- I have now updated to Singularity v3.5.2.
- I see no symlink to /usr/share/zoneinfo/… when I run the ls -l command. i.e. I see only a file:
Singularity> ls -l /etc/localtime
-rw-r–r-- 2 root root 2197 Sep 26 21:34 /etc/localtime
Singularity> cat /etc/redhat-release
CentOS Linux release 7.6.1810 (Core)
Singularity> A cat of the /etc/localtime file reveals (last line) :
AEST-10AEDT,M10.1.0,M4.1.0/3
Singularity> stat /etc/localtime
File: ‘/etc/localtime’
Size: 2197 Blocks: 8 IO Block: 4096 regular file
Device: 802h/2050d Inode: 1914324 Links: 2
Access: (0644/-rw-r–r--) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2020-03-04 13:54:02.781566605 +1100
Modify: 2019-09-26 21:34:09.000000000 +1000
Change: 2019-11-19 13:53:06.189162281 +1100
Running Rstudio from within OOD logs the following:
cat “output.log”
Script starting…
Waiting for RStudio Server to open port 45478…
- echo ‘Starting up rserver…’
Starting up rserver… - singularity run -B /tmp/tmp.ujSIvTJhJe:/tmp /config/binaries/singularity/containers_devel/rserver-launcher-centos7.simg --www-port 45478 -
-auth-none 0 --auth-pam-helper-path /home/bioinf/ondemand/data/sys/dashboard/batch_connect/dev/RStudio/output/e2fc0b08-15f7-418c-b16f-e88815
048e3a/bin/auth --auth-encrypt-password 0 --rsession-path /home/bioinf/ondemand/data/sys/dashboard/batch_connect/dev/RStudio/output/e2fc0b08
-15f7-418c-b16f-e88815048e3a/rsession.sh
ESC[33mWARNING:ESC[0m Skipping mount /etc/localtime [binds]: /etc/localtime doesn’t exist in container - echo ‘Singularity as exited…’
Singularity as exited…
Timed out waiting for RStudio Server to open port 45478!
Cleaning up…
Changes made to script.sh are as follows. nothing else has been changed.
Additional environment which could be moved into a module
Change these to suit
export RSTUDIO_SERVER_IMAGE="/config/binaries/singularity/containers_devel/rserver-launcher-centos7.simg"
export SINGULARITY_BINDPATH="/etc,/media,/mnt,/opt,/srv,/usr,/var"
export PATH="$PATH:/usr/lib/rstudio-server/bin"
export SINGULARITYENV_PATH="$PATH"
In Singularity 3.5.x it became necessary to explicitly pass LD_LIBRARY_PATH
to the singularity process
export SINGULARITYENV_LD_LIBRARY_PATH="$LD_LIBRARY_PATH"
module load singularity/3.5.2
module load R/3.6.0
Hmmm… I will try the --debug option…