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launcher_creator.py -h |
Short option | Long option | Required | Description | |
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-n | name | Yes | The name of the job. | |
-at | allocationtime | The allocation you want to charge the run toYes | Time allotment for job, format must be hh:mm:ss. | |
-qb | queue | Default: Development | The queue to submit to, like 'normal' or 'largemem', etc. | |
-w | wayness | Optional The number of jobs in a job list you want to give to each node. (Default is 12 for Lonestar, 16 for Stampede.) | ||
-N | number of nodes | Optional Specifies a certain number of nodes to use. You probably don't need this option, as the launcher calculates how many nodes you need based on the job list (or Bash command string) you submit. It sometimes comes in handy when writing pipelines. | ||
-t | time | Yes | Time allotment for job, format must be hh:mm:ss. | |
-e | Optional Your email address if you want to receive an email from Lonestar when your job starts and ends. | |||
-l | launcher | Optional Filename of the launcher. (Default is | ||
-m | modules | Optional String of module management commands. | ||
-b | Bash commands | Optional String of Bash commands to execute. | ||
-j | Command list | Optional Filename of list of commands to be distributed to nodes. | ||
-Bash commands | -b OR -j must be used | Optional String of Bash commands to execute. | ||
-j | Command list | -b OR -j must be used | Optional Filename of list of commands to be distributed to nodes. | |
-a | allocation | The allocation you want to charge the run to. If you only have one allocation you don't need this option | ||
-m | modules | Optional String of module management commands. | ||
-q | queue | Default: Development | The queue to submit to, like 'normal' or 'largemem', etc. You will usually want to change this to 'normal' | |
-w | wayness | Optional The number of jobs in a job list you want to give to each node. (Default is 12 for Lonestar, 16 for Stampede.) | ||
-N | number of nodes | Optional Specifies a certain number of nodes to use. You probably don't need this option, as the launcher calculates how many nodes you need based on the job list (or Bash command string) you submit. It sometimes comes in handy when writing pipelines. | ||
-e | Optional Your email address if you want to receive an email from Lonestar when your job starts and ends. If you set an environmental variable EMAIL_ADDRESS it will use that variable if you don't put anything after the -e | |||
-l | launcher | Optional Filename of the launcher. (Default is | ||
-s | stdout | Optional Setting this flag outputs the name of the launcher to stdout. |
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# remember that things after the # sign are ignored by bash and most all programing languages cds # move to your scratch directory nano commands # the following lines should be entered into nano echo "My name is _____ and todays date is:" > BDIB.output.txt date >> BDIB.output.txt echo "I have just demonstrated that I know how to redirect output to a new file, and to append things to an already created file. Or at least thats what I think I did" >> BDIB.output.txt echo "i'm going to test this by counting the number of lines in the file that I am writing to. So if the next line reads 4 I remember I'm on the right track" >> BDIB.output.txt wc -l BDIB.output.txt >> BDIB.output.txt echo "I know that normally i would be typing commands on each line of this file, that would be executed on a compute node instead of the head node so that my programs run faster, in parallel, and do not slow down others or risk my tacc account being locked out" >> BDIB.output.txt echo "i'm currently in my scratch directory on lonestar. there are 2 main ways of getting here: cds and cd $SCRATCH:" >>BDIB.output.txt pwd >> BDIB.output.txt echo "over the last week I've conducted multiple different types of analysis on a variety of sample types and under different conditions. Each of the exercises was taken from the website https://wikis.utexas.edu/display/bioiteam/Genome+Variant+Analysis+Course+20162017" >> BDIB.output.txt echo "using the ls command i'm now going to try to remind you (my future self) what tutorials I did" >> BDIB.output.txt ls -1 >> BDIB.output.txt echo "the contents of those directories (representing the data i downloaded and the work i did) are as follows: ">> BDIB.output.txt ls */* >> BDIB.output.txt echo "the commands that i have run on the headnode are: " >> BDIB.output.txt history >> BDIB.output.txt echo "the contents of this, my commands file, which i will use in the launcher_creator.py script are: ">>BDIB.output.txt cat commands >> BDIB.output.txt echo "finally, I will be generating a job.slurm file using the launcher_creator.py script using the following command:" >> BDIB.output.txt echo 'launcher_creator.py -w 1 -N 1 -n "what_i_did_at_BDIB_20162017" -t 00:02:00 -a "UT-2015-05-18"' >> BDIB.output.txt # this will create a my_first_job.slurm file that will run for 2 minutes echo "and i will send this job to the que using the the command: sbatch what_i_did_at_BDIB_20162017.slurm" >> BDIB.output.txt # this will actually submit the job to the Queue Manager and if everything has gone right, it will be added to the development queue. ctrlo #keyboard command to write your nano output crtlx # keyboard command to close the nano interface launcher_creator.py -w 1 -N 1 -n "what_i_did_at_BDIB_20162017" -t 00:02:00 -a "UT-2015-05-18" sbatch what_i_did_at_BDIB_20162017.slurm |
Interrogating the launcher queue
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Based on our example you may have expected 1 new file to have been created during the job submission (BDIB.output.txt), but instead you will find 3 2 extra files as follows: what_i_did.e(job-ID), and what_i_did.peo(job-ID), and what_i_did.o(job-ID). . When things have worked well, these files are typically ignored. When your job fails, these files offer insight into the why so you can fix things and resubmit.
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# remember that things after the # sign are ignored by bash cat BDIB.output.txt > first# remember that things after the # sign are ignored by bash cat BDIB.output.txt > end_of_class_job_submission.final.output mkdir $WORK/BDIB_GVA_2017 mkdir $WORK/BDIB_GVA_2017/end_of_course_summary/ # each directory must be made in order to avoid getting a no such file or directory error cp end_of_class_job_submission.final.output mkdir $WORK/BDIB_GVA_2016 mkdir_2017/end_of_course_summary/ cp what_i_did* $WORK/BDIB_GVA_20162017/end_of_course_summary/ # note this # each directory must be made in order to avoid getting a no such file or directory error cp first_job_submission.final.output $WORK/BDIB_GVA_2016/end_of_course_summary/ cp what_i_did*grabs the 2 output files generated by tacc about your job run as well as the .slurm file you created to tell it how to run your commands file cp commands $WORK/BDIB_GVA_20162017/end_of_course_summary/ |
Return to GVA2017 to work on any additional tutorials you are interested in.