[Sciserver-users] SciServer new user questions

[Jonas Haase]

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> 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 <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 <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

--  
Rainforest Restriction (n.): The state of not being able to shower because an Amazonian delivery may come while you're wet and undressed.

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