[OOD-users] R Server

[Shawn Doughty]

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


On Fri, Mar 2, 2018 at 12:22 PM, Shawn Doughty <capsaicin420 at gmail.com>
wrote:

> 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>
>>
>
>


-- 
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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