default Containerfile excludes mkl_fft

podman/Containerfile

@@ -40,11 +40,11 @@ RUN wget --no-check-certificate -nv https://www.mpich.org/static/downloads/$mpic
 
 RUN /sbin/ldconfig
 
-# Try to prevent MKL from throttling AMD
-# https://gitlab.com/NERSC/python-benchmark/-/tree/main/amd
-COPY fakeintel.c /src/fakeintel.c
-RUN gcc -shared -fPIC -o /usr/local/lib/libfakeintel.so /src/fakeintel.c
-ENV LD_PRELOAD=/usr/local/lib/libfakeintel.so
+## Try to prevent MKL from throttling AMD
+## https://gitlab.com/NERSC/python-benchmark/-/tree/main/amd
+#COPY fakeintel.c /src/fakeintel.c
+#RUN gcc -shared -fPIC -o /usr/local/lib/libfakeintel.so /src/fakeintel.c
+#ENV LD_PRELOAD=/usr/local/lib/libfakeintel.so
 
 # Install Miniconda
 ENV CONDA_DIR=/opt/miniconda
@@ -86,7 +86,7 @@ RUN conda install -y -c conda-forge \
 RUN conda install -y -c conda-forge \
     libblas=*=*mkl \
     # also tried mkl_fft<1.3.9
-    mkl_fft \
+    # mkl_fft \
     intel-cmplr-lib-rt \
     && conda clean --all -y
 
@@ -99,7 +99,7 @@ ENV DESIMODEL_VERSION=0.19.2
 ENV DESITARGET_VERSION=2.8.0
 ENV DESISPEC_VERSION=0.68.1
 ENV SPECLITE_VERSION=v0.20
-ENV FASTSPECFIT_VERSION=pure-MPI
+ENV FASTSPECFIT_VERSION=main
 #ENV FASTSPECFIT_VERSION=3.1.1
 
 RUN pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil

podman/Containerfile-mkl

@@ -0,0 +1,131 @@
+FROM ubuntu:24.04
+
+WORKDIR /src
+
+RUN mkdir -p /src
+RUN apt-get -y clean && apt -y update && apt install -y apt-utils && apt -y upgrade
+
+RUN DEBIAN_FRONTEND=noninteractive \
+    apt install -y --no-install-recommends \
+    build-essential \
+    ca-certificates \
+    gfortran \
+    wget \
+    git \
+    libbz2-dev \
+    libgsl-dev \
+    libssl-dev \
+    libcfitsio-dev \
+    libcfitsio-bin \
+    # libhdf5 needed by h5py
+    libhdf5-dev \
+    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ARG mpich=3.4.3
+ARG mpich_prefix=mpich-$mpich
+
+ENV FFLAGS="-fallow-argument-mismatch" \
+    FCFLAGS="-fallow-argument-mismatch"
+
+RUN wget --no-check-certificate -nv https://www.mpich.org/static/downloads/$mpich/$mpich_prefix.tar.gz \
+    && tar xvzf $mpich_prefix.tar.gz \
+    && cd $mpich_prefix \
+    && ./configure --with-device=ch4:ofi \
+    && make -j 16 \
+    && make install \
+    && make clean \
+    && cd .. \
+    && rm -rf $mpich_prefix \
+    && rm -f $mpich_prefix.tar.gz
+
+RUN /sbin/ldconfig
+
+# Try to prevent MKL from throttling AMD
+# https://gitlab.com/NERSC/python-benchmark/-/tree/main/amd
+COPY fakeintel.c /src/fakeintel.c
+RUN gcc -shared -fPIC -o /usr/local/lib/libfakeintel.so /src/fakeintel.c
+ENV LD_PRELOAD=/usr/local/lib/libfakeintel.so
+
+# Install Miniconda
+ENV CONDA_DIR=/opt/miniconda
+
+ENV MINICONDA_VERSION=Miniforge3-Linux-x86_64.sh
+ENV MINICONDA=https://github.com/conda-forge/miniforge/releases/latest/download/$MINICONDA_VERSION
+
+RUN wget --no-check-certificate $MINICONDA \
+    && bash $MINICONDA_VERSION -b -p $CONDA_DIR \
+    && rm -f $MINICONDA_VERSION
+
+# Update PATH environment variable
+ENV PATH="$CONDA_DIR/bin:$PATH"
+
+# Verify Miniconda installation and initialize environment
+RUN conda init bash && conda update -n base -c defaults conda -y
+
+# Set default shell to bash
+SHELL ["/bin/bash", "-c"]
+
+# Install all our dependencies
+RUN conda install -y -c conda-forge \
+    "python<3.13" \
+    wheel \
+    setuptools \
+    pytest \
+    "numpy<2.0" \
+    scipy \
+    astropy \
+    healpy \
+    fitsio \
+    numba \
+    seaborn \
+    matplotlib \
+    ipython \
+    ipykernel \
+    h5py
+
+RUN conda install -y -c conda-forge \
+    libblas=*=*mkl \
+    # also tried mkl_fft<1.3.9
+    mkl_fft \
+    intel-cmplr-lib-rt \
+    && conda clean --all -y
+
+# Need to install mpi4py from source to link it properly to MPICH.
+ENV PIP_ROOT_USER_ACTION=ignore
+RUN pip install --no-cache-dir --no-binary=mpi4py mpi4py
+
+ENV DESIUTIL_VERSION=3.4.3
+ENV DESIMODEL_VERSION=0.19.2
+ENV DESITARGET_VERSION=2.8.0
+ENV DESISPEC_VERSION=0.68.1
+ENV SPECLITE_VERSION=v0.20
+ENV FASTSPECFIT_VERSION=main
+#ENV FASTSPECFIT_VERSION=3.1.1
+
+RUN pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
+RUN pip install git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}#egg=desimodel
+RUN pip install git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}#egg=desitarget
+RUN pip install git+https://github.com/desihub/desispec.git@${DESISPEC_VERSION}#egg=desispec
+RUN pip install git+https://github.com/desihub/speclite.git@${SPECLITE_VERSION}#egg=speclite
+RUN pip install git+https://github.com/desihub/fastspecfit.git@${FASTSPECFIT_VERSION}#egg=fastspecfit
+
+ENV DESI_SPECTRO_REDUX=/dvs_ro/cfs/cdirs/desi/spectro/redux
+ENV DUST_DIR=/dvs_ro/cfs/cdirs/cosmo/data/dust/v0_1
+ENV FPHOTO_DIR=/dvs_ro/cfs/cdirs/desi/external/legacysurvey/dr9
+ENV FTEMPLATES_DIR=/dvs_ro/cfs/cdirs/desi/public/external/templates/fastspecfit
+
+# Some environment variables to ensure good performance with MKL.
+# https://www.diracprogram.org/doc/master/installation/mkl.html
+ENV MKL_NUM_THREADS=1
+ENV MKL_DYNAMIC="FALSE"
+ENV OMP_NUM_THREADS=1
+
+# Create the numba cache.
+ENV HOME=/homedir
+ENV NUMBA_CACHE_DIR=$HOME/numba_cache
+
+RUN mkdir -p /homedir/numba_cache \
+    && chmod -R 777 /homedir*
+RUN pytest /opt/miniconda/lib/python3.12/site-packages/fastspecfit/test/test_fastspecfit.py
+
+LABEL Maintainer="John Moustakas [email protected]"