BLAS_LIBRARIES not found

General
1

I am building a Docker image with fenicsx as part of it. During the basix config, it reports BLAS_LIBRARIES not found error.

I already have built the BLAS and LAPACK with MPI while building PETSc. Can those be used at all? or do I have to install libopenblas-dev, boost-dev etc for compiling fenicsx?

Thanks
~anoop

2

PETSc doesn’t install BLAS and LAPACK in a central place that a general cmake config can find. You would need to add their installation paths to CMAKE_PREFIX_PATH, as specified in: CMAKE_PREFIX_PATH — CMake 3.30.3 Documentation

3

Thanks !

I as much thought so - but using CMAKE_PREFIX_PATH did not succeed in compilation either.

Is there a difference between using openblas-dev vs those from PETSc - as the earlier seems an easier solution

thanks
~anoop

4

See: The Use of BLAS and LAPACK in PETSc and external libraries — PETSc v3.21.5-480-gbfe78e4cfe0 documentation
and
Configuring PETSc — PETSc 3.21.5 documentation

It would be helpful to have a reproducible environment and a traceback for this.
Could you tell me the exact way you installed PETSc, and how you are setting the relevant paths afterwards?
For instance, the following runs nicely for me:

FROM ubuntu:24.04 as base


ENV DEB_PYTHON_INSTALL_LAYOUT=deb_system

# PETSC vars
ARG PETSC_VERSION=3.21.1
ENV PETSC_DIR=/usr/local/petsc
ENV PETSC_ARCH=linux-gnu-real-32

# Arguments that can be overridden by a user building the docker image
# Compiler optimisation flags for SLEPc and PETSc, all languages.
ARG PETSC_SLEPC_OPTFLAGS="-O2"
ARG PETSC_SLEPC_DEBUGGING="no"
ARG MPI="mpich"
ARG PETSC_VERSION

# Environment variables
ENV OPENBLAS_NUM_THREADS=1 \
    OPENBLAS_VERBOSE=0
ENV DEB_PYTHON_INSTALL_LAYOUT=deb_system
WORKDIR /tmp



# Install dependencies available via apt-get.
# - First set of packages are required to build and run FEniCS.
# - Second set of packages are recommended and/or required to build
#   documentation or tests.
RUN export DEBIAN_FRONTEND=noninteractive && \
    apt-get -qq update && \
    apt-get -yq --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
    apt-get -y install \
    clang \
    cmake \
    g++ \
    git \
    gfortran \
    lib${MPI}-dev \
    ninja-build \
    pkg-config \
    python3-dev \
    python3-pip \
    python3-setuptools \
    python3-numpy \
    python3.12-venv \
    wget && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV VIRTUAL_ENV /dolfinx-env
ENV PATH /dolfinx-env/bin:$PATH
RUN python3 -m venv ${VIRTUAL_ENV}


# Install Python packages (via pip)
RUN python3 -m pip install --upgrade pip setuptools
RUN python3 -m pip install pytest pkgconfig
RUN python3 -m pip install --no-cache-dir mpi4py


# Install PETSc with real and complex types
RUN apt-get -qq update && \
    apt-get -y install bison flex && \
    git clone -b v${PETSC_VERSION} --single-branch https://gitlab.com/petsc/petsc.git ${PETSC_DIR} && \
    cd ${PETSC_DIR} && \
    # Real, 32-bit int
    python3 ./configure \
    --COPTFLAGS=${PETSC_SLEPC_OPTFLAGS} \
    --CXXOPTFLAGS=${PETSC_SLEPC_OPTFLAGS} \
    --FOPTFLAGS=${PETSC_SLEPC_OPTFLAGS} \
    --with-64-bit-indices=no \
    --with-debugging=${PETSC_SLEPC_DEBUGGING} \
    --with-fortran-bindings=no \
    --with-shared-libraries \
    --download-ptscotch \
    --download-openblas \
    --with-scalar-type=real && \
    make ${MAKEFLAGS} all && \
    # Install petsc4py
    cd src/binding/petsc4py && \
    python3 -m pip install --no-cache-dir . && \
    # Cleanup
    apt-get -y purge bison flex && \
    apt-get -y autoremove && \
    apt-get clean && \
    rm -rf \
    ${PETSC_DIR}/**/tests/ \
    ${PETSC_DIR}/**/obj/ \
    ${PETSC_DIR}/**/externalpackages/  \
    ${PETSC_DIR}/CTAGS \
    ${PETSC_DIR}/RDict.log \
    ${PETSC_DIR}/TAGS \
    ${PETSC_DIR}/docs/ \
    ${PETSC_DIR}/share/ \
    ${PETSC_DIR}/src/ \
    ${PETSC_DIR}/systems/ && \ 
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

ENV CMAKE_PREFIX_PATH=${PETSC_DIR}/${PETSC_ARCH}/lib
RUN python3 -m pip install nanobind scikit-build-core[pyproject]
RUN git clone https://github.com/fenics/basix.git
RUN cmake -G Ninja -B build-dir-basix -DCMAKE_INSTALL_PREFIX=${DOLFINX_DIR} -DBLAS_blas_LIBRARY=${BLAS_PATH} -DLAPACK_LIBRARIES=${LAPACK_PATH} -DCMAKE_BUILD_TYPE="Release" -S ./basix/cpp
RUN cmake --build  build-dir-basix
RUN cmake --install  build-dir-basix
RUN python3 -m pip -v install --check-build-dependencies --config-settings=build-dir=build-dir-basix --config-settings=install.strip=false --config-settings=cmake.build-type="Release" --config-settings=cmake.define.CMAKE_BUILD_PARALLEL_LEVEL=${CMAKE_NUM_PROCESSES}  --no-build-isolation -e ./basix/python/

Note the line: ENV CMAKE_PREFIX_PATH=${PETSC_DIR}/${PETSC_ARCH}/lib

5

Thank you so much for sharing your working Dockerfile. I will compare it with mine and figure out my errors. Much appreciated.

BTW, my Dockerfile is rather lengthy, but here is an extract of how I build the PETSc

FROM ubuntu:22.04

ENV TOPDIR="/opt"
ENV WORKDIR=${TOPDIR}

# Install packages for PETSc and openCARP
RUN export DEBIAN_FRONTEND="noninteractive" \
 && apt update && apt install -y --no-install-recommends \
    ca-certificates \
    curl \
    dpkg-dev \
    file \
    g++ \
    gengetopt \
    gfortran \
    git \
    libfftw3-dev \
    libgomp1 \
    make \
    pkg-config \
    python3 \
    python3-distutils \
    ssh \
    valgrind \
    zlib1g-dev \
    libjpeg-dev \
    cmake \
    vim \
 && ln -sf /usr/bin/python3 /usr/bin/python \
 && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install PETSc
RUN git clone -b release https://gitlab.com/petsc/petsc.git petsc \
 && mkdir ${TOPDIR}/petsc_build \
 && cd $(ls | grep petsc) \
 && ./configure \
        PETSC_ARCH=arch-linux-c-opt \
        --prefix=${TOPDIR}/petsc_build \
        --download-mpich \
        --download-fblaslapack \
        --download-metis \
        --download-parmetis \
        --download-hypre \
        --with-debugging=0 \
        COPTFLAGS='-O2' \
        CXXOPTFLAGS='-O2' \
        FOPTFLAGS='-O2' \
 && make \
 && make install \
 && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
 && cd ${TOPDIR}

ENV PETSC_DIR="${TOPDIR}/petsc"
ENV PETSC_ARCH="arch-linux-c-opt"

I was then using it with CMAKE_PREFIX_PATH=/opt/petsc_build/lib

Thanks and regards
~anoop

6

I do not think --download-fblaslapack gives you a sufficient installation of blas and lapack.
See: The Use of BLAS and LAPACK in PETSc and external libraries — PETSc v3.21.5-480-gbfe78e4cfe0 documentation

Available BLAS/LAPACK libraries
Most systems (besides Microsoft Windows) come with pre-installed BLAS/LAPACK which are satisfactory for many PETSc simulations.
The freely available Intel MKL mathematics libraries provide BLAS/LAPACK that are generally better performing than the system provided libraries and are generally fine for most users.
For systems that do not provide BLAS/LAPACK, such as Microsoft Windows, PETSc provides the Fortran reference version --download-fblaslapack and a f2c generated C version --download-f2cblaslapack (which also supports 128 bit real number computations). These libraries are less optimized but useful to get started with PETSc easily.
PETSc also provides access to OpenBLAS via the --download-openblas configure option. OpenBLAS uses some highly optimized operations but falls back on reference routines for many other operations. See the OpenBLAS manual for more information. The configure option --download-openblas provides a full BLAS/LAPACK implementation.
BLIS does not bundle LAPACK with it so PETSc’s configure attempts to locate a compatible system LAPACK library to use if --download-blis is selected. One can use --download-f2cblaslapack --download-blis. This is recommended as a portable high-performance option. It is possible if you use --download-blis without --download-f2cblaslapack the BLIS library installed will not be used! Instead, PETSc will link in some LAPACK implementation and the BLAS that comes with that implementation!

7

Yes. That was it… thanks for guiding me through this. my apologies… thanks for your time…

~anoop