Merge pull request #13 from voduchuy/improve_docker

Improve docker

docker/arm/Dockerfile → docker/Dockerfile

@@ -1,6 +1,8 @@
 FROM ubuntu:latest
 MAINTAINER Huy Duc Vo
 
+ARG pacmensl_version=0.1.0
+
 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
 
 RUN apt-get update && \
@@ -9,7 +11,8 @@ RUN apt-get update && \
 RUN apt-get -y install dialog apt-utils
 
 # set environment variables
-ENV USERNAME huy
+ENV USERNAME user
+ENV PACMENSL_VERSION $pacmensl_version
 
 RUN adduser --disabled-password --gecos --create-home ${USERNAME}
 RUN adduser ${USERNAME} sudo
@@ -41,7 +44,6 @@ ENV PACKAGES="\
 
 RUN sudo apt-get install -y ${PACKAGES} && sudo apt-get clean
 
-
 RUN sudo echo "export LD_LIBRARY_PATH=/usr/local/lib" >> /home/${USERNAME}/.bashrc && \
     mkdir /home/${USERNAME}/software && \
     mkdir /home/${USERNAME}/software/src && \
@@ -59,7 +61,6 @@ RUN sudo chmod +x ./install_cmake.sh && ./install_cmake.sh
 COPY install_scripts/install_metis.sh ./
 RUN sudo chmod +x ./install_metis.sh && ./install_metis.sh
 
-
 # install Zoltan
 COPY install_scripts/install_zoltan.sh ./
 RUN sudo chmod +x ./install_zoltan.sh && ./install_zoltan.sh
@@ -69,14 +70,13 @@ COPY install_scripts/install_arma.sh ./
 RUN sudo chmod +x ./install_arma.sh && ./install_arma.sh
 
 # install anaconda
-COPY install_scripts/install_conda_arm.sh ./
+COPY install_scripts/install_conda.sh ./
 ENV PATH /home/${USERNAME}/anaconda/bin:${PATH}
-RUN sudo chmod +x ./install_conda_arm.sh && ./install_conda_arm.sh  \
+RUN sudo chmod +x ./install_conda.sh && ./install_conda.sh  \
     && \
     conda update conda && \
     conda init bash
 
-
 # install petsc
 COPY install_scripts/install_petsc.sh ./
 RUN sudo chmod +x ./install_petsc.sh && ./install_petsc.sh
@@ -95,3 +95,8 @@ RUN sudo chmod +x ./install_pacmensl.sh && ./install_pacmensl.sh
 
 # Set OMPI environment variable to prevent spurious printing, see issue 4948 openmpi github page
 ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
+
+# Cleanup
+RUN sudo rm *.sh && \
+    sudo rm -rf /home/${USERNAME}/software/build && \
+    sudo rm -rf /home/${USERNAME}/software/src

docker/build_docker_image.sh

@@ -0,0 +1,4 @@
+PACMENSL_VERSION=0.1.0
+ARCH=$(uname -m)
+
+docker build -t pacmensl:v${PACMENSL_VERSION}_${ARCH} --build-arg pacmensl_version=$PACMENSL_VERSION .

docker/x86/install_scripts/install_arma.sh → docker/install_scripts/install_arma.sh

@@ -10,8 +10,11 @@ rm *.xz
 cd ../build
 mkdir arma
 cd arma
-cmake -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install ../../src/arma
+cmake -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install -DBUILD_SHARED_LIBS=OFF ../../src/arma
 make -j4
 make install
 
+# Cleanup
+rm -rf /home/${user}/software/src/arma
+
 

docker/x86/install_scripts/install_cmake.sh → docker/install_scripts/install_cmake.sh

@@ -8,4 +8,7 @@ tar -zxvf cmake-3.20.0.tar.gz
 cd cmake-3.20.0
 cmake .
 make -j4
-sudo make install
+sudo make install
+
+# Cleanup
+rm -rf /home/${user}/software/src/cmake-3.20.0

docker/install_scripts/install_conda.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+user=${USERNAME}
+
+arch=$(uname -m)
+
+if [ "$arch" = "arm64" ] || [ "$arch" = "aarch64" ]; then
+  conda_link="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
+else
+  conda_link="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
+fi
+
+cd /home/${user}/software/src
+wget ${conda_link} -O conda.sh
+
+sudo chmod u+x ./conda.sh
+bash ./conda.sh -b -p /home/${user}/anaconda
+rm ./conda.sh

docker/arm/install_scripts/install_metis.sh → docker/install_scripts/install_metis.sh

@@ -17,6 +17,8 @@ make config prefix=/home/${user}/software/install shared=1
 make -j4
 make install
 
+# Cleanup
+rm -rf /home/${user}/software/src/*metis*
 
 
 

docker/install_scripts/install_mpi.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+sudo apt-get install -y libopenmpi-dev openmpi-bin openmpi-common
+

docker/install_scripts/install_pacmensl.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+user=${USERNAME}
+
+export CPATH=${CPATH};/home/${user}/software/install/include
+
+cd /home/${user}/software/src
+wget https://github.com/voduchuy/pacmensl/archive/refs/tags/v${PACMENSL_VERSION}.tar.gz -O pacmensl.tar.gz
+tar -xf pacmensl.tar.gz
+rm *.tar.gz
+mv pacmensl* pacmensl
+
+cd /home/${user}/software/build
+mkdir pacmensl
+cd pacmensl
+
+cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DCMAKE_POSITION_INDPENDENT_CODE=ON -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install /home/${user}/software/src/pacmensl
+make -j4
+
+# Now install
+make install

docker/install_scripts/install_petsc.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+user=${USERNAME}
+
+cd /home/${user}/software/src
+
+wget https://gitlab.com/petsc/petsc/-/archive/v3.13.6/petsc-v3.13.6.tar.gz -O petsc.tar.gz
+tar -xvf petsc.tar.gz
+rm petsc.tar.gz
+mv petsc* petsc
+
+cd petsc
+
+arch=$(uname -m)
+
+if [ "$arch" = "arm64" ] || [ "$arch" = "aarch64" ]; then
+  export PETSC_DIR=`pwd`; unset PETSC_ARCH; ./configure PETSC_ARCH=linux-c-opt --with-precision=double --with-scalar-type=real --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 --with-fc=0 --with-shared-libraries=1 --prefix=/home/${user}/software/install/petsc
+else
+  export PETSC_DIR=`pwd`; unset PETSC_ARCH; ./configure PETSC_ARCH=linux-c-opt --with-precision=double --with-scalar-type=real --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 --with-fc=0 --with-shared-libraries=1 --with-avx512-kernels 1 --prefix=/home/${user}/software/install/petsc
+fi
+
+make -j4 PETSC_DIR=/home/${user}/software/src/petsc PETSC_ARCH=linux-c-opt all
+make PETSC_DIR=/home/${user}/software/src/petsc PETSC_ARCH=linux-c-opt install
+
+# add petsc to environment variables
+echo "export PETSC_DIR=/home/${user}/software/install/petsc" >> /home/${user}/.bashrc
+echo "export PETSC_ARCH=linux-c-opt" >> /home/${user}/.bashrc
+echo "export LD_LIBRARY_PATH=/home/${user}/software/install/petsc/lib:/usr/local/lib:/home/${user}/software/install/lib:${LD_LIBRARY_PATH}" >> /home/${user}/.bashrc
+echo "export LIBRARY_PATH=home/${user}/software/install/petsc/lib:/usr/local/lib:/home/${user}/software/install/lib:${LIBRARY_PATH}" >> /home/${user}/.bashrc
+
+# cleanup
+rm -rf /home/${user}/software/src/petsc

docker/x86/install_scripts/install_sundials.sh → docker/install_scripts/install_sundials.sh

@@ -19,6 +19,9 @@ cd sundials
 echo ${PETSC_DIR}
 
 cmake -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install -DPETSC_ENABLE=ON -DMPI_ENABLE=ON -DPETSC_LIBRARIES=${PETSC_DIR}/lib/libpetsc.so -DPETSC_INCLUDES=${PETSC_DIR}/include \
--DSUNDIALS_INDEX_SIZE=32 /home/${user}/software/src/sundials
+-DSUNDIALS_INDEX_SIZE=32 -DBUILD_SHARED_LIBS=ON -DCMAKE_POSITION_INDEPENDENT_CODE=ON /home/${user}/software/src/sundials
 make -j4
 make install
+
+# Cleanup
+rm -rf /home/${user}/software/src/sundials

docker/x86/install_scripts/install_zoltan.sh → docker/install_scripts/install_zoltan.sh

@@ -1,15 +1,20 @@
 #!/bin/bash
 user=${USERNAME}
 
-
+trilinos_link=https://github.com/trilinos/Trilinos/archive/refs/tags/trilinos-release-13-0-1.tar.gz
 
 cd /home/${user}/software/src
-git clone https://github.com/trilinos/Trilinos.git --depth 1 --branch master --single-branch
+wget ${trilinos_link} -O trilinos.tar.gz
+tar -xf trilinos.tar.gz
+rm trilinos.tar.gz
+mv Trilinos* Trilinos
+
 cd ../build
 mkdir zoltan
 cd zoltan
 cmake \
 -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install \
+-DCMAKE_POSITION_INDEPENDENT_CODE=ON \
 -DTPL_ENABLE_MPI=ON \
 -DTrilinos_ENABLE_Zoltan=ON \
 -DBUILD_SHARED_LIBS=ON \
@@ -21,5 +26,8 @@ cmake \
 make -j4
 make install
 
+# Cleanup
+rm -rf /home/${user}/software/src/Trilinos
+