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--- research:containers [2019/02/27 11:42]
itshililo [Using Singularity on Lengau Cluster]
+++ research:containers [2021/12/09 16:42] (current)
@@ Line 1: / Line 1: @@
-====== Singularity in a Nutshell ======
+======Singularity in a Nutshell======
-Singularity is a container solution created for scientific and application workloads. The objective of this guide is to demonstrate how to use Singularity on the CHPC  Lengau cluster.
-The diagram below is a visual depiction of the Singularity work-flow process. This process can be categorised into two environments:
-  * **Build** environment: for testing and building containers (user needs sudo privileges). This would ideally be the user's workstation or VM.
-  * **Production** environment where users run containers. E.g (Lengau Cluster)
-For more details please read the user manual: [[https://www.sylabs.io/guides/2.6/user-guide/index.html]]
-{{ :research:flow.png?900 |}}
-Based on the image above, it is clear that the CHPC Lengau cluster will only provide a production (container execution) environment for the Singularity workflow. Therefore, users are only allowed to run already built containers images on this platform.
-**NB:** Please note that the computes nodes on Lengau do not have access to the internet, which means that users will not be able to use the Singularity **pull** command. However, users can use the **scp.chpc.ac.ca** node to facilitate the transfer of images to and from the platform.
-==== Using Singularity on Lengau Cluster ====
-Using Singularity on Lengau can be summarised as a two-stage process:
-  - **Transferring images to the Lengau cluster:** Users can use cp, SCP, rsync or FTP to copy their images on the cluster using the node://** scp.chpc.ac.za**//. They can also use the **Singularity pull** command on the same node.
-  - **Container Execution** Users can only interact with the computes nodes through the scheduler using the **qsub** command. Users also need to load the chpc/singularity module to enable execution of Singularity commands.
-=== Singularity: MPI Hello World ===
-Below is an example of a recipe file for building a Centos-7 image and installing mpich-3.2.1 inside that image.
-  BootStrap: yum
-  OSVersion: 7
-  MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
-  Include: yum
-  UpdateURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/updates/$basearch/
-  %runscript
-      echo "This build MVAPICH onto the base Centos7"
-  %post
-      echo -e "Installing vim, wget, bzip2, Development Tools and Infiniband Support"
-      yum -y install vim wget bzip2 git unzip
-      yum -y groupinstall "Development Tools"
-      yum -y groupinstall "Infiniband Support"
-      yum -y update
-      echo -e "Compiling mpich-3.2.1"
-      pushd /tmp
-      if [ ! -f /tmp/mpich-3.2.1.tar.gz ]; then
-          wget http://www.mpich.org/static/downloads/3.2.1/mpich-3.2.1.tar.gz
-      fi
-      tar -xf mpich-3.2.1.tar.gz
-      cd mpich-3.2.1
-      ./configure --prefix=/usr/local
-      make -j 4
-      make install
-      mpicc examples/hellow.c -o /usr/local/bin/hellow
-      popd
-      rm -rf /tmp/mpich-3.2.1
-      echo -e "Install another Hello work"
-      cd /tmp
-      if [ ! -f /tmp/gh-pages.zip ]; then
-         wget https://github.com/wesleykendall/mpitutorial/archive/gh-pages.zip
-      fi
-      unzip gh-pages.zip
-      cd  mpitutorial-gh-pages/tutorials/mpi-hello-world/code/
-      make clean
-      make
-      cp mpi_hello_world /usr/local/bin/
-  %runscript
-      # used with singularity run
-      echo "Running hello world"
-      exec hellow
-      # Alternative mpi singularity run
-      echo "Running hello world"
-      exec mpi_hello_world
+Moved to [[howto:singularity|Singularity in a Nutshell]].

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