Bogus change

.github/workflows/CIT_derecho.yml

@@ -0,0 +1,53 @@
+# This is a basic workflow to help you get started with Actions
+
+name: CIT on derecho
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pull request events but only for the "feature_CIT" branch
+  pull_request:
+    branches: 
+      - feature_CIT 
+    paths-ignore:
+      - 'docs/**'
+      - '.github/pull_request_template.md'
+      - '.github/ISSUE_TEMPLATE/**'
+      - '**/README.md'
+      - '**/LICENSE.md'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # Only do the actions when merged or manually run
+    if: github.event.label.name == 'run-pr-tests' || github.event_name == 'workflow_dispatch'
+    # The type of runner that the job will run on
+    #runs-on: ubuntu-latest
+    runs-on: shr-derecho
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it  v2 or v4? (Julie's example shows v2)
+      - uses: actions/checkout@v4
+
+      # Runs a single command using the runners shell
+      - name: Run a one-line script
+        run: echo Hello, world!
+
+      # Compile the FastEddy code
+      #- name: Compile FastEddy
+      #  run: |
+      #    cd SRC/FEMAIN
+      #    module load cuda
+      #    make clean
+      #    make
+
+      # Runs a set of commands using the runners shell
+      #- name: Run a multi-line script
+      #  run: |
+      #    echo Append datetime to a file
+      #    /glade/work/fasteddyrt/actions-runner/appendDatetimeRun.sh
+

README.md

@@ -1,6 +1,8 @@
 # FastEddy® 
 ©2016 University Corporation for Atmospheric Research
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11042754.svg)](https://doi.org/10.5281/zenodo.11042754)
+
 # Open-source License 
 The FastEddy® model is licensed under the Apache License, Version 2.0 (the "License");
 you may not use any source code in this repository except in compliance with the License.

SRC/FEMAIN/Makefile.hip

@@ -0,0 +1,213 @@
+################################################################################
+# FastEddy®: SRC/FEMAIN/Makefile
+# ©2016 University Corporation for Atmospheric Research
+#
+# This file is licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# ################################################################################
+#
+# ################################################################################
+# # Available build targets
+# ################################################################################
+
+TARGETS = \
+       FastEddy 
+
+
+################################################################################
+## Compiler and flags
+################################################################################
+
+TEST_CC = mpicc
+TEST_CU_CC = hipcc -Rpass-analysis=kernel-resource-usage --gpu-max-threads-per-block=256
+ROCM_PATH ?= /opt/rocm
+MPI_ROOT ?= ""
+NETCDF_C_ROOT ?= ""
+GPU_ARCH ?= gfx90a
+
+# For compilation on NCAR's Casper or Derecho supercomputers use the OTHER_INCLUDES below
+OTHER_INCLUDES = -I${MPI_ROOT}/include
+
+DEBUG_CFLAGS = -g 
+
+DEFINES = -DCUB_IGNORE_DEPRECATED_CPP_DIALECT -DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT
+
+TEST_CFLAGS = -Wall -m64 $(shell ${ROCM_PATH}/bin/hipconfig --cpp_config) ${DEFINES} ${INCLUDES} ${OTHER_INCLUDES}
+ARCH_CU_FLAGS = --offload-arch=${GPU_ARCH}
+TEST_CU_CFLAGS = ${ARCH_CU_FLAGS} -m64 -std=c++14 ${DEFINES} ${INCLUDES} ${OTHER_INCLUDES}
+
+L_CPPFLAGS =
+
+
+TEST_LDFLAGS = -L.
+TEST_CU_LDFLAGS = -L.  -fgpu-rdc
+
+TEST_LIBS = -lm -L${MPI_ROOT}/lib -lmpi -lstdc++ -L${ROCM_PATH}/lib -lamdhip64 -lhiprand -L${NETCDF_C_ROOT}/lib -lnetcdf
+TEST_CU_LIBS = -lmpi -L${ROCM_PATH}/lib -lhiprtc
+
+
+################################################################################
+# Sub-directories to INCLUDE 
+# ################################################################################
+
+INCLUDES = \
+	-I. \
+	-I../TIME_INTEGRATION/ \
+	-I../TIME_INTEGRATION/CUDA \
+	-I../HYDRO_CORE \
+	-I../HYDRO_CORE/CUDA \
+	-I../GRID \
+	-I../GRID/CUDA \
+	-I../FECUDA \
+	-I../IO/ \
+	-I../MEM_UTILS/ \
+	-I../FEMPI/ \
+	-I../PARAMETERS/
+
+################################################################################
+# Headers
+# ###############################################################################
+
+TEST_HDRS = \
+	../TIME_INTEGRATION/time_integration.h \
+        ../TIME_INTEGRATION/CUDA/cuda_timeInt.h \
+        ../TIME_INTEGRATION/CUDA/cuda_timeIntDevice_cu.h \
+	../HYDRO_CORE/hydro_core.h \
+	../HYDRO_CORE/CUDA/cuda_hydroCore.h \
+	../HYDRO_CORE/CUDA/cuda_hydroCoreDevice_cu.h \
+	../GRID/grid.h \
+	../GRID/CUDA/cuda_grid.h \
+	../GRID/CUDA/cuda_gridDevice_cu.h \
+        ../FECUDA/fecuda.h \
+        ../FECUDA/fecuda_Device_cu.h \
+	../IO/io.h \
+	../MEM_UTILS/mem_utils.h \
+	../FEMPI/fempi.h \
+	../PARAMETERS/parameters.h \
+	../PARAMETERS/hashTable.h
+
+################################################################################
+# Objects
+# ###############################################################################
+
+TEST_LIB_OBJS =
+
+TEST_OBJS = ./FastEddy.o \
+	../TIME_INTEGRATION/time_integration.o \
+        ../TIME_INTEGRATION/CUDA/cuda_timeInt.o \
+        ../TIME_INTEGRATION/CUDA/cuda_timeIntDevice.o \
+	../HYDRO_CORE/hydro_core.o \
+	../HYDRO_CORE/CUDA/cuda_hydroCore.o \
+	../HYDRO_CORE/CUDA/cuda_hydroCoreDevice.o \
+	../GRID/grid.o \
+	../GRID/CUDA/cuda_grid.o \
+	../GRID/CUDA/cuda_gridDevice.o \
+        ../FECUDA/fecuda.o \
+        ../FECUDA/fecuda_Device.o \
+	../IO/io.o \
+	../IO/ioVarsList.o \
+	../MEM_UTILS/mem_utils.o \
+	../FEMPI/fempi.o \
+	../PARAMETERS/parameters.o \
+	../PARAMETERS/hashTable.o
+
+################################################################################
+# Targets
+# ###############################################################################
+
+all: hipify FastEddy
+
+hipify:
+	find ../ -name "*.cu" -exec hipify-perl -inplace {} \;
+	find ../ -name "*.h" -exec hipify-perl -inplace {} \;
+	find ../ -name "*.prehip" -exec rm {} \;
+
+
+################################################################################
+# Generic compile rules
+# ################################################################################
+%.o: %.cu
+	rm -rf ./FastEddy_devlink.o; \
+	$(TEST_CU_CC) $(TEST_CU_CFLAGS) -fgpu-rdc -c $< -o $@
+
+.c.o:
+	${COMP_FLAGS} -c $< -o $@
+
+################################################################################
+# Module=specific compile rules
+# ################################################################################
+
+../TIME_INTEGRATION/CUDA/cuda_timeIntDevice.o: ../TIME_INTEGRATION/CUDA/cuda_timeIntDevice.cu \
+        ../TIME_INTEGRATION/CUDA/cuda_RKschemes.cu
+	rm -rf ./FastEddy_devlink.o; \
+	$(TEST_CU_CC) $(TEST_CU_CFLAGS) -fgpu-rdc -c $< -o $@
+
+../IO/io.o: ../IO/io.c \
+	../IO/io_netcdf.c \
+	../IO/io_binary.c 
+	$(COMP_FLAGS) -c $< -o $@
+
+../FECUDA/fecuda_Device.o: ../FECUDA/fecuda_Device.cu \
+	../FECUDA/fecuda_Utils.cu \
+	../FECUDA/fecuda_PlugIns.cu 
+	rm -rf ./FastEddy_devlink.o; \
+	$(TEST_CU_CC) $(TEST_CU_CFLAGS) -fgpu-rdc -c $< -o $@
+
+../HYDRO_CORE/CUDA/cuda_hydroCoreDevice.o: ../HYDRO_CORE/CUDA/cuda_hydroCoreDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_BaseStateDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_buoyancyDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_coriolisDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_pressureDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_BCsDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_rayleighDampingDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_advectionDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_molecularDiffDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_surfaceLayerDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_sgsTurbDevice.cu \
+        ../HYDRO_CORE/CUDA/cuda_sgstkeDevice.cu \
+	../HYDRO_CORE/CUDA/cuda_canopyDevice.cu \
+        ../HYDRO_CORE/CUDA/cuda_largeScaleForcingsDevice.cu \
+        ../HYDRO_CORE/CUDA/cuda_moistureDevice.cu \
+        ../HYDRO_CORE/CUDA/cuda_filtersDevice.cu
+	rm -rf ./FastEddy_devlink.o; \
+	$(TEST_CU_CC) $(TEST_CU_CFLAGS) -fgpu-rdc -c $< -o $@
+################################################################################
+# Generic Executable
+# ###############################################################################
+
+FastEddy: COMP_FLAGS = ${TEST_CC} ${TEST_CFLAGS}
+
+TEST_DEPENDENCIES = ${TEST_OBJS} ${TEST_HDRS} FastEddy_devlink.o
+
+FastEddy_devlink.o:
+	$(TEST_CU_CC) ${ARCH_CU_FLAGS} ${TEST_OBJS} ${TEST_LDFLAGS} ${TEST_LIBS} -fgpu-rdc --hip-link --emit-static-lib -o FastEddy_devlink.o
+FastEddy: ${TEST_DEPENDENCIES}
+	${COMP_FLAGS} -o FastEddy ${TEST_OBJS} ./FastEddy_devlink.o ${TEST_LDFLAGS} ${TEST_LIBS}
+
+################################################################################
+# Clean
+# ################################################################################
+
+clean:
+	rm -rf ${TARGETS} ${TEST_OBJS} ${TEST_LIB_OBJS} ./FastEddy_devlink.o
+
+################################################################################
+# Check
+# ###############################################################################
+
+check:
+	@echo CC = ${CC}
+	@echo CFLAGS = ${CFLAGS} 
+	@echo LDFLAGS = ${LDFLAGS} 
+	@echo LIBS = ${LIBS}
+	@echo DEPENDENCIES = ${TEST_DEPENDENCIES}

docs/BOGUS.txt

@@ -0,0 +1,2 @@
+Just a bogus document to provide a change with which to try a pull request.  Trying to
+see if I can make it trigger the workflow!

docs/index.rst

@@ -15,6 +15,9 @@ and multiscale, turbulence-resolving, atmospheric boundary layer
 modeling into local scale weather prediction or actionable science and
 engineering applications.
 
+Citations
+---------
+
 The FastEddy code is located in an open, public
 `GitHub FastEddy-model repository <https://github.com/NCAR/FastEddy-model>`_.
 FastEddy should be cited as shown here:
@@ -25,11 +28,23 @@ FastEddy should be cited as shown here:
   |   https://doi.org/10.1029/2020MS002100
 
 
+Contributing Authors
+--------------------
+
+The following authors have contributed to this documentation of FastEddy:
+
+* Jeremy Sauer
+* Domingo Muñoz-Esparza
+* Eric Hendricks
+* Julie Prestopnik
+
+
 .. toctree::
    :hidden:
 
    release_notes.rst
    run_ncar_hpcs.rst
+   run_amd_gpus.rst
    downloads.rst
    Tutorials/index
    publications.rst

docs/publications.rst

@@ -4,6 +4,14 @@
 Publications
 ************
 
+.. _urban_climate_2025:
+
+| Munoz-Esparza, D., J. Sauer, P.A. Jimenez, J. Boehnert, D. Hahn, and M. Steiner.
+|   “Multiscale Weather Forecasting Sensitivities to Urban Characteristics and Atmospheric
+|   Conditions During a Cold Front Passage Over the Dallas-Fort Worth Metroplex”.
+|   *Urban Climate*, 60 (102334) 2025
+|   https://doi.org/10.1016/j.uclim.2025.102334
+
 .. _wind_energy_2024:
 
 | Sanchez Gomez, M., D. Muñoz-Esparza, J.A. Sauer. "Implementation and Validation

docs/run_amd_gpus.rst

@@ -0,0 +1,37 @@
+.. _run_fasteddy_amdgpu:
+
+**************************************************
+Building FastEddy on AMD GPU Accelerated platforms
+**************************************************
+
+These instructions will help users get started with building FastEddy for systems with AMD GPU accelerators. This can be beneficial for users who have allocations on 
+
+   * `Oak Ridge National Laboratory's Frontier <https://www.olcf.ornl.gov/frontier/>`_
+   * `Pawsey Supercomputing Centre's Setonix <https://pawsey.org.au/systems/setonix/>`_
+   * `CSCS's Lumi <https://www.lumi-supercomputer.eu/may-we-introduce-lumi/>`_
+   * `Fluid Numerics' Galapagos <https://galapagos.fluidnumerics.com>`_
+
+
+Compilation
+===========
+
+FastEddy requires a C-compiler, MPI, and CUDA. 
+
+   1. Download the source code from the `Releases <https://github.com/NCAR/FastEddy-model/releases>`_ page and unpack the release in the desired location or clone the `repository <https://github.com/NCAR/FastEddy-model>`_ in the desired location.
+
+   2. Navigate to the **SRC/FEMAIN** directory.
+
+   3. To build the FastEddy executable run :code:`make -f Makfile.hip` (optionally run :code:`make clean` first if appropriate).
+
+You may need to define a few environment variables that influence the build process to properly set the paths to various dependencies and to select the target GPU.
+
+   * :code:`ROCM_PATH` : This is the path to your ROCm installation. This variable defaults to :code:`/opt/rocm`. However, on some systems, multiple versions of ROCm may be available via environment modules and this variable may need to be adjusted accordingly.
+   * :code:`MPI_ROOT` : This is the path to your MPI installation. Since this environment variable is not necessarily defined through an HPC center's environment modules, it is recommended that you set this variable appropriately.
+   * :code:`NETCDF_C_ROOT`: This is the path to your NetCDF-C installation. Since this environment variable is not necessarily defined through an HPC center's environment modules, it is recommended that you set this variable appropriately.
+   * :code:`GPU_ARCH` : This is the AMD GPU architecture code for the target GPU you want to build for. This variable defaults to :code:`gfx90a`, which corresponds to the MI210, MI250, and MI250X GPUs.
+
+The :code:`FastEddy` executable will be located in the **SRC/FEMAIN** directory. To
+build on other HPC systems with NVIDIA GPUs, check for availability of the aformentioned
+modules/dependencies. Successful compilation may require modifications to shell environment
+variable include or library paths, or alternatively minor adjustments to the include or library
+flags in **SRC/FEMAIN/Makefile.hip**.