GPU Cuda variant

.github/workflows/ubuntu-basic.yml

@@ -55,11 +55,9 @@ jobs:
         --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
         --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
         --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
-        --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \
-        --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
+        --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" 
       ext_pkg_build_command: |
         cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
-        cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
         cd $ISSM_DIR/externalpackages/petsc    && ./install-3.22-linux.sh
         cd $ISSM_DIR/externalpackages/semic    && ./install.sh
       test_cases: '["101:399", "401:899"]'

.github/workflows/ubuntu-codipack.yml

@@ -59,12 +59,10 @@ jobs:
         --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
         --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
         --with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \
-        --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
         --with-medipack-dir="${ISSM_DIR}/externalpackages/medipack/install" \
         --with-codipack-dir="${ISSM_DIR}/externalpackages/codipack/install"
       ext_pkg_build_command: |
         cd $ISSM_DIR/externalpackages/triangle   && ./install-linux.sh
-        cd $ISSM_DIR/externalpackages/m1qn3      && ./install-linux.sh
         cd $ISSM_DIR/externalpackages/petsc      && ./install-3.22-linux.sh
         cd $ISSM_DIR/externalpackages/gsl        && ./install.sh
         cd $ISSM_DIR/externalpackages/codipack   && ./install.sh

.github/workflows/ubuntu-python.yml

@@ -59,11 +59,9 @@ jobs:
         --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
         --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
         --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
-        --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \
-        --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
+        --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" 
       ext_pkg_build_command: |
         cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
-        cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
         cd $ISSM_DIR/externalpackages/petsc    && ./install-3.22-linux.sh
         cd $ISSM_DIR/externalpackages/semic    && ./install.sh
       test_cases: '["101:399", "401:899"]'

.gitignore

@@ -37,6 +37,7 @@ config.h.in~
 config.log
 config.status
 configure
+configure~
 configure.sh
 libtool
 stamp-h1
@@ -96,3 +97,5 @@ examples/Data/*.txt
 examples/Data/*.zip
 examples/Data/Jakobshavn_2008_2011_Composite
 examples/Helheim/Models
+examples/Inversion/*.mat
+examples/Inversion/*.tar.gz

CLAUDE.md

@@ -21,7 +21,6 @@ External packages must be installed before configuring ISSM. The minimum require
 
 ```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
 ```
 
@@ -35,7 +34,7 @@ make -j$(nproc)
 make install
 ```
 
-Key `configure` flags: `--prefix=$ISSM_DIR`, `--with-matlab-dir`, `--with-python`, `--with-petsc-dir`, `--with-triangle-dir`, `--with-m1qn3-dir`, `--enable-debugging`.
+Key `configure` flags: `--prefix=$ISSM_DIR`, `--with-matlab-dir`, `--with-python`, `--with-petsc-dir`, `--with-triangle-dir`, `--enable-debugging`.
 
 ## Running Tests
 
@@ -49,7 +48,9 @@ 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
+./runme.py -b nightly             # benchmark filter (-b/--benchmark: all/nightly/ismip/eismint/thermal/mesh/slc/qmu/...)
+./runme.py -e Dakota              # exclude tests by ID or name (-e/--exclude)
+./runme.py -p update              # update reference archive (-p/--procedure: check/update)
 ```
 
 **MATLAB** (from within MATLAB):
@@ -61,18 +62,20 @@ 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).
+To update a test's reference archive (after an intentional result change), use `procedure='update'` (MATLAB) or `-p 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.).
+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` / `model.js`), 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.
 
+3. **JavaScript interface** (`src/m/js/`, `src/m/classes/model.js`) — browser/WebAssembly interface built via Emscripten, with wrappers in `src/wrappers/javascript/`.
+
 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
@@ -81,7 +84,7 @@ The high-level interface generates input files (`.bin`, `.queue`, and `.toolkits
 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`.
+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` for ice dynamics, `bin/issm_slc.exe` for sea-level change), and loads results back into `md.results`.
 
 ### C++ core layout (`src/c/`)
 
@@ -92,21 +95,29 @@ Each step corresponds to functions in `src/m/parameterization/` and `src/m/solve
 - **`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.
+- **`shared/`** — Shared utilities (I/O helpers, exceptions, enum definitions, math routines) used across the core.
+- **`bamg/`** — BAMG anisotropic mesh generator (alternative to Triangle).
+- **`main/`** — Entry-point source files for the compiled executables (`issm.cpp`, `issm_slc.cpp`, `kriging.cpp`).
 
 ### 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.
+Glue code that compiles C++ modules as shared libraries loadable from MATLAB (`*_matlab.la`), Python (`*_python.la`), and JavaScript (`javascript/` via Emscripten/WebAssembly). 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)
+Some optional packages that can be useful depending on the application:
+- **Dakota** (UQ/sampling)
+- **CoDiPack** / **ADOL-C** (automatic differentiation)
+- **GDAL** / **PROJ** (geospatial data I/O and coordinate transforms)
+- **NetCDF** / **HDF5** (scientific data file formats)
+- **Boost** (C++ utilities)
+- **GSL** (GNU Scientific Library)
+- **Gmsh** (alternative mesh generation)
+- **ESMF** (Earth System Modeling Framework coupling)
 
 ### Path setup for interfaces
 

LICENSE

@@ -1,7 +1,7 @@
 Ice-sheet and Sea-level System Model (ISSM) is a California Institute of 
 Technology Copyright, distributed under BSD 3-Clause License.
 
-Copyright (c) 2002-2024, California Institute of Technology. All rights 
+Copyright (c) 2002-2026, California Institute of Technology. All rights 
 reserved. Based on Government Sponsored Research under contracts NAS7-1407 
 and/or NAS7-03001.
 

configure.ac

@@ -10,6 +10,11 @@ AC_MSG_NOTICE(==================================================================
 AC_MSG_NOTICE(=      AC_PACKAGE_NAME AC_PACKAGE_VERSION configuration    =)
 AC_MSG_NOTICE(============================================================================)
 
+#Make sure options were provided
+AS_IF([test "x$prefix" = "xNONE"],[AC_MSG_ERROR([--prefix is not provided.
+		 Did you run ./configure without any option?
+		 Maybe you meant to run ./configure.sh?])])
+
 #Determine System type and OS
 AC_CANONICAL_TARGET
 

examples/Greenland/runme.py

@@ -17,6 +17,8 @@
 from BamgTriangulate import BamgTriangulate
 from InterpFromMeshToMesh2d import InterpFromMeshToMesh2d
 from scipy.interpolate import griddata
+import matplotlib.pyplot as plt
+import numpy as np
 
 steps = [1]
 
@@ -152,7 +154,7 @@
               'title', 'Surface (m)')
 
     #Line Plots
-    figure
+    plt.figure
 
     #Plot surface mass balance, velocity and volume
     surfmb = []
@@ -190,7 +192,7 @@
     t = np.arange(years_of_simulation[0], years_of_simulation[-1] + 11 / 12, 1 / 12)
     #Area of grid for 5km box
     area_of_grid = 5000 * 5000
-    totalsmb = reshape(np.nansum(smbbox / 1000, axis=(-2, -1)), (len(t), 1)) * area_of_grid
+    totalsmb = np.reshape(np.nansum(smbbox / 1000, axis=(-2, -1)), (len(t), 1)) * area_of_grid
 
     #save surface mass balance mat dataset
     smbmean = np.nanmean(smbbox, axis=(0, 1))

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