Merge pull request #1 from hyschive/soliton

Update the soliton setup in Bondi

.github/workflows/copy-doc-to-wiki.yml

@@ -2,13 +2,17 @@ name: Copy doc to wiki
 
 on:
   workflow_dispatch:
+  pull_request_target:
+    types:
+      - closed
 
 env:
-  GIT_AUTHOR_NAME: Actionbot
-  GIT_AUTHOR_EMAIL: [email protected]
+  GIT_AUTHOR_NAME: ${{ github.actor }}
+  GIT_AUTHOR_EMAIL: ${{ secrets.MY_EMAIL }}
 
 jobs:
   job-copy-doc-to-wiki:
+    if: github.event_name == 'workflow_dispatch' || github.event.pull_request.merged == true
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repo

.github/workflows/copy-wiki-to-doc.yml

@@ -4,8 +4,8 @@ on:
   workflow_dispatch:
 
 env:
-  GIT_AUTHOR_NAME: Actionbot
-  GIT_AUTHOR_EMAIL: [email protected]
+  GIT_AUTHOR_NAME: ${{ github.actor }}
+  GIT_AUTHOR_EMAIL: ${{ secrets.MY_EMAIL }}
 
 jobs:
   job-copy-wiki-to-doc:

.github/workflows/update_all_parameter_page.yml

@@ -0,0 +1,40 @@
+name: Update all parameters wiki page
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'example/test_problem/Template/Input__Parameter'
+      - 'tool/wiki/sync_runtime_parameter.py'
+      - 'src/Init/Init_Load_Parameter.cpp'
+
+env:
+  GIT_AUTHOR_NAME: ${{ github.actor }}
+  GIT_AUTHOR_EMAIL: ${{ secrets.MY_EMAIL }}
+
+jobs:
+  Update-all-parameters-page:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.TOKEN_FOR_WIKI }}
+      - name: run script
+        run: |
+          cd tool/wiki
+          python --version
+          python sync_runtime_parameter.py
+      - name: move markdown
+        run: |
+          mv tool/wiki/Runtime-Parameters:-All.md doc/wiki/Runtime-Parameters-related
+      - name: set git config
+        run: |
+          git config --global user.email "${{env.GIT_AUTHOR_EMAIL}}"
+          git config --global user.name "${{env.GIT_AUTHOR_NAME}}"
+      - name: make a commit and push if the file changed
+        run: |
+          git diff --exit-code doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md || \
+          ( git add doc/wiki/Runtime-Parameters-related/Runtime-Parameters:-All.md && \
+          git commit -m "[Workflow] Update all parameters wiki page" && \
+          git push )

.gitignore

@@ -2,6 +2,8 @@
 .DS_Store
 
 *.o
+*.bin
+*~
 
 bin/**
 src/generate_make.sh
@@ -10,6 +12,6 @@ GAMER_CompareData
 GAMER_ExtractUniform
 GAMER_ExtractProfile
 .vscode
-*~
 src/Makefile
 src/Makefile.log
+src/.local_settings

configs/eureka_gnu.config

@@ -7,6 +7,7 @@ HDF5_PATH       /software/hdf5/default
 GRACKLE_PATH
 GSL_PATH        /software/gsl/default
 LIBYT_PATH
+CUFFTDX_PATH    /software/cuFFTDx/default
 
 # compilers
 CXX     g++

configs/eureka_intel.config

@@ -7,6 +7,7 @@ HDF5_PATH       /software/hdf5/default
 GRACKLE_PATH
 GSL_PATH        /software/gsl/default
 LIBYT_PATH
+CUFFTDX_PATH    /software/cuFFTDx/default
 
 # compilers
 CXX     icpc

configs/forerunnerI_gnu.config

@@ -0,0 +1,50 @@
+# forerunnerI
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load gnu_13.2.0/gcc/13.2.0 gnu_13.2.0/fftw/3.3.10 gnu_13.2.0/gsl/2.8.0 gnu_13.2.0/hdf5/1.14.4 gnu_13.2.0/openmpi/5.0.0  gnu_13.2.0/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     g++-13.2.0
+CXX_MPI mpicxx
+
+# flags
+CXXFLAG -g
+CXXFLAG -O3
+#CXXFLAG -std=c++11
+#CXXFLAG -Ofast
+CXXFLAG -Wall
+CXXFLAG -Wextra
+CXXFLAG -Wno-unused-variable
+CXXFLAG -Wno-unused-parameter
+CXXFLAG -Wno-maybe-uninitialized
+CXXFLAG -Wno-unused-but-set-variable
+CXXFLAG -Wno-unused-function
+CXXFLAG -Wno-unused-result
+CXXFLAG -Wno-implicit-fallthrough
+CXXFLAG -Wno-parentheses
+CXXFLAG -Wno-unknown-pragmas
+
+OPENMPFLAG -fopenmp
+
+LIBFLAG
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong
+#CXXFLAG -fsanitize=undefined -fsanitize=address
+#LIBFLAG -fsanitize=undefined -fsanitize=address

configs/forerunnerI_intel.config

@@ -0,0 +1,42 @@
+# forerunnerI
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load intel/2024_01_46 oneapi_2024/fftw/3.3.10 oneapi_2024/gsl/2.8.0 oneapi_2024/hdf5/1.14.4 oneapi_2024/openmpi/5.0.0 oneapi_2024/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     icpx
+CXX_MPI mpicxx
+
+# flags
+# for warning flags fro oneapi, see: https://www.intel.com/content/dam/develop/external/us/en/documents/oneapi_dpcpp_cpp_compiler.pdf
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -fp-model precise -fstack-protector-all
+#CXXFLAG -std=c++11
+#CXXFLAG -gxx-name=YOUR_G++
+CXXFLAG -Werror -Wfatal-errors -Woverflow
+CXXFLAG -Wno-uninitialized -Wno-absolute-value -Wno-unknown-pragmas -diag-disable 3180 -diag-disable 10441
+
+OPENMPFLAG -qopenmp
+
+LIBFLAG -limf
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong  # somehow it can capture issues not detected by -fstack-protector-all
+#LIBFLAG -lssp

configs/mac_clang.config

@@ -0,0 +1,41 @@
+# A "typical" macOS installation without GPU
+FFTW2_PATH      /usr/local/fftw-2.1.5
+MPI_PATH        /usr/local/mpich-3.2
+GSL_PATH        /usr/local/gsl-1.16
+HDF5_PATH       ${HOME}/mambaforge/envs/py312
+
+# compilers
+CXX     clang++
+CXX_MPI mpicxx
+
+# clang flags
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -std=c++11
+#CXXFLAG -Ofast
+CXXFLAG -Wall
+CXXFLAG -Wextra
+CXXFLAG -Wno-unused-variable
+CXXFLAG -Wno-unused-parameter
+CXXFLAG -Wno-uninitialized
+CXXFLAG -Wno-unused-but-set-variable
+CXXFLAG -Wno-unused-function
+CXXFLAG -Wno-unused-result
+CXXFLAG -Wno-implicit-fallthrough
+CXXFLAG -Wno-parentheses
+CXXFLAG -Wno-unknown-pragmas
+CXXFLAG -Wno-mismatched-tags
+CXXFLAG -Wno-deprecated-declarations
+CXXFLAG -Wno-missing-braces
+
+OPENMPFLAG -Xclang -fopenmp
+
+LIBFLAG -lomp
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+#gpu
+GPU_COMPUTE_CAPABILITY -1

configs/mac.config → configs/mac_gnu.config

@@ -1,17 +1,17 @@
 # A "typical" macOS installation without GPU
 FFTW2_PATH      /usr/local/fftw-2.1.5
 MPI_PATH        /usr/local/mpich-3.2
-HDF5_PATH       ${HOME}/miniconda3
 GSL_PATH        /usr/local/gsl-1.16
+HDF5_PATH       ${HOME}/mambaforge/envs/py312
 
 # compilers
-CXX     g++
+CXX     g++-12
 CXX_MPI mpicxx
 
 # gnu flags
 CXXFLAG -g
 CXXFLAG -O3
-#CXXFLAG -std=c++11
+CXXFLAG -std=c++11
 #CXXFLAG -Ofast
 CXXFLAG -Wall
 CXXFLAG -Wextra

configs/spock_intel.config

@@ -7,6 +7,7 @@ HDF5_PATH       /software/hdf5/1.10.6-intel-2023.1.0
 GRACKLE_PATH
 GSL_PATH        /software/gsl/2.6-intel-2023.1.0
 LIBYT_PATH
+CUFFTDX_PATH    /software/cuFFTDx/22.11
 
 # compilers
 CXX     icpc

configs/taiwania3_gnu.config

@@ -0,0 +1,51 @@
+# TaiwaniaIII
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load gcc/13.2.0 gnu_13.2.0/fftw/3.3.10 gnu_13.2.0/gsl/2.8.0 gnu_13.2.0/hdf5/1.14.4 gnu_13.2.0/openmpi/5.0.5  gnu_13.2.0/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     g++
+CXX_MPI mpicxx
+
+# flags
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -std=c++11
+#CXXFLAG -Ofast
+CXXFLAG -Wall
+CXXFLAG -Wextra
+CXXFLAG -Wno-unused-variable
+CXXFLAG -Wno-unused-parameter
+CXXFLAG -Wno-maybe-uninitialized
+CXXFLAG -Wno-unused-but-set-variable
+CXXFLAG -Wno-unused-function
+CXXFLAG -Wno-unused-result
+CXXFLAG -Wno-implicit-fallthrough
+CXXFLAG -Wno-parentheses
+CXXFLAG -Wno-unknown-pragmas
+CXXFLAG -Wno-cast-function-type
+
+OPENMPFLAG -fopenmp
+
+LIBFLAG
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong
+#CXXFLAG -fsanitize=undefined -fsanitize=address
+#LIBFLAG -fsanitize=undefined -fsanitize=address

configs/taiwania3_intel.config

@@ -0,0 +1,41 @@
+# TaiwaniaIII
+### Caution!! Load modules under module_CALAB on TwnIII first before compiling, such that FFTW3_PATH, MPI_PATH, HDF5_PATH and GSL_PATH can be found:
+###     module use  /home/d07222009/module_CALAB
+###     module load intel/2024 intel_2024/fftw/3.3.10 intel_2024/gsl/2.8.0 intel_2024/hdf5/1.14.4 intel_2024/openmpi/5.0.5 intel_2024/openucx/1.18.0
+###
+CUDA_PATH
+FFTW2_PATH
+FFTW3_PATH      $(FFTW3_PATH)
+MPI_PATH        $(MPI_PATH)
+HDF5_PATH       $(HDF5_PATH)
+GRACKLE_PATH
+GSL_PATH        $(GSL_PATH)
+LIBYT_PATH
+CUFFTDX_PATH
+
+# compilers
+CXX     icpx
+CXX_MPI mpicxx
+
+# flags
+CXXFLAG -g
+CXXFLAG -O3
+CXXFLAG -fp-model precise -fstack-protector-all
+#CXXFLAG -std=c++11
+#CXXFLAG -gxx-name=YOUR_G++
+CXXFLAG -Werror -Wfatal-errors -Woverflow
+CXXFLAG -Wno-uninitialized -Wno-absolute-value -Wno-unknown-pragmas -diag-disable 3180 -diag-disable 10441
+
+OPENMPFLAG -qopenmp
+
+LIBFLAG -limf
+
+NVCCFLAG_COM -O3
+#NVCCFLAG_COM -use_fast_math
+NVCCFLAG_FLU -Xptxas -dlcm=ca -prec-div=false -ftz=true
+NVCCFLAG_POT -Xptxas -dlcm=ca
+
+# for debugging
+#CXXFLAG -fstack-protector-all
+#CXXFLAG -fstack-protector-strong  # somehow it can capture issues not detected by -fstack-protector-all
+#LIBFLAG -lssp

configs/template.config

@@ -9,6 +9,7 @@ HDF5_PATH       /path/to/hdf5
 GRACKLE_PATH    /path/to/grackle
 GSL_PATH        /path/to/gsl
 LIBYT_PATH      /path/to/libyt
+CUFFTDX_PATH    /path/to/cufftdx
 
 # 2. Compiler type
 CXX     icpc                    # Serial compiler