diff --git a/docker/arm/Dockerfile b/docker/Dockerfile similarity index 88% rename from docker/arm/Dockerfile rename to docker/Dockerfile index da4b831..cb19bfc 100644 --- a/docker/arm/Dockerfile +++ b/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 diff --git a/docker/arm/install_scripts/install_arma.sh b/docker/arm/install_scripts/install_arma.sh deleted file mode 100755 index ac162c2..0000000 --- a/docker/arm/install_scripts/install_arma.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -cd /home/${user}/software/src -wget http://sourceforge.net/projects/arma/files/armadillo-9.880.1.tar.xz -O arma.tar.xz -tar -xvf arma.tar.xz -mv armadillo-9.880.1 arma - -rm *.xz -cd ../build -mkdir arma -cd arma -cmake -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install ../../src/arma -make -j4 -make install - - diff --git a/docker/arm/install_scripts/install_cmake.sh b/docker/arm/install_scripts/install_cmake.sh deleted file mode 100644 index 20f61a4..0000000 --- a/docker/arm/install_scripts/install_cmake.sh +++ /dev/null @@ -1,11 +0,0 @@ -user=${USERNAME} - -sudo apt-get -y install build-essential libssl-dev cmake - -cd /home/${user}/software/src -wget https://github.com/Kitware/CMake/releases/download/v3.20.0/cmake-3.20.0.tar.gz -tar -zxvf cmake-3.20.0.tar.gz -cd cmake-3.20.0 -cmake . -make -j4 -sudo make install \ No newline at end of file diff --git a/docker/arm/install_scripts/install_conda_arm.sh b/docker/arm/install_scripts/install_conda_arm.sh deleted file mode 100755 index a07fdff..0000000 --- a/docker/arm/install_scripts/install_conda_arm.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -conda_link="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh" -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 diff --git a/docker/arm/install_scripts/install_mpi.sh b/docker/arm/install_scripts/install_mpi.sh deleted file mode 100755 index 93ef605..0000000 --- a/docker/arm/install_scripts/install_mpi.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/sh - -sudo apt-get install -y libopenmpi-dev openmpi-bin openmpi-common - -#user=${USERNAME} -# -#cd /home/${user}/software/src -# -#wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz -#tar -xvf openmpi-4.0.3.tar.gz -#cd openmpi-4.0.3 -#mkdir build -#cd build -#../configure prefix=/usr/local/openmpi -#make -j4 -#sudo make install -# -#echo "export PATH=${PATH}:/usr/local/openmpi/bin" >> ~/.bashrc -#echo "export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/openmpi/lib" >> ~/.bashrc -#echo "export CPATH=${CPATH}:/usr/local/openmpi/include" -# -## clean up -#cd /home/${user} -#rm -rf software/src/openmpi* diff --git a/docker/arm/install_scripts/install_pacmensl.sh b/docker/arm/install_scripts/install_pacmensl.sh deleted file mode 100755 index 0f62972..0000000 --- a/docker/arm/install_scripts/install_pacmensl.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -cd /home/${user}/software/src -git clone https://github.com/voduchuy/pacmensl pacmensl - -cd /home/${user}/software/build -mkdir pacmensl -cd pacmensl - -cmake -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install /home/${user}/software/src/pacmensl -make -j4 -make install diff --git a/docker/arm/install_scripts/install_petsc.sh b/docker/arm/install_scripts/install_petsc.sh deleted file mode 100755 index 6a60d1e..0000000 --- a/docker/arm/install_scripts/install_petsc.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/sh - -user=${USERNAME} - -cd /home/${user}/software/src - -wget https://gitlab.com/petsc/petsc/-/archive/v3.13.6/petsc-v3.13.6.tar.gz -O petsc.tar.gz -tar -xvf petsc.tar.gz -rm petsc.tar.gz -mv petsc* petsc -# git clone -b maint https://gitlab.com/petsc/petsc.git petsc -cd petsc -export PETSC_DIR=`pwd`; unset PETSC_ARCH; ./configure PETSC_ARCH=linux-c-opt --with-precision=double --with-scalar-type=real --with-debugging=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 --with-fc=0 --with-shared-libraries=1 --with-avx512-kernels 1 --prefix=/home/${user}/software/install/petsc -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/${user}/.bashrc - - diff --git a/docker/arm/install_scripts/install_sundials.sh b/docker/arm/install_scripts/install_sundials.sh deleted file mode 100755 index 23af83a..0000000 --- a/docker/arm/install_scripts/install_sundials.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -sundials_link="https://github.com/LLNL/sundials/releases/download/v5.7.0/sundials-5.7.0.tar.gz" - -source /home/${user}/.bashrc -echo ${PETSC_DIR} - -cd /home/${user}/software/src -wget ${sundials_link} -O sundials.tar.gz -tar -xf sundials.tar.gz -rm sundials.tar.gz -mv sundials* sundials - -cd /home/${user}/software/build -mkdir sundials -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/${user}/software/src/sundials -make -j4 -make install diff --git a/docker/arm/install_scripts/install_zoltan.sh b/docker/arm/install_scripts/install_zoltan.sh deleted file mode 100755 index 86e134a..0000000 --- a/docker/arm/install_scripts/install_zoltan.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash -user=${USERNAME} - - - -cd /home/${user}/software/src -git clone https://github.com/trilinos/Trilinos.git --depth 1 --branch master --single-branch -cd ../build -mkdir zoltan -cd zoltan -cmake \ --DCMAKE_INSTALL_PREFIX=/home/${user}/software/install \ --DTPL_ENABLE_MPI=ON \ --DTrilinos_ENABLE_Zoltan=ON \ --DBUILD_SHARED_LIBS=ON \ --DTPL_ENABLE_ParMETIS=ON \ --DParMETIS_INCLUDE_DIRS=/usr/local/include \ --DTrilinos_GENERATE_REPO_VERSION_FILE=OFF \ --DParMETIS_LIBRARY_DIRS=/home/${user}/software/install/lib \ -../../src/Trilinos -make -j4 -make install - - - diff --git a/docker/build_docker_image.sh b/docker/build_docker_image.sh new file mode 100755 index 0000000..92ff3c5 --- /dev/null +++ b/docker/build_docker_image.sh @@ -0,0 +1,4 @@ +PACMENSL_VERSION=0.1.0 +ARCH=$(uname -m) + +docker build -t pacmensl:v${PACMENSL_VERSION}_${ARCH} --build-arg pacmensl_version=$PACMENSL_VERSION . \ No newline at end of file diff --git a/docker/x86/install_scripts/install_arma.sh b/docker/install_scripts/install_arma.sh similarity index 63% rename from docker/x86/install_scripts/install_arma.sh rename to docker/install_scripts/install_arma.sh index ac162c2..cb9613b 100755 --- a/docker/x86/install_scripts/install_arma.sh +++ b/docker/install_scripts/install_arma.sh @@ -10,8 +10,11 @@ rm *.xz cd ../build mkdir arma cd arma -cmake -DCMAKE_INSTALL_PREFIX=/home/${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 + diff --git a/docker/x86/install_scripts/install_cmake.sh b/docker/install_scripts/install_cmake.sh similarity index 77% rename from docker/x86/install_scripts/install_cmake.sh rename to docker/install_scripts/install_cmake.sh index 20f61a4..757bbb4 100644 --- a/docker/x86/install_scripts/install_cmake.sh +++ b/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 \ No newline at end of file +sudo make install + +# Cleanup +rm -rf /home/${user}/software/src/cmake-3.20.0 \ No newline at end of file diff --git a/docker/install_scripts/install_conda.sh b/docker/install_scripts/install_conda.sh new file mode 100755 index 0000000..8063652 --- /dev/null +++ b/docker/install_scripts/install_conda.sh @@ -0,0 +1,17 @@ +#!/bin/bash +user=${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 diff --git a/docker/arm/install_scripts/install_metis.sh b/docker/install_scripts/install_metis.sh similarity index 90% rename from docker/arm/install_scripts/install_metis.sh rename to docker/install_scripts/install_metis.sh index ea5ac1f..a28f616 100755 --- a/docker/arm/install_scripts/install_metis.sh +++ b/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* diff --git a/docker/install_scripts/install_mpi.sh b/docker/install_scripts/install_mpi.sh new file mode 100755 index 0000000..62ec193 --- /dev/null +++ b/docker/install_scripts/install_mpi.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +sudo apt-get install -y libopenmpi-dev openmpi-bin openmpi-common + diff --git a/docker/install_scripts/install_pacmensl.sh b/docker/install_scripts/install_pacmensl.sh new file mode 100755 index 0000000..cae4dfa --- /dev/null +++ b/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 \ No newline at end of file diff --git a/docker/install_scripts/install_petsc.sh b/docker/install_scripts/install_petsc.sh new file mode 100755 index 0000000..86fd24d --- /dev/null +++ b/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 diff --git a/docker/x86/install_scripts/install_sundials.sh b/docker/install_scripts/install_sundials.sh similarity index 77% rename from docker/x86/install_scripts/install_sundials.sh rename to docker/install_scripts/install_sundials.sh index 23af83a..a56a4fb 100755 --- a/docker/x86/install_scripts/install_sundials.sh +++ b/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/${user}/software/src/sundials \ No newline at end of file diff --git a/docker/x86/install_scripts/install_zoltan.sh b/docker/install_scripts/install_zoltan.sh similarity index 60% rename from docker/x86/install_scripts/install_zoltan.sh rename to docker/install_scripts/install_zoltan.sh index 86e134a..4e32e4e 100755 --- a/docker/x86/install_scripts/install_zoltan.sh +++ b/docker/install_scripts/install_zoltan.sh @@ -1,15 +1,20 @@ #!/bin/bash user=${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 + diff --git a/docker/x86/Dockerfile b/docker/x86/Dockerfile deleted file mode 100644 index 88bf4e1..0000000 --- a/docker/x86/Dockerfile +++ /dev/null @@ -1,98 +0,0 @@ -FROM ubuntu:latest - -RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections - -RUN apt-get update && \ - apt-get -y install sudo && \ - apt-get clean -RUN apt-get -y install dialog apt-utils - -# set environment variables -ENV USERNAME huy - -RUN adduser --disabled-password --gecos --create-home ${USERNAME} -RUN adduser ${USERNAME} sudo -RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers - -WORKDIR /home/${USERNAME} -USER ${USERNAME} -RUN chmod a+rwx /home/${USERNAME}/ - -RUN sudo apt update && \ - sudo apt install -y software-properties-common && \ - sudo add-apt-repository -y ppa:deadsnakes/ppa && \ - sudo apt update && \ - sudo apt-get clean - -# install GCC and other basic libraries -ENV PACKAGES="\ - gcc \ - g++ \ - gfortran \ - libopenblas-base \ - libopenblas-dev \ - wget \ - xz-utils \ - git \ - python3.8 \ -" - -RUN sudo apt-get install -y ${PACKAGES} && sudo apt-get clean - - -RUN sudo echo "export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}" >> /home/${USERNAME}/.bashrc && \ - sudo echo "export LD_LIBRARY_PATH=/home/${USERNAME}/software/install/lib:${LD_LIBRARY_PATH}" >> /home/${USERNAME}/.bashrc && \ - mkdir /home/${USERNAME}/software && \ - mkdir /home/${USERNAME}/software/src && \ - mkdir /home/${USERNAME}/software/build - -# install open-mpi 4.0 -COPY install_scripts/install_mpi.sh ./ -RUN sudo chmod +x ./install*.sh && ./install_mpi.sh - -# install CMake 3.20 -COPY install_scripts/install_cmake.sh ./ -RUN sudo chmod +x ./install_cmake.sh && ./install_cmake.sh - -# install metis -COPY install_scripts/install_metis.sh ./ -RUN sudo chmod +x ./install_metis.sh && ./install_metis.sh - -# install Zoltan -COPY install_scripts/install_zoltan.sh ./ -RUN sudo chmod +x ./install_zoltan.sh && ./install_zoltan.sh - -# install armadillo -COPY install_scripts/install_arma.sh ./ -RUN sudo chmod +x ./install_arma.sh && ./install_arma.sh - -# install anaconda -COPY install_scripts/install_conda.sh ./ -ENV PATH /home/${USERNAME}/anaconda/bin:${PATH} -RUN sudo chmod +x ./install_conda.sh && ./install_conda.sh \ - && \ - conda update conda && \ - conda init bash - - -# install petsc -COPY install_scripts/install_petsc.sh ./ -RUN sudo chmod +x ./install_petsc.sh && ./install_petsc.sh - - - -# install sundials -COPY install_scripts/install_sundials.sh ./ -ENV PETSC_DIR=/home/${USERNAME}/software/install/petsc -ENV PETSC_ARCH=linux-c-opt -RUN sudo chmod +x ./install_sundials.sh && ./install_sundials.sh - -# install pacmensl -COPY install_scripts/install_pacmensl.sh ./ -ENV CPATH=/home/${USERNAME}/software/install/include -ENV LIBRARY_PATH=/home/${USERNAME}/software/install/lib -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 - diff --git a/docker/x86/install_scripts/install_conda.sh b/docker/x86/install_scripts/install_conda.sh deleted file mode 100755 index 06edb97..0000000 --- a/docker/x86/install_scripts/install_conda.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -conda_link="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -cd /home/${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 diff --git a/docker/x86/install_scripts/install_metis.sh b/docker/x86/install_scripts/install_metis.sh deleted file mode 100755 index ea5ac1f..0000000 --- a/docker/x86/install_scripts/install_metis.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -cd /home/${user}/software/src -wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz -tar -xvf metis-5.1.0.tar.gz -cd metis-5.1.0 -make config prefix=/home/${user}/software/install shared=1 -make -j4 -make install - -cd /home/${user}/software/src -wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz -tar -xvf parmetis-4.0.3.tar.gz -cd parmetis-4.0.3 -make config prefix=/home/${user}/software/install shared=1 -make -j4 -make install - - - - diff --git a/docker/x86/install_scripts/install_mpi.sh b/docker/x86/install_scripts/install_mpi.sh deleted file mode 100755 index 717727c..0000000 --- a/docker/x86/install_scripts/install_mpi.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/sh - -sudo apt-get install -y libopenmpi-dev openmpi-bin openmpi-common -# -# user=${USERNAME} -# -# cd /home/${user}/software/src -# -# wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz -# tar -xvf openmpi-4.0.3.tar.gz -# cd openmpi-4.0.3 -# mkdir build -# cd build -# ../configure prefix=/usr/local/openmpi -# make -j4 -# sudo make install -# -# echo "export PATH=${PATH}:/usr/local/openmpi/bin" >> ~/.bashrc -# echo "export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/openmpi/lib" >> ~/.bashrc -# echo "export CPATH=${CPATH}:/usr/local/openmpi/include" -# -# # clean up -# cd /home/${user} -# rm -rf software/src/openmpi* diff --git a/docker/x86/install_scripts/install_pacmensl.sh b/docker/x86/install_scripts/install_pacmensl.sh deleted file mode 100755 index 0f62972..0000000 --- a/docker/x86/install_scripts/install_pacmensl.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash -user=${USERNAME} - -cd /home/${user}/software/src -git clone https://github.com/voduchuy/pacmensl pacmensl - -cd /home/${user}/software/build -mkdir pacmensl -cd pacmensl - -cmake -DCMAKE_INSTALL_PREFIX=/home/${user}/software/install /home/${user}/software/src/pacmensl -make -j4 -make install diff --git a/docker/x86/install_scripts/install_petsc.sh b/docker/x86/install_scripts/install_petsc.sh deleted file mode 100755 index 6a60d1e..0000000 --- a/docker/x86/install_scripts/install_petsc.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/sh - -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 -# git clone -b maint https://gitlab.com/petsc/petsc.git petsc -cd petsc -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/${user}/software/install/petsc -make -j4 PETSC_DIR=/home/${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 - -