Merge pull request #108 from cpmech/remove-mpi-dependency

Remove mpi dependency

.github/workflows/test_and_coverage.yml

@@ -7,20 +7,27 @@ jobs:
       - uses: actions/checkout@v4
       - name: Install Libraries
         run: |
-          bash case-a-openblas-debian.bash
+          sudo apt-get update -y && \
+          sudo apt-get install -y --no-install-recommends \
+              liblapacke-dev \
+              libopenblas-dev \
+              libsuitesparse-dev
+      - name: Compile MUMPS
+        run: |
+          bash zscripts/compile-and-install-mumps.bash
       - name: Install Rust
         run: |
           rustup toolchain install nightly --component llvm-tools-preview
           rustup default nightly
       - name: Run tests
         run: |
-          RUST_BACKTRACE=1 cargo test
+          RUST_BACKTRACE=1 cargo test --features with_mumps
       - name: Install cargo-llvm-cov
         run: |
           curl -LsSf https://github.com/taiki-e/cargo-llvm-cov/releases/latest/download/cargo-llvm-cov-x86_64-unknown-linux-gnu.tar.gz | tar xzf - -C ~/.cargo/bin
       - name: Generate code coverage
         run: |
-          cargo llvm-cov --workspace --ignore-filename-regex 'build.rs|mem_check.rs|mem_check_lab.rs|solve_matrix_market.rs|amplifier1t.rs|brusselator_pde.rs' --lcov --output-path lcov.info
+          cargo llvm-cov --workspace --features with_mumps --ignore-filename-regex 'build.rs|mem_check.rs|mem_check_lab.rs|solve_matrix_market.rs|amplifier1t.rs|brusselator_pde.rs' --lcov --output-path lcov.info
       - name: Upload to codecov.io
         uses: codecov/codecov-action@v4
         with:

.github/workflows/test_on_arch_linux.yml

@@ -0,0 +1,10 @@
+name: Test on Arch Linux
+on: [pull_request]
+jobs:
+  test_on_arch_linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build docker image
+        run: |
+          bash zscripts/docker-build-image.bash arch

.github/workflows/test_with_intel_mkl.yml

@@ -5,11 +5,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Install Libraries
+      - name: Compile MUMPS
         run: |
-          bash case-b-intel-mkl-local-libs.bash
+          bash zscripts/compile-and-install-mumps.bash mkl
+      - name: Compile SuiteSparse
+        run: |
+          bash zscripts/compile-and-install-suitesparse.bash mkl
       - name: Run tests
         run: |
           source /opt/intel/oneapi/setvars.sh
-          RUST_BACKTRACE=1 cargo test --features intel_mkl
+          RUST_BACKTRACE=1 cargo test --features local_suitesparse,with_mumps,intel_mkl
 

.github/workflows/test_with_local_libs.yml

@@ -5,9 +5,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Install Libraries
+      - name: Compile MUMPS
         run: |
-          bash case-a-openblas-local-libs.bash
+          bash zscripts/compile-and-install-mumps.bash
+      - name: Compile SuiteSparse
+        run: |
+          bash zscripts/compile-and-install-suitesparse.bash
       - name: Run tests
         run: |
-          RUST_BACKTRACE=1 cargo test --features local_libs
+          RUST_BACKTRACE=1 cargo test --features local_suitesparse,with_mumps

.vscode/c_cpp_properties.json

@@ -5,12 +5,8 @@
       "includePath": [
         "${default}",
         "/usr/include",
-        "/usr/include/mumps",
-        "/usr/lib/x86_64-linux-gnu/openmpi/include",
-        "/usr/include/suitesparse",
-        "/opt/intel/oneapi/mkl/latest/include",
         "/usr/local/include/mumps",
-        "/usr/local/include/umfpack"
+        "/usr/local/include/suitesparse"
       ],
       "defines": [
         "USE_INTEL_MKL"

Dockerfile.Arch

@@ -0,0 +1,36 @@
+FROM archlinux:base-devel
+
+# initialize
+RUN pacman -Sy go git --noconfirm
+
+# set user
+RUN useradd -G wheel -m user
+RUN echo "user ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+RUN chown -R user:wheel /usr/local/src/
+USER user
+WORKDIR /usr/local/src/
+
+# install yay
+RUN git clone https://aur.archlinux.org/yay.git
+RUN cd yay && makepkg -si --noconfirm
+RUN sudo rm -f \
+      /var/cache/pacman/pkg/* \
+      /var/lib/pacman/sync/* \
+      /README \
+      /etc/pacman.d/mirrorlist.pacnew
+
+# install libraries for russell
+RUN yay -Y --gendb --noconfirm && yay -Y --devel --save
+RUN yay -Syu blas-openblas --noconfirm
+RUN yay -Syu suitesparse --noconfirm
+
+# install rust
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | bash -s -- -y
+ENV PATH="/home/user/.cargo/bin:${PATH}"
+
+# copy files
+COPY --chown=user:user . russell
+WORKDIR russell
+
+# run tests
+RUN cargo test

Dockerfile.Rocky

@@ -2,18 +2,14 @@ FROM rockylinux/rockylinux
 
 # initialize
 RUN dnf update -y
-RUN dnf check-update 
 RUN dnf install epel-release -y
 RUN crb enable
 RUN dnf install cmake gcc make curl clang -y
 
 # dependencies
 RUN dnf install -y \
-  gcc-toolset-13 \
   lapack-devel \
-  MUMPS-devel \
   openblas-devel \
-  openmpi-devel \
   suitesparse-devel
 
 # install rust
@@ -24,9 +20,5 @@ ENV PATH="/root/.cargo/bin:${PATH}"
 COPY . /tmp/russell
 WORKDIR /tmp/russell
 
-# set environment variables
-ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/lib64/openmpi/lib"
-ENV PSM3_DEVICES='self,shm'
-
 # run tests
 RUN cargo test

Dockerfile.Ubuntu

@@ -15,11 +15,8 @@ RUN apt-get update -y && \
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
   ca-certificates \
   curl \
-  g++ \
-  gdb \
-  gfortran \
+  build-essential \
   liblapacke-dev \
-  libmumps-dev \
   libopenblas-dev \
   libsuitesparse-dev \
   && apt-get clean && rm -rf /var/lib/apt/lists/*

Dockerfile.Ubuntu.Mumps

@@ -0,0 +1,36 @@
+FROM ubuntu:22.04
+
+# disable tzdata questions
+ENV DEBIAN_FRONTEND=noninteractive
+
+# use bash
+SHELL ["/bin/bash", "-c"]
+
+# install apt-utils
+RUN apt-get update -y && \
+  apt-get install -y apt-utils 2> >( grep -v 'debconf: delaying package configuration, since apt-utils is not installed' >&2 ) \
+  && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# essential tools
+RUN apt-get update -y && apt-get install -y --no-install-recommends \
+  ca-certificates \
+  curl \
+  build-essential \
+  liblapacke-dev \
+  libopenblas-dev \
+  libsuitesparse-dev \
+  && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# install rust
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | bash -s -- -y
+ENV PATH="/root/.cargo/bin:${PATH}"
+
+# copy files
+COPY . /tmp/russell
+WORKDIR /tmp/russell
+
+# compile MUMPS
+RUN bash zscripts/compile-and-install-mumps.bash
+
+# run tests
+RUN cargo test --features with_mumps