Merge branch 'new_docker'

docker/ubuntu_20_04_gcc_13_OneAPI_2024_2_gpu_12_5/Dockerfile

+FROM ubuntu:20.04
+
+ENV LINUX_CPP_COMPONENTS='intel-oneapi-compiler-dpcpp-cpp'
+ENV LINUX_FORTRAN_COMPONENTS='intel-oneapi-compiler-fortran'
+ENV LINUX_MKL_COMPONENTS='intel-oneapi-mkl'
+ENV LINUX_MKL1_COMPONENTS='intel-oneapi-mkl-devel'
+
+RUN apt-get update 
+RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get install -y apt-utils wget pkg-config ca-certificates gnupg git python3-pip openssh-client graphviz gnuplot curl zip unzip
+#RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get install -y build-essential  gfortran
+
+RUN apt-get install software-properties-common -y
+RUN add-apt-repository ppa:ubuntu-toolchain-r/test -y
+RUN apt update
+RUN apt install g++-13 gcc-13 gfortran-13 -y
+
+RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-13 13 --slave /usr/bin/g++ g++ /usr/bin/g++-13 --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-13
+
+RUN update-alternatives --config gcc
+
+
+RUN apt-get remove cmake -y
+RUN pip install --upgrade fypp ford cmake fprettify
+
+RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
+RUN dpkg -i cuda-keyring_1.1-1_all.deb
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get -y install cuda-12-5
+
+COPY setup_apt_repo_linux_no_sudo.sh /
+RUN /setup_apt_repo_linux_no_sudo.sh
+RUN apt-get install -y ${LINUX_FORTRAN_COMPONENTS}-2024.2 ${LINUX_CPP_COMPONENTS}-2024.2 ${LINUX_MKL_COMPONENTS}-2024.2 ${LINUX_MKL1_COMPONENTS}-2024.2
+#
+#RUN apt-get clean all
+#RUN apt-cache pkgnames intel
+#RUN apt-cache search intel
+
+RUN apt-get clean all

docker/ubuntu_20_04_gcc_13_OneAPI_2024_2_gpu_12_5/README.md

+# Instruction to build and push the container on WUR Gitlab
+
+```shell
+TOKEN=<generated_token_in_gitlad_with_read_registry_and_write_registry>
+echo "$TOKEN" | sudo docker login docker-registry.wur.nl -u jeremie.vandenplas@wur.nl --password-stdin
+sudo docker build -t docker-registry.wur.nl/vande018/containers/2024:ubuntu_20_04_gcc_13_OneAPI_2024_2_gpu_12_5 .
+sudo docker push docker-registry.wur.nl/vande018/containers/2024:ubuntu_20_04_gcc_13_OneAPI_2024_2_gpu_12_5
+```
+
+```shell
+sudo docker run --rm -it -v ~/snpblup_software_tmp:/container/local:z docker-registry.wur.nl/vande018/containers/2024:ubuntu_20_04_gcc_13_OneAPI_2024_2_gpu_12_5 bash
+```

docker/ubuntu_20_04_gcc_13_OneAPI_2024_2_gpu_12_5/setup_apt_repo_linux_no_sudo.sh

+#!/bin/bash
+
+apt-get update
+apt-get install -y gpg-agent wget
+
+# download the key to system keyring
+wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+| gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+
+# add signed entry to apt sources and configure the APT client to use Intel repository:
+echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
+
+apt-get update

docker/ubuntu_20_04_gcc_13_OneAPI_2025_0_gpu_12_5/Dockerfile

+FROM ubuntu:20.04
+
+ENV LINUX_CPP_COMPONENTS='intel-oneapi-compiler-dpcpp-cpp'
+ENV LINUX_FORTRAN_COMPONENTS='intel-oneapi-compiler-fortran'
+ENV LINUX_MKL_COMPONENTS='intel-oneapi-mkl'
+ENV LINUX_MKL1_COMPONENTS='intel-oneapi-mkl-devel'
+
+RUN apt-get update 
+RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get install -y apt-utils wget pkg-config ca-certificates gnupg git python3-pip openssh-client graphviz gnuplot curl zip unzip
+#RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get install -y build-essential  gfortran
+
+RUN apt-get install software-properties-common -y
+RUN add-apt-repository ppa:ubuntu-toolchain-r/test -y
+RUN apt update
+RUN apt install g++-13 gcc-13 gfortran-13 -y
+
+RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-13 13 --slave /usr/bin/g++ g++ /usr/bin/g++-13 --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-13
+
+RUN update-alternatives --config gcc
+
+
+RUN apt-get remove cmake -y
+RUN pip install --upgrade fypp ford cmake fprettify
+
+RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
+RUN dpkg -i cuda-keyring_1.1-1_all.deb
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get -y install cuda-12-5
+
+COPY setup_apt_repo_linux_no_sudo.sh /
+RUN /setup_apt_repo_linux_no_sudo.sh
+RUN apt-get install -y ${LINUX_FORTRAN_COMPONENTS}-2025.0 ${LINUX_CPP_COMPONENTS}-2025.0 ${LINUX_MKL_COMPONENTS}-2025.0 ${LINUX_MKL1_COMPONENTS}-2025.0
+#
+#RUN apt-get clean all
+#RUN apt-cache pkgnames intel
+#RUN apt-cache search intel
+
+RUN apt-get clean all

docker/ubuntu_20_04_gcc_13_OneAPI_2025_0_gpu_12_5/README.md

+# Instruction to build and push the container on WUR Gitlab
+
+```shell
+TOKEN=<generated_token_in_gitlad_with_read_registry_and_write_registry>
+echo "$TOKEN" | sudo docker login docker-registry.wur.nl -u jeremie.vandenplas@wur.nl --password-stdin
+sudo docker build -t docker-registry.wur.nl/vande018/containers/2025:ubuntu_20_04_gcc_13_OneAPI_2025_0_gpu_12_5 .
+sudo docker push docker-registry.wur.nl/vande018/containers/2025:ubuntu_20_04_gcc_13_OneAPI_2025_0_gpu_12_5
+```

docker/ubuntu_20_04_gcc_13_OneAPI_2025_0_gpu_12_5/setup_apt_repo_linux_no_sudo.sh

+#!/bin/bash
+
+apt-get update
+apt-get install -y gpg-agent wget
+
+# download the key to system keyring
+wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+| gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+
+# add signed entry to apt sources and configure the APT client to use Intel repository:
+echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
+
+apt-get update

docker/ubuntu_22_04_gcc_13_OneAPI_2024_2_gpu_12_5/Dockerfile

+FROM ubuntu:22.04
+
+ENV LINUX_CPP_COMPONENTS='intel-oneapi-compiler-dpcpp-cpp'
+ENV LINUX_FORTRAN_COMPONENTS='intel-oneapi-compiler-fortran'
+ENV LINUX_MKL_COMPONENTS='intel-oneapi-mkl'
+ENV LINUX_MKL1_COMPONENTS='intel-oneapi-mkl-devel'
+
+RUN apt-get update 
+RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get install -y apt-utils wget pkg-config ca-certificates gnupg git python3-pip openssh-client graphviz gnuplot curl zip unzip
+#RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get install -y build-essential  gfortran
+
+RUN apt-get install software-properties-common -y
+RUN add-apt-repository ppa:ubuntu-toolchain-r/test -y
+RUN apt update
+RUN apt install g++-13 gcc-13 gfortran-13 -y
+
+RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-13 13 --slave /usr/bin/g++ g++ /usr/bin/g++-13 --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-13
+
+RUN update-alternatives --config gcc
+
+
+RUN apt-get remove cmake -y
+RUN pip install --upgrade fypp ford cmake fprettify
+
+RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
+RUN dpkg -i cuda-keyring_1.1-1_all.deb
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt-get -y install cuda-12-5
+
+COPY setup_apt_repo_linux_no_sudo.sh /
+RUN /setup_apt_repo_linux_no_sudo.sh
+RUN apt-get install -y ${LINUX_FORTRAN_COMPONENTS}-2024.2 ${LINUX_CPP_COMPONENTS}-2024.2 ${LINUX_MKL_COMPONENTS}-2024.2 ${LINUX_MKL1_COMPONENTS}-2024.2
+#
+#RUN apt-get clean all
+#RUN apt-cache pkgnames intel
+#RUN apt-cache search intel
+
+RUN apt-get clean all

docker/ubuntu_22_04_gcc_13_OneAPI_2024_2_gpu_12_5/README.md

+# Instruction to build and push the container on WUR Gitlab
+
+```shell
+TOKEN=<generated_token_in_gitlad_with_read_registry_and_write_registry>
+echo "$TOKEN" | sudo docker login docker-registry.wur.nl -u jeremie.vandenplas@wur.nl --password-stdin
+sudo docker build -t docker-registry.wur.nl/vande018/containers/2024:ubuntu_22_04_gcc_13_OneAPI_2024_2_gpu_12_5 .
+sudo docker push docker-registry.wur.nl/vande018/containers/2024:ubuntu_22_04_gcc_13_OneAPI_2024_2_gpu_12_5
+```
+
+```shell
+sudo docker run --rm -it -v ~/snpblup_software_tmp:/container/local:z docker-registry.wur.nl/vande018/containers/2024:ubuntu_22_04_gcc_13_OneAPI_2024_2_gpu_12_5 bash
+```

docker/ubuntu_22_04_gcc_13_OneAPI_2024_2_gpu_12_5/setup_apt_repo_linux_no_sudo.sh

+#!/bin/bash
+
+apt-get update
+apt-get install -y gpg-agent wget
+
+# download the key to system keyring
+wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \
+| gpg --dearmor | tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+
+# add signed entry to apt sources and configure the APT client to use Intel repository:
+echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | tee /etc/apt/sources.list.d/oneAPI.list
+
+apt-get update