Get information on jobs currently on the SGE queue

read_qstat(file = NULL)

Arguments

file: A file, a connection, or NULL. If NULL (default), then the output of system call qstat -xml -u '*' is read.

Value

A tibble::tibble

Examples

pathname <- system.file("exdata", "qstat.xml", package = "wyntonquery")

qstat <- read_qstat(pathname)
print(qstat)
#> # A tibble: 2,119 × 13
#>    job_number prio.x name        owner state.x submission_time     slots tasks.x
#>         <dbl>  <dbl> <chr>       <chr> <chr>   <dttm>              <int> <chr>  
#>  1     198026  0.65  wt_D842Z_Z… owne… qw      2021-06-11 19:34:47     3 NA     
#>  2     198027  0.5   wt_D842Z_Z… owne… qw      2021-06-11 19:34:47     3 NA     
#>  3     198028  0.41  wt_D842Z_Z… owne… qw      2021-06-11 19:34:47     3 NA     
#>  4    3050724  0.365 relioncpu   owne… Eqw     2021-04-11 00:22:52   100 NA     
#>  5     127221  0.232 relion4GPU… owne… Eqw     2021-06-06 17:46:46     4 NA     
#>  6     245277  0.200 singularit… owne… qw      2021-06-15 09:28:30     4 NA     
#>  7    2316670  0.171 run_phylop… owne… Eqw     2021-03-09 17:11:46    24 NA     
#>  8    1125632  0.128 blast_abor… owne… Eqw     2021-01-12 16:59:26     4 NA     
#>  9      77151  0.126 genomegene… owne… Eqw     2021-06-04 12:27:36     5 NA     
#> 10    1280060  0.108 atac.sh     owne… qw      2020-04-23 12:27:00     8 NA     
#> # ℹ 2,109 more rows
#> # ℹ 5 more variables: prio.y <dbl>, state.y <chr>, start_time <dttm>,
#> #   queue_name <chr>, tasks.y <chr>

## Anonymize (although actually already anonymized)
qstat_anon <- anonymize(qstat)
print(qstat_anon)
#> # A tibble: 2,119 × 13
#>    job_number prio.x name        owner state.x submission_time     slots tasks.x
#>         <dbl>  <dbl> <chr>       <chr> <chr>   <dttm>              <int> <chr>  
#>  1     198026  0.65  wt_D842Z_Z… owne… qw      2021-06-11 19:34:47     3 NA     
#>  2     198027  0.5   wt_D842Z_Z… owne… qw      2021-06-11 19:34:47     3 NA     
#>  3     198028  0.41  wt_D842Z_Z… owne… qw      2021-06-11 19:34:47     3 NA     
#>  4    3050724  0.365 relioncpu   owne… Eqw     2021-04-11 00:22:52   100 NA     
#>  5     127221  0.232 relion4GPU… owne… Eqw     2021-06-06 17:46:46     4 NA     
#>  6     245277  0.200 singularit… owne… qw      2021-06-15 09:28:30     4 NA     
#>  7    2316670  0.171 run_phylop… owne… Eqw     2021-03-09 17:11:46    24 NA     
#>  8    1125632  0.128 blast_abor… owne… Eqw     2021-01-12 16:59:26     4 NA     
#>  9      77151  0.126 genomegene… owne… Eqw     2021-06-04 12:27:36     5 NA     
#> 10    1280060  0.108 atac.sh     owne… qw      2020-04-23 12:27:00     8 NA     
#> # ℹ 2,109 more rows
#> # ℹ 5 more variables: prio.y <dbl>, state.y <chr>, start_time <dttm>,
#> #   queue_name <chr>, tasks.y <chr>