Working 0-1D Chemistry (among other things) (#653)

Co-authored-by: Dimitrios Adam <[email protected]>
Co-authored-by: Henry Le Berre <[email protected]>

Author: henryleberre

.github/CODEOWNERS

@@ -13,3 +13,5 @@ CMakeLists.txt     @sbryngelson @henryleberre
 .vscode/           @sbryngelson @henryleberre
 .github/workflows/ @sbryngelson @henryleberre
 
+# Spencer H. Bryngelson & Ben Wilfong
+.typos.toml        @sbryngelson @wilfonba

.github/file-filter.yml

@@ -7,7 +7,7 @@ fortran_src: &fortran_src
 
 python_src: &python_src
   - '**/*.py'
-  - 'toolchain/requirements.txt'
+  - 'toolchain/pyproject.toml'
 
 cmakelist: &cmakelist
   - 'CMakeLists.txt'

CMakeLists.txt

@@ -133,6 +133,8 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
             -fimplicit-none
             #-ffpe-trap=invalid,zero,denormal,overflow
             -fsignaling-nans
+            -finit-real=snan
+            -finit-integer=-99999999
 	    )
     endif()
 

README.md

@@ -68,7 +68,7 @@ cd MFC
 ```
 and be sure MFC knows where to find Boost by appending to your dotfiles and sourcing them again
 ```shell
-echo -e 'export BOOST_INCLUDE=/opt/homebrew/' | tee -a ~/.bash_profile ~/.zshrc
+echo -e "export BOOST_INCLUDE='$(brew --prefix --installed boost)/include'" | tee -a ~/.bash_profile ~/.zshrc
 . ~/.bash_profile 2>/dev/null || . ~/.zshrc 2>/dev/null
 ! [ -z "${BOOST_INCLUDE+x}" ] && echo 'Environment is ready!' || echo 'Error: $BOOST_INCLUDE is unset. Please adjust the previous commands to fit with your environment.'
 ```

benchmarks/5eq_rk3_weno3_hllc/case.py

@@ -14,11 +14,13 @@
     description="This MFC case was created for the purposes of benchmarking MFC.",
     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-parser.add_argument("dict", type=str, metavar="DICT", help=argparse.SUPPRESS)
-parser.add_argument("gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
+parser.add_argument("--mfc", type=json.loads, default='{}', metavar="DICT",
+                    help="MFC's toolchain's internal state.")
+parser.add_argument("--gbpp", type=int, metavar="MEM", default=16,
+                    help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
 
 ARGS = vars(parser.parse_args())
-DICT = json.loads(ARGS["dict"])
+DICT = ARGS["mfc"]
 
 size = 1 if DICT["gpu"] else 0
 

benchmarks/hypo_hll/case.py

@@ -12,11 +12,13 @@
     description="This MFC case was created for the purposes of benchmarking MFC.",
     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-parser.add_argument("dict", type=str, metavar="DICT", help=argparse.SUPPRESS)
-parser.add_argument("gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
+parser.add_argument("--mfc", type=json.loads, default='{}', metavar="DICT",
+                    help="MFC's toolchain's internal state.")
+parser.add_argument("--gbpp", type=int, metavar="MEM", default=16,
+                    help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
 
 ARGS = vars(parser.parse_args())
-DICT = json.loads(ARGS["dict"])
+DICT = ARGS["mfc"]
 
 size = 1 if DICT["gpu"] else 0
 

benchmarks/ibm/case.py

@@ -11,11 +11,13 @@
     description="This MFC case was created for the purposes of benchmarking MFC.",
     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-parser.add_argument("dict", type=str, metavar="DICT", help=argparse.SUPPRESS)
-parser.add_argument("gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
+parser.add_argument("--mfc", type=json.loads, default='{}', metavar="DICT",
+                    help="MFC's toolchain's internal state.")
+parser.add_argument("--gbpp", type=int, metavar="MEM", default=16,
+                    help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
 
 ARGS = vars(parser.parse_args())
-DICT = json.loads(ARGS["dict"])
+DICT = ARGS["mfc"]
 
 size = 1 if DICT["gpu"] else 0
 

benchmarks/viscous_weno5_sgb_acoustic/case.py

@@ -16,11 +16,13 @@
     description="This MFC case was created for the purposes of benchmarking MFC.",
     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-parser.add_argument("dict", type=str, metavar="DICT", help=argparse.SUPPRESS)
-parser.add_argument("gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
+parser.add_argument("--mfc", type=json.loads, default='{}', metavar="DICT",
+                    help="MFC's toolchain's internal state.")
+parser.add_argument("--gbpp", type=int, metavar="MEM", default=16,
+                    help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
 
 ARGS = vars(parser.parse_args())
-DICT = json.loads(ARGS["dict"])
+DICT = ARGS["mfc"]
 
 size = 1 if DICT["gpu"] else 0
 

docs/documentation/case.md

@@ -34,24 +34,26 @@ Input files can accept command line arguments, forwarded by `mfc.sh run`.
 Consider this example from the `scaling` case:
 
 ```python
-import argparse
+import json, argparse
 
 parser = argparse.ArgumentParser(
     prog="scaling",
     description="Weak- and strong-scaling benchmark case.",
     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-parser.add_argument("dict", type=str, metavar="DICT")
-parser.add_argument("-s", "--scaling",  type=str, metavar="SCALING",  choices=["weak", "strong"], help="Whether weak- or strong-scaling is being exercised.")
+parser.add_argument("--mfc", type=json.loads, default='{}', metavar="DICT",
+                    help="MFC's toolchain's internal state.")
+parser.add_argument("-s", "--scaling", type=str, metavar="SCALING", choices=["weak", "strong"],
+                    help="Whether weak- or strong-scaling is being exercised.")
 
 # Your parsed arguments are here
 args = parser.parse_args()
 ```
 
-The first argument is always a JSON string representing `mfc.sh run`'s internal
-state.
+The `--mfc` argument is a JSON string representing `mfc.sh run`'s internal
+state, passed in when MFC runs your input file.
 It contains all the runtime information you might want from the build/run system.
-You can add as many additional arguments as you may need.
+You can add as many additional arguments and options as you may need.
 
 To run such a case, use the following format:
 

docs/documentation/getting-started.md

@@ -106,7 +106,7 @@ before configuring your environment:
 
 ```shell
 brew install coreutils python cmake fftw hdf5 gcc boost open-mpi
-echo -e 'export BOOST_INCLUDE=/opt/homebrew/' | tee -a ~/.bash_profile ~/.zshrc
+echo -e "export BOOST_INCLUDE='$(brew --prefix --installed boost)/include'" | tee -a ~/.bash_profile ~/.zshrc
 . ~/.bash_profile 2>/dev/null || . ~/.zshrc 2>/dev/null
 ! [ -z "${BOOST_INCLUDE+x}" ] && echo 'Environment is ready!' || echo 'Error: $BOOST_INCLUDE is unset. Please adjust the previous commands to fit with your environment.'
 ```