schism-dev · tomsail · Oct 28, 2025 · Oct 29, 2025 · Oct 29, 2025 · Nov 3, 2025
diff --git a/.github/workflows/build_docs_latest.yml b/.github/workflows/build_docs_latest.yml
@@ -3,31 +3,38 @@ on:
   push:
     branches:
       - master
-      - docs
+      - docs_update
+permissions:
+  contents: write
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
+      - name: Configure git user
+        run: |
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+
       - name: Setup python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: '3.11'
+          cache: 'pip'
+
       - name: Install python packages
-        run: pip install mkdocs==1.5.2 mkdocs-material==8.3.4 mike==1.1.2 setuptools
-      - name: Configure git user
         run: |
-          git config --local user.email "github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-      - name: Get tag of the version
-        uses: olegtarasov/get-tag@v2.1
-        id: tag_name
+          pip install --upgrade pip
+          pip install mike mkdocs mkdocs-material
+
       - name: Deploy with mike
         run: |
-          mike deploy --force --update-aliases master stable
-          mike retitle master stable
+          VERSION=${GITHUB_REF_NAME}
+          mike deploy --push --update-aliases $VERSION stable
           mike set-default --push stable
 
diff --git a/.github/workflows/build_docs_version.yml b/.github/workflows/build_docs_version.yml
@@ -1,33 +1,40 @@
 name: release documentation 
+
 on:
   push:
     branches:
       - 'v*.*'
+
+permissions:
+  contents: write
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
+      - name: Configure git user
+        run: |
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
+          ref: ${{ github.ref_name }}
           fetch-depth: 0
+
       - name: Setup python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: '3.11'
+          cache: 'pip'
+
       - name: Install python packages
-        run: pip install mkdocs==1.5.2 mkdocs-material==8.3.4 mike==1.1.2 setuptools
-      - name: Configure git user
         run: |
-          git config --local user.email "github-actions[bot]@users.noreply.github.com"
-          git config --local user.name "github-actions[bot]"
-      - name: Get tag of the version
-        uses: olegtarasov/get-tag@v2.1
-        id: tag_name
-      - name: Get branch names
-        id: branch-name
-        uses: tj-actions/branch-names@v9.0.0
+          pip install --upgrade pip
+          pip install mike mkdocs mkdocs-material
+
       - name: Deploy with mike
         run: |
-          mike deploy --force --push ${{ steps.branch-name.outputs.current_branch }} ${{ steps.tag_name.outputs.tag }}
+          mike deploy --push ${{ github.ref_name }}
           mike set-default --push stable
diff --git a/cmake/SCHISM.local.bora.gnu b/cmake/SCHISM.local.bora.gnu
@@ -14,4 +14,4 @@ set(NetCDF_C_DIR  "$ENV{NETCDF}"  CACHE PATH "Path to NetCDF C library")
 
 ###Compile flags
 #CMAKE_EXE_LINKER_FLAGS did not work so I had to remove -static
-set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -ffree-line-length-none -static-libgfortran -finit-local-zero" CACHE STRING "Fortran flags" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -ffree-line-length-none -finit-local-zero" CACHE STRING "Fortran flags" FORCE)
diff --git a/cmake/SCHISM.local.build b/cmake/SCHISM.local.build
@@ -19,12 +19,14 @@ set(SH_MEM_COMM ON CACHE BOOLEAN "Use shared memory communicator")
 set(NO_PARMETIS OFF CACHE BOOLEAN "Turn off ParMETIS")
 
 #   Algorithm choices
+set (USE_SPK OFF CACHE BOOLEAN "Use sphere harmonic for SAL via spherepack - not working")
 # TVD_LIM must be one of SB, VL, MM or OS for Superbee, Van Leer, Minmod, or Osher.")
 set (TVD_LIM VL CACHE STRING "Flux limiter")
 #Turn OLDIO off to use the new scribe based I/O
 set (OLDIO OFF CACHE BOOLEAN "Old nc output (each rank dumps its own data)")
 
 set (USE_ATMOS OFF CACHE BOOLEAN "Coupling with atmospheric model via ESMF")
+##At the moment, must compile USE_BMI with NO_PARMETIS and OLDIO turned on
 set (USE_BMI OFF CACHE BOOLEAN "Build a library that can be used from BMI, with sources and some b.c. provided by BMI")
 set (PREC_EVAP OFF CACHE BOOLEAN "Include precipitation and evaporation calculation")
 set (USE_BULK_FAIRALL OFF CACHE BOOLEAN "Enable Fairall bulk scheme for air-sea exchange")
@@ -44,6 +46,7 @@ set( USE_WWM OFF CACHE BOOLEAN "Use wind-wave module")
 set( USE_WW3 OFF CACHE BOOLEAN "Use Wave Watch III")
 set( USE_ICE OFF CACHE BOOLEAN "Use 1-class ICE module")
 set( USE_MICE OFF CACHE BOOLEAN "Use multi-class ICE module")
+set( USE_CICE OFF CACHE BOOLEAN "Coupled to CICE via ESMF/UFS")
 
 #Tracer models
 set( USE_GEN OFF CACHE BOOLEAN "Use generic tracer module")

diff --git a/cmake/SCHISM.local.james b/cmake/SCHISM.local.james
@@ -3,7 +3,7 @@
 set (SCHISM_EXE_BASENAME pschism_JAMES CACHE STRING "Base name (modules and file extension to be added of the executable. If you want a machine name, add it here")
 
 ###Relative paths won't work
-set(CMAKE_Fortran_COMPILER ifort CACHE PATH "Path to serial Fortran compiler")
+set(CMAKE_Fortran_COMPILER ifx CACHE PATH "Path to serial Fortran compiler")
 set(NetCDF_FORTRAN_DIR "$ENV{NETCDF_FORTRAN}" CACHE PATH "Path to NetCDF Fortran library")
 set(NetCDF_C_DIR  "$ENV{NETCDF}"  CACHE PATH "Path to NetCDF C library")
 ###Compile flags. If USE_WWM, change to -O2

diff --git a/cmake/SCHISM.local.kuro b/cmake/SCHISM.local.kuro
@@ -5,11 +5,11 @@ set (SCHISM_EXE_BASENAME pschism_KURO CACHE STRING "Base name (modules and file
 ###Relative paths won't work
 #set(CMAKE_Fortran_COMPILER ifort CACHE PATH "Path to serial Fortran compiler")
 set(CMAKE_Fortran_COMPILER ifx CACHE PATH "Path to serial Fortran compiler")
-set(CMAKE_C_COMPILER icx  CACHE PATH "Path to serial Fortran compiler")
-set(CMAKE_CXX_COMPILER icpx  CACHE PATH "Path to serial Fortran compiler")
-set(CMAKE_Fortran_COMPILER mpiifort CACHE PATH "Path to serial Fortran compiler")
-set(CMAKE_C_COMPILER mpiicc  CACHE PATH "Path to serial Fortran compiler")
+set(CMAKE_C_COMPILER icx  CACHE PATH "Path to serial C compiler")
+set(CMAKE_CXX_COMPILER icpx  CACHE PATH "Path to serial C++ compiler")
+set(CMAKE_Fortran_COMPILER mpiifort CACHE PATH "Path to parallel Fortran compiler")
+set(CMAKE_C_COMPILER mpiicc  CACHE PATH "Path to parallel C compiler")
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -mcmodel=medium -march=x86-64-v3 -init=zero" CACHE STRING "Fortran flags" FORCE)
 #set(CMAKE_Fortran_FLAGS_RELEASE "-O1 -ipo -mcmodel=medium -march=core-avx2 -init=zero " CACHE STRING "Fortran flags" FORCE)
-set(CMAKE_C_FLAGS_RELEASE "-O1 -march=core-avx2 " CACHE STRING "Fortran flags" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O1 -march=core-avx2 " CACHE STRING "C flags" FORCE)
 
diff --git a/cmake/SCHISM.local.ursa b/cmake/SCHISM.local.ursa
@@ -0,0 +1,27 @@
+### NOAA RDHPC Ursa Cluster (GCC/OpenMPI)
+# Executable basename
+set (SCHISM_EXE_BASENAME pschism_Ursa CACHE STRING "Base name of the executable")
+
+### Compilers
+set(CMAKE_Fortran_COMPILER gfortran CACHE PATH "Path to serial Fortran compiler")
+set(CMAKE_C_COMPILER gcc CACHE PATH "Path to serial C compiler")
+
+### NetCDF Locations
+# Note: On Ursa, if environment variables are not set, use 'nc-config --prefix' 
+# and 'nf-config --prefix' to find absolute paths.
+if(DEFINED ENV{NETCDF_FORTRAN_ROOT})
+    set(NetCDF_FORTRAN_DIR "$ENV{NETCDF_FORTRAN_ROOT}" CACHE PATH "Path to NetCDF Fortran")
+else()
+    # Placeholder path based on Feb 2026 Spack build
+    set(NetCDF_FORTRAN_DIR "/apps/spack-2024-12/linux-rocky9-x86_64/gcc-11.4.1/netcdf-fortran-4.6.1-rxwle72kj3anm4uess3ixiqg7ezgq4vk" CACHE PATH "Path to NetCDF Fortran")
+endif()
+
+if(DEFINED ENV{NETCDF_ROOT})
+    set(NetCDF_C_DIR "$ENV{NETCDF_ROOT}" CACHE PATH "Path to NetCDF C")
+else()
+    # Placeholder path based on Feb 2026 Spack build
+    set(NetCDF_C_DIR "/apps/spack-2024-12/linux-rocky9-x86_64/gcc-11.4.1/netcdf-c-4.9.2-dzmdg3ly7avioysvapk37klgegbsq3js" CACHE PATH "Path to NetCDF C")
+endif()
+
+### Compile flags
+set(CMAKE_Fortran_FLAGS_RELEASE "-O2 -mcmodel=medium -ffree-line-length-none -finit-local-zero" CACHE STRING "Fortran flags" FORCE)
diff --git a/docs/assets/pdaf_data_format.png b/docs/assets/pdaf_data_format.png
diff --git a/docs/assets/pdaf_folder_structures.png b/docs/assets/pdaf_folder_structures.png
diff --git a/docs/coupling/esmf.md b/docs/coupling/esmf.md
@@ -2,6 +2,8 @@ The Earth System Modeling Framework (ESMF) is a suite of software tools for deve
 
 SCHISM can be such a model component within an ESMF-coupled system.  A so-called "cap" wraps SCHISM and exposes it via the ESMF Application Programming Interface (API).  The interfaces exposed through the API are (1) import of fields, (2) export of fields, and (3) control structure.
 
+A live manual can be found [here](https://schism-esmf.readthedocs.io/en/latest/).
+
 ## Obtaining and building the cap
 
 The [ESMF](esmf.html) and the [NUOPC](nuopc.html) caps are jointly hosted in a separate repository on [https://github.com/schism-dev/schism-esmf](https://github.com/schism-dev/schism-esmf).  It requires that the SCHISM core is built and pointed to by the environment variable `$SCHISM_BUILD_DIR` 

diff --git a/docs/faq.md b/docs/faq.md
@@ -44,5 +44,5 @@ Besides the following info, you may also search archived messages from the SCHIS
     This can be caused by a number of reasons, but a common one is that when user switches from 2D to 3D, they forgot to set itur=3 to use turbulence closure.
 
 ???faq "fatal.error indicates “Could not find suitable element in input”"
-    This is likely because your `sflux*.nc` is not prepared properly: either the grid in `.nc` does not cover `hgrid.ll`, or the structured grid in `.nc` is not ordered counter-clockwise.
+    This is likely because your `sflux*.nc` is not prepared properly: either the grid in `.nc` does not cover `hgrid.ll`, or the structured grid in `.nc` has a mixture of clockwise and counter-clockwise orientations.
 
diff --git a/docs/getting-started/pre-processing-with-pyschism/atmos.md b/docs/getting-started/pre-processing-with-pyschism/atmos.md
@@ -5,11 +5,11 @@ There are four types of files needed:
 
 sflux_input.txt (<font color="red">required</font>): a namelist file
 
-sflux_air_1.[XXXX].nc (<font color="red">required</font>): NetCDF files that have time (in days), wind speed at 10m above MSL (u, v), air temperatue and spedific humidity at 2m above MSL, sea level pressure;
+sflux_air_1.[1-].nc (<font color="red">required</font>): NetCDF files that have time (in days), wind speed at 10m above MSL (u, v), air temperatue and spedific humidity at 2m above MSL, sea level pressure;
 
-sflux_prc_1.[XXXX].nc (<font color="blue">needed</font> if isconsv=1): NetCDF files that have time and precipitation rate;
+sflux_prc_1.[1-]nc (<font color="blue">needed</font> if isconsv=1): NetCDF files that have time and precipitation rate;
 
-sflux_rad_1.[XXXX].nc (<font color="blue">needed</font> if ihconsv=1): NetCDF files that have time, downward longwave and shortwave radiation fluxes.
+sflux_rad_1.[1-].nc (<font color="blue">needed</font> if ihconsv=1): NetCDF files that have time, downward longwave and shortwave radiation fluxes.
 
 PySCHISM supports three types of atmpsheric datasets.
 

diff --git a/docs/getting-started/test_suite.md b/docs/getting-started/test_suite.md
@@ -9,9 +9,9 @@ The command to checkout the tests is:
 
 `svn co https://columbia.vims.edu/schism/schism_verification_tests`
 
-(You can also simply use wget to download)
+(You can also simply use wget to download, but using svn allows easy updates later)
 
-Note that the test suite is kept up to date with the latest master branch on the [SCHISM's git repo](https://github.com/schism-dev/schism/tree/master).
+Note that the test suite is kept up to date with the latest `master branch` on the [SCHISM's git repo](https://github.com/schism-dev/schism/tree/master).
 As a result, there may be some differences (some parameters may have been removed or added) between the param.nml you are using and the one from the verification tests (master branch).
  It's important to use a correct `param.nml` corresponding to the version of SCHISM you are using. A sample param.nml is always provided under your SCHISM source code directory:
 

diff --git a/docs/input-output/optional-inputs.md b/docs/input-output/optional-inputs.md
@@ -259,3 +259,7 @@ NHAGE, NHAGV = flags that indicate whether or not harmonic analysis is performed
     - FMV: fraction of the harmonic analysis period (extending back from the end of the harmonic analysis period) to use for comparing the water elevation and velocity means and variances from the raw model time series with corresponding means and variances of a time series resynthesized from the harmonic constituents. This comparison is helpful for identifying numerical instabilities and for determining how complete the harmonic analysis was. Examples: FMV = 0. - do not compute any means and vars. FMV = 0.1 - compute means and vars. over final 10% of period used in harmonic analysis FMV = 1.0 - compute means and vars. over entire period used in harmonic analysis.
     - NHAGE: NHAGE= 0 no harmonic analysis is performed for global elevations; NHAGE =1 harmonic analysis is performed for global elevations (output on harme.53);
     - NHAGV: NHAGV is for velocity which is not active right now.
+
+### metadata.nc
+
+This optional file can contain global and variable metadata in the form of NetCDF attributes that will be copied over to the SCHISM output NetCDF files.  This file is useful for adding project- or institution-specific metadata.   In particular, you should use it to fill the contact and institution information required by CF, and to add a coordinate reference system to SCHISM output on projected coordinates (`ics = 1`) if you add a grid mapping variable called `crs` with appropriate attributes.  See the CF conventions for details on required and recommended metadata: https://cfconventions.org/.