PBS Pro qsub Options
Version 1.2 2021-04-28
-l select and similar is a lower case "L", -I for interactive is an upper case "I"
| Cobalt CLI | PBS CLI | PBS Directive | Function and Page Reference |
|---|---|---|---|
| -A \ |
-A \ |
#PBS Account_Name=\ |
"Specifying Accounting String” UG-29 |
| -n NODES --nodecount NODES |
-l select=NODES:system=\ |
One or more #PBS -l \ directives |
"Requesting Resources” UG-51 |
| -t --walltime |
-l walltime=1:00:00 | One or more #PBS -l \ directives |
"Requesting Resources” UG-51 |
| --attrs filesystems=\ |
-l filesystems=\ |
One or more #PBS -l \ directives |
"Requesting Resources” UG-51 |
| -q | -q \ |
#PBS -q \ #PBS -q @\ #PBS -q \ |
"Specifying Server and/or Queue” UG-29 |
| --env | -v \ |
"Exporting Specific Environment Variables” UG-126 | |
| --env | -V | #PBS -V | "Exporting All Environment Variables” UG-126 |
| --attrs | Done via custom resources and select statements | "Setting Job Attributes” UG-16 | |
--dependencies=\ |
-W depend=afterok:\ |
#PBS depend=... | "Using Job Dependencies” UG-107 |
| -I --interactive |
-I | Deprecated for use in a script | "Running Your Job Interactively” UG-121 |
| -e --error= |
-e \ |
#PBS -e \ #PBS Error_Path=\ |
"Paths for |
| -o --output= |
-o \ |
#PBS -o \ #PBS Output_Path=\ |
"Paths for Output and Error Files” UG-42 |
| -M --notify see note #1 |
-M \ -m \ -m be is suggested |
#PBS -M \ #PBS -WMail_Users=\ #PBS -m \ #PBS -WMail_Points=\ |
"Setting Email Recipient List” UG-26 |
| -u --umask |
-W umask=\ |
#PBS umask=\ |
"Changing Linux Job umask” UG-45 |
| -h | -h | #PBS -h | "Holding and Releasing Jobs” UG-115 |
| --proccount See Note #2 |
-l mpiprocs Not needed to get equivalent Cobalt functionality |
One or more #PBS -l \ |
"Requesting Resources” UG-51 |
PBS options that provide functionality above and beyond Cobalt
Depending on policy decisions not all of these options may be available.
| Cobalt CLI | PBS CLI | PBS Directive | Function and Page Reference |
|---|---|---|---|
| N/A | -a \ |
#PBS -a | "Deferring Execution” UG-119 |
| N/A | -C “\ |
"Changing the Directive Prefix” UG-16 | |
| N/A | -c \ |
#PBS -c | "Using Checkpointing” UG-113 |
| N/A | -G | "Submitting Interactive GUI Jobs on Windows” UG-125 | |
| N/A | -J X-Y[:Z] | #PBS -J | "Submitting a Job Array” UG-150 |
| N/A | -j \ |
#PBS Join_Path=\ |
"Merging Output and Error Files” UG-43 |
| N/A | -k \ |
#PBS Keep_Files=\ |
"Keeping Output and Error Files on Execution Host” UG-44 |
| N/A | -p \ |
#PBS -p | "Setting Priority for Your Job” UG-120 |
| N/A | -P \ |
#PBS project=\ |
"Specifying a Project for a Job” UG-27 |
| N/A | -r \ |
#PBS -r | "Allowing Your Job to be Re-run” UG-118 |
| N/A | -R \ |
"Avoiding Creation of stdout and/or stderr” UG-43 | |
| N/A | -S \ |
"Specifying the Top Shell for Your Job” UG-19 | |
| N/A See Note #3 |
-u \ |
#PBS User_List=\ |
"Specifying Job Username” UG-28 |
| N/A | -W block=true | #PBS block=true | "Making qsub Wait Until Job Ends” UG-120 |
| N/A | -W group_list=\ |
#PBS group_list=\ |
"Specifying Job Group ID” UG-28 |
| N/A | -W release_nodes_on_stageout=\ |
"Releasing Unneeded Vnodes from Your Job” UG-127 | |
| N/A | -W run_count=\ |
"Controlling Number of Times Job is Re-run” UG-119 | |
| N/A | -W sandbox=\ |
"Staging and Execution Directory: User Home vs. Job-specific” UG-31 | |
| N/A | -W stagein=\ |
#PBS -W stagein=\ |
"Input/Output File Staging” UG-31 |
| N/A | -W stageout=\ |
#PBS -W stageout=\ |
"Input/Output File Staging” UG-31 |
| N/A | -X | "Receiving X Output from Interactive Linux Jobs” UG-124 | |
| N/A | -z | #PBS -z | "Suppressing Printing Job Identifier to stdout” UG-30 |
| #Notes | |||
| 1. To get the equivalent mail notifications from PBS it requires two parameters the -M just like Cobalt, but also -m be (the be stands for beginning and end) to specify when the mails should go out. This will give you the same behavior as Cobalt. | |||
| 2. --proccount, while available, only changed behavior on the Blue Gene machines. To get equivalent functionality just drop it from the CLI. In PBS it does influence the PBS_NODES file. See Section 5.1.3 in the PBS Users Guide page UG-78 | |||
| 1. The following Cobalt options have no equivalent in PBS | |||
| - --cwd - use a script and cd to the directory you want to run from | |||
| - --user_list - There is no way to do this. We will work on adding this functionality | |||
| - --debuglog - Are we going to try and generate the equivalent of a .cobalt file? | |||
| 2. The following Cobalt options were Blue Gene specific and no longer apply | |||
| - --kernel | |||
| - -K KERNELOPTIONS | |||
| - --ion_kernel | |||
| - --ion_kerneloption | |||
| - --mode - see notes on running scripts, python, and executables | |||
| - --geometry | |||
| - --disable_preboot |