Merge branch 'main' into fpm

Author: pibion

.gitattributes

@@ -0,0 +1,14 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.f90 text
+*.py text
+*.md text
+*.toml text
+*.yaml text
+Dockerfile* text
+
+# Denote all files that are truly binary and should not be modified.
+*.sif binary

Dockerfile_tau

@@ -0,0 +1,88 @@
+# Use Ubuntu 22.04 as base image
+FROM gmao/llvm-flang
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install necessary packages
+RUN apt-get update && apt-get install -y \
+    software-properties-common \
+    wget \
+    bzip2 \
+    libz-dev \
+    g++ \
+    ca-certificates \
+    curl \
+    git \
+    nano \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN add-apt-repository ppa:ubuntu-toolchain-r/test \
+    && apt-get install -y gfortran-14
+
+# Set up working directory
+WORKDIR /packages
+
+# Install Anaconda
+RUN wget https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Linux-x86_64.sh -O /tmp/anaconda.sh \
+    && bash /tmp/anaconda.sh -b -p /opt/anaconda \
+    && rm /tmp/anaconda.sh
+
+# Add Anaconda to PATH
+ENV PATH="/opt/anaconda/bin:${PATH}"
+
+# Initialize conda for bash shell
+RUN echo ". /opt/anaconda/etc/profile.d/conda.sh" >> ~/.bash_profile
+RUN echo ". /opt/anaconda/etc/profile.d/conda.sh" >> ~/.bashrc
+
+# Copy environment.yaml file
+COPY NR_Fano_dan_env.yaml .
+
+# Create conda environment from the yaml file
+# this installs fpm and intel compiler
+RUN conda env create -f NR_Fano_dan_env.yaml
+RUN echo "conda activate NR_Fano" >> ~/.bash_profile
+RUN echo "conda activate NR_Fano" >> ~/.bashrc
+
+# Source - https://stackoverflow.com/a/39777387
+# Posted by Ahmad Abdelghany, modified by community. See post 'Timeline' for change history
+# Retrieved 2025-11-09, License - CC BY-SA 4.0
+# this command, together with putting conda activation in .bash_profile, means we have
+# enabled the conda environment for every command
+SHELL ["/bin/bash", "--login", "-c"] 
+
+# Check out TAU
+RUN git clone https://github.com/UO-OACISS/tau2.git --depth=1
+
+# Build TAU
+# From Nicholas Chaimov
+# -pthread to enable pthread
+# Don’t specify -mpi to build without MPI
+# Most builds of TAU should use bfd, unwind, dwarf, otf to support sampling and tracing
+#RUN cd tau2 \
+#    && ./configure -cc=gcc -c++=g++ -fortran=gfortran -bfd=download -unwind=download -dwarf=download -otf=download -pthread \
+#    && make -j install
+
+
+WORKDIR /app
+
+# Copy the fortran code over
+# first we build the expected directory structure
+# and then we copy files
+RUN mkdir /app/src
+RUN mkdir /app/test
+
+COPY src /app/src/
+COPY test /app/test
+COPY fpm.toml /app/
+
+# also copy over the python functions for testing
+RUN mkdir /app/python
+COPY python /app/python/
+COPY *.py /app
+
+# Now compile the fortran code
+RUN fpm test --compiler flang-new --profile release --flag -O3 \
+    && fpm install --prefix=.  --compiler flang-new --profile release --flag -O3
+

NR_Fano_dan_env.yaml

@@ -8,6 +8,8 @@ dependencies:
   - ifx_linux-64
   - mpi4py
   - fpm
+  - ford
+  - graphviz
   - lmfit
   - ipykernel
   - matplotlib

README.md

@@ -10,16 +10,25 @@ With `fpm` releases more recent than 0.12.0, one can replace `flang-new` with `f
 
 |Vendor| Version(s)      |  Build/Test Command                                          |
 |------|-----------------|--------------------------------------------------------------|
-|GNU   | 14.3.0, 15.2.0  | `fpm test --compiler gfortran --profile release --flag "-march=native -fopenmp -ftree-parallelize-loops=4"` |
-|      | 13.4.0          | `fpm test --compiler gfortran --profile release --flag "-march=native -fopenmp -ftree-parallelize-loops=4 -ffree-line-length-none"` |
+|GNU   | 14.3.0, 15.2.0  | `fpm test --compiler gfortran --profile release --flag "-cpp -march=native -fopenmp -ftree-parallelize-loops=4"` |
+|      | 13.4.0          | `fpm test --compiler gfortran --profile release --flag "-cpp -march=native -fopenmp -ftree-parallelize-loops=4 -ffree-line-length-none"` |
 |Intel | 2025.2.1        | `FOR_COARRAY_NUM_IMAGES=1 fpm test --compiler ifx --flag "-fpp -O3 -coarray" --profile release` |
-|LLVM  | 20-22           | `fpm test --compiler flang-new --profile release --flag -O3` |
-|      | 19              | `fpm test --compiler flang-new --profile release --flag "-O3 -mmlir -allow-assumed-rank"` |
+|LLVM  | 20-22           | `fpm test --compiler flang-new --profile release --flag "-cpp -O3"` |
+|      | 19              | `fpm test --compiler flang-new --profile release --flag "-cpp -O3 -mmlir -allow-assumed-rank"` |
 |NAG   | 7.2, Build 7235 | `fpm test --compiler nagfor --flag "-fpp -O4"`               |
 
 **Caveat:** In the case of LLVM 19-20, the above commands succeed for testing band_distribution's Julienne dependency.
 A future pull request could test band_distribution itself with LLVM 19-20 via GitHub Actions.
 
+### Preprocessor macros
+* Add `-DPREFER_DO_CONCURRENT` in the `--flag` argument to switch from array statements or `do` loops to `do concurrent`
+
+### Experimental parallelization
+To multithread `do concurrent` on CPUs with LLVM `flang` 21 or later, try the following:
+```
+fpm test --compiler flang-new --profile release --flag "-O3 -cpp -DPREFER_DO_CONCURRENT -fopenmp -fdo-concurrent-to-openmp=host"
+```
+
 # Testing the python calls
 This code builds a library that may be called within python (this is the original intent of the code).  To test the python calls, run