Last updated: 2019-05-27
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Knit directory: W_shredder/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | b70693c | lukeholman | 2019-05-20 | tweak |
| Rmd | 063e21f | lukeholman | 2019-05-20 | tweak |
| Rmd | 41aa9f7 | lukeholman | 2019-05-20 | tweak |
| html | 4d78c50 | lukeholman | 2019-05-06 | Build site. |
| Rmd | 8d839bb | lukeholman | 2019-05-06 | wflow_publish(files = "*") |
| html | 216445e | lukeholman | 2019-05-06 | Build site. |
| Rmd | 635d151 | lukeholman | 2019-05-06 | wflow_publish(files = "*") |
| html | 635d151 | lukeholman | 2019-05-06 | wflow_publish(files = "*") |
| Rmd | 1fca665 | lukeholman | 2019-04-26 | increase SLURM time, and writing |
| Rmd | 0ccc722 | Luke Holman | 2018-12-28 | change to 48h |
| Rmd | a587610 | Luke Holman | 2018-12-21 | bigger chunks |
| Rmd | e882e57 | Luke Holman | 2018-12-04 | single core for faster queueing |
| Rmd | 8a6ce50 | Luke Holman | 2018-12-03 | change resources |
| Rmd | 3b94528 | Luke Holman | 2018-12-03 | Tweaks |
| Rmd | ab69fc7 | Luke Holman | 2018-11-23 | fix else |
| Rmd | e60d0d1 | Luke Holman | 2018-11-23 | bug hunt |
| Rmd | b531be6 | Luke Holman | 2018-11-23 | Tweak handling of parameter set up |
| Rmd | e01c7fe | Luke Holman | 2018-11-22 | bug fix |
| Rmd | 6c2a74e | Luke Holman | 2018-11-22 | Added new slurm script to check paras |
| Rmd | 68469d2 | Luke Holman | 2018-11-22 | fix wd typo |
| Rmd | 79a4634 | Luke Holman | 2018-11-21 | Change counting of old parameters |
| Rmd | 7bf9997 | Luke Holman | 2018-11-20 | added print to find bug |
| Rmd | ed47ecc | Luke Holman | 2018-11-20 | go to single core again |
| Rmd | 9d2045c | Luke Holman | 2018-11-20 | Fix parameter file |
| Rmd | ee185ed | Luke Holman | 2018-11-19 | Extra params |
| Rmd | 64ce9e9 | Luke Holman | 2018-11-18 | Less memory? |
| Rmd | 0e180bc | Luke Holman | 2018-11-18 | Fix memory spec |
| Rmd | a9c7dfb | Luke Holman | 2018-11-16 | More memory pls |
| Rmd | 4c91977 | Luke Holman | 2018-11-16 | Get more computation time |
| Rmd | 4e630f4 | Luke Holman | 2018-11-15 | Make combine_results_files.R |
| Rmd | 2416673 | Luke Holman | 2018-11-15 | missed bracket |
| Rmd | 2c0e001 | Luke Holman | 2018-11-15 | Bug fix |
| Rmd | 4be43ee | Luke Holman | 2018-11-14 | fixing bugs |
| Rmd | b02f7d0 | Luke Holman | 2018-11-14 | more nodes pls |
| Rmd | 1cafc43 | Luke Holman | 2018-11-14 | Added fitness to density calculation |
| Rmd | fb9316c | Luke Holman | 2018-11-13 | Request 32GB memory |
| Rmd | 7560af7 | Luke Holman | 2018-11-13 | change node number |
| Rmd | b0fdeed | Luke Holman | 2018-11-13 | multicore again |
| Rmd | 8983cff | Luke Holman | 2018-11-13 | Fixed chunks |
| Rmd | 710d342 | Luke Holman | 2018-11-13 | cpu = 1 |
| Rmd | 5f4f83b | Luke Holman | 2018-11-13 | fixed job chunks |
| Rmd | 9440576 | Luke Holman | 2018-11-13 | change name |
| Rmd | de9e0ff | Luke Holman | 2018-11-13 | Added slurm capacity |
| Rmd | 99e93c7 | Luke Holman | 2018-11-03 | Many bug fixes with density dependence |
| html | 99e93c7 | Luke Holman | 2018-11-03 | Many bug fixes with density dependence |
# This bit is for the unimelb cluster, Spartan
working_directory <- "/data/projects/punim0243/W_shredder"
setwd(working_directory)source_rmd <- function(file){
options(knitr.duplicate.label = "allow")
tempR <- tempfile(tmpdir = ".", fileext = ".R")
on.exit(unlink(tempR))
knitr::purl(file, output = tempR, quiet = TRUE)
source(tempR, local = globalenv())
}
source_rmd("analysis/model_functions.Rmd")
custom_functions <- ls()This is defined in an R script that sets up the parameter space, and runs everything that has not already completed.
source("code/set_up_parameters.R")chunk_size <- 4000
cpus <- 1
sopt <- list(time = '168:00:00', # max run time per node in hours
mem = '32768') # 32GB memory across all 8 cores
chunks <- split(1:nrow(parameters),
ceiling(seq_along(1:nrow(parameters))/chunk_size))
number_of_chunks <- length(chunks)
sjob <- slurm_apply(
f = function(i) {
try(do_all_parameters(parameters[chunks[[i]],],
over_write = FALSE,
cores = cpus,
wd = working_directory))
},
params = data.frame(i = 1:length(chunks)),
add_objects = c("do_all_parameters",
"parameters", "cpus",
"working_directory",
"chunks", "number_of_chunks",
custom_functions),
jobname = 'W_shredder',
nodes = number_of_chunks,
cpus_per_node = cpus,
slurm_options = sopt)
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] tibble_2.0.99.9000 readr_1.1.1 rslurm_0.4.0
[4] Rcpp_1.0.1 reshape2_1.4.3 stringr_1.4.0
[7] tidyr_0.8.2 purrr_0.3.2 dplyr_0.8.0.1
loaded via a namespace (and not attached):
[1] knitr_1.22 whisker_0.3-2 magrittr_1.5
[4] workflowr_1.3.0 hms_0.4.2 tidyselect_0.2.5
[7] R6_2.4.0 rlang_0.3.4 plyr_1.8.4
[10] tools_3.5.1 xfun_0.6 git2r_0.23.0
[13] htmltools_0.3.6 yaml_2.2.0 rprojroot_1.3-2
[16] digest_0.6.18 assertthat_0.2.1 crayon_1.3.4
[19] fs_1.3.1 glue_1.3.1.9000 evaluate_0.13
[22] rmarkdown_1.10 stringi_1.4.3 compiler_3.5.1
[25] pillar_1.3.1.9000 backports_1.1.2 pkgconfig_2.0.2