[Neurodebian-users] running neurodebian Singularity container on Redhat EL6?

[Craig Hamilton]

I’m making progress, lots of googling for answers.  What menu are you referring to ‘at first use from the menu’?  Is there indeed a ‘software suite’, or is that just the collection of packages that I decide to install myself?  I’ll try to contact the maintainer you suggested.

Thanks 

> On Aug 28, 2017, at 1:25 PM, Bennet Fauber <bennet at umich.edu> wrote:
> 
> Craig,
> 
> It might be a stock NeuroDebian, in which case the software is
> designed to install at first use from the menu.  Probably that
> question is best aimed at the maintainer of the Singularity Hub ND
> container.  I don't know if that's handled on the ND mailing list or
> on the Singularity mailing list.
> 
> But, yes, I think you'll end up running something to actually install
> what you want.
> 
> Be careful about the container size, too!  I have ended up making
> multiple containers because I didn't know how large it would be with
> the final software suite installed.
> 
> Good luck!  Let me know how it turns out, if you have a moment.  I'm
> curious whether this might be good on our cluster or not.
> 
> -- bennet
> 
> 
> 
> 
> On Mon, Aug 28, 2017 at 1:19 PM, Craig Hamilton <crhamilt at gmail.com> wrote:
>> Thanks for the speedy reply, Bennet!  You are right about uname.  os-release does show debian, so I think
>> it is working.  It seems that there is no neuro software installed, I will need to apt-get lots of stuff.  I guess I
>> didn’t understand that the neurodebian container is just a bare OS, and all the packages I want to use have
>> to be manually installled.   I initially thought that neurodebian meant you download one big package and
>> you get a multitude of tools at once.   Am I understanding this correctly?  (The documentation could
>> really use some work…)
>> 
>> Best,
>>  Craig
>> 
>> 
>>> On Aug 28, 2017, at 1:02 PM, Bennet Fauber <bennet at umich.edu> wrote:
>>> 
>>> Craig,
>>> 
>>> I think uname will return the host kernel version, not the container version.
>>> 
>>> From the Singularity shell, try
>>> 
>>> $ cat /etc/os-release
>>> 
>>> You will almost certainly have to set up your paths inside the
>>> container as part of setting up the application you want to run.
>>> Singularity isn't a VM, it's really an application container, so
>>> setting paths and the like would be part of the application you run,
>>> which might be a shell script.
>>> 
>>> So, try something like this from the container shell.
>>> 
>>> $ export FLSDIR=/usr/share/fsl/5.0
>>> $ source $FSLDIR/etc/fslconf/fsl.sh
>>> $ which bet2
>>> 
>>> and see if you get something useful.
>>> 
>>> -- bennet
>>> 
>>> 
>>> 
>>> On Mon, Aug 28, 2017 at 12:52 PM, Craig Hamilton <crhamilt at gmail.com> wrote:
>>>> I have a system running Redhat EL6 and want to be able to use neurodebian on it.  One solution I tried is:
>>>>  1. Build singularity from source
>>>>  2. Run “singularity pull shub://neurodebian/neurodebian”  which downloads a 12GB Singularity container.
>>>>  3. Run “singularity shell neurodebian-neurodebian-master.img”
>>>>  4. I get a shell prompt within the container, but don’t find any neuro software available anywhere.
>>>>      If I run ‘uname -a’ at the container shell prompt, it returns redhat linux, not debian. The file system is
>>>>      very different than the underlying system’s file system, so I think I am inside the container.
>>>> 
>>>> Am I wasting my time trying to do this?   Singularity seems like a great solution, but do I need to be
>>>> running inside a debian VM?  That seems like an extra, unnecessary layer.
>>>> 
>>>> As you can tell, I’m new to all this, any help much appreciated!
>>>> 
>>>> Thanks,
>>>>  Craig Hamilton
>>>>  Wake Forest Sch of Med
>>>> 
>>>> 
>>>> 
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>>