Tuesday Exercise 2.2: Software Differences in the OSG

The goal of this exercise is to see the differences in availability of software in the OSG. At your local cluster, you may be used to having certain versions of software but out on the OSG, it's possible that the software you need won't even be installed.

Refresher - condor_status

The OSG pool, like the local pool you used yesterday, is just another HTCondor pool. This means that the commands you use will be the same and the jobs you submit can have similar payloads but there is one major difference: the slots are different! You can use the condor_status command just as you did yesterday to inspect these differences.

  1. Open two terminal windows side-by-side
  2. Log in to learn.chtc.wisc.edu in one window and osg-learn.chtc.wisc.edu in the other
  3. Run condor_status in both windows

Notice any differences?

Comparing operating systems

To really see differences between slots in the local cluster vs the OSG, you will want to compare the slot ClassAds between the two pools. Rather than inspecting the very long ClassAd for each slot, you will look at a specific attribute called OpSysAndVer, which tells us the operating system version of the machine where a slot resides. An easy way to show this attribute for all slots is by using condor_status in conjunction with the -autoformat option. -autoformat like the -format option you learned about yesterday will print out the attributes you're interested in for each slot but as you probably guessed, it does some automatic formatting for you. So to show the operating system and version of each slot, run the following command in both of your terminal windows:

[email protected] $ condor_status -autoformat OpSysAndVer

You will see many values with the type of operating system at the front and the version number at the end (i.e. SL6 stands for Scientific Linux 6). The only problem is that with hundreds or thousands of slots, it's difficult to get a feel for the composition of each pool from this output. You can find a count for each operating system by passing the condor_status output into the sort and uniq commands. Your command line should look something like this:

[email protected] $ condor_status -autoformat OpSysAndVer | sort | uniq -c

Can you spot the differences between the two pools now?

Submitting probe jobs

Knowing the type and version of the operating systems is a step in the right direction to knowing what kind of software will be available on the machines that your jobs land on. However it still only serves as a proxy to the information that you really want: does the machine have the software that you want? Does it have the correct version?

Software probe code

The following shell script probes for software and returns the version if it is installed:

#!/bin/sh

get_version(){
    program=$1
    $program --version > /dev/null 2>&1
    double_dash_rc=$?
    $program -version > /dev/null 2>&1
    single_dash_rc=$?
    which $program > /dev/null 2>&1
    which_rc=$?
    if [ $double_dash_rc -eq 0 ]; then
        $program --version 2>&1
    elif [ $single_dash_rc -eq 0 ]; then
        $program -version 2>&1
    elif [ $which_rc -eq 0 ]; then
        echo "$program installed but could not find version information"
    else
        echo "$program not installed"
    fi
}

get_version 'R'
get_version 'cmake'
get_version 'python'

If there's a specific command line program that your research requires, feel free to add it to the script! For example, if you wanted to test for the existence and version of nslookup, you would add the following to the end of the script:

get_version 'nslookup'

Probing several machines

For this part of the exercise, try creating a submit file without referring to previous exercises!

  1. Log in to osg-learn.chtc.wisc.edu
  2. Create and change into a new folder for this exercise, e.g. tuesday-2.2
  3. Save the above script as a file named sw_probe.sh
  4. As always, make sure that you can run your script from the command line before asking HTCondor to do so
  5. Create a submit file that runs sw_probe.sh 100 times and uses macros to write different output, error, and log files
  6. Submit your job and wait for the results

Will you be able to do your research on the OSG with what's available? Don't fret if it doesn't look like you can: over the next few days, you'll learn how to make your jobs portable enough so that they can run anywhere!