diff --git a/README.Rmd b/README.Rmd index e211765..d1d8a5a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -7,7 +7,7 @@ output: [![DOI](http://joss.theoj.org/papers/10.21105/joss.01493/status.svg)](https://doi.org/10.21105/joss.01493) [![R CI release](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml/badge.svg)](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml) -[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/slurmR) +[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/USCbiostats/slurmR) [![CRAN status](https://www.r-pkg.org/badges/version/slurmR)](https://CRAN.R-project.org/package=slurmR) [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/slurmR)](https://cran.r-project.org/package=slurmR) [![status](https://tinyverse.netlify.com/badge/slurmR)](https://CRAN.R-project.org/package=slurmR) diff --git a/README.md b/README.md index d521c85..d8bca88 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![DOI](http://joss.theoj.org/papers/10.21105/joss.01493/status.svg)](https://doi.org/10.21105/joss.01493) [![R CI release](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml/badge.svg)](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml) -[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/slurmR) +[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/USCbiostats/slurmR) [![CRAN status](https://www.r-pkg.org/badges/version/slurmR)](https://CRAN.R-project.org/package=slurmR) [![CRAN @@ -122,10 +122,10 @@ We can use the function `Slurm_lapply` to distribute computations ``` r ans <- Slurm_lapply(x, mean, plan = "none") # Warning in normalizePath(file.path(tmp_path, job_name)): path[1]="/home/ -# george/Documents/development/slurmR/slurmr-job-27165393bf6bf": No such file or +# george/Documents/development/slurmR/slurmr-job-2855312d50503": No such file or # directory # Warning: [submit = FALSE] The job hasn't been submitted yet. Use sbatch() to submit the job, or you can submit it via command line using the following: -# sbatch --job-name=slurmr-job-27165393bf6bf /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/01-bash.sh +# sbatch --job-name=slurmr-job-2855312d50503 /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/01-bash.sh Slurm_clean(ans) # Cleaning after you ``` @@ -137,10 +137,10 @@ get more info, we can set the verbose mode on opts_slurmR$verbose_on() ans <- Slurm_lapply(x, mean, plan = "none") # Warning in normalizePath(file.path(tmp_path, job_name)): path[1]="/home/ -# george/Documents/development/slurmR/slurmr-job-27165393bf6bf": No such file or +# george/Documents/development/slurmR/slurmr-job-2855312d50503": No such file or # directory # -------------------------------------------------------------------------------- -# [VERBOSE MODE ON] The R script that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/00-rscript.r and has the following contents: +# [VERBOSE MODE ON] The R script that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/00-rscript.r and has the following contents: # -------------------------------------------------------------------------------- # .libPaths(c("/home/george/R/x86_64-pc-linux-gnu-library/4.2", "/usr/local/lib/R/site-library", "/usr/lib/R/site-library", "/usr/lib/R/library")) # message("[slurmR info] Loading variables and functions... ", appendLF = FALSE) @@ -168,7 +168,7 @@ ans <- Slurm_lapply(x, mean, plan = "none") # sprintf("%s/%s/%s", tmp_path, job_name, type) # } # TMP_PATH <- "/home/george/Documents/development/slurmR" -# JOB_NAME <- "slurmr-job-27165393bf6bf" +# JOB_NAME <- "slurmr-job-2855312d50503" # # # The -tcq- function is a wrapper of tryCatch that on error tries to recover # # the message and saves the outcome so that slurmR can return OK. @@ -195,19 +195,19 @@ ans <- Slurm_lapply(x, mean, plan = "none") # } # message("done loading variables and functions.") # tcq({ -# INDICES <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/INDICES.rds") +# INDICES <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/INDICES.rds") # }) # tcq({ -# X <- readRDS(sprintf("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/X_%04d.rds", ARRAY_ID)) +# X <- readRDS(sprintf("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/X_%04d.rds", ARRAY_ID)) # }) # tcq({ -# FUN <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/FUN.rds") +# FUN <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/FUN.rds") # }) # tcq({ -# mc.cores <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/mc.cores.rds") +# mc.cores <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/mc.cores.rds") # }) # tcq({ -# seeds <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/seeds.rds") +# seeds <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/seeds.rds") # }) # set.seed(seeds[ARRAY_ID], kind = NULL, normal.kind = NULL) # tcq({ @@ -217,24 +217,24 @@ ans <- Slurm_lapply(x, mean, plan = "none") # mc.cores = mc.cores # ) # }) -# saveRDS(ans, sprintf("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/03-answer-%03i.rds", ARRAY_ID), compress = TRUE) +# saveRDS(ans, sprintf("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/03-answer-%03i.rds", ARRAY_ID), compress = TRUE) # message("[slurmR info] job-status: OK.\n") # -------------------------------------------------------------------------------- -# The bash file that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/01-bash.sh and has the following contents: +# The bash file that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/01-bash.sh and has the following contents: # -------------------------------------------------------------------------------- # #!/bin/sh -# #SBATCH --job-name=slurmr-job-27165393bf6bf -# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/02-output-%A-%a.out +# #SBATCH --job-name=slurmr-job-2855312d50503 +# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/02-output-%A-%a.out # #SBATCH --array=1-2 -# #SBATCH --job-name=slurmr-job-27165393bf6bf +# #SBATCH --job-name=slurmr-job-2855312d50503 # #SBATCH --cpus-per-task=1 # #SBATCH --ntasks=1 -# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/00-rscript.r +# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/00-rscript.r # -------------------------------------------------------------------------------- # EOF # -------------------------------------------------------------------------------- # Warning: [submit = FALSE] The job hasn't been submitted yet. Use sbatch() to submit the job, or you can submit it via command line using the following: -# sbatch --job-name=slurmr-job-27165393bf6bf /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/01-bash.sh +# sbatch --job-name=slurmr-job-2855312d50503 /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/01-bash.sh Slurm_clean(ans) # Cleaning after you ``` @@ -381,15 +381,15 @@ ans <- Slurm_lapply(1:10, mean, plan = "none", preamble = "module load pandoc") # Printing out the bashfile cat(readLines(ans$bashfile), sep = "\n") # #!/bin/sh -# #SBATCH --job-name=slurmr-job-27165393bf6bf -# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/02-output-%A-%a.out +# #SBATCH --job-name=slurmr-job-2855312d50503 +# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/02-output-%A-%a.out # #SBATCH --array=1-2 -# #SBATCH --job-name=slurmr-job-27165393bf6bf +# #SBATCH --job-name=slurmr-job-2855312d50503 # #SBATCH --cpus-per-task=1 # #SBATCH --ntasks=1 # module load gcc/6.0 # module load pandoc -# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/00-rscript.r +# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/00-rscript.r Slurm_clean(ans) # Cleaning after you ```