Difference between revisions of "Note about container"

Revision as of 17:24, 31 January 2018

• warning
  • if you are running singularity-2.4 on a centos7.2 host, you could have kernel panic if you use ROOT TMD5 and load your host dir

• installation
  • refer to installation instruction and the latest version is recommend.
  • singularity-2.4 can run singularity-2.3 images and has many new features and we should use it instead of 2.3 whenever possible
  • On redhat-kind linux, build an rpm first and install it.
  • On windows and Mac, the official way is cumbersome and not good enough to run image with graphic. The better alternative is to use a linux virtual machine. (see below)

• the linux virtual machine to run singularity
  • (It's nice, but not a must, to run singularity image in shared folder because it keeps the virtual machine size small. Vmware's shared folder doesn't work for this, but virtualbox does)
  • download and install virtualbox https://www.virtualbox.org/wiki/Downloads
  • download the linux virtual machine at http://www.phy.duke.edu/~zz81/CentOS7_x86_64_20171030.ova (a centos7.4 with latest on 20171030 and singularity-2.4 installed)
  • import the virtual machine into virtualbox, set up a shared folder with name "share" in setting and put the singularity image into the shared folder on host
  • boot up the linux virtual machine and login with both "root" and user "user" password are "111111"
  • install the latest singularity or a particular version you want
  • mount the shared folder "sudo mount -t vboxsf -o uid=$uid,gid=$gid share share" and use /home/user/share" as your working dir, then you can test singularity

• singularity at jlab
  • jlab farm and ifarm has singularity-2.3.1 installed as default
  • on ifarm1402, you can also test singularity-2.4.2 and singularity-2.3.2 by using module with "module load singularity-2.4.2" or "module load singularity-2.3.2" and "module rm singularity-2.4.2" or "module rm singularity-2.3.2". They are not on farm nodes, so we can't run jobs yet

• test singularity
  • cd some_where_with_enough_space
  • "setenv http_proxy http://jprox.jlab.org:8082" "setenv https_proxy http://jprox.jlab.org:8082" if you are on jlab ifarm
  • setenv SINGULARITY_CACHEDIR ./ (change cache dir from default ~/.singularity, MUST do at jlab ifarm with very limited space at hom)
  • singularity pull docker://godlovedc/lolcow
  • singularity run lolcow.img
  • setenv PYTHONHTTPSVERIFY 0 (sometime needed to bypass singularity hub certificate check)
  • singularity pull shub://GodloveD/lolcow
  • singularity run GodloveD-lolcow-master-latest.simg

questions and comments should go to Zhiwen Zhao zwzhao at jlab.org