MANUAL USAGE

Mahameru LIPI HPC Usage

Apply for Account

A LIPI HPC user account is needed for using LIPI HPC. You can apply for it by registering an account in ELSA. For LIPI user, you can use Single Sign-On (Intra LIPI) account to log in. Once your proposal is accepted, your account will be activated for a number of days you applied for.

SSH to LIPI HPC

The SSH client is used to establish remote connections using the command-line. For windows users, you can use SmarTTY or another SSH client, for LINUX users, you can use a terminal as an SSH client.

Simply connect to LOGIN node using the name “masuk.hpc.lipi.go.id”. Replace “user” with your user account name. The first time around the system will ask you to accept the remote computer into the list of known hosts before you accept it as a trustworthy computer from LIPI HPC by typing “yes” followed by pressing enter (return, here represented by the “↵” symbol). At the first time logging in, you need to change your password.

ssh username@masuk.hpc.lipi.go.id"↵"

Storage

The Grid@LIPI will have shared storage, we will update this section if the shared storage is ready. For now, for each account, the size of the storage is 100 GB quota in each user’s home directory.

Software

List of installed softwares are provided in LIPI HPC. We use Module to manage software modules. You can run module command to query, load, and unload of software modules.

  • Use “module avail” to list what software modules available at the LIPI HPC batch
    module load blast "↵"
  • Use “module list” to list what software modules already been loaded
  • Use PBS script as follows to submit your job. Simply copy and paste by using text editor (sublimeText, Notepad, Notepad++, etc).
    #!/bin/bash
    ### This is parameter for job management
    ### Don't remove '#' sign before PBS
    ### The '###' is a comment
    ### PBS Parameters
    ### -N Job's name
    ### -o Output name
    ### -e Error name
    ### -q queue name 
    ### -l resource
    ### Example:
    #PBS -N "hello_world_job"
    #PBS -q public
    #PBS -l walltime=04:00:00
    #PBS -l nodes=2:ppn=8
    #PBS -m ae
    #PBS -M your@email.address
    ### Go to 'your home' dir
    cd $PBS_O_WORKDIR
    exec 2>&1
    # set to debug
    #set -x
    # how many nodes have been assigned to this job?
    NP=`wc -l $PBS_NODEFILE | awk '{print $1}'`
    ### load module you need
    ### you can check the available module by command: module avail
    module load openmpi
    ### Call your script/code
    ### Example:
    echo "Hostname = $HOSTNAME"
    echo "Number of nodes = $NP"
    echo "Start = `date`"
    mpirun -np $NP /home/user/hello_world/hello_world
    echo "Finish = `date`"
    
  • Save your pbs script, for example “hello_world.pbs”
  • Run the “hello_world.pbs” script as follows
    qsub hello_world.pbs "↵"
  • You can use qstat command as follows to check your job status
    qstat #JOB_ID "↵"
     Job ID Name User Time Use S Queue
     ------------------------- ---------------- --------------- -------- - -----
     #JOB_ID.borneo02 ...lo_world_job" test101 0 R nongpu
    
  • If you want to undo the submit job, you can use “qdel”
    qdel #JOB_ID "↵"
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