start from vagrant box bento/ubuntu-16.04

[alaindomissy]

Replacing the initial vagrant box from "ubuntu/trusty64" with "ubuntu/xenial64" was a great move :

• xenial is the latest ubuntu long term support release,
• also this avoids an issue which is specific to older versions of ubuntu : when running multiprocessing python inside the image the OS needs to create temporary files in /run/shm and /run/lock and this does not work unless the /etc/singularity/singularity.conf is modified with an additional line: "bind path = /run" )
  However when testing more, I found that box the ubuntu/xenial64 does not have a system python2 installed, just a python3, Because of that , several steps fail unless python2 is installed: some python scripts have a she-bang line like this:
  #!/usr/bin/env python and in absence of python2 , the python command is not found. So this is another hassle which would need to be documented in the instructions
  The solution I found is to use an alternative ubuntu1604 box from the bento project : http://chef.github.io/bento/ Bento is an impressive project and their vagrant boxes are well made and well regarded. https://atlas.hashicorp.com/bento

[vsoch]

should this guy be bento/ubuntu-16.04 too?

[vsoch]

hey @alaindomissy let me know if you want to fix this - I'd be happy to do a quick PR to change it on my end, since it's pretty small. Let me know!

[alaindomissy]

Good catch. I fixed it. Thanks

[vsoch]

I'm a huge fan of hasicorp! I know almost nothing about them, but I especially like Packer, Vagrant, and some of the other tools they have created.

[alaindomissy]

There is a docker Packer builder : https://www.packer.io/docs/builders/docker.html
Would a singularity Packer builder be feasible / a good idea ? :-)

[vsoch]

yes, definitely! I'll take a look at what constitutes a builder. I've been using packer for a custom deployment of a builder to google cloud, but we could equally use to make singularity locally. Thanks for testing and fixing the mac doc! Without Mac, I am badly in need of this help :)

[alaindomissy]

My pleasure. Did you notice my comment in slack : I made a Vagrant Box with has singularity pre-installed
https://atlas.hashicorp.com/alaindomissy/boxes/singularity-2.2.99
This can simplify the installation procedure for mac users :

1) first install vagrant
             https://www.vagrantup.com/docs/installation
1.5)  if on windows, also install git, as this is the easiest way to have ssh (which we need)
2) then create a new directory in your home and navigate to it: (your syntax may vary)
             mkdir -p /Users/me/testing-singularity-vagrant-box
              cd  /Users/me/testing-singularity-vagrant-box
3) then run these 2 commands to download and start the VM:
            vagrant init alaindomissy/singularity-2.2.99
            vagrant up --provider virtualbox
4) to enter the VM run:
            vagrant ssh
5) download your favorite container from singularity-hub:
             singularity pull shub://vsoch/hello-world:master
6) Play with it:
             chmod +x bunchofnumbers.img
             ./bunchofnumbers.img

Also it should also work for windows users
( there are no instructions for windows at the moment at : http://singularity.lbl.gov/install-windows )

I'd be happy to rename, relocate, document etc... if that could be useful for the Singularity project.....

[vsoch]

I just tested - it works great! (sorry for delay, had a few issues with my kernel). How does it work to create a box on Atlas? Is it a service you need to pay for? I think this would be fantastic to provide for Singularity - especially for version 2.3 (if you saw is being released next Wednesday!) If this is something that we are able to make a singularityware account to serve the image from, I think that would be fantastic. If that's not possible, and you don't mind maintaining, then we can definitely use this uri. What do you think?

[alaindomissy]

Creating a box on Atlas is very easy to do and it is free: you create an account, fill up a little form to say what you want to share, and you upload your .box file. This box (https://atlas.hashicorp.com/alaindomissy/boxes/singularity-2.2.99) I made "manually" following the instructions we now have for mac users (with the bento box). Then I followed the "package the box" instructions form this blog: https://blog.engineyard.com/2014/building-a-vagrant-box There is another (cleaner) way which is automated and based on a "Packerfile" (or something like that) but I have not tried that (yet). I am very happy if you want to rename and republish the box under a Singularity account. It is relatively straightforward but let me know if I can help. I did see the planned release for Wed! Yay!! I have been testing out hoping to find out soon enough in case we have any issue.... especially the new feature to pull singularity hub feature. I am still trying to make this work for our next singularity+cwl pipeline to be released very soon.... I do have trouble with getting a particular container automatically build on Singularity-hub. I am still not sure if its a mistake in my setup... Is there a more suitable then here to ask singularity-hub questions ? Thanks!

…

On Fri, May 26, 2017 at 10:55 PM, Vanessa Sochat ***@***.***> wrote: I just tested - it works great! (sorry for delay, had a few issues with my kernel). How does it work to create a box on Atlas? Is it a service you need to pay for? I think this would be fantastic to provide for Singularity - especially for version 2.3 (if you saw is being released next Wednesday!) If this is something that we are able to make a singularityware account to serve the image from, I think that would be fantastic. If that's not possible, and you don't mind maintaining, then we can definitely use this uri. What do you think? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#80 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEVrE5t-XvqTLGyB27Fb7cJY1qPSuxiks5r97rsgaJpZM4NnK2W> .

-- --Alain 619-884-5450

[alaindomissy]

I renamed my account to singularityware, so the link to the vagrantbox is now:
https://atlas.hashicorp.com/singularityware/boxes/singularity-2.2.99/
and people can download it with:
vagrant init singularityware/singularity-2.2.99
Is that ok ?
I see that I can add you to the singularityware account if you create a username on https://atlas.hashicorp.com/vagrant
Let me know if you prefer setting this up another way

[vsoch]

Hey @alaindomissy ! Apologies for the delay, I went for a run this morning :) I just made an account (or I believe it's called "organization") called vanessa, I'm not sure if this link will work for you but this seems to be one of it's bases:

https://atlas.hashicorp.com/settings/organizations/vanessa

Can you find me on there and add to Singularityware? Then we can add this to the docs! This was a really great idea - it's really much easier using vagrant with already to go images than coming up with a new one on the fly.

[vsoch]

oh! And @alaindomissy if you want to point me at the container you are having trouble building on singularity hub, I'd be glad to look into it. If it's an issue of using the older singularity, then that will be resolved when I update the builders on Wednesday. If not, I'll help you figure it out sooner. For future / any and all help that you need with Singularity Hub, please post on the repo here! https://github.com/singularityhub/singularityhub.github.io/issues

[alaindomissy]

Hi @vsoch , your vanessa hashicorp account is now added to the owners team for the singularityware organisation on atlas :-)
I posted this singularity-hub github issue regarding my troublesome singularity container building
Thanks!

[vsoch]

awesome! I just added the singularityware vagrant box to the docs page, take a look and let me know if everything looks ok: https://github.com/singularityware/singularityware.github.io/blob/docs/2.3/pages/docs/install/install-mac.md