pandoc:singularity:01_introduction:singularity [VSC Wiki]

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====== Singularity ======

  * Article written by Markus Stöhr (VSC Team)



===== Containerization (historical, pre 1955) =====

{{.:hafenarbeiter_bei_der_verladung_von_sackgut_-_ms_rothenstein_ndl,_port_sudan_1960.png}} {{.:stevedores_ny_1912.jpg}}


(pictures from Wikipedia)

===== Containerization (historical, post 1955) =====

{{.:container_ship_loading-700px.jpg}}


(picture from Wikimedia, see also [[http://www.worldshipping.org/about-the-industry/history-of-containerization|http:%%//%%www.worldshipping.org]])

===== HPC Situation =====

{{.:personal-container-mngmnt2.jpg}}


(picture from [[http://www.bricoleurbanism.org/whimsicality/personal-container-management/|http:%%//%%www.bricoleurbanism.org]])

===== Virtualization vs. Containerization =====

{{.:virtualization.png}}


===== Docker vs. Singularity =====


**Singularity:**

  * container runs in user namespace
  * no privilege escalation
  * can be used in a multi-user environment



===== Container concepts =====

{{.:containerconcepts.png}}


  * image: stored in a single file
  * build images with ‘recipes’
  * work interactively within container

===== Recipes in Singularity =====


^section    ^                                   ^
|setup      |executed before post               |
|post       |install commands                   |
|files      |executed after post                |
|environment|add variables for runtime          |
|runscript  |commands when container is executed|
|labels     |metadata                           |
|test       |                                   |
|apps       |                                   |


===== OpenMPI example =====

**Filename: OpenMPI-3.0.0**

<code>
BootStrap: docker
From: centos:7.4.1708

%setup
     cp openmpi-3.0.0.tar.bz2 \
        ${SINGULARITY_ROOTFS}/usr/local/src/openmpi-3.0.0.tar.bz2
</code>
<code>
%post
    yum install -y gcc gcc-c++ gcc-gfortran 
    yum install -y wget tar make bzip2 gzip perl rsync zip
    yum install -y infinipath-psm-devel infinipath-psm 
    yum install -y libibverbs-devel libibverbs

    cd /usr/local/src 
    tar -xjf openmpi-3.0.0.tar.bz2
    cd openmpi-3.0.0  

    ./configure --prefix=/usr/local --with-hwloc --with-psm --with-verbs
    make -j 16
    make install
    ldconfig
</code>

===== Container build =====

**on your local system as root user:**

<code>
#singularity must be present
module load singularity/2.4.2

singularity build OpenMPI-3.0.0.img OpenMPI-3.0.0

</code>
===== Derive from existing container =====

**Filename: MPI-Hello**

<code>
BootStrap: localimage
From: .../OpenMPI-3.0.0.img

%post
    yum install -y git
    mkdir /usr/local/src/git 
    cd /usr/local/src/git  

    git clone https://github.com/wesleykendall/mpitutorial 
    cd mpitutorial/tutorials/mpi-hello-world/code 
    make 
    cp mpi_hello_world /usr/local/bin 

%runscript
    /usr/local/bin/mpi_hello_world $@


</code>
<code>
singularity build MPI-Hello.img MPI-Hello
</code>
===== Run Container =====

  * Copy image to VSC-3
  * Job script:

<code>
#!/bin/bash
#SBATCH -J singularity
#SBATCH -N 2


module purge
module load intel/18 openmpi/3.0.0 singularity/2.4.2

mpirun -np 32 ./MPI-Hello.img
</code>
===== MPI call stack =====



===== Performance =====

{{.:scaling_vasp.eps.jpg}}


===== Further reading =====

<html><br></html> <html><br></html> <html><br></html> <html><br></html> <html><br></html> <html><br></html> <html><br></html> http://singularity.lbl.gov