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| − | == j-perdue random links for 8/10/2018 ==
| + | See [[SW:Singularity:Examples]] |
| − | === Placeholder ===
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| − | To be added to SW:Singlularity:Examples or something.... just a placeholder for now to dump all my URLs at home for access at work:
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| − | https://github.com/singularityware/singularity/issues/1076
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| − | https://github.com/singularityware/singularity/issues/1165
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| − | http://singularity.lbl.gov/quickstart#build-images-from-scratch
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| − | https://hub.docker.com/_/fedora/
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| − | https://github.com/NIH-HPC/singularity-examples/blob/master/torch/Singularity.torch
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| − | https://www.sylabs.io/docs/
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| − | | |
| − | === history ===
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| − | | |
| − | * random notes from .bash_history on hprclab2
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| − | | |
| − | <pre>
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| − | [j-perdue@hprclab2 ~]$ history | grep docker | |
| − | 460 git clone https://github.com/fedora-cloud/docker-brew-fedora.git
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| − | 466 less prep-docker-brew-branch.sh
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| − | 468 ./prep-docker-brew-branch.sh 28
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| − | 470 sudo docker pull fedora:28
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| − | 472 sudo docker run --rm -ti fedora:28 bash
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| − | 484 sudo docker run -ti fedora:28 bash
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| − | 494 sudo docker run -ti fedora:28 bash
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| − | 495 man docker
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| − | 496 man docker-run
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| − | 497 sudo docker build --writable Fedora28.img fedora:28
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| − | 515 sudo singularity build --writable FedoraLatest.img docker://fedora:latest
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| − | 516 sudo singularity build --writable Fedora28.img docker://fedora:28
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| − | 523 # sudo singularity build --writable --size Fedora28.img docker://fedora:28
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| − | 541 history | grep docker
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| − | [j-perdue@hprclab2 ~]$ history | grep singularit | |
| − | 510 sudo singularity build --writable Fedora28.img fedora:28
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| − | 511 sudo singularity build --writable Fedora28.img fedora:27
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| − | 512 sudo singularity build --writable Fedora28.img
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| − | XXX sudo singularity shell --writable Fedora28-HPRCLAB.img
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| − | </pre>
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| − | | |
| − | === nearing in on objective ===
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| − | The objective in this case is a Fedora28-HPRCLAB.img file that has space for users to manuever around and install stuff:
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| − | # that we can provide to users, a Singularity .img file (self-contained), for them to update as needed (as root on their own workstations) that also runs on our clusters.
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| − | # is already populated with HPRCLAB RPMs
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| − | # has plenty of disk space for the user to add files (as non-root) while on the cluster
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| − | # Example below was created on HPRCLAB workstations.
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| − | Things not included yet include:
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| − | # setting mount/bind points for HPRC clusters
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| − | ==== Latest ====
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| − | | |
| − | * create a Singularity sandbox from one of Fedora's Docker images
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| − | <pre>
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| − | sudo singularity build --sandbox Fedora28-HPRCLAB.sandbox docker://fedora:28
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| − | </pre>
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| − | * create a list of packages to install into the image and place in /root. In this case we use the HPRCLAB/Fedora28 workstations current list of software. So on the workstation/host (not in the image):
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| − | <pre>
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| − | sudo su - # need root for redirect
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| − | rpm -qa --qf "%{NAME}\n" | sort > /root/rpmlist
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| − | </pre>
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| − | which results in something that looks like this:
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| − | <pre>
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| − | [root@hprclab4 ~]# head -5 rpmlist
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| − | a2ps
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| − | a52dec
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| − | aajohan-comfortaa-fonts
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| − | aalib-libs
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| − | aalto-xml
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| − | </pre>
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| − | Log out of root shell with exit/logout/Ctrl-D.
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| − | * open a sudo --writable shell in the sandbox (requires sudo for next steps)
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| − | <pre>
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| − | sudo singularity shell --writable Fedora28-HPRCLAB.sandbox/
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| − | </pre>
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| − | * Install the RPMFUSION repos (needed for below)
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| − | <pre>
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| − | dnf -y install\
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| − | https://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-28.noarch.rpm\
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| − | https://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-28.noarch.rpm
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| − | </pre>
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| − | * populate the sandbox with all the RPMs (we do them in groups at first in case there a problems and then do all to see what those problems were. (get a snack, take a walk... it can take awhile)
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| − | <pre>
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| − | for x in {a..z} ; do
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| − | dnf -y install `grep ^$x /root/rpmlist`
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| − | done
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| − | dnf -y install `cat /root/rpmlist`
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| − | </pre>
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| − | or maybe
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| − | <pre>
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| − | for x in `cat /root/rpmlist` ; do
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| − | dnf -y install $x
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| − | done
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| − | </pre>
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| − | There will still be packages that have "No match" due to not including the repos for them.
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| − | * add users (best done after populating with software in case anything added something to /etc/skel) '''ACTUALLY THIS LOOKS TO BE A BAD IDEA... SKIP FOR NOW'''
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| − | <pre>
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| − | useradd mynetid
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| − | </pre>
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| − | * once you are happy with the sandbox log out from it (logout/exit/Ctrl-D).
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| − | * To make an .img file that provides space for the user to work in (e.g. download/install software). These steps do not require sudo since they don't really create anything in the image. This example is for a 20GB /.
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| − | <pre>
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| − | singularity image.create Fedora28-HPRCLAB.img # create .img file
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| − | singularity image.expand -s 20480 Fedora28-HPRCLAB.img # expand to 20GB (works because there is no real filesystem yet [some ext3/4 systems seem to have a problem with expand once the image has filesystems?]... also, get another snack while you wait)
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| − | </pre>
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| − | * Now import the sandbox into the 20GB image (more snacks/time)
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| − | <pre>
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| − | sudo tar -cvf - -C Fedora28-HPRCLAB.sandbox/ . | sudo singularity image.import Fedora28-HPRCLAB.img # see the last/tar example in 'singularity image.import --help'
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| − | </pre>
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| − | * open a non-sudo shell and see if you can do "things" '''GIVING ME PROBLEMS AT THE MOMENT... I THINK DUE TO TO THE useradd ABOVE'''
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| − | <pre>
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| − | singularity shell Fedora28-HPRCLAB.img
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| − | </pre>
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