## [1] "iris"## [1] "svm" "forest"The flow to define experiments is summarized in the following figure:
If we want to peek into the R log file of a job to see more context for the error we can use showLog() which opens a pager or use getLog() to get the log as character vector:
writeLines(getLog(id = 9))## ### [bt 2017-01-02 16:19:05]: This is batchtools v0.9.1
-## ### [bt 2017-01-02 16:19:05]: Starting calculation of 1 jobs
-## ### [bt 2017-01-02 16:19:05]: Setting working directory to '/tmp'
-## ### [bt 2017-01-02 16:19:05]: Memory measurement disabled
-## ### [bt 2017-01-02 16:19:05]: Starting job [batchtools job.id=9]
+## ### [bt 2017-01-03 14:40:17]: This is batchtools v0.9.1
+## ### [bt 2017-01-03 14:40:17]: Starting calculation of 1 jobs
+## ### [bt 2017-01-03 14:40:17]: Setting working directory to '/tmp'
+## ### [bt 2017-01-03 14:40:17]: Memory measurement disabled
+## ### [bt 2017-01-03 14:40:17]: Starting job [batchtools job.id=9]
## Error in (function (value) : Ooops.
##
-## ### [bt 2017-01-02 16:19:05]: Job terminated with an exception [batchtools job.id=9]
-## ### [bt 2017-01-02 16:19:05]: Calculation finished!
+## ### [bt 2017-01-03 14:40:17]: Job terminated with an exception [batchtools job.id=9]
+## ### [bt 2017-01-03 14:40:17]: Calculation finished!You can also grep for error or warning messages:
ids = grepLogs(pattern = "ooops", ignore.case = TRUE)
print(ids)This R package is licensed under the LGPL-3. If you encounter problems using this software (lack of documentation, misleading or wrong documentation, unexpected behaviour, bugs, …) or just want to suggest features, please open an issue in the issue tracker. Pull requests are welcome and will be included at the discretion of the author. If you have customized a template file for your (larger) computing site, please share it: fork the repository, place your template in inst/templates and send a pull request.
tmp = makeRegistry(file.dir = NA, make.default = FALSE)#>print(tmp)#> Job Registry #> Name : Interactive -#> File dir: /scratch/registry7d217ec115a +#> File dir: /scratch/registryb13153650b8 #> Work dir: /home/lang/Projekte/batchtools/docs/reference #> Jobs : 0 #> Seed : 396414167diff --git a/docs/reference/showLog.html b/docs/reference/showLog.html index 5dbee55b..4eb70952 100644 --- a/docs/reference/showLog.html +++ b/docs/reference/showLog.html @@ -127,14 +127,14 @@Examp #> Done : 4 ( 80.0%) #> Error : 1 ( 20.0%) #> Expired : 0 ( 0.0%)
-writeLines(getLog(ids[1], reg = tmp))#> ### [bt 2017-01-02 16:19:01]: This is batchtools v0.9.1 -#> ### [bt 2017-01-02 16:19:01]: Starting calculation of 1 jobs -#> ### [bt 2017-01-02 16:19:01]: Setting working directory to '/home/lang/Projekte/batchtools/docs/reference' -#> ### [bt 2017-01-02 16:19:01]: Memory measurement disabled -#> ### [bt 2017-01-02 16:19:01]: Starting job [batchtools job.id=1] +writeLines(getLog(ids[1], reg = tmp))#> ### [bt 2017-01-03 14:40:13]: This is batchtools v0.9.1 +#> ### [bt 2017-01-03 14:40:13]: Starting calculation of 1 jobs +#> ### [bt 2017-01-03 14:40:13]: Setting working directory to '/home/lang/Projekte/batchtools/docs/reference' +#> ### [bt 2017-01-03 14:40:13]: Memory measurement disabled +#> ### [bt 2017-01-03 14:40:13]: Starting job [batchtools job.id=1] #> -#> ### [bt 2017-01-02 16:19:01]: Job terminated successfully [batchtools job.id=1] -#> ### [bt 2017-01-02 16:19:01]: Calculation finished!## Not run: ------------------------------------ +#> ### [bt 2017-01-03 14:40:13]: Job terminated successfully [batchtools job.id=1] +#> ### [bt 2017-01-03 14:40:13]: Calculation finished!## Not run: ------------------------------------ # showLog(ids[1], reg = tmp) ## --------------------------------------------- diff --git a/docs/reference/submitJobs.html b/docs/reference/submitJobs.html index 2b350222..8eeccc0e 100644 --- a/docs/reference/submitJobs.html +++ b/docs/reference/submitJobs.html @@ -173,13 +173,13 @@Examp submitJobs(ids, resources = res, reg = tmp)
#># Retrive information about memory, combine with parameters info = ijoin(getJobStatus(reg = tmp)[, .(job.id, memory)], getJobPars(reg = tmp))#>print(info)#> job.id memory n p -#> 1: 1 51.1 1e+04 10 +#> 1: 1 51.3 1e+04 10 #> 2: 2 63.6 1e+05 10 #> 3: 3 56.3 1e+04 50 #> 4: 4 124.6 1e+05 50# Combine job info with results -> each job is aggregated using mean() ijoin(info, reduceResultsDataTable(fun = function(res) list(res = mean(res)), reg = tmp))#> job.id memory n p res -#> 1: 1 51.1 1e+04 10 0.4999599 +#> 1: 1 51.3 1e+04 10 0.4999599 #> 2: 2 63.6 1e+05 10 0.5006067 #> 3: 3 56.3 1e+04 50 0.4998562 #> 4: 4 124.6 1e+05 50 0.4999849diff --git a/vignettes/tikz_prob_algo_simple.png b/vignettes/tikz_prob_algo_simple.png new file mode 100644 index 00000000..c95ee7b1 Binary files /dev/null and b/vignettes/tikz_prob_algo_simple.png differ diff --git a/vignettes/tikz_prob_algo_simple.svg b/vignettes/tikz_prob_algo_simple.svg deleted file mode 100644 index bd75f9eb..00000000 --- a/vignettes/tikz_prob_algo_simple.svg +++ /dev/null @@ -1,579 +0,0 @@ - - - diff --git a/vignettes/tikz_prob_algo_simple.tex b/vignettes/tikz_prob_algo_simple.tex index 66fb0bf0..5787900c 100644 --- a/vignettes/tikz_prob_algo_simple.tex +++ b/vignettes/tikz_prob_algo_simple.tex @@ -1,4 +1,4 @@ -\documentclass[crop,tikz,convert={outext=.svg}]{standalone} +\documentclass[crop,tikz,convert]{standalone} \usetikzlibrary{shapes,matrix,positioning,chains,arrows,shadows,decorations.pathmorphing,fit,backgrounds} \begin{document} diff --git a/vignettes/v11_ExampleExperiment.Rmd b/vignettes/v11_ExampleExperiment.Rmd index 12c76b43..7f4b2e4d 100644 --- a/vignettes/v11_ExampleExperiment.Rmd +++ b/vignettes/v11_ExampleExperiment.Rmd @@ -99,7 +99,9 @@ getProblemIds() getAlgorithmIds() ``` The flow to define experiments is summarized in the following figure: - +```{r, echo=FALSE} +knitr::include_graphics("tikz_prob_algo_simple.png") +``` # Creating jobs