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research:containers [2019/02/27 14:20]
itshililo [Using Singularity on Lengau Cluster] 		research:containers [2021/12/09 16:42] (current)
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-====== 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. +Moved to [[howto:singularity|Singularity in a Nutshell]].
- +
-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. This also includes an MPI example code for hello world programs. +
- +
-  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 MPICH-3.2.1 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 +
- +
-Using the definition file above we can build a Singularity image on a system with singularity install and we have sudo privileges (i.e personal work station or VM). Use the command below to build the image: +
- sudo singularity build $image_name $definition_file +
-where **$image_name** is the name of the image your building and **$definition_file** with the filename for code provided above. +
- +
-Once we've built our image we can then transfer it to the Lengau cluster. +
-  rsync -azP $image_name $username@lengau.chpc.ac.za:$DIR_PATH +
-where **$DIR_PATH** is the location you want to store your image. +
- +
-=== Run Image on Lengau === +
-Login to the cluster +
-  ssh $user@lengau.chpc.ca.za +
-Submit your job using the qsub command and the resources you need +
-  qsub -I -P $PROJECT -q $Queue_name -l select=2:ncpus=24:mpiprocs=4:nodetype=haswell_reg +
-where $PROJECT is the project name to draw you alllocation and $QUEUE_NAME is the name of the Queue you want to run. +
-   +
-Then load the Singularity and MPI module avail on the cluster +
-  module load chpc/singularity chcp/mvapich.... +
- +
-Then exec the program from the container +
- +
-  $ mpirun -np 24 singularity exec mpich-3.2.1.simg-v2 hellow +
-    Hello world from process 20 of 24 +
-    Hello world from process 4 of 24 +
-    Hello world from process 5 of 24 +
-    Hello world from process 7 of 24 +
-    Hello world from process 12 of 24 +
-    Hello world from process 14 of 24 +
-    Hello world from process 6 of 24 +
-    Hello world from process 15 of 24 +
-    Hello world from process 22 of 24 +
-    Hello world from process 23 of 24 +
-    Hello world from process 13 of 24 +
-    Hello world from process 9 of 24 +
-    Hello world from process 11 of 24 +
-    Hello world from process 21 of 24 +
-    Hello world from process 16 of 24 +
-    Hello world from process 8 of 24 +
-    Hello world from process 0 of 24 +
-    Hello world from process 3 of 24 +
-    Hello world from process 18 of 24 +
-    Hello world from process 17 of 24 +
-    Hello world from process 10 of 24 +
-    Hello world from process 1 of 24 +
-    Hello world from process 19 of 24 +
-    Hello world from process 2 of 24 +
-     +
-Alternative MPI code, with ranks and hostname +
- +
-  $ mpirun -np 24 singularity exec mpich-3.2.1.simg-v2 mpi_hello_world +
-    Hello world from processor cnode0241, rank 4 out of 24 processors +
-    Hello world from processor cnode0241, rank 15 out of 24 processors +
-    Hello world from processor cnode0241, rank 5 out of 24 processors +
-    Hello world from processor cnode0241, rank 6 out of 24 processors +
-    Hello world from processor cnode0241, rank 20 out of 24 processors +
-    Hello world from processor cnode0241, rank 21 out of 24 processors +
-    Hello world from processor cnode0241, rank 22 out of 24 processors +
-    Hello world from processor cnode0241, rank 13 out of 24 processors +
-    Hello world from processor cnode0241, rank 7 out of 24 processors +
-    Hello world from processor cnode0241, rank 14 out of 24 processors +
-    Hello world from processor cnode0241, rank 12 out of 24 processors +
-    Hello world from processor cnode0241, rank 23 out of 24 processors +
-    Hello world from processor cnode0215, rank 9 out of 24 processors +
-    Hello world from processor cnode0215, rank 19 out of 24 processors +
-    Hello world from processor cnode0215, rank 8 out of 24 processors +
-    Hello world from processor cnode0215, rank 0 out of 24 processors +
-    Hello world from processor cnode0215, rank 16 out of 24 processors +
-    Hello world from processor cnode0215, rank 3 out of 24 processors +
-    Hello world from processor cnode0215, rank 11 out of 24 processors +
-    Hello world from processor cnode0215, rank 18 out of 24 processors +
-    Hello world from processor cnode0215, rank 2 out of 24 processors +
-    Hello world from processor cnode0215, rank 10 out of 24 processors +
-    Hello world from processor cnode0215, rank 1 out of 24 processors +
-    Hello world from processor cnode0215, rank 17 out of 24 processors+
  
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