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bioinfo
datautils
Commits
583a235d
Commit
583a235d
authored
Nov 09, 2015
by
Holger Brandl
Browse files
continued blastx fix
parent
2347d9df
Changes
1
Hide whitespace changes
Inline
Side-by-side
bash/CreateJobReport.R
View file @
583a235d
...
...
@@ -3,8 +3,8 @@
#sessionInfo()
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.1
4
/R/core_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.1
4
/R/ggplot_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.1
8
/R/core_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.1
8
/R/ggplot_commons.R"
)
require.auto
(
lubridate
)
...
...
@@ -34,8 +34,22 @@ jobData <- read.table(paste0(reportName, ".cluster_snapshots.txt"), header=F, fi
set_names
(
c
(
"jobid"
,
"user"
,
"stat"
,
"queue"
,
"from_host"
,
"exec_host"
,
"job_name"
,
"submit_time"
,
"proj_name"
,
"cpu_used"
,
"mem"
,
"swap"
,
"pids"
,
"start_time"
,
"finish_time"
,
"snapshot_time"
))
%>%
transform
(
jobid
=
factor
(
jobid
))
%>%
arrange
(
jobid
)
%>%
subset
(
stat
==
"RUN"
)
%>%
transform
(
num_cores
=
str_match
(
exec_host
,
"([0-9]+)[*]n"
)[,
2
])
%>%
mutate
(
num_cores
=
ifelse
(
is.na
(
num_cores
),
1
,
num_cores
))
subset
(
stat
==
"RUN"
)
if
(
nrow
(
jobData
)
==
0
){
system
(
paste
(
"mailme 'no jobs were run in "
,
normalizePath
(
reportName
),
"'"
))
stop
(
-1
)
}
#jobData %>% count(jobid) %>% nrow
## extract multi-threading number
jobData
%<>%
transform
(
num_cores
=
str_match
(
exec_host
,
"([0-9]+)[*]n"
)[,
2
])
%>%
mutate
(
num_cores
=
ifelse
(
is.na
(
num_cores
),
1
,
num_cores
))
jobData
%>%
count
(
exec_host
)
jobData
%>%
select
(
submit_time
,
start_time
,
finish_time
)
%>%
head
# filter(finish_time!="-") %>% head
...
...
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