Test running RStudio on Nimbus VMs

[georgiesamaha]

Check RStudio can run on Nimbus VMs without issue. If any issues, create new ticket.

[nandan75]

• The RServer was run using the updated RStudio singularity containers as documented at https://github.com/Sydney-Informatics-Hub/rnaseqOct23_Testing/blob/Nandan/Scripts/Day2/Runtime-testing.md#run-the-singularity-container-to-start-the-rstudio-server

• The Rmarkdown file https://github.com/Sydney-Informatics-Hub/rnaseqOct23_Testing/blob/Nandan/Scripts/Day2/rnaseq_DE_analysis_Day2.Rmd was executed and it ran successfully.

  • The updated R packages were tested for loading.
  • The R script which was modified at a few steps was tested
  • In summary the R script for the downstream analysis with plot generation works fine

• The loop unavailable error pops up and can be solved locally using the workaround as document ed here - https://github.com/Sydney-Informatics-Hub/rnaseqOct23_Testing/blob/Nandan/Scripts/Day2/Runtime-testing.md#intermittent-problems-when-running-the-rserver

  • This needs to get solved for the instance in general.

[georgiesamaha]

2022 run

For 2022 workshop we ran RStudio Singularity image from CVMFS

Ran successfully with:

PASSWORD='abc' singularity exec \
    -B /home/ubuntu/rnaseq23/day2_RStudio/working_dir/rstudio-server:/var/lib/rstudio-server \
    -B /home/ubuntu/rnaseq23/day2_RStudio/working_dir/rstudio-server:/var/run/rstudio-server \
    -B /home/ubuntu/rnaseq23/day2_RStudio/working_dir:/home \
    /cvmfs/containers.biocommons.aarnet.edu.au/r/n/rnaseq_rstudio.sif \
    rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user ubuntu

To quit we ran:

CTRL + C

2023 run

This year, when running an updated version of RStudio Singularity image (stored locally on VM)

 PASSWORD='abc' singularity exec \
-B /home/ubuntu/rnaseq23/day2_RStudio/working_dir/rstudio-server:/var/lib/rstudio-server \
-B /home/ubuntu/rnaseq23/day2_RStudio/working_dir/rstudio-server:/var/run/rstudio-server \
-B /home/ubuntu/rnaseq23/day2_RStudio/working_dir:/home \
rstudio_4.1.0.wCP.sif \
rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user ubuntu

Intermittently receiving this error:

FATAL:   container creation failed: mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error: while mounting image /proc/self/fd/3: failed to find loop device: could not attach image file to loop device: no loop devices available

Current workaround:

1. Check if the loop module is loaded:

lsmod | grep loop

2. If the loop module is not listed, you can load it using:

sudo modprobe loop

3. Verify the loop devices availability:

sudo losetup -f

This issue has been observed intermittently on current bioimage when running Singularity, RStudio, and Nextflow. Contacting Pawsey Helpdesk for support.