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

[Craig Hamilton]

Thanks, Yaroslav.  I don’t have overlays enabled, so didn’t get got by that gotcha.   Another user (Bennet Fauber) explained that uname returns info on the host kernel.  /etc/os-release shows that I am indeed in a Debian container, so that is good.  It seems there are no neuro packages installed by default, I need to be doing a lot of apt-get.  I found that my /etc/apt/sources.list needed updating for apt-get to be able to find packages.  There could certainly be better instructions on getting this up and running!

Craig

> On Aug 28, 2017, at 1:21 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> 
> 
> On Mon, 28 Aug 2017, Craig Hamilton 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.  
> 
> nah, no VM must be needed as long as the host system is linux as well (which is
> in your case)
> 
> the gotcha [more in 1] could be that by default you have overlays enabled
> 
> $> grep overlay /etc/singularity/singularity.conf  
> enable overlay = yes
> 
> but your kernel is too old and doesn't support them (run lsmod | grep overlay)
> so disable them in the config and try again please.  
> 
> [1] https://github.com/singularityware/singularity/issues/721#issuecomment-307196365
> 
> -- 
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik