Hoffman2:Job Submission Templates - Revision history

Dmargolis: /* To work with these example scripts */

2017-12-04T23:28:40Z

To work with these example scripts

← Older revision		Revision as of 23:28, 4 December 2017
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	#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. ''Watch out for line ending errors caused by copying/pasting from a Mac or PC.'' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.		#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. ''Watch out for line ending errors caused by copying/pasting from a Mac or PC.'' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
	#*For jobs longer than 24 hours, you must specify the 'highp' option, e.g. <code>-l h_rt=8:00:00,h_data=4G,highp</code>		#*For jobs longer than 24 hours, you must specify the 'highp' option, e.g. <code>-l h_rt=36:00:00,h_data=4G,highp</code>
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.
	#*Edit the mail notification options: '-m bea' means you want to receive a message when your job Begins, Ends, or Aborts (quits due to an error). You may use any combination of 'b', 'e', and 'a' for this setting.		#*Edit the mail notification options: '-m bea' means you want to receive a message when your job Begins, Ends, or Aborts (quits due to an error). You may use any combination of 'b', 'e', and 'a' for this setting.
	#Put your script content at the bottom.		#Put your script content at the bottom.
	#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>		#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>

Dmargolis: /* To work with these example scripts */

2017-12-04T23:27:40Z

To work with these example scripts

← Older revision		Revision as of 23:27, 4 December 2017
Line 13:		Line 13:
	#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. ''Watch out for line ending errors caused by copying/pasting from a Mac or PC.'' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.		#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. ''Watch out for line ending errors caused by copying/pasting from a Mac or PC.'' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
			#*For jobs longer than 24 hours, you must specify the 'highp' option, e.g. <code>-l h_rt=8:00:00,h_data=4G,highp</code>
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.
	#*Edit the mail notification options: '-m bea' means you want to receive a message when your job Begins, Ends, or Aborts (quits due to an error). You may use any combination of 'b', 'e', and 'a' for this setting.		#*Edit the mail notification options: '-m bea' means you want to receive a message when your job Begins, Ends, or Aborts (quits due to an error). You may use any combination of 'b', 'e', and 'a' for this setting.
	#Put your script content at the bottom.		#Put your script content at the bottom.
	#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>		#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>

Dmargolis at 19:36, 29 November 2017

2017-11-29T19:36:42Z

← Older revision		Revision as of 19:36, 29 November 2017
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			[[Hoffman2\|Back to all things Hoffman2]]
	===Job submission templates===		===Job submission templates===
	'''[[Hoffman2:Submit_job\|Submit job]]'''		'''[[Hoffman2:Submit_job\|Submit job]]'''

Dmargolis at 19:26, 29 November 2017

2017-11-29T19:26:49Z

← Older revision		Revision as of 19:26, 29 November 2017
Line 10:		Line 10:

	===To work with these example scripts===		===To work with these example scripts===
	#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. '''Watch out for ~~non-Linux (~~Mac or PC~~) line endings~~.''' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.		#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. ''Watch out for line ending errors caused by copying/pasting from a Mac or PC.'' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.

Dmargolis: /* To work with these example scripts */

2017-11-29T19:25:23Z

To work with these example scripts

← Older revision		Revision as of 19:25, 29 November 2017
Line 10:		Line 10:

	===To work with these example scripts===		===To work with these example scripts===
	#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. '''Watch out for non-Linux (Mac or PC) line endings.''' Line ending issues can be fixed with <code>dos2unix</code>.		#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. '''Watch out for non-Linux (Mac or PC) line endings.''' Line ending issues can be fixed with <code>dos2unix myscript.sh</code>.
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.

Dmargolis: /* To work with these example scripts */

2017-11-29T19:25:01Z

To work with these example scripts

← Older revision		Revision as of 19:25, 29 November 2017
Line 10:		Line 10:

	===To work with these example scripts===		===To work with these example scripts===
			#Copy the contents of the script template into a new script, e.g. <code>myscript.sh</code>. '''Watch out for non-Linux (Mac or PC) line endings.''' Line ending issues can be fixed with <code>dos2unix</code>.
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.

Dmargolis: /* To work with these example scripts */

2017-11-29T19:23:34Z

To work with these example scripts

← Older revision		Revision as of 19:23, 29 November 2017
Line 12:		Line 12:
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.
			#*Edit the mail notification options: '-m bea' means you want to receive a message when your job Begins, Ends, or Aborts (quits due to an error). You may use any combination of 'b', 'e', and 'a' for this setting.
	#Put your script content at the bottom.		#Put your script content at the bottom.
	#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>		#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>

Dmargolis: /* Job submission templates */

2017-11-29T19:16:42Z

Job submission templates

← Older revision		Revision as of 19:16, 29 November 2017
Line 1:		Line 1:
	===Job submission templates===		===Job submission templates===
	'''[[Hoffman2:~~Submit_job_example~~\|Submit job]]'''		'''[[Hoffman2:Submit_job\|Submit job]]'''
	*example script for submitting a single job		*example script for submitting a single job
	'''[[Hoffman2:~~Submit_job_example_~~(tcsh)\|Submit job (tcsh)]]'''		'''[[Hoffman2:Submit_job_(tcsh)\|Submit job (tcsh)]]'''
	*same as above, written for tcsh		*same as above, written for tcsh
	'''[[Hoffman2:~~Submit_jobarray_example~~\|Submit jobarray]]'''		'''[[Hoffman2:Submit_jobarray\|Submit jobarray]]'''
	*example script for submitting a jobarray with hard-coded array values		*example script for submitting a jobarray with hard-coded array values
	'''[[Hoffman2:~~Submit_jobarray_example_~~(readarray)\|Submit jobarray (readarray)]]'''		'''[[Hoffman2:Submit_jobarray_(readarray)\|Submit jobarray (readarray)]]'''
	*example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'		*example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'

Dmargolis: /* Job submission templates */

2017-11-29T19:14:45Z

Job submission templates

← Older revision		Revision as of 19:14, 29 November 2017
Line 1:		Line 1:
	===Job submission templates===		===Job submission templates===
	'''[[Hoffman2:Submit_job_example\|Submit job ~~example~~]]'''		'''[[Hoffman2:Submit_job_example\|Submit job]]'''
	*example script for submitting a single job		*example script for submitting a single job
	'''[[Hoffman2:Submit_job_example_(tcsh)\|Submit job ~~example~~ (tcsh)]]'''		'''[[Hoffman2:Submit_job_example_(tcsh)\|Submit job (tcsh)]]'''
	*same as above, written for tcsh		*same as above, written for tcsh
	'''[[Hoffman2:Submit_jobarray_example\|Submit jobarray ~~example~~]]'''		'''[[Hoffman2:Submit_jobarray_example\|Submit jobarray]]'''
	*example script for submitting a jobarray with hard-coded array values		*example script for submitting a jobarray with hard-coded array values
	'''[[Hoffman2:Submit_jobarray_example_(readarray)\|Submit jobarray ~~example~~ (readarray)]]'''		'''[[Hoffman2:Submit_jobarray_example_(readarray)\|Submit jobarray (readarray)]]'''
	*example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'		*example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'

Dmargolis at 22:54, 14 November 2017

2017-11-14T22:54:06Z

← Older revision		Revision as of 22:54, 14 November 2017
Line 1:		Line 1:
			===Job submission templates===
	'''[[Hoffman2:Submit_job_example\|Submit job example]]'''		'''[[Hoffman2:Submit_job_example\|Submit job example]]'''
	*example script for submitting a single job		*example script for submitting a single job
Line 8:		Line 9:
	*example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'		*example script for submitting a jobarray with an array read in from a file, e.g. 'subjects.txt'

	To work with these example scripts:		===To work with these example scripts===
	#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).		#Edit the "preamble" content at the top to adjust the memory (h_data) and run time (h_rt).
	#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.		#*You can also adjust the number of cores: 2 cores is '-pe shared 2'. I recommend 2, 4, or 8 for this value. Be aware that the number of cores is a multiplier for the RAM. h_data=4G and 2 cores is 8G total.
	#Put your script content at the bottom.		#Put your script content at the bottom.
	#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>		#Submit directly to the job scheduler like this: <code>qsub myscript.sh</code>