From f6830cc85ef19995252f1e07947259fb94b5d29c Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Thu, 2 Mar 2023 15:40:53 -0600 Subject: [PATCH 1/4] Move README.md to top level dir --- docs/README.md => README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/README.md => README.md (100%) diff --git a/docs/README.md b/README.md similarity index 100% rename from docs/README.md rename to README.md From b6f3ce41c89d9563902ea050e80cde19c88b118b Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Thu, 2 Mar 2023 15:58:27 -0600 Subject: [PATCH 2/4] Fix second half of page --- docs/running-jobs/pbs-qsub-options-table.md | 96 ++++++++++----------- 1 file changed, 48 insertions(+), 48 deletions(-) diff --git a/docs/running-jobs/pbs-qsub-options-table.md b/docs/running-jobs/pbs-qsub-options-table.md index 6c52aaef5..aeb633daa 100644 --- a/docs/running-jobs/pbs-qsub-options-table.md +++ b/docs/running-jobs/pbs-qsub-options-table.md @@ -6,14 +6,14 @@ Version 1.2 2021-04-28 | 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 +| `-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 |--jobname |-N \ | #PBS -N \
#PBS -WJob_Name=\|"Specifying Job Name” UG-27 @@ -23,48 +23,48 @@ Version 1.2 2021-04-28 | -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 \=\ directives |"Requesting Resources” UG-51| |-l \ |One or more
#PBS -l \=\
directives |"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. -

-## 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 +|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 other executables + - `--geometry` + - `--disable_preboot` From 86ff3ac852dce760e613902feef5cbdd83a1c915 Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Fri, 3 Mar 2023 00:59:36 -0600 Subject: [PATCH 3/4] Cleanup the rest of the page --- docs/running-jobs/pbs-qsub-options-table.md | 35 +++++++++++---------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/docs/running-jobs/pbs-qsub-options-table.md b/docs/running-jobs/pbs-qsub-options-table.md index aeb633daa..7e29bbf1e 100644 --- a/docs/running-jobs/pbs-qsub-options-table.md +++ b/docs/running-jobs/pbs-qsub-options-table.md @@ -1,27 +1,28 @@ -# PBS Pro qsub Options +# 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" +`-l select` and similar options use 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 |--jobname |-N \ | #PBS -N \
#PBS -WJob_Name=\|"Specifying Job Name” UG-27 -| -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 \=\ directives |"Requesting Resources” UG-51| |-l \ |One or more
#PBS -l \=\
directives |"Requesting Resources” UG-51 +| `-n NODES`
`--nodecount NODES` | `-l select=NODES:system=` |One or more
`#PBS -l =`
directives |"Requesting Resources” UG-51 +| `-t`
`--walltime` | `-l walltime=H:MM:SS` |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 +|`--jobname` |`-N ` | `#PBS -N `
`#PBS -WJob_Name=`|"Specifying Job Name” UG-27 +| `-e`
`--error=` | `-e ` | `#PBS -e `
`#PBS Error_Path=`|"Paths for Output and Error Files” UG-42 +| `-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 =` directives |"Requesting Resources” UG-51| |`-l ` |One or more
`#PBS -l =`
directives |"Requesting Resources” UG-51 ## PBS options that provide functionality above and beyond Cobalt From 36df444cd4f1ce79db62dcd24b9c191016a55801 Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Fri, 3 Mar 2023 01:26:33 -0600 Subject: [PATCH 4/4] Move link to internal repo copy of external document --- docs/ai-testbed/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ai-testbed/index.md b/docs/ai-testbed/index.md index 69b51c6c3..5369c1669 100644 --- a/docs/ai-testbed/index.md +++ b/docs/ai-testbed/index.md @@ -34,4 +34,4 @@ Submit your proposal requests at: [Allocation Request Page](https://accounts.alc The documentation is based on [MkDocs](https://www.mkdocs.org/){:target="_blank"} and source files are on [GitHub](https://github.com/argonne-lcf/ai-testbed-userdocs). You can contribute to the documentation by creating a pull request. - [Learn more on how to contribute to documentation.](https://github.com/argonne-lcf/ai-testbed-userdocs/blob/main/docs/HOWTO_CONTRIBUTE.md) + [Learn more on how to contribute to documentation.](howto-contribute.md)