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Containerized versions

Singularity Usage

In this tutorial, we will explain how to download, setup, and run FabSim3 within a singularity container image.

Dependencies

Installation under Ubuntu Linux:

sudo apt install openssh-server
Installations under CentOS Linux:
sudo yum install -y openssh-server

FabSim3 Singularity Installation

Download the singularity image from Singularity Hub:

singularity pull --name fabsim.simg shub://arabnejad/FabSim3

Tip

The download image should be kept as fabsim.simg, this filename will be used later for setting environment variable and alias names in your ~/.bashrc file.

  • To see How to Use Fabsim3 singularity:

    ./fabsim.simg --help
    or
    ./fabsim.simg -h
    

  • Running the following will download the FabSim3 library in your local machine:

    ./fabsim.simg --install [fabsim_INSTALL_DIR]
    or
    ./fabsim.simg -i [fabsim_INSTALL_DIR]
    

    By default, it will be downloaded in sub-folder FabSim3 in your current directory, you also can set the installation directory by setting [fabsim_INSTALL_DIR] parameter.

    At the end of installation part, you will received a message, which explain how you should setup your PC for further usage.

    Please add/load the generated fabsim_env.conf in your ~/.bashrc.

  • To load:

    source \${fabsim_INSTALL_DIR}/fabsim_env.conf
    

  • To add to your ~/.bashrc:

    echo \"source \${fabsim_INSTALL_DIR}/fabsim_env.conf\" >> ~/.bashrc
    source ~/.bashrc
    
    fabsim_INSTALL_DIR will be replaced by your local machine path.

After loading the environment variable from fabsim_env.conf into your into the current shell script, fab command will be available as a alias name to run for singularity image and accept all FabSim3 command.

For QCG users
  • Please make sure, you udpate/replace username: "plg<your-username>" with your username account in {fabsim_INSTALL_DIR}/deploy/machines_user.yml.
  • Sets up SSH key pairs for FabSim3 access:
    fab qcg setup_ssh_keys
    
  • Please create a globus in your $HOME directory, If Not Exist:
    mkdir -p ~/.globus
    
  • Copy usercert.pem and userkey.pem from your account to ~/.globus:
    scp plg<user>@eagle.man.poznan.pl:~/.globus/usercert.pem ~/.globus
    scp plg<user>@eagle.man.poznan.pl:~/.globus/userkey.pem ~/.globus
    

FabSim3 with QCG middleware

To execute jobs through remote resource schedulers, some essential machine-specific configurations are required to be set and stored. These parameters will be applied to all applications run on that remote machine.

First, you need to add your username for remote machine in FabSim3/fabsim/deploy/machines_user.yml file as:

qcg: # machine name
     username: "plg..."
Then, set up configuration for remote machine in FabSim3/fabsim/deploy/machines.yml file. Here is a simple example:
qcg: # machine name
     remote: 'eagle.man.poznan.pl'
     home_path_template: '/home/plgrid/$username'
     manual_ssh: true
     dispatch_jobs_on_localhost: true
     job_dispatch : 'qcg-sub'
     batch_header: qcg-eagle
     stat: 'qcg-list -Q -s all -F "%-22I %-16S %-8H" | awk "{if(NR>2)print}"'
     job_dispatch: 'qcg-sub'
     cancel_job_command: 'qcg-cancel $jobID'
     job_info_command : 'qcg-info -Q $jobID'

  • qcg: the name of target remote machine machine , it will use by FabSim3 as fab qcg <command>. Internally, FabSim3 uses <$user_name>@<$remote> to connect to the remote machine.
  • remote: the remote machine address. FabSim3 uses <$user_name>@<$remote> template internally all connection. The user_name parameter is taken from FabSim3/fabsim/deploy/machines.yml file.
  • home_path_template: used to the storage space to checkout and build on the remote machine.
  • manual_ssh: when enabled, FabSim3 will connect directly using an ssh client instead of using the paramiko api.
  • dispatch_jobs_on_localhost: if it is set to true, job dispatch is done locally. Otherwise, FabSim3 executes commands directly inside the remote machine by ssh connection. To dispatch job locally, the command-line interface for job management should be installed in your local machine.
  • batch_header: it can be used to add some predefined templates to the submitted job script. The template file should be store at FabSim3/fabsim/deploy/templates.
  • stat: filled by the command-line that displays report on the submitted jobs. In this example, according to our grid broker, qcg-list command displays table with information about tasks.