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Remember to replace ".username" with your stats cluster username. This sample submit script can be used for shortjob and longjob groups by replacing "testjob" with either "shortjob" or "longjob".
Remember to replace ".username" with your stats cluster username. This sample submit script can be used for shortjob and longjob groups by replacing "testjob" with either "shortjob" or "longjob".
=== GCC 4.9.2 ===
CentOS 6 uses the default 4.4.7 GCC compiler. The version 4.9.2 is available but it needs to be set by the user. To do this, it is recommended to include it in your job's executable. For example, you could make /bin/bash your executable and then transfer an executable bash script. Within this bash script, you can set gcc to 4.9.2 and then execute your code.
The submit file
<pre>
...
Executable = /bin/bash
Arguments = myBashScript
# if your script takes in arguments, write it like below
Arguments = myBashScript arg1 arg2 ...
transfer_input_files = myBashScript
...
</pre>
myBashScript (make sure this is executable, chmod +x myBashScript)
<pre>
# At the very beginning of your script you should add this line
source scl_source enable devtoolset-3
# If you want to convince yourself that you are now using gcc 4.9.2, add the following line to get the gcc version in your output file
gcc --version
# Now include the necessary commands in the remaining bash script to execute your code
exe="root"
opt1="-l"
opt2="-b"
macro="runDSelector.C(\"$1\")"
command=( "$exe" "$opt1" "$opt2" "$macro" )
"${command[@]}"
</pre>
This is just an example bash script that will open the software ROOT and execute a macro called runDSelector.C with a solitary argument. This is not the only way to structure a bash script.
== Some guidelines ==
=== Memory ===
If you find that your job is being held, it's possible that your job is going over its memory (resident set) quota. This can be checked by examining your log file and seeing how much disk and memory used compared to what was requested. If the disk usage far exceeds the requested amount, you are likely thrashing the cluster by using swap (hard disk) instead of memory.
To request more memory for your job, add the following line to your submit file
<pre>
request_memory = <size in MB>
</pre>
If you had a job that was held because of a memory quota issue, you should try testing it before submitting a large batch. Add the amount of hard disk you used to your initial memory request and do a test run. Once you're satisfied that you're within the request limits, submit a full set of jobs.
=== Large job queues ===
Never submit more than 5,000 jobs at once. The cluster can only negotiate so many queued jobs. Overloading the queue will prevent the resource manager from properly negotiating the resources.
Remember, other users might also submit a large set of jobs. Try to keep smaller batches.