update Docker container for Fujilupe

bin/fastspecfit-setup.sh

@@ -1,32 +1,34 @@
 #!/bin/bash
-# Simple script to run fastspecfit in interactive / development mode.
+# Simple script to run fastspecfit in interactive / development mode. Run with
+# % fastspecfit-setup.sh shifter
+# % source fastspecfit-setup.sh env
 
 if [ $1 = "shifter" ]; then
     # Load the desigal Docker container using shifter
     #SHIFTER=docker:desihub/fastspecfit:latest
-    SHIFTER=docker:desihub/fastspecfit:v0.2
+    SHIFTER=docker:desihub/fastspecfit:v1.0
 
     echo 'Updating and loading the shifter image '$SHIFTER
     echo 'Load the environment with: '
-    echo '  source fastspecfit-setup.sh env'
+    echo '  source ./fastspecfit-setup.sh env'
 
     shifterimg pull $SHIFTER
-    shifter --image $SHIFTER bash
+    shifter --module=mpich-cle6 --image $SHIFTER bash
 elif [ $1 = "env" ]; then
-    package=fastspecfit
+    #for package in fastspecfit; do
+    #    echo Loading local check-out of $package
+    #    export PATH=/global/homes/i/ioannis/code/desihub/$package/bin:$PATH
+    #    export PYTHONPATH=/global/homes/i/ioannis/code/desihub/$package/py:$PYTHONPATH
+    #done
 
-    if [ "$NERSC_HOST" == "cori" ]; then
-        #export PATH=/opt/conda/bin:$PATH # NERSC hack!
-
-        export DESI_ROOT=/global/cfs/cdirs/desi
-        export FASTSPECFIT_TEMPLATES=$DESI_ROOT/science/gqp/templates/SSP-CKC14z
-        export DUST_DIR=/global/cfs/cdirs/cosmo/data/dust/v0_1
-
-        export OMP_NUM_THREADS=1
-        export MKL_NUM_THREADS=1
-        export KMP_AFFINITY=disabled
-        export MPICH_GNI_FORK_MODE=FULLCOPY
-    fi
+    export DESI_ROOT='/global/cfs/cdirs/desi'
+    export DUST_DIR='/global/cfs/cdirs/cosmo/data/dust/v0_1'
+    export FASTSPECFIT_TEMPLATES='/global/cfs/cdirs/desi/science/gqp/templates/SSP-CKC14z'
+
+    export OMP_NUM_THREADS=1
+    export MKL_NUM_THREADS=1
+    export KMP_AFFINITY=disabled
+    export MPICH_GNI_FORK_MODE=FULLCOPY
 
     # Config directory nonsense
     export TMPCACHE=$(mktemp -d)

bin/jupyter-kernel.sh

@@ -39,7 +39,8 @@ if __name__ == '__main__':
     from ipykernel import kernelapp as app
     app.launch_new_instance()
 EOF
-/opt/conda/bin/python $TMPSCRIPT --ignore-cwd -f $1
+/usr/bin/python $TMPSCRIPT --ignore-cwd -f $1
+#/opt/conda/bin/python $TMPSCRIPT --ignore-cwd -f $1
 rm $TMPSCRIPT
 
 # Clean up config directory nonsense.

bin/mpi-fastspecfit.sh

@@ -21,13 +21,13 @@ program=$4
 coadd_type=cumulative
 
 #for package in desispec desitarget desiutil desimodel speclite specsim; do
-for package in fastspecfit desispec; do
+for package in fastspecfit; do
     echo Loading local check-out of $package
     export PATH=/global/homes/i/ioannis/code/desihub/$package/bin:$PATH
     export PYTHONPATH=/global/homes/i/ioannis/code/desihub/$package/py:$PYTHONPATH
 done
-echo 'Loading local check-out of speclite'
-export PYTHONPATH=/global/homes/i/ioannis/code/desihub/speclite:$PYTHONPATH
+#echo 'Loading local check-out of speclite'
+#export PYTHONPATH=/global/homes/i/ioannis/code/desihub/speclite:$PYTHONPATH
 
 outdir_data=/global/cfs/cdirs/desi/users/ioannis/fastspecfit/vitiles
 outdir_html=/global/cfs/cdirs/desi/users/ioannis/fastspecfit/vitiles
@@ -52,13 +52,13 @@ export MPICH_GNI_FORK_MODE=FULLCOPY
 if [ $stage = "test" ]; then
     time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --help
 elif [ $stage = "fastspec" ]; then
-    time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 244 245 246 --outdir-data $outdir_data
-    #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 80605 80606 80613 --outdir-data $outdir_data
+    time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 142 --outdir-data $outdir_data
+    #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 80648 80666 136 141 142 244 245 246 80605 80606 80613 --outdir-data $outdir_data
     #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --survey $survey --program $program --outdir-data $outdir_data
     #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --survey $survey --program $program --outdir-data $outdir_data
 elif [ $stage = "fastphot" ]; then
-    time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 80605 80606 80613 244 245 246 --outdir-data $outdir_data --fastphot --overwrite
-    #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 80605 80606 80613 --outdir-data $outdir_data --fastphot
+    time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 80648 80666 136 141 142 --outdir-data $outdir_data --fastphot
+    #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --coadd-type $coadd_type --tile 244 245 246 80605 80606 80613 --outdir-data $outdir_data --fastphot
     #time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --mp $mp --survey $survey --program $program --outdir-data $outdir_data --fastphot 
 elif [ $stage = "qafastspec" ]; then
     time python /global/homes/i/ioannis/code/desihub/fastspecfit/bin/mpi-fastspecfit --makeqa --mp $mp --coadd-type $coadd_type --tile 80605 80606 80613 --outdir-data $outdir_data --outdir-html $outdir_html

doc/changes.rst

@@ -5,6 +5,7 @@ FastSpecFit Change Log
 1.0 (not released yet)
 ----------------------
 
+* Update Docker container and tag all dependencies [`PR #76`_].
 * Numerous backwards-incompatible improvements and changes to the code engine
   and data model in preparation for processing Fuji (EDR)+Guadalupe [`PR #69`_].
 * Initial set-up of GitHub Actions and unit tests [`PR #61`_].
@@ -15,6 +16,7 @@ FastSpecFit Change Log
 .. _`PR #60`: https://github.com/desihub/fastspecfit/pull/60
 .. _`PR #61`: https://github.com/desihub/fastspecfit/pull/61
 .. _`PR #69`: https://github.com/desihub/fastspecfit/pull/69
+.. _`PR #76`: https://github.com/desihub/fastspecfit/pull/76
 
 0.3 (2022-01-19)
 ----------------

docker/Dockerfile

@@ -1,163 +1,81 @@
-FROM registry.services.nersc.gov/nersc/intel_cxx_fort_mpi_mkl_devel as builder
+FROM ubuntu:22.04
 
-RUN apt-get -y clean && apt -y update && apt install -y apt-utils && echo 4
+RUN mkdir -p /src
+WORKDIR /src
+
+RUN apt-get -y clean && apt -y update && apt install -y apt-utils && apt -y upgrade && echo 1
 
 RUN DEBIAN_FRONTEND=noninteractive \
     apt install -y --no-install-recommends \
-    make \
-    git \
-    file \
-    patch \
-    # pkg-config \
+    build-essential \
+    gfortran \
     wget \
-    subversion \
-    emacs \
-    less \
-    # gcc \
-    zlib1g-dev \
-    # gfortran \
-    libbz2-dev \
-    libgsl-dev \
-    libcfitsio-dev \
-    libcfitsio-bin \
-    # python3 \
-    # python3-dev \
-    # python3-pip \
-    # python3-pil \
-    # python3-tk \
-    # # Remove APT files
+    git \
+    pkg-config \
+    libbz2-dev \ 
+    libgsl-dev \ 
+    libssl-dev \
+    # mpich \
+    python3-dev \
+    python3-pip \
+    # python3-mpi4py \
     && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN echo 'PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
-
-RUN wget -nv https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
-    bash miniconda.sh -b -p /opt/conda && \
-    conda config --add channels intel && \
-    conda config --set always_yes yes && \
-    conda update conda && \
-    conda install python=3.9 pip numpy scipy && \
-    conda clean -a -y
-
-ENV CC icc
-ENV CXX icpc
-ENV LDSHARED icc -shared
-ENV CFLAGS -O3 -g -fPIC -std=gnu99 -pthread -x=haswell -ax=knl
-ENV ARCH_FLAGS ""
+# python = python3
+RUN ln -s "$(which python3)" /usr/bin/python
 
-ENV PYTHON python3
-ENV PYTHON_CONFIG python3-config
-ENV PYTHON_SCRIPT "/usr/bin/env python3"
+ARG mpich=4.0.2
+ARG mpich_prefix=mpich-$mpich
 
-RUN mkdir -p /src
-WORKDIR /src
+ENV FFLAGS="-fallow-argument-mismatch" \
+    FCFLAGS="-fallow-argument-mismatch"
 
-ENV BLAS -L${MKLROOT}/lib/intel64 -lmkl_rt -fopenmp -lpthread -limf -lsvml -ldl
-ENV CPPFLAGS -I${MKLROOT}/include
-
-RUN wget --no-check-certificate -nv https://www.mpich.org/static/downloads/3.4.3/mpich-3.4.3.tar.gz \
-    && tar xvzf mpich-3.4.3.tar.gz \
-    && cd mpich-3.4.3 \
+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 \
-    && make -j4 \
+    && make -j 4 \
     && make install \
     && make clean \
-    && cd .. && rm -Rf mpich-3.4.3
-# defaults to installing in /usr/local
-
-# mpi4py / mpicc can't handle -ax=knl
-ENV CFLAGS -O3 -g -fPIC -std=gnu99 -pthread
-RUN git clone https://github.com/mpi4py/mpi4py.git \
-         && (cd mpi4py \
-         && python setup.py build \
-         && python setup.py install) \
-         && rm -Rf mpi4py
-
-# Pip installs -- built from source
-RUN pip --no-cache-dir install fitsio && echo 1
+    && cd .. \
+    && rm -rf $mpich_prefix
 
 RUN /sbin/ldconfig
 
-######## Stage 2 ########
-FROM registry.services.nersc.gov/nersc/intel_cxx_fort_mpi_mkl_runtime
-
-ENV PYTHON python3
-ENV PYTHON_CONFIG python3-config
-ENV PYTHON_SCRIPT "/usr/bin/env python3"
-RUN echo 'PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh
-
-RUN rm /root/.profile
-
-RUN apt -y update && apt install -y apt-utils \
- && DEBIAN_FRONTEND=noninteractive \
-    apt install -y --no-install-recommends \
-    make \
-    git \
-    file \
-    pkg-config \
-    wget \
-    # gcc \
-    zlib1g-dev \
-    # gfortran \
-    subversion \
-    emacs \
-    less \
-    patch \
-    libbz2-dev \
-    libgsl-dev \
-    libcfitsio-dev \
-    libcfitsio-bin \
-    imagemagick \
-    # # Remove APT files
-    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-COPY --from=builder /usr/local /usr/local
-COPY --from=builder /opt/conda /opt/conda
-
-RUN conda update --no-deps certifi
 RUN for x in \
-    setuptools \
     wheel \
-    numpy \
+    setuptools \
+    pytest \
+    numpy==1.22.4 \
     scipy \
-    matplotlib \
     astropy \
-    numba \
-    pyyaml \
-    requests \
-    scikit-learn \
     healpy \
+    fitsio \
+    numba \
+    mpi4py \
     seaborn \
-    photutils \
+    matplotlib \
     ipython \
     ipykernel \
     h5py \
-    pytest \
-    configobj \
-    sqlalchemy \
     ; do pip3 install $x; done \
     && rm -Rf /root/.cache/pip \
-    && echo 3
-
-WORKDIR /src
-
-# python = python3
-RUN ln -s $(which python3) /usr/bin/python
-
-WORKDIR /src
+    && echo 1
 
-ENV DESIMODEL /src/desimodel
+# ENV DESIMODEL /src/desimodel
 ENV DESIUTIL_VERSION 3.2.5
+ENV DESIMODEL_VERSION 0.17.0
+ENV DESITARGET_VERSION 2.5.0
+ENV DESISPEC_VERSION 0.53.2
+ENV SPECLITE_VERSION v0.16
 ENV FASTSPECFIT_VERSION main
 
-# Install desiutil, fastspecfit, and then the other desihub dependencies.
-RUN python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
-
-RUN git clone https://github.com/desihub/fastspecfit.git@{FASTSPECFIT_VERSION} \
-    && cd $package \
-    && git describe --always \
-    && python -m pip install -r requirements.txt \
-    && python setup.py install \
-    && echo 1
+RUN pip3 install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
+RUN pip3 install git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}#egg=desimodel
+RUN pip3 install git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}#egg=desitarget
+RUN pip3 install git+https://github.com/desihub/speclite.git@${SPECLITE_VERSION}#egg=speclite
+RUN pip3 install git+https://github.com/desihub/desispec.git@{DESISPEC_VERSION}#egg=desispec
+RUN pip3 install git+https://github.com/desihub/fastspecfit.git
 
 ENV PYTHONPATH /src/fastspecfit/py
 ENV PATH /src/fastspecfit/bin:/opt/conda/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
@@ -186,9 +104,4 @@ RUN echo "export PS1='[container] \\u@\\h:\\w$ '" >> $HOME/.bashrc \
   && chmod -R a+rwX $HOME/.ipython \
   && echo 2
 
-# Curses upon you, astropy
-RUN wget -O /opt/conda/lib/python3.9/site-packages/astropy/utils/iers/data/Leap_Second.dat \
-    https://raw.githubusercontent.com/astropy/astropy/master/astropy/utils/iers/data/Leap_Second.dat \
-    && rm $HOME/.wget-hsts
-
 LABEL Maintainer="John Moustakas jmoustakas@siena.edu"

docker/README → docker/README.md

@@ -1,12 +1,14 @@
 Build a Docker container for fastspecfit.
 =========================================
 
+Build a cross-platform docker container as documented [here](https://www.docker.com/blog/faster-multi-platform-builds-dockerfile-cross-compilation-guide), [here](https://blog.jaimyn.dev/how-to-build-multi-architecture-docker-images-on-an-m1-mac/), and [here](https://docs.nersc.gov/development/shifter/how-to-use/).
 ```
-./build.sh 
-docker push desihub/fastspecfit:latest
+export DOCKER_BUILDKIT=0
+export COMPOSE_DOCKER_CLI_BUILD=0
 
-docker tag desihub/fastspecfit:latest desihub/fastspecfit:v0.3
-docker push desihub/fastspecfit:v0.3
+docker buildx create --use
+docker buildx build --platform linux/amd64,linux/arm64/v8 --push -t desihub/fastspecfit:v1.0 .
+docker buildx build --platform linux/amd64,linux/arm64/v8 --push -t desihub/fastspecfit:latest .
 ```
 
 To enter the container (with a shell prompt) on a laptop do:
@@ -16,8 +18,8 @@ docker run -it desihub/fastspecfit:latest
 ```
 or
 ```
-docker pull desihub/fastspecfit:v0.2
-docker run -it desihub/fastspecfit:v0.2
+docker pull desihub/fastspecfit:v1.0
+docker run -it desihub/fastspecfit:v1.0
 ```
 
 Or at NERSC: