:00 bash -lc 'module load openmpi; cp ~/vlasiator/build_libraries.sh .; ./build_libraries.sh arriesgado'
       - name: Build libraries tar
         run: tar -czvf libraries-arriesgado.tar.gz libraries-arriesgado/
       - name: Upload libraries as artifact
@@ -102,8 +96,8 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3 
-      with: 
+      uses: actions/checkout@v3
+      with:
         submodules: true
     - name: Download libraries
       uses: actions/download-artifact@v3
@@ -119,17 +113,22 @@ jobs:
    #  - name: Compile vlasiator (Release build)
    #    run: |
    #      srun -M carrington --job-name release_compile --interactive --nodes=1 -n 1 -c 16 --mem=40G -p short -t 0:10:0 bash -c 'module purge; module load GCC/11.2.0; module load OpenMPI/4.1.1-GCC-11.2.0 ; module load PMIx/4.1.0-GCCcore-11.2.0; module load PAPI/6.0.0.1-GCCcore-11.2.0; export VLASIATOR_ARCH=carrington_gcc_openmpi; make clean; make -j 16'
-      
-  
+
+
   build_testpackage:
     # Build Vlasiator with testpackage flags, on the carrington cluster
     # (for subsequent running of the integration test package)
     runs-on: carrington
 
     steps:
+    - name: Clean workspace
+      run: |
+        rm -rf libraries library-build testpackage
+        rm -f libraries.tar.zst dtestpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt
+        rm -f *.xml
     - name: Checkout source
       uses: actions/checkout@v3
-      with: 
+      with:
         submodules: true
     - name: Make clean
       run: VLASIATOR_ARCH=carrington_gcc_openmpi make clean
@@ -159,8 +158,8 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3 
-      with: 
+      uses: actions/checkout@v3
+      with:
         submodules: true
     - name: Download libraries
       uses: actions/download-artifact@v3
@@ -174,7 +173,7 @@ jobs:
       run: VLASIATOR_ARCH=arriesgado make clean
     - name: Compile vlasiator (RISC-V)
       run: |
-          srun --interactive -p arriesgado-jammy -J vlasiator_build --pty -t 01:00:00 bash -lc 'module load boost papi openmpi; export VLASIATOR_ARCH=arriesgado; make -j4'
+          srun --interactive -p arriesgado-jammy -J vlasiator_build -n 1 -c 4 --pty -t 01:00:00 bash -lc 'module load boost papi openmpi; export VLASIATOR_ARCH=arriesgado; make -j4'
     - name: Upload riscv binary
       uses: actions/upload-artifact@v3
       with:
@@ -185,11 +184,16 @@ jobs:
   build_tools:
     # Build vlsvdiff and vlsvextract for testpackage use
     runs-on: carrington
-      
+
     steps:
+    - name: Clean workspace
+      run: |
+        rm -rf libraries library-build testpackage
+        rm -f libraries.tar.zst dtestpackage_check_description.txt testpackage-output.tar.gz metrics.txt stdout.txt stderr.txt testpackage_output_variables.txt
+        rm -f *.xml
     - name: Checkout source
-      uses: actions/checkout@v3 
-      with: 
+      uses: actions/checkout@v3
+      with:
         submodules: true
     - uses: ursg/gcc-problem-matcher@master
     - name: Make clean
@@ -216,7 +220,7 @@ jobs:
     steps:
     - name: Checkout source
       uses: actions/checkout@v3
-      with: 
+      with:
         submodules: true
     - name: Download testpackage binary
       uses: actions/download-artifact@v3
@@ -256,10 +260,10 @@ jobs:
     # Build IonosphereSolverTests miniApp (currently broken)
     runs-on: carrington
       #container: ursg/vlasiator_ci:20230220_1
-    needs: build_libraries
+    needs: [build_libraries]
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3 
+      uses: actions/checkout@v3
       with:
         submodules: true
           #    - name: Download libraries
@@ -283,4 +287,3 @@ jobs:
           mini-apps/ionosphereSolverTests/differentialFlux
           mini-apps/ionosphereSolverTests/sigmaProfiles
         if-no-files-found: error
-

.gitmodules

@@ -2,7 +2,15 @@
 	path = submodules/fsgrid
 	url = git@github.com:fmihpc/fsgrid.git
 
-
 [submodule "submodules/dccrg"]
 	path = submodules/dccrg
-	url = https://github.com/fmihpc/dccrg.git
+	url = git@github.com:fmihpc/dccrg.git
+	branch = vlasiator-version
+
+[submodule "submodules/vectorclass"]
+	path = submodules/vectorclass
+	url = https://github.com/vectorclass/version2
+
+[submodule "submodules/vectorclass-addon"]
+	path = submodules/vectorclass-addon
+	url = https://github.com/vectorclass/add-on

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: Doxyfile|libraries|Makefile|README|INSTALL|testpackage|doc|\.txt|\.tex|\.cfg|\.vtk|\.yml|\.clang-format|\.m$|\.sh|\.py
+exclude: Doxyfile|libraries|Makefile|README|INSTALL|testpackage|doc|\.txt|\.tex|\.cfg|\.vtk|\.clang-format|\.m$|\.sh|\.py
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks

MAKE/Makefile.Freezer

@@ -13,13 +13,13 @@ LNK = mpic++
 ifeq ($(DISTRIBUTION_FP_PRECISION),SPF)
 #Single-precision        
 	VECTORCLASS = VEC8F_AGNER
-	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
+	INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 # 	VECTORCLASS = VEC8F_FALLBACK
 #	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/../vlasiator/vlasovsolver
 else
 #Double-precision
 	VECTORCLASS = VEC4D_AGNER
-	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
+	INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 #	VECTORCLASS = VEC4D_FALLBACK
 #	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/../vlasiator/vlasovsolver
 endif

MAKE/Makefile.carrington_gcc_openmpi

@@ -115,5 +115,5 @@ LIB_PAPI = -lpapi
 INC_EIGEN = -isystem $(LIBRARY_PREFIX)/ -isystem $(LIBRARY_PREFIX)/Eigen/
 INC_FSGRID = -I./submodules/fsgrid/
 INC_DCCRG = -I./submodules/dccrg/
-INC_VECTORCLASS = -isystem $(LIBRARY_PREFIX)/vectorclass/
+INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 

MAKE/Makefile.cubbli20

@@ -53,11 +53,11 @@ LIB_JEMALLOC = #-L$(LIBRARY_PREFIX)/lib -ljemalloc
 
 ifeq ($(DISTRIBUTION_FP_PRECISION),SPF)
 #Single-precision        
-        INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/version1
+        INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 	VECTORCLASS = VEC4F_FALLBACK
 else
 #Double-precision
-        INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/version1
+        INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 	VECTORCLASS = VEC4D_FALLBACK
 endif
 

MAKE/Makefile.docker

@@ -89,5 +89,5 @@ LIB_PAPI = -L$(LIBRARY_PREFIX)/papi/lib -lpapi
 
 INC_EIGEN = -I/usr/include/eigen3
 INC_DCCRG = -I./submodules/dccrg
-INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
+INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 INC_FSGRID = -I./submodules/fsgrid

MAKE/Makefile.github_actions

@@ -84,3 +84,4 @@ LIB_PROFILE = -I $(LIBRARY_PREFIX)/include ${GITHUB_WORKSPACE}/libraries/lib/lib
 INC_PROFILE =
 INC_TOPO =
 
+INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/

MAKE/Makefile.hawk_gcc_mpt

@@ -22,13 +22,13 @@ LNK = mpicxx
 ifeq ($(DISTRIBUTION_FP_PRECISION),SPF)
 #Single-precision        
 	VECTORCLASS = VEC8F_AGNER
-	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass-version1
+	INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 #	VECTORCLASS = VEC8F_FALLBACK
 #	INC_VECTORCLASS = -I$(HOME)/vlasiator/vlasovsolver
 else
 #Double-precision
 	VECTORCLASS = VEC4D_AGNER
-	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass-version1
+	INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 #	VECTORCLASS = VEC4D_FALLBACK
 #	VECTORCLASS = VEC8D_FALLBACK
 #	INC_VECTORCLASS = -I$(HOME)/vlasiator/vlasovsolver
@@ -103,5 +103,5 @@ LIB_PAPI = -L/opt/hlrs/spack/rev-004_2020-06-17/papi/c048e224f-gcc-9.2.0-hxfnx7k
 INC_EIGEN = -I$(LIBRARY_PREFIX)/
 INC_DCCRG = -I./submodules/dccrg
 INC_FSGRID = -I./submodules/fsgrid
-INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass-version1
+INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/
 

MAKE/Makefile.hawk_gcc_openmpi

@@ -85,7 +85,7 @@ LIB_PAPI = -L/opt/hlrs/spack/rev-004_2020-06-17/papi/c048e224f-gcc-9.2.0-hxfnx7k
 INC_EIGEN = -I$(LIBRARY_PREFIX)/
 INC_DCCRG = -I./submodules/dccrg
 INC_FSGRID = -I./submodules/fsgrid
-INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass-version1
+INC_VECTORCLASS = -I ./submodules/vectorclass/ -I ./submodules/vectorclass-addon/vector3d/