Sync Upstream -- 2026.04.15

.github/workflows/common-workflow.yml

@@ -109,7 +109,9 @@ jobs:
           ${{ inputs.build_command }}
 
       - name: Compile ISSM
-        run: make -j4 install
+        run: |
+          make -j4 
+          make install
 
       - name: Compress ISSM artifact
         run: |

CLAUDE.md

@@ -0,0 +1,114 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## What is ISSM
+
+ISSM (Ice-sheet and Sea-level System Model) is a large-scale thermo-mechanical 2D/3D parallelized multi-purpose finite-element software for ice sheet and sea-level modeling. It is written in C++ (computational core) with MATLAB, Python, and JavaScript interfaces.
+
+## Environment Setup
+
+Before building or running anything, set `ISSM_DIR` in your shell profile (`.bashrc`/`.zshrc`) pointing to the repository root, then source the environment script:
+
+```sh
+export ISSM_DIR=/path/to/ISSM
+source $ISSM_DIR/etc/environment.sh
+```
+
+## Build
+
+External packages must be installed before configuring ISSM. The minimum required set for a basic build:
+
+```sh
+cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh    # or install-mac.sh
+cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
+cd $ISSM_DIR/externalpackages/petsc    && ./install-3.22-linux.sh
+```
+
+Then configure and build:
+
+```sh
+source $ISSM_DIR/etc/environment.sh
+autoreconf -ivf
+./configure.sh        # local config script (adjust paths as needed), or run ./configure directly
+make -j$(nproc)
+make install
+```
+
+Key `configure` flags: `--prefix=$ISSM_DIR`, `--with-matlab-dir`, `--with-python`, `--with-petsc-dir`, `--with-triangle-dir`, `--with-m1qn3-dir`, `--enable-debugging`.
+
+## Running Tests
+
+Tests live in `test/NightlyRun/`. Each test is a numbered script (`test101.m` / `test101.py`).
+
+**Python** (from `test/NightlyRun/`):
+```sh
+export PYTHONPATH="$ISSM_DIR/src/m/dev:$PYTHONPATH"
+export PYTHONSTARTUP="$ISSM_DIR/src/m/dev/devpath.py"
+cd $ISSM_DIR/test/NightlyRun
+./runme.py                        # run all nightly tests
+./runme.py -i 101 102             # run specific tests by ID
+./runme.py -i SquareShelf         # run by (partial) name
+./runme.py --benchmark nightly    # benchmark filter
+```
+
+**MATLAB** (from within MATLAB):
+```matlab
+cd([getenv('ISSM_DIR') '/test/NightlyRun'])
+addpath([getenv('ISSM_DIR') '/src/m/dev']); devpath;
+runme                          % run all
+runme('id', [101 102])         % run specific tests
+runme('id', 102, 'procedure', 'update')  % update reference archive (developers only)
+```
+
+To update a test's reference archive (after an intentional result change), use `procedure='update'` (MATLAB) or `--procedure update` (Python).
+
+## Code Architecture
+
+### Dual-layer design
+
+ISSM has two layers that work together:
+
+1. **High-level interfaces** (`src/m/`) — MATLAB (`.m`), Python (`.py`), and JavaScript (`.js`) code for building and parameterizing models, running simulations, and post-processing results. The key object is `model` (defined in `src/m/classes/model.m` / `model.py`), which holds all simulation fields as properties (mesh, geometry, materials, boundary conditions, solver settings, results, etc.).
+
+2. **C++ computational core** (`src/c/`) — compiled finite-element parallel engine that does the actual solving.
+
+The high-level interface generates input files (`.bin`, `.queue`, and `.toolkits`) that are read by the computational core. In turn, the results from the simulation are saved in an `.outbin` file that is read by the High-level interface and added to the model (saved in `md.results`)
+
+### Typical model workflow
+
+```
+triangle/mesh → setmask → parameterize → setflowequation → solve → results
+```
+
+Each step corresponds to functions in `src/m/parameterization/` and `src/m/solve/`. `parameterize()` runs a user-supplied `.par` file that fills the `model` object fields. `solve()` marshals model data to binary, calls the C++ executable (`bin/issm.exe`), and loads results back into `md.results`.
+
+### C++ core layout (`src/c/`)
+
+- **`analyses/`** — One `*Analysis` class per physics type (e.g., `StressbalanceAnalysis`, `ThermalAnalysis`). Each implements the abstract `Analysis` interface: element matrix/vector assembly (`CreateKMatrix`, `CreatePVector`), node/constraint creation, solution update.
+- **`cores/`** — Top-level solution entry points (e.g., `stressbalance_core.cpp`, `transient_core.cpp`). These orchestrate which analyses to run and in what order.
+- **`solutionsequences/`** — Linear/nonlinear/adjoint solvers that call PETSc (via `toolkits/`).
+- **`classes/`** — C++ representations of FEM objects: `Elements/` (Tria, Penta, etc.), `Nodes/`, `Constraints/`, `Loads/`, `Inputs/`, `Params/`, `Materials/`.
+- **`modules/`** — Compiled callable modules exposed as MEX/Python wrappers (e.g., mesh generation, interpolation, partitioning).
+- **`toolkits/`** — Abstraction layer over PETSc, MPI, MUMPS, METIS for linear algebra and distributed computing.
+- **`datastructures/`** — `DataSet` container and `Object` base class used throughout the core.
+
+### Wrappers (`src/wrappers/`)
+
+Glue code that compiles C++ modules as shared libraries loadable from MATLAB (`*_matlab.la`) and Python (`*_python.la`). The `io/` subdirectory handles binary serialization of the `model` object (marshalling) for communication between the interface and the executable.
+
+### External packages (`externalpackages/`)
+
+Each subdirectory has its own `install-linux.sh` / `install-mac.sh` / etc. ISSM only needs a handful of external packages installed depending on the desired configuration. The key dependencies are: 
+- **PETSc** (includes MPI/MPICH, BLAS/LAPACK, MUMPS, METIS/ParMETIS, ScaLAPACK)
+- **Triangle** (mesh generation),
+- **m1qn3** (L-BFGS optimizer for inversions).
+
+Some optional that can be useful depending on the application:
+- **Dakota** (UQ/sampling),
+- **CoDiPack** (automatic differentiation)
+
+### Path setup for interfaces
+
+- **Python**: `src/m/dev/devpath.py` walks `src/m/` and adds all directories containing `.py` files to `sys.path`, plus `$ISSM_DIR/lib` and `$ISSM_DIR/src/wrappers/python/.libs`.
+- **MATLAB**: `src/m/dev/devpath.m` does the equivalent using `addpath` recursively.

configure.ac

@@ -1,13 +1,13 @@
 
 #Initializing configure
-AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[2026.1],[https://github.com/ISSMteam/ISSM/],[issm],[https://issmteam.github.io/ISSM-Documentation/])
+AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[2026.2],[https://github.com/ISSMteam/ISSM/],[issm],[https://issmteam.github.io/ISSM-Documentation/])
 AC_CONFIG_AUX_DIR([./aux-config]) # Put config files in aux-config
 AC_CONFIG_MACRO_DIR([m4])         # m4 macros are located in m4
 m4_include([m4/issm_options.m4])
 
 #print header
 AC_MSG_NOTICE(============================================================================)
-AC_MSG_NOTICE(=      AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration      =)
+AC_MSG_NOTICE(=      AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration    =)
 AC_MSG_NOTICE(============================================================================)
 
 #Determine System type and OS

externalpackages/autotools/install-mac.sh

@@ -4,10 +4,10 @@ set -eu
 
 ## Constants
 #
-AUTOCONF_VER="2.69"
-AUTOMAKE_VER="1.16.1"
-LIBTOOL_VER="2.4.6"
-M4_VER="1.4.19"
+AUTOCONF_VER="2.73"
+AUTOMAKE_VER="1.18.1"
+LIBTOOL_VER="2.5.4"
+M4_VER="1.4.21"
 
 PREFIX="${ISSM_DIR}/externalpackages/autotools/install" # Set to location where external package should be installed
 

externalpackages/chaco/install-linux.sh

@@ -18,7 +18,7 @@ mkdir -p ${PREFIX} src
 
 # Download source
 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/raw/refs/heads/main/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz"
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/blob/main/chaco_user_guide.pdf" "chaco_user_guide.pdf"
+#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/blob/main/chaco_user_guide.pdf" "chaco_user_guide.pdf"
 
 # Unpack source
 tar -xvzf Chaco-${VER}.tar.gz

externalpackages/chaco/install-mac.sh

@@ -18,7 +18,7 @@ mkdir -p ${PREFIX} src
 
 # Download source
 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/raw/refs/heads/main/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz"
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/blob/main/chaco_user_guide.pdf" "chaco_user_guide.pdf"
+#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/blob/main/chaco_user_guide.pdf" "chaco_user_guide.pdf"
 
 # Unpack source
 tar -xvzf Chaco-${VER}.tar.gz

externalpackages/chaco/install-win-msys2-mingw.sh

@@ -14,7 +14,7 @@ mkdir -p ${PREFIX} src
 
 # Download source
 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/raw/refs/heads/main/Chaco-${VER}.tar.gz" "Chaco-${VER}.tar.gz"
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/blob/main/chaco_user_guide.pdf" "chaco_user_guide.pdf"
+#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://github.com/sandialabs/Chaco/blob/main/chaco_user_guide.pdf" "chaco_user_guide.pdf"
 
 # Unpack source
 tar -xvzf Chaco-${VER}.tar.gz

externalpackages/gshhg/install.sh

@@ -4,7 +4,7 @@ set -eu
 
 ## Constants
 #
-VER="2.3.4"
+VER="2.3.7"
 
 PREFIX="${ISSM_DIR}/externalpackages/gshhg/install" # Set to location where external package should be installed
 
@@ -13,7 +13,7 @@ rm -rf ${PREFIX}
 mkdir -p ${PREFIX}
 
 # Download source
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://www.ngdc.noaa.gov/mgg/shorelines/data/gshhg/oldversions/version${VER}/gshhg-gmt-${VER}.tar.gz" "gshhg-gmt-${VER}.tar.gz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://www.soest.hawaii.edu/pwessel/gshhg/gshhg-gmt-${VER}.tar.gz" "gshhg-gmt-${VER}.tar.gz"
 
 # Unpack source
 tar -zxvf gshhg-gmt-${VER}.tar.gz

jenkins/javascript/karma/package.json

@@ -9,7 +9,7 @@
     "karma-junit-reporter": "^1.0.0",
     "karma-phantomjs-launcher": "^1.0.1",
     "karma-requirejs": "^1.0.0",
-    "mathjs": "^13.0.0",
+    "mathjs": "^15.2.0",
     "phantomjs-prebuilt": "^2.1.7",
     "requirejs": "^2.2.0"
   }

m4/analyses.m4

@@ -387,6 +387,20 @@ fi
 AM_CONDITIONAL([HYDROLOGYARMAPW], [test x$HAVE_HYDROLOGYARMAPW = xyes])
 AC_MSG_RESULT($HAVE_HYDROLOGYARMAPW)
 dnl }}}
+dnl with-HydrologyPrescribe{{{
+AC_ARG_WITH([HydrologyPrescribe],
+	AS_HELP_STRING([--with-HydrologyPrescribe = YES], [compile with HydrologyPrescribe capabilities (default is yes)]),
+	[HYDROLOGYPRESCRIBE=$withval],[HYDROLOGYPRESCRIBE=yes])
+AC_MSG_CHECKING(for HydrologyPrescribe capability compilation)
+
+HAVE_HYDROLOGYPRESCRIBE=no 
+if test "x$HYDROLOGYPRESCRIBE" = "xyes"; then
+	HAVE_HYDROLOGYPRESCRIBE=yes
+	AC_DEFINE([_HAVE_HYDROLOGYPRESCRIBE_],[1],[with HydrologyPrescribe capability])
+fi
+AM_CONDITIONAL([HYDROLOGYPRESCRIBE], [test x$HAVE_HYDROLOGYPRESCRIBE = xyes])
+AC_MSG_RESULT($HAVE_HYDROLOGYPRESCRIBE)
+dnl }}}
 dnl with-L2ProjectionBase{{{
 AC_ARG_WITH([L2ProjectionBase],
 	AS_HELP_STRING([--with-L2ProjectionBase = YES], [compile with L2ProjectionBase capabilities (default is yes)]),

m4/issm_options.m4

@@ -2341,6 +2341,32 @@ AC_DEFUN([ISSM_OPTIONS],[
 		AC_MSG_RESULT([${GMSH_VERSION_MAJOR}])
 		AC_DEFINE_UNQUOTED([_GMSH_VERSION_MAJOR_], ${GMSH_VERSION_MAJOR}, [Gmsh major version])
 	fi
+	dnl }}}
+	dnl PyBind11{{{
+	AC_MSG_CHECKING([for pybind11])
+	AC_ARG_WITH(
+		[pybind11-include],
+		AS_HELP_STRING([--with-pybind11-include=DIR], [PyBind11 include directory, necessary for emulator integration]),
+		[PyBind11INCL=${withval}],
+		[PyBind11INCL=""]
+	)
+	AC_ARG_WITH(
+		[pybind11-libflags],
+		AS_HELP_STRING([--with-pybind11-libflags=LIBS], [PyBind11 libraries to be used, necessary for emulator integration]),
+		[PyBind11LIB=${withval}],
+		[PyBind11LIB=""]
+	)
+	if test -z "${PyBind11INCL}"; then
+	   HAVE_PyBind11=no
+	else
+	   HAVE_PyBind11=yes
+
+		AC_DEFINE([_HAVE_PyBind11_], [1], [with PyBind11 in ISSM src])
+		AC_SUBST([PyBind11INCL])
+		AC_SUBST([PyBind11LIB])
+	fi
+	AM_CONDITIONAL([PyBind11], [test "x${HAVE_PyBind11}" == "xyes"])
+   AC_MSG_RESULT([${HAVE_PyBind11}])
 	dnl }}}
 	dnl Capabilities
 	dnl with-bamg{{{

src/c/Makefile.am

@@ -1,4 +1,4 @@
-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @TRIANGLEINCL@ @PETSCINCL@ @AMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @PARMETISINCL@ @METISINCL@ @CHACOINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADOLCINCL@ @CODIPACKINCL@ @ADJOINTPETSCINCL@ @GSLINCL@ @BOOSTINCL@ @ESMFINCL@ @PROJINCL@ @MPLAPACKINCL@
+AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @TRIANGLEINCL@ @PETSCINCL@ @AMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @PARMETISINCL@ @METISINCL@ @CHACOINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADOLCINCL@ @CODIPACKINCL@ @ADJOINTPETSCINCL@ @GSLINCL@ @BOOSTINCL@ @ESMFINCL@ @PROJINCL@ @MPLAPACKINCL@ @PyBind11INCL@
 AM_FCFLAGS = @SEMICINCL@
 
 AUTOMAKE_OPTIONS = subdir-objects
@@ -182,6 +182,7 @@ issm_sources += \
 	./shared/Elements/PrintArrays.cpp \
 	./shared/Elements/PddSurfaceMassBalance.cpp \
 	./shared/Elements/PddSurfaceMassBalanceSicopolis.cpp \
+	./shared/Elements/PddSurfaceMassBalanceFast.cpp \
 	./shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp \
 	./shared/Elements/ComputeMungsmTemperaturePrecipitation.cpp \
 	./shared/Elements/ComputeD18OTemperaturePrecipitationFromPD.cpp \
@@ -492,6 +493,9 @@ endif
 if HYDROLOGYARMAPW
 issm_sources += ./analyses/HydrologyArmapwAnalysis.cpp
 endif
+if HYDROLOGYPRESCRIBE
+issm_sources += ./analyses/HydrologyPrescribeAnalysis.cpp
+endif
 if L2PROJECTIONEPL
 issm_sources += ./analyses/L2ProjectionEPLAnalysis.cpp
 endif
@@ -581,6 +585,11 @@ if OCEAN
 issm_sources += ./modules/OceanExchangeDatax/OceanExchangeDatax.cpp
 endif
 #}}}
+# PyBind11{{{
+if PyBind11
+issm_sources += ./classes/Params/EmulatorParam.cpp
+endif
+#}}}
 # Sampling sources {{{
 if SAMPLING
 issm_sources += \
@@ -860,28 +869,37 @@ LDADD += $(OSLIBS)
 
 issm_SOURCES = main/issm.cpp
 issm_CXXFLAGS= $(CXXFLAGS)
+issm_DEPENDENCIES = libISSMCore.la libISSMModules.la
 
 issm_slc_SOURCES = main/issm_slc.cpp
 issm_slc_CXXFLAGS= $(CXXFLAGS)
+issm_slc_DEPENDENCIES = libISSMCore.la libISSMModules.la
 
 if OCEAN
 bin_PROGRAMS += issm_ocean
 issm_ocean_SOURCES = main/issm_ocean.cpp
 issm_ocean_CXXFLAGS= $(CXXFLAGS)
+issm_ocean_DEPENDENCIES = libISSMCore.la libISSMModules.la
 endif
 
 if KRIGING
 bin_PROGRAMS += kriging
 kriging_SOURCES = main/kriging.cpp
 kriging_CXXFLAGS= $(CXXFLAGS)
+kriging_DEPENDENCIES = libISSMCore.la libISSMModules.la
 endif
 
 if ISSM_DAKOTA
 bin_PROGRAMS += issm_dakota
 issm_dakota_SOURCES = main/issm_dakota.cpp
 issm_dakota_CXXFLAGS= $(CXXFLAGS)
+issm_dakota_DEPENDENCIES = libISSMCore.la libISSMModules.la
 bin_PROGRAMS += issm_post
 issm_post_SOURCES = main/issm_post.cpp
 issm_post_CXXFLAGS= $(CXXFLAGS)
+issm_post_DEPENDENCIES = libISSMCore.la libISSMModules.la
 endif
 #}}}
+
+# Ensure install does not run before build completes
+install-exec-local: $(lib_LTLIBRARIES) $(bin_PROGRAMS)

src/c/analyses/EnthalpyAnalysis.cpp

@@ -45,6 +45,7 @@ void EnthalpyAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomod
 		if(smb_model==SMBpddEnum)				isdynamic=true;
 		if(smb_model==SMBd18opddEnum)			isdynamic=true;
 		if(smb_model==SMBpddSicopolisEnum)	isdynamic=true;
+		if(smb_model==SMBpddFastEnum)	      isdynamic=true;
 	}
 
 	/*Convert spcs from temperatures to enthalpy*/

src/c/analyses/EnumToAnalysis.cpp

@@ -94,6 +94,9 @@ Analysis* EnumToAnalysis(int analysis_enum){
 		#ifdef _HAVE_HYDROLOGYSHREVE_
 		case HydrologyShreveAnalysisEnum : return new HydrologyShreveAnalysis();
 		#endif
+		#ifdef _HAVE_HYDROLOGYPRESCRIBE_
+		case HydrologyPrescribeAnalysisEnum: return new HydrologyPrescribeAnalysis();
+		#endif
 		#ifdef _HAVE_L2PROJECTIONBASE_
 		case L2ProjectionBaseAnalysisEnum : return new L2ProjectionBaseAnalysis();
 		#endif