[OOD-users] R Server

Fri Mar 2 12:22:46 EST 2018

Hi everyone, thanks for all your help. RStudio is now working and I'll
unleash users on it to test.

--
Shawn G. Doughty

On Fri, Mar 2, 2018 at 11:44 AM, Kevin Manalo <kmanalo at jhu.edu> wrote:

> Brian,
>
>
>
> Thanks for putting this out there! I have local static binaries but this
> is helpful.
>
>
>
> -Kevin
>
>
>
> *From: *OOD-users <ood-users-bounces at lists.osc.edu> on behalf of
> "McMichael, Brian" <bmcmichael at osc.edu>
> *Reply-To: *User support mailing list for Open OnDemand <
> ood-users at lists.osc.edu>
> *Date: *Friday, March 2, 2018 at 10:08 AM
> *To: *User support mailing list for Open OnDemand <ood-users at lists.osc.edu
> >
> *Subject: *Re: [OOD-users] R Server
>
>
>
> I forked the PRoot repo last year and added the static binaries to the
> bin/ folder of the repo.
>
>
>
> It’s available here:
>
>
>
> https://github.com/brianmcmichael/PRoot
>
>
>
>
>
> *Brian L. McMichael*
> Web and Interface Applications 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) 292-8091
>
> bmcmichael at osc.edu
>
>
>
>
>
>
>
>
>
> *From:* OOD-users [mailto:ood-users-bounces+bmcmichael=osc.edu at lists.osc.
> edu] *On Behalf Of *Nicklas, Jeremy
> *Sent:* Friday, March 2, 2018 8:42 AM
> *To:* User support mailing list for Open OnDemand
> *Subject:* Re: [OOD-users] R Server
>
>
>
> 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 <+16142926739> • Mobile: (614) 316-6428
> <+16143166428> • Fax: (614) 292-7168 <+16142927168>
> jnicklas at osc.edu
>
> Learn more about OSC at 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>
> 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> 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 <+16142926739> • Mobile: (614) 316-6428
> <+16143166428> • Fax: (614) 292-7168 <+16142927168>
> jnicklas at osc.edu
>
> Learn more about OSC at https://osc.edu
> ------------------------------
>
> *From:* OOD-users [ood-users-bounces at lists.osc.edu] on behalf of Shawn
> Doughty [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 <(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 <(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 <(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>
>
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