R devel - Dec 2019 - running R with users home dirs on a shared filesystems

Hi guys,

I want to ask devel for who knows better - having multiple
nodes serving users home dirs off the same shared network
filesystem : are there any precautions or must-dos &
must-donts in order to assure healthy and efficient parallel
Rs running simultaneously - and I don't mean obvious stuff,
I'm rather asking about R's internals & environment.

simple example: three nodes mount a NFS share and users on
all three nodes run R simultaneously.

many thanks, L.

User home is not used by R directly, so it is really up to whatever package/code
may be using user home. In our setup we have all machines using NFS mounted
homes for years. From experience the only thing to watch for are packages that
use their own cache directories in $HOME instead of tempdir() - it is
technically against CRAN policies but we have seen it in the wild.

Cheers,
Simon


> On Dec 13, 2019, at 1:36 PM, lejeczek via R-devel <r-devel at
r-project.org> wrote:
> 
> Hi guys,
> 
> I want to ask devel for who knows better - having multiple
> nodes serving users home dirs off the same shared network
> filesystem : are there any precautions or must-dos &
> must-donts in order to assure healthy and efficient parallel
> Rs running simultaneously - and I don't mean obvious stuff,
> I'm rather asking about R's internals & environment.
> 
> simple example: three nodes mount a NFS share and users on
> all three nodes run R simultaneously.
> 
> many thanks, L.
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Another thing to avoid are having multiple processes simultaneously access
single sqlite3 database stored on NFS mount.

From sqlite manual: ?Your best defense is to not use SQLite for files on a
network filesystem<https://www.sqlite.org/lockingv3.html>?

So, if you configuring RStudio Server, make sure to follow advice about RStudio
Package Manager<https://docs.rstudio.com/rspm/admin/database.html>: ?This
location must exist on local storage?

And any package that uses sqlite ?under the hood? will similarly want the db on
local storage to avoid such issues stemming from multi-process access.

Cheers,
Malcolm

From: R-devel <r-devel-bounces at r-project.org> On Behalf Of Simon
Urbanek
Sent: Friday, December 13, 2019 12:52 PM
To: lejeczek <peljasz at yahoo.co.uk>
Cc: r-devel <r-devel at r-project.org>
Subject: Re: [Rd] running R with users home dirs on a shared filesystems

CAUTION: This email was received from an External Source


User home is not used by R directly, so it is really up to whatever package/code
may be using user home. In our setup we have all machines using NFS mounted
homes for years. From experience the only thing to watch for are packages that
use their own cache directories in $HOME instead of tempdir() - it is
technically against CRAN policies but we have seen it in the wild.

Cheers,
Simon


> On Dec 13, 2019, at 1:36 PM, lejeczek via R-devel <r-devel at
r-project.org<mailto:r-devel at r-project.org>> wrote:
>
> Hi guys,
>
> I want to ask devel for who knows better - having multiple
> nodes serving users home dirs off the same shared network
> filesystem : are there any precautions or must-dos &
> must-donts in order to assure healthy and efficient parallel
> Rs running simultaneously - and I don't mean obvious stuff,
> I'm rather asking about R's internals & environment.
>
> simple example: three nodes mount a NFS share and users on
> all three nodes run R simultaneously.
>
> many thanks, L.
>
> ______________________________________________
> R-devel at r-project.org<mailto:R-devel at r-project.org> mailing
list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
______________________________________________
R-devel at r-project.org<mailto:R-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

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