Using the RCE submit command line client (for advanced users)¶

Accessing the terminal¶

If you’re working within a NoMachine NX session, open the terminal by selecting Applications → System Tools → Terminal.

You can also SSH to rce.hmdc.harvard.edu if you prefer to launch interactive jobs outside of a NoMachine NX4 session, but, you will still need an X server running client-side. If you’re currently running any variant of the Linux operating system, using ssh -X should suffice, otherwise, follow these links to download X servers for your operating system:

• Windows: Xming
• OS X: Xquartz

Listing available applications¶

While GUI RCE submit tools only supports Matlab for the rest of the 2015 calendar year, the RCE submit tools command line client supports all applications in the RCE. You can list which applications are supported by running the following command:

rce_submit.py -list

which will output a list of supported applications and versions:

** denotes default
Application    Version(s)
-------------  ------------
gauss          14 **
               8
mathematica    10.2.0
               10.1.0
               10.3.0 **
matlab         R2015a **
               R2012a
               R2013a
               R2014b
               R2014a
               R2010b
octave         3.4.3 **
python         3.3
               2.7 **
R              3.2 **
rstudio        0.98 **
SAS            9.3
               9.4 **
shell          2.31.3 **
StatTransfer   12 **
xstata-mp      13.1
               14.0 **
xstata-se      13.1
               14.0 **

Running an application¶

You can run the default version of the application python, by executing:

rce_submit.py -r -a python

You can run python 3.3 by executing:

rce_submit.py -r -a python -v 3.3

Listing running applications¶

You can list which RCE interactive applications you are currently running, whether attached or detached, by executing:

rce_submit.py --jobs

which produces the following output:

  Job Id  Application    Version    Requested Cpus    Requested Memory
--------  -------------  ---------  ----------------  ------------------
     174  xstata-mp      14.0       4                 6144
     183  matlab         R2015a     1                 12288
     113  shell          2.31.3     1                 2048
     110  shell          2.31.3     1                 2048

(Re)attaching an application¶

If you’ve disconnected your application from yoiur desktop, you can re-attach it using the command line tools by first running rce_submit.py --jobs, noting the Job Id of the job you want to re-attach and then executing:

rce_submit.py -attach 174

In the above example, I reattached xstata-mp.

Creating a custom application launcher¶

You may have installed an application locally to your home directory which has GUI capabilities and want to run this application in our HTCondor cluster. RCE cluster tools uses a configuration file format called rceapp.yml to manage application settings.

First, you should copy the existing rceapp.yml into your home directory to get an idea of how this file is structured:

cp /etc/rceapp.yml $HOME

Here is a simple stanza from rceapp.yml describing the gnome-terminal:

shell:
  global:
    memory: 2048
    cpu: 1
    icon: /usr/share/icons/gnome/32x32/apps/gnome-terminal.png
    supports_memory_adjustable: true
    supports_cpu_adjustable: true
    supports_cli_mode: true
  '2.31.3':
    default: true
    command: /usr/bin/gnome-terminal
    command_nogui: $ENV(SHELL)

Presume that I want to run firefox as an interactive job in the RCE cluster. I would first edit my local rceapp.yml at $HOME/rceapp.yml and add the following stanza:

firefox:
  global:
    memory: 2048
    cpu: 1
    icon: /usr/share/icons/gnome/32x32/apps/gnome-terminal.png
    supports_memory_adjustable: true
    supports_cpu_adjustable: true
    supports_cli_mode: true
  '10.0':
    default: true
    command: /usr/bin/firefox

Then, I could run firefox by running the following command, which would create a firefox job that consumes 1 CPU and 2048 MiB of memory:

rce_submit.py -c $HOME/rceapp.yml -r -a firefox

The -c switch designates that you’re using a custom rceapp.yml rather than the system-wide rceapp.yml in /etc

Getting help¶

Running the following command will print out inline help for rce_submit.py:

rce_submit.py -help