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Compute Resources

Docker Usage

Software Included

Overview

From the Intel® oneAPI HPC Toolkit Docker Hub,

The Intel oneAPI HPC Toolkit delivers what developers need to build, analyze, optimize, and scale high-performance computing (HPC) applications with the latest techniques in vectorization, multithreading, multi-node parallelization, and memory optimization.

For a complete list of libraries included in the Intel® oneAPI HPC Toolkit, please visit the Intel® oneAPI HPC Toolkit Documentation.

Interactive Command-Line Session

To use the Intel® compilers in an interactive command-line session, follow the steps below.

  1. Submit an interactive job.

LSF_DOCKER_VOLUMES="/scratch1/fs1/ris/application/intel/oneapi/:/opt/intel/oneapi" \
bsub -Is -q general-interactive -a 'docker(us.gcr.io/ris-appeng-shared-dev/compiler-base:oneapi2021.1.1_centos7)' \
/bin/bash

  1. Set up the Intel® oneAPI environment.

. /opt/intel/oneapi/setvars.sh

  1. Compile code.

Multi-Stage Docker Image Build

Compile, Keep Only Binaries

A multi-stage build leverages the compilers in the Intel® oneAPI HPC Toolkit Docker image and copies the compiled binaries and runtime dependencies to a new base image. This method results in a smaller Docker image, reducing computing time/resources/cost, and allows withholding source code from public consumption.

For more information on Docker multi-stage builds, please see the Docker multi-stage build documentation.

Sample Multi-Stage Dockerfile

# Begin Stage 1 with the base compiler image.
FROM us.gcr.io/ris-appeng-shared-dev/compiler-base:oneapi2021.1.1_centos7 as build

# Add any additional build dependencies here.

# copy source code to a new location inside the container.
COPY /path/to/source/code /opt/app_name/src

# Change directory to location of source code,
# set up the Intel environment,
# compile,
# copy binary to standard location.
RUN cd /opt/app_name/src/ && \
  . /opt/intel/oneapi/setvars.sh && \
  make && \
  cp -f example.binary /usr/local/bin

# Begin Stage 2 with a new base image.
FROM centos:7

# Copy only the needed parts of Stage 1.
COPY --from=build /usr/local/bin/example.binary /usr/local/bin
COPY --from=build /usr/local/lib /usr/local/lib
COPY --from=build /usr/local/include /usr/local/include

# Add any additional runtime dependencies here.

# Set up MLNX_OFED driver.
ENV MOFED_VERSION 5.4-3.1.0.0
ENV OS_VERSION rhel7.7
ENV PLATFORM x86_64
RUN wget -q http://content.mellanox.com/ofed/MLNX_OFED-${MOFED_VERSION}/MLNX_OFED_LINUX-${MOFED_VERSION}-${OS_VERSION}-${PLATFORM}.tgz && \
  tar -xvf MLNX_OFED_LINUX-${MOFED_VERSION}-${OS_VERSION}-${PLATFORM}.tgz && \
  MLNX_OFED_LINUX-${MOFED_VERSION}-${OS_VERSION}-${PLATFORM}/mlnxofedinstall --user-space-only --without-fw-update -q  --distro ${OS_VERSION} && \
  cd .. && \
  rm -rf ${MOFED_DIR} && \
  rm -rf *.tgz

Single-Stage Docker Image Build

Compile, Compile, Keep Source Code and Binaries

A single-stage build leverages the compilers in the Intel® oneAPI HPC Toolkit Docker image and keeps the compiled binaries, runtime dependencies and source code in the resulting image. This method results in a larger Docker image which may cause increased computing time/resources/cost. This method also caches the source code in build layers resulting in public exposure, which may be unwanted.

Sample Single-Stage Dockerfile

FROM us.gcr.io/ris-appeng-shared-dev/compiler-base:oneapi2021.1.1_centos7

# Add any additional build dependencies here.

# copy source code to a new location inside the container
COPY /path/to/source/code /opt/app_name/src

# Change directory to location of source code,
# set up the Intel environment,
# compile.
RUN cd /opt/app_name/src/ && \
  . /opt/intel/oneapi/setvars.sh && \
  make

Building and Pushing the Docker image

To build and push a Docker image using one of the above methods, please refer to the our existing documentation for guidance.

Intel® Base Compiler Tutorial

Please see our Intel® Base Compiler Tutorial to learn how to leverage the Intel® Base Compiler Docker image on the RIS Scientific Compute Platform.

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