[OOD-users] R Server

Fri Mar 2 08:42:21 EST 2018

Obtaining or compiling proot is a headache. We managed to snag the precompiled binary before the mirrors went down last year. If you would like a copy of x86_64 binary feel free to send me a private msg at jnicklas at osc.edu.

The reason we use proot is because RStudio Server is hardcoded to use predefined directories under /tmp. This is a problem in a multi-user environment as ownership and file permissions will wreak havoc when multiple users try to launch RStudio Server. Through the magic of proot we are able to perform a "fake" bind-mount for /tmp as the user, so that RStudio Server will use a different /tmp directory.

This is also resolved with Singularity as you can setup "real" bind-mounts, and it won't have the overhead introduced by proot which scans and intercepts system calls.

--
Jeremy Nicklas
Web and Interface App Engineer
Ohio Supercomputer Center (OSC)<https://osc.edu/>
A member of the Ohio Technology Consortium<https://oh-tech.org/>
1224 Kinnear Road, Columbus, Ohio 43212
Office: (614) 292-6739<tel:+16142926739> • Mobile: (614) 316-6428<tel:+16143166428> • Fax: (614) 292-7168<tel:+16142927168>
jnicklas at osc.edu<mailto:jnicklas at osc.edu>

Learn more about OSC at https://osc.edu<https://osc.edu/>
________________________________
From: OOD-users [ood-users-bounces at lists.osc.edu] on behalf of Shawn Doughty [shawn.doughty at tufts.edu]
Sent: Thursday, March 01, 2018 5:59 PM
To: User support mailing list for Open OnDemand
Subject: Re: [OOD-users] R Server

Has anyone managed to get a safe copy of the binary or tarball for proot? Every time I've ever gone to the site the download section is in the wrong language and it just doesn't look like something one should be accessing.

Ideas?

On Tue, Feb 27, 2018 at 12:44 PM, Doughty, Shawn <Shawn.Doughty at tufts.edu<mailto:Shawn.Doughty at tufts.edu>> wrote:
Jerey, Excellent, thanks for the information. Tufts will be happy to test out the rpms. In the meantime I try the solutions you suggested.
Kevin, I've found the upgrade process to 1.2 and 1.3 to be 99% glitch free. The only major issue was on my end after messing up file permissions on the OOD source tree and then rsyncing those to the destination This made a couple of the apps break until I noticed the permission error in nginx log files.

On Tue, Feb 27, 2018 at 8:50 AM, Nicklas, Jeremy <jnicklas at osc.edu<mailto:jnicklas at osc.edu>> wrote:
Hi Shawn,

> So far I get "no implicit conversion of Hash into Array" when submitting the job.

If you copied the source from OSC's "bc_osc_rstudio_server" Interactive App:

https://github.com/OSC/bc_osc_rstudio_server/

then it sounds like your "submit.yml.erb" might have PBS/Torque specific references in it (this is what OSC uses). You should probably copy your "submit.yml.erb" that you used in your Jupyter app.

> Has anyone managed to get R Server working?

A couple centers have got RStudio Server working, although caution should be taken if you use OSC's "bc_osc_rstudio_server" Interactive App as it takes advantage of some features in the latest Dashboard app that aren't present in the OnDemand 1.2 release.

That leaves you with three options:

1. Manually update the Dashboard code from the GitHub repo, or wait until OnDemand 1.3 release in March
2. Volunteer to install the beta RPM we are currently developing
3. Modify the "bc_osc_rstudio_server" app so it works with the current Dashboard
  - I believe this means replacing "$(find_port ${host})" with just "$(find_port)" in the template files
  - Also, removing the "template/after.sh.erb" since it calls "wait_until_port_used" which doesn't exist yet

Also, you will need to install the dependencies on the compute nodes (see README.md). I believe both HPC centers went the route of using a Singularity image.

--
Jeremy Nicklas
Web and Interface App Engineer
Ohio Supercomputer Center (OSC)<https://osc.edu/>
A member of the Ohio Technology Consortium<https://oh-tech.org/>
1224 Kinnear Road, Columbus, Ohio 43212
Office: (614) 292-6739<tel:+16142926739> • Mobile: (614) 316-6428<tel:+16143166428> • Fax: (614) 292-7168<tel:+16142927168>
jnicklas at osc.edu<mailto:jnicklas at osc.edu>

Learn more about OSC at https://osc.edu<https://osc.edu/>
________________________________
From: OOD-users [ood-users-bounces at lists.osc.edu<mailto:ood-users-bounces at lists.osc.edu>] on behalf of Shawn Doughty [shawn.doughty at tufts.edu<mailto:shawn.doughty at tufts.edu>]
Sent: Monday, February 26, 2018 8:56 PM
To: User support mailing list for Open OnDemand
Subject: [OOD-users] R Server

Hi,

Has anyone managed to get R Server working? I know it is not officially supported until the next release...  We have jupyter and jupyterlab working with pilot users (way cool!) and they are now clamoring to test R Server... and Matlab.

So far I get "no implicit conversion of Hash into Array" when submitting the job.

--
Shawn G. Doughty
Senior Research Technology Specialist, Research Technology
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville, MA 02144
617-627-5462<tel:(617)%20627-5462>
http://it.tufts.edu/<https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f>

--
Shawn G. Doughty
Senior Research Technology Specialist, Research Technology
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville, MA 02144
617-627-5462<tel:(617)%20627-5462>
http://it.tufts.edu/<https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f>

--
Shawn G. Doughty
Senior Research Technology Specialist, Research Technology
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville, MA 02144
617-627-5462
http://it.tufts.edu/<https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f>
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