Merge pull request #10 from hpc4cmb/hdf5mpi

Package updates
hpc4cmb · Nov 26, 2021 · 1dba33d · 1dba33d
2 parents 1ea249a + 8e69ddf
commit 1dba33d
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -21,7 +21,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
       - name: Create Dockerfile
-        run: ./cmbenv -c docker-py3.8-debian -p /usr/local
+        run: ./cmbenv -c docker-py3.9-debian -p /usr/local
       - name: Set tag name
         run: tag=$(echo "${GITHUB_REF}" | sed -e 's/.*\/\(v.*\)/\1/') && echo "TAGNAME=${tag}" >> $GITHUB_ENV
       - name: Build Docker Image

diff --git a/cmbenv b/cmbenv
@@ -78,7 +78,7 @@ if [ "x${prefix}" = "x" ]; then
         show_help
         exit 1
     else
-        prefix="none"
+        prefix="NONE"
     fi
 fi
 

diff --git a/configs/cori-gcc b/configs/cori-gcc
@@ -6,7 +6,7 @@ OSTYPE = linux
 TEMPLATE = linux
 
 # Python version to use
-PYVERSION = 3.7
+PYVERSION = 3.9
 
 # Packages to install with pip
 PIP_PKGS =
@@ -41,7 +41,7 @@ MPI_EXTRA_LINK = -shared
 
 CFLAGS = -O3 -g -fPIC -pthread
 CXXFLAGS = -O3 -g -fPIC -pthread -std=c++11
-FCFLAGS = -O3 -g -fPIC -pthread
+FCFLAGS = -O3 -g -fPIC -pthread -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/cori-gcc.pkgs b/configs/cori-gcc.pkgs
@@ -27,7 +27,7 @@ openblas:static=1
 # a virtualenv or a conda environment.  This will also install a set of
 # common base packages.
 #python:virtualenv
-python:conda nomkl
+python:conda
 #python:default
 #
 # Install MPICH.  This step is optional and only needed in 2 cases:
@@ -53,7 +53,7 @@ bzip2
 # Install Boost.
 boost
 #
-# Install HDF5 (serial version).
+# Install HDF5.
 hdf5
 #
 # Install h5py (using our HDF5).

diff --git a/configs/cori-intel b/configs/cori-intel
@@ -6,7 +6,7 @@ OSTYPE = linux
 TEMPLATE = linux
 
 # Python version to use
-PYVERSION = 3.7
+PYVERSION = 3.9
 
 # Packages to install with pip
 PIP_PKGS =

diff --git a/configs/cori-intel.pkgs b/configs/cori-intel.pkgs
@@ -27,7 +27,7 @@ zlib
 # a virtualenv or a conda environment.  This will also install a set of
 # common base packages.
 #python:virtualenv
-python:conda nomkl
+python:conda
 #python:default
 #
 # Install MPICH.  This step is optional and only needed in 2 cases:
@@ -53,7 +53,7 @@ bzip2
 # Install Boost.
 boost
 #
-# Install HDF5 (serial version).
+# Install HDF5.
 hdf5
 #
 # Install h5py (using our HDF5).

diff --git a/configs/docker-py3.7-debian b/configs/docker-py3.7-debian
@@ -9,7 +9,7 @@ TEMPLATE = docker-debian
 PYVERSION = 3.7
 
 # Specify the docker base image
-DOCKER_BASE = python:3.7-slim-buster
+DOCKER_BASE = python:3.7-slim-bullseye
 
 # Specify additional packages to install for docker builds
 DOCKER_SYS_PKGS = m4 libtool autoconf automake llvm libsuitesparse-dev libfftw3-dev libcfitsio-dev libflac-dev zlib1g-dev libbz2-dev libopenblas-dev liblapack-dev libhdf5-dev
@@ -47,7 +47,7 @@ MPI_EXTRA_LINK =
 
 CFLAGS = -O2 -g -fPIC -pthread
 CXXFLAGS = -O2 -g -fPIC -pthread -std=c++11
-FCFLAGS = -O2 -g -fPIC -pthread
+FCFLAGS = -O2 -g -fPIC -pthread -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/docker-py3.7-debian.pkgs b/configs/docker-py3.7-debian.pkgs
@@ -53,11 +53,11 @@ mpi4py
 # Install Boost.
 #boost
 #
-# Install HDF5 (serial version).
-#hdf5
+# Install HDF5.
+hdf5
 #
 # Install h5py (using our HDF5).
-h5py:pkg-config
+h5py
 #
 # Install healpy
 healpy

diff --git a/configs/docker-py3.8-debian b/configs/docker-py3.8-debian
@@ -9,7 +9,7 @@ TEMPLATE = docker-debian
 PYVERSION = 3.8
 
 # Specify the docker base image
-DOCKER_BASE = python:3.8-slim-buster
+DOCKER_BASE = python:3.8-slim-bullseye
 
 # Specify additional packages to install for docker builds
 DOCKER_SYS_PKGS = m4 libtool autoconf automake llvm libsuitesparse-dev libfftw3-dev libcfitsio-dev libflac-dev zlib1g-dev libbz2-dev libopenblas-dev liblapack-dev libhdf5-dev
@@ -47,7 +47,7 @@ MPI_EXTRA_LINK =
 
 CFLAGS = -O2 -g -fPIC -pthread
 CXXFLAGS = -O2 -g -fPIC -pthread -std=c++11
-FCFLAGS = -O2 -g -fPIC -pthread
+FCFLAGS = -O2 -g -fPIC -pthread -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/docker-py3.9-debian b/configs/docker-py3.9-debian
@@ -9,7 +9,7 @@ TEMPLATE = docker-debian
 PYVERSION = 3.9
 
 # Specify the docker base image
-DOCKER_BASE = python:3.9-slim-buster
+DOCKER_BASE = python:3.9-slim-bullseye
 
 # Specify additional packages to install for docker builds
 DOCKER_SYS_PKGS = m4 libtool autoconf automake llvm libsuitesparse-dev libfftw3-dev libcfitsio-dev libflac-dev zlib1g-dev libbz2-dev libopenblas-dev liblapack-dev libhdf5-dev
@@ -47,7 +47,7 @@ MPI_EXTRA_LINK =
 
 CFLAGS = -O2 -g -fPIC -pthread
 CXXFLAGS = -O2 -g -fPIC -pthread -std=c++11
-FCFLAGS = -O2 -g -fPIC -pthread
+FCFLAGS = -O2 -g -fPIC -pthread -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/docker-toastdeps-py37.pkgs b/configs/docker-toastdeps-py37.pkgs
@@ -53,11 +53,11 @@ mpi4py
 # Install Boost.
 #boost
 #
-# Install HDF5 (serial version).
-#hdf5
+# Install HDF5.
+hdf5
 #
 # Install h5py (using our HDF5).
-h5py:pkg-config
+h5py
 #
 # Install healpy
 healpy

diff --git a/configs/linux-conda b/configs/linux-conda
@@ -6,7 +6,7 @@ OSTYPE = linux
 TEMPLATE = linux
 
 # Python version to use
-PYVERSION = 3.7
+PYVERSION = 3.9
 
 # Packages to install with pip
 PIP_PKGS =
@@ -41,7 +41,7 @@ MPI_EXTRA_LINK =
 
 CFLAGS = -O3 -fPIC -pthread
 CXXFLAGS = -O3 -fPIC -pthread -std=c++11
-FCFLAGS = -O3 -fPIC -pthread
+FCFLAGS = -O3 -fPIC -pthread -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/linux-conda-mkl b/configs/linux-conda-mkl
@@ -0,0 +1 @@
+linux-conda
diff --git a/configs/linux-conda-nomkl.pkgs → configs/linux-conda-mkl.pkgs b/configs/linux-conda-nomkl.pkgs → configs/linux-conda-mkl.pkgs
@@ -27,7 +27,7 @@ openblas
 # a virtualenv or a conda environment.  This will also install a set of
 # common base packages.
 #python:virtualenv
-python:conda nomkl
+python:conda mkl
 #python:default
 #
 # Install MPICH.  This step is optional and only needed in 2 cases:
@@ -53,7 +53,7 @@ bzip2
 # Install Boost.
 boost
 #
-# Install HDF5 (serial version).
+# Install HDF5.
 hdf5
 #
 # Install h5py (using our HDF5).

diff --git a/configs/linux-conda-nomkl b/configs/linux-conda-nomkl
diff --git a/configs/linux-conda.pkgs b/configs/linux-conda.pkgs
@@ -53,7 +53,7 @@ bzip2
 # Install Boost.
 boost
 #
-# Install HDF5 (serial version).
+# Install HDF5.
 hdf5
 #
 # Install h5py (using our HDF5).

diff --git a/configs/linux-venv b/configs/linux-venv
@@ -41,7 +41,7 @@ MPI_EXTRA_LINK =
 
 CFLAGS = -O3 -fPIC -pthread
 CXXFLAGS = -O3 -fPIC -pthread -std=c++11
-FCFLAGS = -O3 -fPIC -pthread
+FCFLAGS = -O3 -fPIC -pthread -std=legacy -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/linux-venv.pkgs b/configs/linux-venv.pkgs
@@ -53,7 +53,7 @@ bzip2
 # Install Boost.
 boost
 #
-# Install HDF5 (serial version).
+# Install HDF5.
 hdf5
 #
 # Install h5py (using our HDF5).

diff --git a/configs/cori-gcc-gpu → configs/old/cori-gcc-gpu b/configs/cori-gcc-gpu → configs/old/cori-gcc-gpu
diff --git a/configs/cori-gcc-gpu.mod → configs/old/cori-gcc-gpu.mod b/configs/cori-gcc-gpu.mod → configs/old/cori-gcc-gpu.mod
diff --git a/configs/cori-gcc-gpu.pkgs → configs/old/cori-gcc-gpu.pkgs b/configs/cori-gcc-gpu.pkgs → configs/old/cori-gcc-gpu.pkgs
diff --git a/configs/cori-gcc-gpu.sh → configs/old/cori-gcc-gpu.sh b/configs/cori-gcc-gpu.sh → configs/old/cori-gcc-gpu.sh
diff --git a/configs/docker-intel → configs/old/docker-intel b/configs/docker-intel → configs/old/docker-intel
diff --git a/configs/osx-homebrew-clang.notes b/configs/osx-homebrew-clang.notes
@@ -0,0 +1,12 @@
+
+# Before running the install, run these commands once
+# to get dependencies from OS packages.
+
+brew install \
+mpich \
+cmake \
+suite-sparse \
+boost \
+fftw \
+cfitsio \
+hdf5
diff --git a/configs/osx-homebrew-clang.pkgs b/configs/osx-homebrew-clang.pkgs
@@ -53,8 +53,8 @@ mpi4py
 # Install Boost.
 #boost
 #
-# Install HDF5 (serial version).
-hdf5
+# Install HDF5.
+#hdf5
 #
 # Install h5py (using our HDF5).
 h5py
@@ -75,8 +75,8 @@ fitsio
 aatm
 #
 # GMP and MPFR are needed by SuiteSparse
-gmp
-mpfr
+#gmp
+#mpfr
 #
 # Install suitesparse
 #suitesparse

diff --git a/configs/osx-macports-gcc b/configs/osx-macports-gcc
@@ -4,9 +4,9 @@ OSTYPE = osx
 
 # Serial compilers
 
-CC = gcc-mp-9
-CXX = g++-mp-9
-FC = gfortran-mp-9
+CC = gcc-mp-10
+CXX = g++-mp-10
+FC = gfortran-mp-10
 
 # Compiler to use for packages needed on the build machine
 
@@ -29,7 +29,7 @@ MPI_EXTRA_LINK =
 
 CFLAGS = -O3 -fPIC
 CXXFLAGS = -O3 -fPIC -std=c++11
-FCFLAGS = -O3 -fPIC
+FCFLAGS = -O3 -fPIC -fallow-argument-mismatch
 
 OPENMP_CFLAGS = -fopenmp
 OPENMP_CXXFLAGS = -fopenmp

diff --git a/configs/osx-macports-gcc.notes b/configs/osx-macports-gcc.notes
@@ -0,0 +1,15 @@
+
+# Before running the install, run these commands once
+# to get dependencies from OS packages.
+
+sudo port install \
+gcc10 \
+mpich-gcc10 \
+cmake \
+OpenBLAS +gcc10 \
+OpenBLAS-devel +gcc10 \
+SuiteSparse +gcc10 \
+boost176 \
+fftw-3 +gcc10 \
+cfitsio +gcc10 \
+hdf5 +gcc10