Running Singularity on a HPC

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Nidhal Ghanmi

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Nov 25, 2021, 5:47:34 AM11/25/21
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Hi

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 !
Nidhal

Meng Tang

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Nov 25, 2021, 3:33:03 PM11/25/21
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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.

Best,
Meng Tang (Candice)

Nidhal Ghanmi

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Nov 28, 2021, 4:28:01 AM11/28/21
to singularity, mta...@hawk.iit.edu, Nidhal Ghanmi
Heey

Thanks Meng

Got it fixed due to some cache issue


regards
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