Running Singularity on a HPC

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Nidhal Ghanmi

Nov 25, 2021, 5:47:34 AM11/25/21
to singularity

does any one please have some experience with singularity installed and running on an HPC , I am doing this for the first time

envirement managed by Bright cluster , Redhat 7,9 and workload manager is PBS Pro

I am trying to make it work for local users , I think it is fine , but in some points , can not build images from definition file , getting this actually :

INFO:    Starting build...
FATAL:   While performing build: conveyor failed to get: error getting username and password: error reading JSON file "/run/user/0/containers/auth.json": open /run/user/0/containers/auth.json: permission denied

also is there any security issues regarding singularity usage ? as I saw a configuration names %setup can touch settings into local host

Thanks !

Meng Tang

Nov 25, 2021, 3:33:03 PM11/25/21
to singularity,
Hi Nidhal,

I think you need sudo to build Singularity image, if you have root access.

$ sudo singularity build lolcow.sif lolcow.def
The command requires sudo just as installing software on your local machine requires root privileges.

Once you build the image, you can copy this image to all machines you intend to use the container. I think you don't need root access for most other operations on the container.

Meng Tang (Candice)

Nidhal Ghanmi

Nov 28, 2021, 4:28:01 AM11/28/21
to singularity,, Nidhal Ghanmi

Thanks Meng

Got it fixed due to some cache issue

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