Merge pull request #17 from gjbex/development

Development

Author: gjbex

containers_for_hpc.pptx

@@ -8,9 +8,17 @@ recipe.
 ## What is it?
 
 1. `simple.py`: very simple example.
+1. `development_base.py`: base recipe for a development container.
+1. `development_c++.py`: recipe for a C++ development container.
+1. `development_cuda_base.py`: base recipe for CUDA development.
+1. `development_cuda.py`: recipe for CUDA development.
+1. `development_intel_base.py`: base recipe for development using
+   Intel compilers.
 1. `development_node`: definition of a development node.
 1. `mssql_client`: defintion of a container with Microsoft
    SQL Server drivers, ODBC, FreeTDS and a conda environment
    for a client script.
 1. `r_container`: definition of an image to run R.
 1. `oneapi`: examples of images containing OneAPI development tools.
+1. `nvidia_hpc_sdk.py`: recipe for development using NVIDA HPC SDK.
+1 `rapids.py`: recipe for an image to run NVIDIA Rapids.

examples/hpccm/README.md

@@ -0,0 +1,19 @@
+'''Recipe to create either a docker container or Singularity image
+for a compute node on which users can log in using password authentication.
+A number of editors, git, make, CMake, GCC and Open-MPI
+
+Usage:
+    $ hpccm  --recipe development_cuda.py  --format docker
+    $ hpccm  --recipe development_cuda.py  --format singularity
+'''
+
+from pathlib import Path
+
+# Choose a base image
+Stage0.baseimage('nvcr.io/nvidia/nvhpc:24.3-devel-cuda_multi-ubuntu22.04')
+ 
+# Install CMake
+Stage0 += cmake(eula=True)
+
+# add run script, i.e., start bash
+Stage0 += runscript(commands=['/bin/bash'])

examples/hpccm/development_cuda.py

@@ -10,7 +10,7 @@
 from pathlib import Path
 
 # Choose a base image
-Stage0.baseimage('nvcr.io/nvidia/nvhpc:23.11-devel-cuda_multi-ubuntu22.04')
+Stage0.baseimage('nvcr.io/nvidia/nvhpc:24.3-devel-cuda_multi-ubuntu22.04')
 
 # Install CMake
 Stage0 += cmake(eula=True)

examples/hpccm/development_cuda_base.py

@@ -0,0 +1,34 @@
+'''Recipe to create either a docker container or Singularity image
+for a compute node on which users can log in using password authentication.
+A number of editors, git, make, CMake, GCC and Open-MPI
+
+Usage:
+    $ hpccm  --recipe development_cuda.py  --format docker
+    $ hpccm  --recipe development_cuda.py  --format singularity
+'''
+
+from pathlib import Path
+
+# Choose a base image
+Stage0.baseimage('nvcr.io/nvidia/nvhpc:24.7-devel-cuda_multi-ubuntu22.04')
+ 
+# Install CMake
+Stage0 += cmake(eula=True)
+
+# Install editor and other tools
+Stage0 += apt_get(ospackages=['vim', 'less', 'ack', ])
+
+# Install archive and compression software and utitlies
+Stage0 += apt_get(ospackages=['tar', 'gzip', 'bzip2', 'wget', 'ca-certificates', ])
+
+# Install version control
+Stage0 += apt_get(ospackages=['git', 'openssh-client', ])
+
+# Install debugging tools
+Stage0 += apt_get(ospackages=['valgrind', 'strace', ])
+
+# Install benchmarking tools
+Stage0 += apt_get(ospackages=['hyperfine'])
+
+# add run script, i.e., start bash
+Stage0 += runscript(commands=['/bin/bash'])

examples/hpccm/nvidia_hpc_sdk.py

@@ -12,8 +12,16 @@
 
 
 # Choose a base image
-Stage0.baseimage('intel/oneapi-hpckit')
+Stage0.baseimage('intel/hpckit:2024.1.0-devel-ubuntu22.04')
 
+# Install NVIDIA backend
+Stage0 += copy(src='oneapi-for-nvidia-gpus-2024.1.0-cuda-12.0-linux.sh',
+            dest='/')
+Stage0 += shell(commands=['/oneapi-for-nvidia-gpus-2024.1.0-cuda-12.0-linux.sh -y'])
+
+# Install build tools
+Stage0 += cmake(eula=True)
+
 # Install editor and other tools
 Stage0 += apt_get(ospackages=['vim', 'neovim', 'less', 'ack', 'tmux', ])
 

examples/hpccm/oneapi/oneapi-for-nvidia-gpus-2024.1.0-cuda-12.0-linux.sh

@@ -12,13 +12,26 @@
 # Install utilities
 Stage0 += apt_get(ospackages=['gist', 'wget', 'rclone', ])
 
+# Install tools to install R
+Stage0 += apt_get(ospackages=['software-properties-common', 'apt-transport-https', 'dirmngr', 'gnupg'])
+
+# Add signature key for CRAN
+Stage0 += shell(commands=['wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc'])
+
+# Add CRAN repository
+Stage0 += shell(commands=['add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"'])
+
 # Install build tools
 Stage0 += apt_get(ospackages=['build-essential', 'make'])
+Stage0 += cmake(eula=True)
 
 # Install GNU compilers (upstream)
 compilers = gnu()
 Stage0 += compilers
 
+# Install HDF5 libraries
+Stage0 += hdf5(configure_opts=['--enable-cxx', '--enable-fortran',])
+
 # Install libraries required to build R
 Stage0 += apt_get(ospackages=['openssl', 'libxml2-dev', 'libcurl4-openssl-dev', 'libz-dev', 'libssl-dev',
                               'libjpeg-dev', ])

examples/hpccm/oneapi/oneapi_hpc.py

@@ -11,13 +11,48 @@ From: ubuntu:22.04
         wget
     rm -rf /var/lib/apt/lists/*
 
+%post
+    apt-get update -y
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        apt-transport-https \
+        dirmngr \
+        gnupg \
+        software-properties-common
+    rm -rf /var/lib/apt/lists/*
+
+%post
+    cd /
+    wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+
+%post
+    cd /
+    add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+
 %post
     apt-get update -y
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
         build-essential \
         make
     rm -rf /var/lib/apt/lists/*
 
+# CMake version 3.25.1
+%post
+    apt-get update -y
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        make \
+        wget
+    rm -rf /var/lib/apt/lists/*
+%post
+    cd /
+    mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.sh
+    mkdir -p /usr/local
+    /bin/sh /var/tmp/cmake-3.25.1-linux-x86_64.sh --prefix=/usr/local --skip-license
+    rm -rf /var/tmp/cmake-3.25.1-linux-x86_64.sh
+%environment
+    export PATH=/usr/local/bin:$PATH
+%post
+    export PATH=/usr/local/bin:$PATH
+
 # GNU compiler
 %post
     apt-get update -y
@@ -27,6 +62,37 @@ From: ubuntu:22.04
         gfortran
     rm -rf /var/lib/apt/lists/*
 
+# HDF5 version 1.12.0
+%post
+    apt-get update -y
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+        bzip2 \
+        file \
+        make \
+        wget \
+        zlib1g-dev
+    rm -rf /var/lib/apt/lists/*
+%post
+    cd /
+    mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.bz2
+    mkdir -p /var/tmp && tar -x -f /var/tmp/hdf5-1.12.0.tar.bz2 -C /var/tmp -j
+    cd /var/tmp/hdf5-1.12.0 &&   ./configure --prefix=/usr/local/hdf5 --enable-cxx --enable-fortran
+    make -j$(nproc)
+    make -j$(nproc) install
+    rm -rf /var/tmp/hdf5-1.12.0 /var/tmp/hdf5-1.12.0.tar.bz2
+%environment
+    export CPATH=/usr/local/hdf5/include:$CPATH
+    export HDF5_DIR=/usr/local/hdf5
+    export LD_LIBRARY_PATH=/usr/local/hdf5/lib:$LD_LIBRARY_PATH
+    export LIBRARY_PATH=/usr/local/hdf5/lib:$LIBRARY_PATH
+    export PATH=/usr/local/hdf5/bin:$PATH
+%post
+    export CPATH=/usr/local/hdf5/include:$CPATH
+    export HDF5_DIR=/usr/local/hdf5
+    export LD_LIBRARY_PATH=/usr/local/hdf5/lib:$LD_LIBRARY_PATH
+    export LIBRARY_PATH=/usr/local/hdf5/lib:$LIBRARY_PATH
+    export PATH=/usr/local/hdf5/bin:$PATH
+
 %post
     apt-get update -y
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \