Introduction to research computing on the Palmetto cluster

Running your first job

Learning objectives

  • Distinguish between the login node and compute nodes
  • Run your first interactive job on the Palmetto cluster
  • Learn how to load modules

The Palmetto cluster consists of several hundred “compute” nodes, each equipped with CPUs and GPUs to do heavy computation. The login node user001 is a “service” node, shared by all users, and is meant only for tasks such as managing projects (editing and moving files and directories), and submitting batch scripts (about which we will learn shortly).

We’d like to start analyzing the data we’ve downloaded. So let’s get access to a compute node to begin:

$ qsub -I
qsub (Warning): Interactive jobs will be treated as not rerunnable
qsub: waiting for job 2725837.pbs02 to start
qsub: job 2725837.pbs02 ready

[username@node1466 ~]$ 

The prompt indicates that you are no longer running a shell on the login node (user001), but a compute node (node1466 or similar). The qsub command is used to submit “jobs” to the cluster. A job is a request for cluster resources, like hardware (like cpu cores, memory, interconnect) and time (minutes or hours). The -I flag in the qsub command stands for “interactive”. This job is interactive because commands are entered interactively into a shell running on a compute node. (This is opposed to a batch job, in which the commands are included in a script—more on that later).

Your home directory (and all the files inside it) are still accessible from the compute nodes:

$ ls

Let’s navigate to the directory where our data files are:

$ cd data-hpc/north-pacific-gyre/2012-07-03/
$ ls
goostats        NENE01736A.csv  NENE01812A.csv  NENE01971Z.csv  NENE02018B.csv  NENE02040Z.csv  plots
NENE01729A.csv  NENE01751A.csv  NENE01843A.csv  NENE01978A.csv  NENE02040A.csv  NENE02043A.csv  results
NENE01729B.csv  NENE01751B.csv  NENE01843B.csv  NENE01978B.csv  NENE02040B.csv  NENE02043B.csv

The script we have to analyze our file is called It’s a Python script, and needs specific Python modules to run. Try:

{.bash} $ python{.output}

And you should see an error about missing modules.

“Missing software” is a common problem when working with HPC clusters such as Palmetto. Software that you are used to having/using on your personal machines are generally missing from the cluster. Several commonly used software packages are installed on the cluster - however, you will manually have to “load” them. The specific software package we need is called anaconda. So let’s load that package:

$ module load anaconda/2.5.0

You can see a list of software packages that can be loaded in this way by using module avail:

$ module avail
------------------------------------------------------------------- /software/modulefiles --------------------------------------------------------------------
abaqus/6.10                    cufflinks/2.1.1                gromacs/5.0.5-gpu              mpich2/1.4                     opensees/2.4.6
abaqus/6.13                    cusp/0.5.1                     gromacs/5.0.5-nogpu            namd/20150610                  openvswitch/2.4.0
abaqus/6.14                    divvy/0.9                      gsl/1.15                       namd/20150610-intel            paraview/4.1.0
amber/14                       dmol/3.0                       gsl/1.16                       namd/2.11b1                    paraview/5.0
anaconda/1.9.1                 earlang/18.2.1                 gurobi/6.5.0                   namd/2.9                       postgis/2.2.1
anaconda/2.3.0                 emboss/6.6                     hadoop/1.2.1                   namd/2.9-k20                   postgresql/9.4.0
anaconda/2.4.0                 espresso/5.1                   hdf5/1.10.0                    netcdf/                 python/2.7.6
anaconda/2.5.0                 fastqc/0.10.1                  hdf5/1.8.15                    netcdf/4.4.0                   python/3.3.3
anaconda/4.0.0                 ffmpeg/2.4                     houdini/13.0.547               netcdf-parallel/1.6.1          python/3.4
anaconda3/2.5.0                fftw/3.3.3-dp-gcc              hwloc/1.10.1                   nvbio/20150213                 qemu/1.7.0

You can have more than one package loaded, but take care not to load conflicting packages. Some software is licensed and can only be used by a limited number of users at a given time. If you don’t see a software package that you want to use listed above, then you will have to install and configure that software for yourself. You can learn more about this from the Palmetto User’s Guide.

Now that you’ve loaded the anaconda module, you can run Luckily, has some documentation that you can access using the -h switch:

$ python -h
usage: [-h] [--fname FNAME]

Script to analyze assay machine output. For a given input file, this script
computes the least abundant and most abundant protein. It also plots the
relative abundance of all proteins. The statistics are put in the results/
directory and the plot is put in the plots/ directory.

optional arguments:
  -h, --help     show this help message and exit
    --fname FNAME  Input file name

So, to analyze the file NENE01729A.csv using, we can run the following command:

$ python --fname NENE01729A.csv

This takes a while, but after the script is done, you should see two things:

  1. A results file called NENE01729A-results.out in the results/ directory.
  2. A plot called NENE01729A.png in the plots/ directory.

You can copy these files back to your local machine in the same way you copied files in to the cluster. Mac OS X/Linux users will use scp:

$ scp -r .

Windows user’s can use the file transfer client as before.

You’ll notice that running the script took a while (about a minute). Let’s say we had a few hundred files to analyze, even with a loop to automate the analysis, we would have to wait at least a few hours for our results. Later in the lesson, we’ll learn how we can bring this time down to a few minutes.