Last updated: 2021-09-20
Checks: 2 0
Knit directory: misc/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
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Unstaged changes:
Modified: analysis/index.Rmd
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | da4d3fa | Dongyue Xie | 2021-09-20 | wflow_publish(“analysis/command.Rmd”) |
| html | 22ea1c8 | DongyueXie | 2020-09-23 | Build site. |
| Rmd | d2b54b1 | DongyueXie | 2020-09-23 | wflow_publish(c(“analysis/index.Rmd”, “analysis/genelength.Rmd”, |
| html | 53029fc | Dongyue Xie | 2020-01-15 | Build site. |
| Rmd | cfac861 | Dongyue Xie | 2020-01-15 | wflow_publish(“analysis/command.Rmd”) |
| html | 1313b6f | Dongyue Xie | 2019-12-12 | Build site. |
| Rmd | c07c0dc | Dongyue Xie | 2019-12-12 | wflow_publish(“analysis/command.Rmd”) |
cd $SCRATCH
htop: check login mode cpu use
Get compute node:
sinteractive --time=10:00:00 --mem=8G -c 4 -p mstephens --account=pi-mstephens
--exclusive:
squeue -u dyxie : see job status
squeue -p mstephens: see who’s using nodes.
scontrol show node=midway2-0437
squeue -p broadwl | less -S
export OPENLABS_NUM_THREADS=4: use 4 cpus to compute
Open another command window, login to midway2 then ssh midway2-0437, htop --user=dyxie monitor the computations on the other command window.
Use screen to back up screens.
nano myscript.R to write an R script.
module load R then Rscript myscript.R
sbatch myscript.sbatch
gzip -d file.gz or gunzip file.gz
head, less
transfer from my laptop to my home directory:
Single files: scp <some file> <CNetID>@midway2.rcc.uchicago.edu
Directories: scp -r <some dir> <CNetID>@midway2.rcc.uchicago.edu
To other directory:
scp -r <some dir> <CNetID>@midway2.rcc.uchicago.edu:/project2