accounting | R Documentation |
For a given set of SGE job IDs, these functions extract the data from SGE
using qacct
and then parse it to produce a data.frame with the summary
information recorded by SGE on the performance of these SGE jobs.
accounting(
job_ids,
accounting_files = "/cm/shared/apps/sge/sge-8.1.9/default/common/accounting",
tz = "EST"
)
accounting_read(
job_ids,
accounting_files = "/cm/shared/apps/sge/sge-8.1.9/default/common/accounting"
)
accounting_parse(accounting_info, tz = "EST")
job_ids |
A |
accounting_files |
A |
tz |
Time zone for your SGE cluster. Defaults to |
accounting_info |
A named list where each element contains the output
from |
accounting_read
: A list with the output from qacct
by SGE for
each of the SGE job IDs.
accounting_parse
and accounting
: a data.frame
with the SGE
accounting information parsed.
Leonardo Collado-Torres
Leonardo Collado-Torres, Andrew E. Jaffe and Emily E. Burke (2019). jaffelab: Commonly used functions by the Jaffe lab. R package version 0.99.27. https://github.com/LieberInstitute/jaffelab
## Requires JHPCE to run
accounting_file <- "/cm/shared/apps/sge/sge-8.1.9/default/common/accounting_20191007_0300.txt"
if (file.exists(accounting_file)) {
head(
accounting(
c("92500", "77672"),
accounting_file
)
)
}
## Example for a single job
acc_info <- list("92500" = readLines(
system.file("extdata", "accounting", "92500.txt",
package = "sgejobs"
)
))
acc_info
## Requires JHPCE access
accounting_file <- "/cm/shared/apps/sge/sge-8.1.9/default/common/accounting_20191007_0300.txt"
if (file.exists(accounting_file)) {
acc_info_jhpce <- accounting_read("92500", accounting_file)
identical(acc_info_jhpce, acc_info)
}
## The example file has been subset to just the first two tasks
acc_info_array <- list("77672" = readLines(
system.file("extdata", "accounting", "77672.txt",
package = "sgejobs"
)
))
## Requires JHPCE access
#' ## Example for an array job
if (file.exists(accounting_file)) {
acc_info_jhpce_array <- accounting_read("77672", accounting_file)
}
## Requires JHPCE access
accounting_file <- "/cm/shared/apps/sge/sge-8.1.9/default/common/accounting_20191007_0300.txt"
if (file.exists(accounting_file)) {
accounting_info_jhpce <- accounting_read(
c("92500", "77672"),
accounting_file
)
}
## Here we use the data included in the package to avoid depending on JHPCE
## where the data for job 77672 has been subset for the first two tasks.
accounting_info <- list(
"92500" = readLines(system.file("extdata", "accounting", "92500.txt",
package = "sgejobs"
)),
"77672" = readLines(system.file("extdata", "accounting", "77672.txt",
package = "sgejobs"
))
)
## Here we parse the data from `qacct` into a data.frame
res <- accounting_parse(accounting_info)
res
## Check the maximum memory use
as.numeric(res$maxvmem)
## And the absolute maximum
pryr:::show_bytes(max(res$maxvmem))
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