Merge branch 'main' into plot

Author: In-Woo Park

.github/workflows/common-workflow.yml

@@ -27,6 +27,7 @@ on:
       python_version:
         required: false
         type: string
+
 env:
   ISSM_DIR: ${{ github.workspace }}
 

.github/workflows/ubuntu-basic.yml

@@ -3,8 +3,29 @@ name: Ubuntu Basic
 on:
   push:
     branches: [ "main" ]
+    paths:
+      - ".github/workflows/common-workflow.yml"
+      - ".github/workflows/ubuntu-basic.yml"
+      - "etc/**"
+      - "externalpackages/**"
+      - "m4/**"
+      - "src/**"
+      - "test/**"
+      - "Makefile.am"
+      - "configure.ac"
   pull_request:
     branches: [ "main" ]
+    paths:
+      - ".github/workflows/common-workflow.yml"
+      - ".github/workflows/ubuntu-basic.yml"
+      - "etc/**"
+      - "externalpackages/**"
+      - "m4/**"
+      - "src/**"
+      - "test/**"
+      - "Makefile.am"
+      - "configure.ac"
+
 env:
   ISSM_DIR: ${{ github.workspace }}
 

.github/workflows/ubuntu-codipack.yml

@@ -3,8 +3,29 @@ name: Ubuntu CodiPack
 on:
   push:
     branches: [ "main" ]
+    paths:
+      - ".github/workflows/common-workflow.yml"
+      - ".github/workflows/ubuntu-codipack.yml"
+      - "etc/**"
+      - "externalpackages/**"
+      - "m4/**"
+      - "src/**"
+      - "test/**"
+      - "Makefile.am"
+      - "configure.ac"
   pull_request:
     branches: [ "main" ]
+    paths:
+      - ".github/workflows/common-workflow.yml"
+      - ".github/workflows/ubuntu-codipack.yml"
+      - "etc/**"
+      - "externalpackages/**"
+      - "m4/**"
+      - "src/**"
+      - "test/**"
+      - "Makefile.am"
+      - "configure.ac"
+
 env:
   ISSM_DIR: ${{ github.workspace }}
 

.github/workflows/ubuntu-python.yml

@@ -3,8 +3,29 @@ name: Ubuntu Python
 on:
   push:
     branches: [ "main" ]
+    paths:
+      - ".github/workflows/common-workflow.yml"
+      - ".github/workflows/ubuntu-python.yml"
+      - "etc/**"
+      - "externalpackages/**"
+      - "m4/**"
+      - "src/**"
+      - "test/**"
+      - "Makefile.am"
+      - "configure.ac"
   pull_request:
     branches: [ "main" ]
+    paths:
+      - ".github/workflows/common-workflow.yml"
+      - ".github/workflows/ubuntu-basic.yml"
+      - "etc/**"
+      - "externalpackages/**"
+      - "m4/**"
+      - "src/**"
+      - "test/**"
+      - "Makefile.am"
+      - "configure.ac"
+
 env:
   ISSM_DIR: ${{ github.workspace }}
 

configure.ac

@@ -29,20 +29,71 @@ AM_PROG_AR
 #Libtool
 LT_INIT([win32-dll])
 
-#Run issm_options.m4
+# =====================================================================
+#  Automatic-Differentiation switches
+# =====================================================================
+AC_ARG_ENABLE([ad],
+  AS_HELP_STRING([--enable-ad],
+                 [Build ISSM with CoDiPack+MediPack (disables PETSc)]),
+  [enable_ad=$enableval],
+  [enable_ad=no])
+
+AC_ARG_WITH([codipack-dir],
+  AS_HELP_STRING([--with-codipack-dir=DIR],  [Prefix of CoDiPack install]),
+  [CODIPACK_DIR=$withval],
+  [CODIPACK_DIR=])
+
+AC_ARG_WITH([medipack-dir],
+  AS_HELP_STRING([--with-medipack-dir=DIR],  [Prefix of MediPack install]),
+  [MEDIPACK_DIR=$withval],
+  [MEDIPACK_DIR=])
+
+# --- Validation & flag embedding -------------------------------------
+if test "x$enable_ad" = "xyes"; then
+  if test -z "$CODIPACK_DIR" || test -z "$MEDIPACK_DIR"; then
+    AC_MSG_ERROR([--enable-ad needs BOTH --with-codipack-dir and --with-medipack-dir])
+  fi
+
+  # Tell source files we are in AD mode
+  AC_DEFINE([ISSM_USE_AD], [1], [Define to 1 if building with automatic differentiation])
+
+  # Drop PETSc automatically (picked up by m4/issm_options.m4)
+  ENABLE_PETSC=no
+  AM_CONDITIONAL([USE_AD], [true])
+else
+  ENABLE_PETSC=yes
+  AM_CONDITIONAL([USE_AD], [false])
+fi
+
+dnl ---- Embed include-paths, lib-paths & libs globally -----------------
+if test "x$enable_ad" = "xyes"; then
+  AM_CPPFLAGS="$AM_CPPFLAGS -I$CODIPACK_DIR/include -I$MEDIPACK_DIR/include -DCODI_ForcedInlines"
+  AM_LDFLAGS="$AM_LDFLAGS -L$CODIPACK_DIR/lib -L$MEDIPACK_DIR/lib"
+  LIBS="$LIBS -lcodi -lmedi"
+fi
+
+dnl  Export the variables so Automake can substitute them
+AC_SUBST([AM_CPPFLAGS])
+AC_SUBST([AM_LDFLAGS])
+AC_SUBST([LIBS])
+
+# ---------------------------------------------------------------------
+#  Run ISSM’s usual option-detection macro collection
+# ---------------------------------------------------------------------
 ISSM_OPTIONS
 
-#List all Makefiles
+# ---------------------------------------------------------------------
+#  Output files
+# ---------------------------------------------------------------------
 AC_CONFIG_FILES([
-	Makefile
-	src/Makefile
-	src/c/Makefile
-	src/wrappers/Makefile
-	src/wrappers/python/Makefile
-	src/wrappers/matlab/Makefile
-	src/wrappers/javascript/Makefile
-	src/m/Makefile
+        Makefile
+        src/Makefile
+        src/c/Makefile
+        src/m/Makefile
+        src/wrappers/Makefile
+        src/wrappers/python/Makefile
+        src/wrappers/matlab/Makefile
+        src/wrappers/javascript/Makefile
 ])
 
-#End of configure.ac
 AC_OUTPUT

etc/environment.sh

@@ -2,22 +2,20 @@
 # have been installed.
 #
 # ISSM_DIR and ISSM_ARCH should have been defined already in your shell
-# settings file (i.e. .bashrc, .cshrc).
+# settings file (i.e., .bashrc, .zshrc, .cshrc).
 #
 # NOTE:
 # - We use <PKG>_ROOT_TEMP variables because all variables are exported to 
 #	environment when this script is source'd. In some cases, this may cause 
 #	conflicts (e.g. on Pleiades, we use the module copy of PETSc, which 
 #	defines PETSC_ROOT).
-#
 
+# Silence `zsh: no matches found: <file>`
 if [[ -n "$ZSH_VERSION" ]]; then
-	# Silence `zsh: no matches found: <file>`
 	setopt +o nomatch 1> /dev/null 2>&1
 fi
 
 ## Functions
-#
 c_include_path_append(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${C_INCLUDE_PATH}" ]; then
@@ -36,7 +34,6 @@ c_include_path_prepend(){ #{{{
 		fi
 	fi
 } #}}}
-
 cpath_append(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${CPATH}" ]; then
@@ -55,7 +52,6 @@ cpath_prepend(){ #{{{
 		fi
 	fi
 } #}}}
-
 cplus_include_path_append(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${CPLUS_INCLUDE_PATH}" ]; then
@@ -74,7 +70,6 @@ cplus_include_path_prepend(){ #{{{
 		fi
 	fi
 } #}}}
-
 dyld_library_path_append(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${DYLD_LIBRARY_PATH}" ]; then
@@ -89,7 +84,6 @@ dyld_library_path_append(){ #{{{
 		fi
 	fi
 } #}}}
-
 dyld_library_path_prepend(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${DYLD_LIBRARY_PATH}" ]; then
@@ -104,7 +98,6 @@ dyld_library_path_prepend(){ #{{{
 		fi
 	fi
 } #}}}
-
 ld_library_path_append(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${LD_LIBRARY_PATH}" ]; then
@@ -119,7 +112,6 @@ ld_library_path_append(){ #{{{
 		fi
 	fi
 } #}}}
-
 ld_library_path_prepend(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${LD_LIBRARY_PATH}" ]; then
@@ -134,7 +126,6 @@ ld_library_path_prepend(){ #{{{
 		fi
 	fi
 } #}}}
-
 library_path_append(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${LIBRARY_PATH}" ]; then
@@ -144,7 +135,6 @@ library_path_append(){ #{{{
 		fi
 	fi
 } #}}}
-
 library_path_prepend(){ #{{{
 	if [ -d "${1}" ]; then
 		if [ -z "${LIBRARY_PATH}" ]; then
@@ -154,7 +144,6 @@ library_path_prepend(){ #{{{
 		fi
 	fi
 } #}}}
-
 path_append(){ #{{{
 	if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then
 		PATH_IN="${1}"
@@ -164,7 +153,6 @@ path_append(){ #{{{
 		export PATH="${PATH}:${PATH_IN}"
 	fi
 } #}}}
-
 path_prepend(){ #{{{
 	if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then
 		PATH_IN="${1}"
@@ -178,11 +166,10 @@ path_prepend(){ #{{{
 path_append "${ISSM_DIR}/aux-config"
 path_append "${ISSM_DIR}/scripts"
 
-# Default path to external packages. Redefine this constant if they are 
-# installed to a different directory. Alternatively, export it on the command 
-# line or in a profile initialization file (that is why we check here if it is 
+# Default path to external packages. Redefine this constant if they are
+# installed to a different directory. Alternatively, export it on the command
+# line or in a profile initialization file (that is why we check here if it is
 # set already).
-#
 if [ -z "${ISSM_EXT_DIR+x}" ]; then
 	export ISSM_EXT_DIR="${ISSM_DIR}/externalpackages"
 fi

scripts/patch_bin.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python3
+import argparse, struct, pathlib
+from typing import Union
+
+FMT2CODE = {"bool":1,"int":2,"double":3}
+
+def locate(fp, field):
+    with fp.open('rb') as f:
+        while (raw:=f.read(4)):
+            namelen = struct.unpack('i', raw)[0]
+            name    = f.read(namelen).decode()
+            reclen  = struct.unpack('q', f.read(8))[0]
+            codepos = f.tell(); code = struct.unpack('i', f.read(4))[0]
+            datapos = f.tell()
+            if name == field: return datapos, code
+            f.seek(reclen-4,1)
+    raise KeyError(field)
+
+def patch(fp: pathlib.Path, field: str, value: Union[str,int,float]):
+    datapos, code = locate(fp, field)
+    with fp.open('r+b') as f:
+        f.seek(datapos)
+        if code==FMT2CODE["double"]:
+            f.write(struct.pack('d', float(value)))
+        elif code==FMT2CODE["int"]:
+            f.write(struct.pack('i', int(value)))
+        elif code==FMT2CODE["bool"]:
+            f.write(struct.pack('i', 1 if value.lower()=='true' else 0))
+        else:
+            raise TypeError("Only scalar bool/int/double supported in-place")
+
+if __name__ == "__main__":
+    p = argparse.ArgumentParser()
+    p.add_argument("-f","--file", required=True)
+    p.add_argument("-n","--name", required=True)
+    p.add_argument("-v","--value", required=True)
+    args = p.parse_args()
+    patch(pathlib.Path(args.file), args.name, args.value)

src/c/classes/Elements/Element.cpp

@@ -3850,6 +3850,7 @@ void       Element::PositiveDegreeDayGCM(){/*{{{*/
 	IssmDouble* smb         = xNew<IssmDouble>(NUM_VERTICES);
 	IssmDouble* accumulation= xNew<IssmDouble>(NUM_VERTICES);
 	IssmDouble* ablation    = xNew<IssmDouble>(NUM_VERTICES);
+	IssmDouble* downscaleT  = xNew<IssmDouble>(NUM_VERTICES);
 	IssmDouble* refreezing	= xNew<IssmDouble>(NUM_VERTICES);
 	/*variables*/
 	IssmDouble rlaps, ref_surf, surface;
@@ -3884,8 +3885,9 @@ void       Element::PositiveDegreeDayGCM(){/*{{{*/
 		ref_s_input->GetInputValue(&ref_surf,gauss);
 		surface_input->GetInputValue(&surface,gauss);
 
-		/*Step 2: downsampling temp with elevation and lapse rate*/
+		/*Step 2: downscaling temp with elevation and lapse rate*/
 		temperature = temperature + rlaps*(ref_surf - surface);
+		downscaleT[iv] = temperature;
 
 		/*Step 3: Accumulation*/
 		if (temperature <= temp_all_solid){
@@ -3912,9 +3914,11 @@ void       Element::PositiveDegreeDayGCM(){/*{{{*/
 	/*Add input to element and Free memory*/
 	this->AddInput(SmbAccumulationEnum,accumulation,P1Enum);
 	this->AddInput(SmbAblationEnum,ablation,P1Enum);
+	this->AddInput(SmbDownscaleTemperatureEnum,downscaleT,P1Enum);
 	this->AddInput(SmbMassBalanceEnum,smb,P1Enum);
 	xDelete<IssmDouble>(accumulation);
 	xDelete<IssmDouble>(ablation);
+	xDelete<IssmDouble>(downscaleT);
 	xDelete<IssmDouble>(refreezing);
 	xDelete<IssmDouble>(smb);
 	delete gauss;

src/c/shared/Enum/Enum.vim

@@ -1166,6 +1166,7 @@ syn keyword cConstant SmbFACEnum
 syn keyword cConstant SmbFACSubstepEnum
 syn keyword cConstant SmbGCMLapseratesEnum
 syn keyword cConstant SmbGCMRefSurfaceEnum
+syn keyword cConstant SmbDownscaleTemperatureEnum
 syn keyword cConstant SmbGdnEnum
 syn keyword cConstant SmbGdniniEnum
 syn keyword cConstant SmbGspEnum

src/c/shared/Enum/EnumDefinitions.h

@@ -1162,6 +1162,7 @@ enum definitions{
 	SmbFACSubstepEnum,
 	SmbGCMLapseratesEnum,
 	SmbGCMRefSurfaceEnum,
+	SmbDownscaleTemperatureEnum,
 	SmbGdnEnum,
 	SmbGdniniEnum,
 	SmbGspEnum,