Sync upstream -- 2026.02.05

.github/workflows/common-workflow.yml

@@ -12,7 +12,7 @@ on:
       build_command:
         required: true
         type: string
-      ext_install_command:
+      ext_pkg_build_command:
         required: true
         type: string
       test_cases:
@@ -39,46 +39,20 @@ jobs:
       test_matrix: ${{ steps.createTestMatrix.outputs.test_output }}
     steps:
       - name: Free disk space
-        run: |
-          # Source: https://dev.to/mathio/squeezing-disk-space-from-github-actions-runners-an-engineers-guide-3pjg#6-how-to-automate-cleanup-in-your-ci
-          #
-
-          # Remove Java (JDKs)
-          #sudo rm -rf /usr/lib/jvm
-
-          # Remove .NET SDKs
-          sudo rm -rf /usr/share/dotnet
-
-          # Remove Swift toolchain
-          sudo rm -rf /usr/share/swift
-
-          # Remove Haskell (GHC)
-          sudo rm -rf /usr/local/.ghcup
-
-          # Remove Julia
-          sudo rm -rf /usr/local/julia*
-
-          # Remove Android SDKs
-          sudo rm -rf /usr/local/lib/android
-
-          # Remove Chromium (optional if not using for browser tests)
-          sudo rm -rf /usr/local/share/chromium
-
-          # Remove Microsoft/Edge and Google Chrome builds
-          sudo rm -rf /opt/microsoft /opt/google
-
-          # Remove Azure CLI
-          sudo rm -rf /opt/az
-
-          # Remove PowerShell
-          sudo rm -rf /usr/local/share/powershell
-
-          # Remove CodeQL and other toolcaches
-          sudo rm -rf /opt/hostedtoolcache
-
-          docker system prune -af || true
-          docker builder prune -af || true
-          df -h
+        uses: jlumbroso/free-disk-space@main
+        with:
+            # this might remove tools that are actually needed,
+            # if set to "true" but frees about 6 GB
+            tool-cache: false
+
+            # all of these default to true, but feel free to set to
+            # "false" if necessary for your workflow
+            android: true
+            dotnet: true
+            haskell: true
+            large-packages: true
+            docker-images: true
+            swap-storage: true
       - name: Check out copy of repository
         uses: actions/checkout@v4
 
@@ -96,7 +70,7 @@ jobs:
       - name: Prepare external packages
         if: ${{ steps.cache-externalpackages.outputs.cache-hit != 'true' }}
         run: |
-          ${{ inputs.ext_install_command }}
+          ${{ inputs.ext_pkg_build_command }}
 
       - name: Get MATLAB
         if: ${{ inputs.interface == 'matlab' }}
@@ -138,7 +112,12 @@ jobs:
         run: make -j4 install
 
       - name: Compress ISSM artifact
-        run: tar --exclude='./externalpackages/petsc/src' -cvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar -C ${{ env.ISSM_DIR }}/ .
+        run: |
+          rm -rf .git
+          find externalpackages -maxdepth 1 -name src -exec rm -rf {} \;
+          find externalpackages -maxdepth 1 -name *tar.gz -exec rm -rf {} \;
+          find externalpackages -maxdepth 1 -name *zip -exec rm -rf {} \;
+          tar --exclude='./externalpackages/petsc/src' -cvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar -C ${{ env.ISSM_DIR }}/ .
 
       - name: Upload ISSM artifact
         uses: actions/upload-artifact@v4
@@ -166,6 +145,7 @@ jobs:
       - name: Unpack ISSM artifact
         run: |
           tar -xvf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar
+          rm -rf ISSM_artifact-${{ runner.os }}-${{ inputs.build_type }}.tar
           source $ISSM_DIR/etc/environment.sh
         working-directory: ${{ env.ISSM_DIR }}
         shell: 'bash'
@@ -175,7 +155,7 @@ jobs:
         id: setup-matlab
         uses: matlab-actions/setup-matlab@v2
         with:
-          release: R2023b
+          release: R2025b
           cache: true
 
       - name: Creating matlab_ci.m

.github/workflows/ubuntu-basic.yml

@@ -57,7 +57,7 @@ jobs:
         --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
         --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \
         --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
-      ext_install_command: |
+      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

.github/workflows/ubuntu-codipack.yml

@@ -62,7 +62,7 @@ jobs:
         --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_install_command: |
+      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

.github/workflows/ubuntu-python.yml

@@ -61,7 +61,7 @@ jobs:
         --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
         --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \
         --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
-      ext_install_command: |
+      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

.gitignore

@@ -95,3 +95,4 @@ examples/Data/*.mat
 examples/Data/*.txt
 examples/Data/*.zip
 examples/Data/Jakobshavn_2008_2011_Composite
+examples/Helheim/Models

README.md

@@ -8,11 +8,12 @@
 ISSM is a large-scale thermo-mechanical 2D/3D parallelized multi-purpose finite-element software dedicated to ice sheet and sea-level modeling.
 
 ## Documentation
-<a href="https://issmteam.github.io/ISSM-Documentation" target="_blank">Just The Docs</a>
+A complete <a href="https://issmteam.github.io/ISSM-Documentation" target="_blank">documentation</a> is available <a href="https://issmteam.github.io/ISSM-Documentation" target="_blank">here</a>.
 
 ## Contact
  - Bug Reporting: Please direct compile and run time bug reports strictly related to ISSM's core code or API's to the 'Issues' page.
  - Questions: Please direct all other questions (e.g. model setup, configuration/compiling on a particular platform, compute cluster configuration) to the 'Discussions' page.
+ - <a href="https://github.com/ISSMteam/ISSM/discussions/113" target="_blank">Slack Workspace</a>
  - Website:	https://issm.jpl.nasa.gov (will be decommissioned soon)
 
 ## Checking Out a Copy of the Repository

configure.ac

@@ -1,8 +1,8 @@
 
 #Initializing configure
-AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.24],[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
+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_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

etc/environment.csh

@@ -98,11 +98,6 @@ if ( -d {$PETSC_ROOT} ) then
 	endif
 endif
 
-set SCOTCH_ROOT="{$ISSM_EXT_DIR}/scotch/install"
-if ( -d {$SCOTCH_ROOT} ) then
-	setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SCOTCH_ROOT}/lib
-endif
-
 set DAKOTA_ROOT="{$ISSM_EXT_DIR}/dakota/install"
 if ( -d {$DAKOTA_ROOT} ) then
 	setenv PATH {$PATH}:{$DAKOTA_ROOT}/bin
@@ -202,11 +197,6 @@ if ( -d {$TRIANGLE_ROOT} ) then
 	setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:{$TRIANGLE_ROOT}/lib
 endif
 
-set YAMS_ROOT="{$ISSM_EXT_DIR}/yams/install"
-if ( -d {$YAMS_ROOT} ) then
-	setenv PATH {$PATH}:{$YAMS_ROOT}
-endif
-
 set VALGRIND_ROOT="{$ISSM_EXT_DIR}/valgrind/install"
 if ( -d {$VALGRIND_ROOT} ) then
 	setenv PATH {$VALGRIND_ROOT}/bin:{$PATH}

etc/environment.sh

@@ -339,9 +339,6 @@ if [ -d "${ADJOINTPETSC_TEMP}" ]; then
 	ld_library_path_append "${ADJOINTPETSC_TEMP}/lib"
 fi
 
-SCOTCH_ROOT_TEMP="${ISSM_EXT_DIR}/scotch/install"
-ld_library_path_append "${SCOTCH_ROOT_TEMP}/lib"
-
 BOOST_ROOT_TEMP="${ISSM_EXT_DIR}/boost/install"
 if [ -d "${BOOST_ROOT_TEMP}" ]; then
 	export BOOST_ROOT=${BOOST_ROOT_TEMP} # Used in installation of Dakota
@@ -445,16 +442,6 @@ if [ -d "${TRIANGLE_ROOT_TEMP}" ]; then
 	fi
 fi
 
-BBFTP_ROOT_TEMP="${ISSM_EXT_DIR}/bbftp/install"
-if [ -d "${BBFTP_ROOT_TEMP}" ]; then
-	path_append "${BBFTP_ROOT_TEMP}/bin"
-fi
-
-SHAPELIB_ROOT_TEMP="${ISSM_EXT_DIR}/shapelib/install"
-if [ -d "${SHAPELIB_ROOT_TEMP}" ]; then
-	path_append "${SHAPELIB_ROOT_TEMP}/exec"
-fi
-
 ESMF_ROOT_TEMP="${ISSM_EXT_DIR}/esmf/install"
 if [ -d "${ESMF_ROOT_TEMP}" ]; then
 	path_prepend "${ESMF_ROOT_TEMP}/bin"
@@ -466,11 +453,6 @@ if [ -d "${NEOPZ_ROOT_TEMP}" ]; then
 	export REFPATTERNDIR="${NEOPZ_ROOT_TEMP}/include/refpatterns"
 fi
 
-YAMS_ROOT_TEMP="${ISSM_EXT_DIR}/yams/install"
-if [ -d "${YAMS_ROOT_TEMP}" ]; then
-	path_prepend "${YAMS_ROOT_TEMP}"
-fi
-
 VALGRIND_ROOT_TEMP="${ISSM_DIR}/externalpackages/valgrind/install"
 if [ -d "${VALGRIND_ROOT_TEMP}" ]; then
 	path_prepend "${VALGRIND_ROOT_TEMP}/bin"

externalpackages/adjointpetsc/install-andes.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf install src build
+
+#Download development version
+git clone https://github.com/SciCompKL/adjoint-PETSc.git src
+mkdir install
+mkdir build
+
+grep -rl 'remove_cvref_t' . | xargs sed -i 's/std::remove_cvref_t<\([A-Za-z0-9_]*\)>/std::remove_cv_t<std::remove_reference_t<\1>>/g'
+
+$ISSM_DIR/externalpackages/cmake/install/bin/cmake src \
+    -B build \
+    -DBUILD_TESTING=OFF \
+    -DBUILD_EXAMPLES=OFF \
+    -DCMAKE_BUILD_TYPE=RELEASE \
+    -DBUILD_SHARED_LIBS=ON \
+    -DCMAKE_INSTALL_PREFIX=$ISSM_DIR/externalpackages/adjointpetsc/install \
+    -DCoDiPack_DIR=$ISSM_DIR/externalpackages/codipack/install/cmake \
+    -DPETSc_DIR=$ISSM_DIR/externalpackages/petsc/install
+
+if [ $# -eq 0 ]; then
+  cmake --build build
+else
+  cmake --build build -j $1
+fi
+cmake --install build

externalpackages/cppcheck/install.sh

@@ -1,23 +1,21 @@
 #!/bin/bash
 set -eu
 
-#Erase install
-rm -rf install  src cppcheck-1.48
-mkdir src
 
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/cppcheck-1.48.tar' 'cppcheck-1.48.tar'
-tar -xvf cppcheck-1.48.tar
+## Constants
+#
+PREFIX="${ISSM_DIR}/externalpackages/cppcheck/install" # Set to location where external package should be installed
 
-mv cppcheck-1.48/* src
-rm -rf cppcheck-1.48
+# Cleanup
+rm -rf ${PREFIX} src
 
-#compile
+# Download source
+git clone [email protected]:danmar/cppcheck.git src
+
+# Compile and install
 cd src
 if [ $# -eq 0 ]; then
-	make 
-else 
-	make -j $1
-fi  
-make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install
-cd ..
+	make MATCHCOMPILER=yes FILESDIR="${PREFIX}" HAVE_RULES=yes CXXFLAGS="-O2 -DNDEBUG -Wall -Wno-sign-compare -Wno-unused-function"
+else
+	make -j $1 MATCHCOMPILER=yes FILESDIR="${PREFIX}" HAVE_RULES=yes CXXFLAGS="-O2 -DNDEBUG -Wall -Wno-sign-compare -Wno-unused-function"
+fi

externalpackages/esmf/install.sh

@@ -1,21 +1,30 @@
 #!/bin/bash
 set -eu
 
-#DOC: https://earthsystemmodeling.org/docs/nightly/develop/ESMC_crefdoc/node5.html#SECTION05063000000000000000
-# https://cpp.hotexamples.com/examples/-/-/ESMC_MeshAddNodes/cpp-esmc_meshaddnodes-function-examples.html
-
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/ESMF_8_0_1.tar.gz" "ESMF_8_0_1.tar.gz"
-tar -zxvf ESMF_8_0_1.tar.gz
-mv ESMF_8_0_1 esmf
-export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf
-export ESMF_INSTALL_PREFIX=$ISSM_DIR/externalpackages/esmf/install
-
-#Compile and install esmf
-cd esmf
-if [ $# -eq 0 ]; then
-	make
-	make install
-else
-	make -j $1
-	make -j $1 install
-fi
+## Sources
+# - https://earthsystemmodeling.org/docs/nightly/develop/ESMC_crefdoc/node5.html#SECTION05063000000000000000
+# - https://cpp.hotexamples.com/examples/-/-/ESMC_MeshAddNodes/cpp-esmc_meshaddnodes-function-examples.html
+
+## Constants
+#
+PREFIX="${ISSM_DIR}/externalpackages/math77/install" # Set to location where external package should be installed
+
+VER="8_0_1"
+
+export ESMF_DIR="${ISSM_DIR}/externalpackages/esmf/src"
+export ESMF_INSTALL_PREFIX="${PREFIX}"
+
+# Cleanup
+rm -rf ${PREFIX} src
+
+# Download source
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://github.com/esmf-org/esmf/archive/refs/tags/ESMF_${VER}.tar.gz" "ESMF_${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf ESMF_${VER}.tar.gz
+mv esmf-ESMF_${VER} ${ESMF_DIR}
+
+# Compile and install
+cd ${ESMF_DIR}
+make
+make install