FORUMR keeps being killed when loading Bioconductor packages
Karen Gonçalves asked 2 months ago



I am running R on cedar soft.mugqic (/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/) and when I try to load “GenomicFeatures”, “GenomicAlignments” or “Rsamtools”, it starts fine loading the dependencies but finishes with this:
This is after library(“Rsamtools”)
“/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/lib64/R/bin/exec.wrap/R: line 1: 58085 Killed /cvmfs/soft.mugqic/yum/centos7/1.0/lib64/ld-linux-x86-64.so.2 –library-path /cvmfs/soft.mugqic/yum/centos7/1.0/usr/local/c3g/rpm/usr/lib64:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/local/c3g/compile/lib:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/local/lib64:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/lib64:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/lib:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/lib64/mysql:/cvmfs/soft.mugqic/yum/centos7/1.0/lib64/mysql:/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/lib64/R/lib /cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/lib64/R/bin/exec/R ${args} ${@}

This after library(“GenomicFeatures”)
“Welcome to Bioconductor
Vignettes contain introductory material; view with
‘browseVignettes()’. To cite Bioconductor, see
‘citation(“Biobase”)’, and for packages ‘citation(“pkgname”)’.
/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/lib64/R/bin/exec.wrap/R: line 1: 62945 Killed /cvmfs/soft.mugqic/yum/centos7/1.0/lib64/ld-linux-x86-64.so.2 –library-path /cvmfs/soft.mugqic/yum/centos7/1.0/usr/local/c3g/rpm/usr/lib64:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/local/c3g/compile/lib:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/local/lib64:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/lib64:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/lib:/cvmfs/soft.mugqic/yum/centos7/1.0/usr/lib64/mysql:/cvmfs/soft.mugqic/yum/centos7/1.0/lib64/mysql:/cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/lib64/R/lib /cvmfs/soft.mugqic/CentOS6/software/R_Bioconductor/R_Bioconductor-3.5.3_3.8/lib64/R/bin/exec/R ${args} ${@}”

flefebvre Staff replied 2 months ago

Hi Karen, can you describe in more details what you are doing (commands or submission script)? Are you trying to load a large file to memory?

I am not able to reproduce the error, e.g.

module load mugqic/R_Bioconductor/3.5.3_3.8 && R -e “library(GenomicFeatures)”

Works fine on cedar1 at the moment.

Karen Gonçalves replied 2 months ago

I started a interactive job. then did this
export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6
module use $MUGQIC_INSTALL_HOME/modulefiles
loaded R and opened it and ran the library command.
module add mugqic/R_Bioconductor/3.5.1_3.7 # I also tried other versions
R
library(“AnyOfTheOnesISaidBefore”)
## and see the error

flefebvre Staff replied 2 months ago

Ok thank you, there is actually this problem on beluga as well. The maintainers of the mugqic software stack are on it, I will open a ticket with them for you.

1 Answers
flefebvre Staff answered 2 months ago



Hi Karen, the solution is to request an interactive job with more memory, the default is 256Mb which is not even sufficient to just load the packages. I tried with –mem=20G -N 1 -n 6 and it worked fine.