[Sciserver-users] SciServer new user questions

[Tom Dwelly]

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
> 
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> 
> 
> 
> -- 
> --------------------------------------------------------------------
>   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
> --------------------------------------------------------------------