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Howto use Host libraries: GPU drivers and OpenMPI BTLs

Note: Much of the GPU portion of this tutorial is deprecated by the --nv option that automatically binds host system driver libraries into your container at runtime. See the exec command for an example

Singularity does a fantastic job of isolating you from the host so you don’t have to muck about with LD_LIBRARY_PATH, you just get exactly the library versions you want. However, in some situations you need to use library versions that match host exactly. Two common ones are NVIDIA gpu driver user-space libraries, and OpenMPI transport drivers for high performance networking. There are many ways to solve these problems. Some people build a container and copy the version of the libs (installed on the host) into the container.

{% include toc.html %}

What We will learn today

This document describes how to use a bind mount, symlinks and ldconfig so that when the host libraries are updated the container does not need to be rebuilt.

Note this tutorial is tested with Singularity commit 945c6ee343a1e6101e22396a90dfdb5944f442b6, which is part of the (current) development branch, and thus it should work with version 2.3 when that is released. The version of OpenMPI used is 2.1.0 (versions above 2.1 should work).

Environment

In our environment we run CentOS 7 hosts with:

  1. slurm located on /opt/slurm-<version> and the slurm user slurm
  2. Mellanox network cards with drivers installed to /opt/mellanox ( Specifically we run a RoCEv1 network for Lustre and MPI communications)
  3. NVIDIA GPUs with drivers installed to /lib64
  4. OpenMPI (by default) for MPI processes

Creating your image

Since we are building an ubuntu image, it may be easier to create an ubuntu VM to create the image. Alternatively you can follow the recipe here.

Use the following def file to create the image.

{% include gist.html username=’l1ll1′ id=’89b3f067d5b790ace6e6767be5ea2851′ file=’hostlibs.def’ %}

The mysterious wget line gets a list of all the libraries that the CentOS host has in /lib64 that we think its safe to use in the container. Specifically these are things like nvidia drivers.

{% include gist.html username=’l1ll1′ id=’89b3f067d5b790ace6e6767be5ea2851′ file=’desired_hostlibs.txt’ %}

Also note:

  1. in hostlibs.def we create a slurm user. Obviously if your SlurmUser is different you should change this name.
  2. We make directories for /opt and /usr/local/openmpi. We’re going to bindmount these from the host so we get all the bits of OpenMPI and Mellanox and Slurm that we need.

Executing your image

On our system we do:

SINGULARITYENV_LD_LIBRARY_PATH=/usr/local/openmpi/2.1.0-gcc4/lib:/opt/munge-0.5.11/lib:/opt/slurm-16.05.4/lib:/opt/slurm-16.05.4/lib/slurm:/desired_hostlibs:/opt/mellanox/mxm/lib/
export SINGULARITYENV_LD_LIBRARY_PATH

then

srun  singularity exec -B /usr/local/openmpi:/usr/local/openmpi -B /opt:/opt -B /lib64:/all_hostlibs hostlibs.img <path to binary>
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