Merge pull request #230 from PrincetonUniversity/make_improvements

Make improvements

Author: matt-pharr

.github/workflows/make_test.yml

@@ -26,7 +26,6 @@ jobs:
       - name: Install dependencies
         if: steps.netcdf-cache.outputs.cache-hit != 'true'
         run: |
-          sudo rm /var/lib/man-db/auto-update
           sudo apt update
           sudo apt install -y build-essential gfortran m4 curl libhdf5-dev libnetcdf-dev
 
@@ -85,7 +84,6 @@ jobs:
       - name: Install Intel oneAPI + deps
         if: steps.netcdf-cache.outputs.cache-hit != 'true'
         run: |
-          sudo rm /var/lib/man-db/auto-update
           wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
           echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
           sudo apt update
@@ -154,13 +152,16 @@ jobs:
 
       - name: Rewrite .gitmodules to use HTTPS
         run: |
-          git config --file .gitmodules submodule.harvest.url https://github.com/gafusion/harvest_client.git
+          git config --file .gitmodules submodule."deps/src/harvest".url https://github.com/gafusion/harvest_client.git
+          git config --file .gitmodules submodule."deps/src/netcdf-c".url https://github.com/Unidata/netcdf-c.git
+          git config --file .gitmodules submodule."deps/src/netcdf-fortran".url https://github.com/Unidata/netcdf-fortran.git
+          git config --file .gitmodules submodule."deps/src/hdf5".url https://github.com/HDFGroup/hdf5.git
+          git config --file .gitmodules submodule."deps/src/OpenBLAS".url https://github.com/OpenMathLib/OpenBLAS.git
           git submodule sync
-          git submodule update --init --recursive
+          git submodule update --init --recursive "deps/src/harvest"
           
       - name: Install Dependencies
         run: |
-          sudo rm /var/lib/man-db/auto-update
           sudo apt update
           sudo apt install -y gfortran libopenblas-dev libx11-dev libnetcdf-dev
 
@@ -173,7 +174,7 @@ jobs:
           export FC=/usr/bin/gfortran
           export CC=/usr/bin/gcc
           export FFLAGS='-fallow-argument-mismatch -O0 -Wall -Wextra -fcheck=all,no-array-temps -fbacktrace -finit-real=snan -finit-integer=-9999 -fstack-protector-all -fsanitize=bounds -Wno-array-temporaries -Wno-unused-variable -Wno-unused-dummy-argument -Wno-compare-reals -Wno-unused-parameter -Wno-unused-label -fno-omit-frame-pointer -frecord-marker=4 -gdwarf-4 -ffloat-store -fbounds-check'
-          make
+          make -j$(nproc)
 
       - name: Run Soloviev ideal example
         run: |
@@ -217,7 +218,6 @@ jobs:
 
       - name: Install Intel oneAPI + deps
         run: |
-          sudo rm /var/lib/man-db/auto-update
           wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
           echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
           sudo apt update
@@ -233,9 +233,12 @@ jobs:
 
       - name: Rewrite .gitmodules to use HTTPS
         run: |
-          git config --file .gitmodules submodule.harvest.url https://github.com/gafusion/harvest_client.git
-          git submodule sync
-          git submodule update --init --recursive
+          git config --file .gitmodules submodule."deps/src/harvest".url https://github.com/gafusion/harvest_client.git
+          git config --file .gitmodules submodule."deps/src/netcdf-c".url https://github.com/Unidata/netcdf-c.git
+          git config --file .gitmodules submodule."deps/src/netcdf-fortran".url https://github.com/Unidata/netcdf-fortran.git
+          git config --file .gitmodules submodule."deps/src/hdf5".url https://github.com/HDFGroup/hdf5.git
+          git config --file .gitmodules submodule."deps/src/OpenBLAS".url https://github.com/OpenMathLib/OpenBLAS.git
+          git submodule update --init --recursive "deps/src/harvest"
 
       - name: Compile
         run: |
@@ -247,7 +250,7 @@ jobs:
           export FC=/opt/intel/oneapi/compiler/2022.2.1/linux/bin/intel64/ifort
           export CC=/usr/bin/gcc
           export FFLAGS='-O0 -warn all -check all -check noarg_temp_created -traceback -fpe3 -fstack-protector -fopenmp'
-          make
+          make -j$(nproc)
 
       - name: Run Soloviev ideal example
         run: |

.gitignore

@@ -9,6 +9,7 @@
 *.mod
 *.pyc
 *~
+*.i
 *.out
 *.bin
 *.nc
@@ -31,6 +32,12 @@ docs/examples/*/gal_solution.dat
 docs/examples/*/delta_gw.dat
 docs/examples/*/gal_solution_cut.dat
 
+deps/bin/*
+deps/hdf5
+deps/include/*
+deps/lib/*
+deps/share/*
+
 *version.inc
 
 dcon/dcon

.gitmodules

@@ -1,3 +1,15 @@
-[submodule "harvest"]
-	path = harvest
-	url = git@github.com:gafusion/harvest_client.git
+[submodule "deps/src/harvest"]
+	path = deps/src/harvest
+	url = https://github.com/gafusion/harvest_client.git
+[submodule "deps/src/OpenBLAS"]
+	path = deps/src/OpenBLAS
+	url = https://github.com/OpenMathLib/OpenBLAS.git
+[submodule "deps/src/netcdf-c"]
+	path = deps/src/netcdf-c
+	url = https://github.com/Unidata/netcdf-c.git
+[submodule "deps/src/netcdf-fortran"]
+	path = deps/src/netcdf-fortran
+	url = https://github.com/Unidata/netcdf-fortran.git
+[submodule "deps/src/hdf5"]
+	path = deps/src/hdf5
+	url = https://github.com/HDFGroup/hdf5.git