Use Spack in Tutorial

[ajyounge]

We need to develop an advanced portion of the tutorial, where users can inherit form our ECP containers image, add a few "spack install x y z" commands, and generate a new image which they push & run on some supercomputer. This will help reinforce the usage of our base-supported images and encourage spack usage within a container.

[ArangoGutierrez]

@tgamblin

[tgamblin]

Sameer's latest repo version (built with spack.yaml files) is looking closer to what this part of the tutorial should be. https://github.com/UO-OACISS/e4s/tree/master/docker/

[ajyounge]

@sameershende do you have a status update? i know you have this in new E4S image, is it ready and incorporated into tutorial?

[sameershende]

Yes, we are putting final touches on E4S images for SC19. https://hub.docker.com/repository/docker/ecpe4s/superlu_sc
is an image for SuperLU. There are other images under exascaleproject and ecpe4s that we are working on.

[scanon]

Here is my version that works the most seamlessly but could use some streamlining.

FROM ecpe4s/ubi7_x86_64_base:1.0

ENV PATH=/spack/bin:$PATH

ADD helloworld.c /helloworld.c


RUN \
   . /spack/share/spack/setup-env.sh && \
   spack load mpich && \
   mkdir /app && mpicc /helloworld.c -o /app/hello
ADD entrypoint.sh /

#SPACK_ROOT=/spack
env LD_LIBRARY_PATH=/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/mpich-3.2.1-lcdvbejz7w7ohecffa2qdng7y6dfxbab/lib
env PATH=/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/mpich-3.2.1-lcdvbejz7w7ohecffa2qdng7y6dfxbab/bin:/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/environment-modules-4.3.0-nhojhnpu7bh7zqf4gouwacpmbeg54cfb/bin:/spack/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin


ENTRYPOINT [ "/entrypoint.sh" ]

[alalazo]

We need to develop an advanced portion of the tutorial, where users can inherit form our ECP containers image, add a few "spack install x y z" commands, and generate a new image which they push & run on some supercomputer.

I think you can use Spack Environments to ease the installation.

With @tgamblin and @ArangoGutierrez we are currently experimenting the automatic generation of recipes for containers and the current state of the art is something like the following:

FROM spack/ubuntu-bionic:prerelease as builder

RUN mkdir /opt/spack-environment \
&&  (echo "spack:" \
&&   echo "  config:" \
&&   echo "    install_tree: /opt/software" \
&&   echo "  specs:" \
&&   echo "  - gromacs+mpi" \
&&   echo "  - mpich" \
&&   echo "  concretization: together" \
&&   echo "  view: /opt/view") > /opt/spack-environment/spack.yaml

RUN cd /opt/spack-environment && spack install && spack autoremove -y
RUN cd /opt/view/bin && strip -s * || exit 0
RUN cd /opt/view/lib && strip -s * || exit 0

RUN cd /opt/spack-environment && \
    spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh

FROM ubuntu:bionic

COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software
COPY --from=builder /opt/view /opt/view
COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh

RUN apt-get -yqq update                                   \
 && apt-get -yqq install libgomp1                         \
 && rm -rf /var/lib/apt/lists/*

ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]

This produces a 143MB image for me that goes down to 50MB when compressed in a registry. gromacs and mpich executables are already in the PATH when you start the container.

[ArangoGutierrez]

I have the current example, works with Buildah + Spack

spack:
  config:
    install_tree: /opt/software
  packages:
    all:
      target: [x86_64]
  specs:
  - hdf5~mpi
  - szip
  view:
    default:
      root: /opt/view

and

FROM spack/centos7 as builder

ADD spack.yaml /opt/spack-environment/spack.yaml

RUN cd /opt/spack-environment && /opt/spack/bin/spack install

FROM registry.access.redhat.com/ubi7/ubi

COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software
COPY --from=builder /opt/view /opt/view

ENV PATH=/opt/view/bin:${PATH}