Changes between Version 6 and Version 7 of Workshops/JobCheckpointing/Examples/R


Ignore:
Timestamp:
09/02/2026 03:46:59 PM (38 hours ago)
Author:
Carl Baribault
Comment:

Updated to tidyverse 4.6.1

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  • Workshops/JobCheckpointing/Examples/R

    v6 v7  
    2020 * [wiki://Workshops/JobCheckpointing/Examples#plot_progress.py plot_progress.py]
    2121
    22 2. Create your own version of the following R application script file '''checkpoint_signal_R.sh'''.
     222. Create your own version of the following R application script file '''checkpoint_signal_iter.R'''.
    2323
    2424{{{
    … …  
    7979
    8080
    81 3. Use the steps in the section [wiki:cypress/RunningRStudioWithSingularity#Alternativefortidyverse Alternative for tidyverse] for constructing a container image file '''tidyverse_latest.sif''' (or '''tidyverse_4.5.2.sif''' as in the following) for use with Singularity.
     813. Use the steps in the section [wiki:cypress/RunningRStudioWithSingularity#Alternativefortidyverse Alternative for tidyverse] for constructing a container image file '''tidyverse_latest.sif''' (or '''tidyverse_4.6.1.sif''' as in the following) for use with Singularity.
    8282
    83834. Install the required R package '''sigterm''' via the following, substituting your own writable R library directory for <R_lib_path>. See [wiki:cypress/InstallingRPackages Installing R Packages on Cypress] for more information on using a writable R library directory.
    … …  
    8686[tulaneID@cypress1 ~]$idev --partition=centos7
    8787[tulaneID@cypress01-XXX ~]$module load singularity/3.9.0
    88 [tulaneID@cypress01-XXX ~]$singularity shell tidyverse_4.5.2.sif
     88[tulaneID@cypress01-XXX ~]$singularity shell tidyverse_4.6.1.sif
    8989Singularity> Rscript --version # confirm Rscript is available
    90 Rscript (R) version 4.5.2 (2025-10-31)
    91 Singularity>Rscript -e "devtools::install_github('atheriel/sigterm', lib='<R_lib_path>')"
     90Rscript (R) version 4.6.1 (2026-06-24)
     91# install required remotes package
     92Singularity> Rscript -e "install.packages('remotes', lib=.libPaths()[3], repos='https://cloud.r-project.org')"
     93Singularity>Rscript -e "remotes::install_github('atheriel/sigterm', lib=.libPaths()[3])"
    9294Singularity>exit # exit the container
    9395[tulaneID@cypress01-XXX ~]$exit # exit the interactive session
    … …  
    9799
    98100{{{
    99 [tulaneID@cypress1 ~]$APP_CMD="singularity exec tidyverse_4.5.2.sif Rscript checkpoint_signal_iter.R" \
     101[tulaneID@cypress1 ~]$APP_CMD="singularity exec tidyverse_4.6.1.sif Rscript checkpoint_signal_iter.R" \
    100102MODULE_LIST="singularity/3.9.0" \
    101103CKPT_PATH=state_iter_r.txt \