Commit 583a235d authored by Holger Brandl's avatar Holger Brandl

continued blastx fix

parent 2347d9df
......@@ -3,8 +3,8 @@
#sessionInfo()
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.14/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.14/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.18/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.18/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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