[Sciserver-users] SciServer new user questions

[Maximilian Fabricius]

Hi Tom,

understood. It is definitely something we should put on a wish list (I has
rsynch in an out of Sciserver).

But with all these things there is also security implications of course,
plus of course a container does not necessarily get a public IP address....

Max


On Tue, Oct 20, 2020 at 6:08 PM Tom Dwelly <dwelly at mpe.mpg.de> wrote:

> Hi Max,
>
> yes I have been using the web-based terminal interface already.
> Unfortunately the subtle differences between that
> interface and the 'real' terminal I'm used to are a bit of a barrier. But
> it's only day one of trying this out, so maybe
> my muscle memory will give in eventually. I'm investigating firefox
> extensions that will enable 'normal' linux-like copy
> and paste operations in the web-terminal.
>
> However, I was mainly interested in the additional functionality that
> would be enabled by being able to pipe stuff in
> and out of a sciserver container via an ssh tunnel. But it sounds like
> that's not possible. Oh well, there are other routes.
>
> Cheers,
>
> Tom
>
>
>
> On 20/10/2020 15:53, Maximilian Fabricius wrote:
> > Hi Tom,
> >
> > (good to hear from you virtually again)
> >
> > ... and you do know that there is a terminal interface in SciServer,
> right?
> >
> > Max
> >
> >
> >
> > On Tue, Oct 20, 2020 at 3:57 PM Jonas Haase <jhaase at mpe.mpg.de <mailto:
> jhaase at mpe.mpg.de>> wrote:
> >
> >     Oh dear I never saw Tom’s original mail, appareantly mailing list
> owners are not automativally subscribers….
> >
> >     Let me anwer now!
> >
> >>     On 20. Oct 2020, at 14:51, Johannes Buchner <jbuchner at mpe.mpg.de
> <mailto:jbuchner at mpe.mpg.de>> wrote:
> >>
> >>     On 19.10.20 14:58, Tom Dwelly wrote:
> >>>     Hi Jonas
> >>>
> >>>     I have a few questions about using the MPE SciServer system. I am
> >>>     sending this to the list in case any of these issues have been
> >>>     encountered by other users.
> >>>     Apologies for where I have got the SciServer nomenclature wrong.
> >>>
> >>>
> >>>     1) Is it possible to ssh from an external machine into a container
> >>>     session running on SciServer compute?
> >>
> >>     This would make SciServer many times more attractive to use for me.
> >>
> >
> >     It is not possible to enter a interactive container that way no,
> however you can use the SciServer Python API to do
> >     interactive work on your machine using the resources on the
> SciServer (database, file sharing) and you can also use
> >     it to launch compute jobs, so running your software inside a new
> container.
> >
> >     The MPE version of it is here:
> >     https://github.com/jonashaase/SciScript-Python
> >
> >     I put some small example at the end of the getting started document
> >     https://datashare.mpcdf.mpg.de/s/1e0CF3yRNcgDL4V
> >     And there is a example usage file with the code as well.
> >     Admittedly a lot of it could be made more userfriendly...
> >
> >>     Cheers,
> >>           Johannes
> >>
> >>>     2) Is there any way for a user to set up persistent settings (e.g.
> >>>     .bashrc file, ssh settings etc) that are sourced/used by new
> terminal
> >>>     sessions within any compute container?
> >>>
> >
> >     You can change .bashrc and everything else the idies user has access
> to and it should stay the same as long as the
> >     container is not deleted. However as soon as you start a new
> container that will all be gone since /home/idies gets
> >     re-built from the original image.
> >
> >     Only the volumes mounted inside /home/idies/workspace/ are
> persistent, so you could of course source a setup scrip
> >     inside your user volume which sets the environment in a way you like.
> >
> >     I am of course happy to adjust the compute images to set up the
> environment better. I am sure I missed a few things,
> >     in particular in connection with the x-ray software.
> >
> >>>     3) Is it possible for users to install standard linux packages
> (e.g. via
> >>>     apt) within a container session?
> >>>
> >
> >     apt-get not, but conda and pip work.
> >
> >     The reason is that we enforce that the user in the container is
> ‘idies’ and not root as it most often is in a Docker
> >     container.
> >     Its mostly a security issue: We don’t want anyone with root to be
> able to write onto the mounted disks on the
> >     underlying system and somehow launch a escalation attack there.
> >
> >>>     3a) if not, please can you add emacs to the default list of
> installed
> >>>     packages in the standard SciServer compute image?
> >>>
> >
> >     absolutely, no problem!
> >
> >     @everyone: Please let me know if any software or libraries you need
> are missing and I’ll install them as quickly as
> >     possible.
> >
> >
> >>>
> >>>     4) Any idea why 'git clone' operations like the following are
> failing
> >>>     within a compute container?
> >>>
> >
> >     unfortunately not, this should work.
> >     I will look into it!
> >
> >
> >     cheers
> >     Jonas
> >
> >     —
> >     Jonas Haase
> >     Max Planck Institute for Extraterrestrial Physics (MPE)
> >     Giessenbachstr. 1, 85748 Garching, Germany
> >     X5 1.3.08
> >     +49 89 30000 3706
> >
> >     --
> >     Sciserver-users mailing list
> >     Sciserver-users at lists.mpe.mpg.de <mailto:
> Sciserver-users at lists.mpe.mpg.de>
> >     https://lists.mpe.mpg.de/cgi-bin/mailman/listinfo/sciserver-users
> >
> >
> >
> > --
> > --------------------------------------------------------------------
> >   Maximilian Fabricius
> >   * Max Planck Institute for Extraterrestrial Physics (MPE)
> >     Giessenbachstrasse, D-85748 Garching, Germany
> >   eMail: mxhf at mpe.mpg.de <mailto:mxhf at mpe.mpg.de>
> >   Phone:  +49 89 30000 3712
> > --------------------------------------------------------------------
>


-- 
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 Maximilian Fabricius
 * Max Planck Institute for Extraterrestrial Physics (MPE)
   Giessenbachstrasse, D-85748 Garching, Germany
 eMail:  mxhf at mpe.mpg.de
 Phone:  +49 89 30000 3712
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