stack size error limit

Question

stack size error limit

mamyAndrianteranagna opened this issue 4 years ago · 11 comments

mamyAndrianteranagna commented 4 years ago

Dear Gregory,

I'm trying to launch too-many-cells on my datasets when I get the following error:

Language.R.Interpreter: Cannot increase stack size limit.Try increasing your stack size limit manually:$ ulimit -s unlimited
too-many-cells: setResourceLimit: permission denied (Operation not permitted)

I do not have the right to change myself the stack limit size (I'm working on a remote server and the system admin does not want to change it too since it requires a reboot of all the system).

It would be helpfull for me if I can launch the tool without having to change this stack size limit.

Best regards,
Mamy Andrianteranagna

Answer 1 · 2020-07-24T14:47:51.000Z

When does this happen? What OS? Docker or not?

Answer 2 · 2020-07-24T15:34:15.000Z

The OS is CentOS (server).
The docker image have been converted into singularity image (I have not the permission to launch docker) and I run the command like this:

"singularity run too-many-cells_20.2.2.0.simg make-tree ..."

(singularity run too-many-cells_20.2.2.0.simg make-tree -h works)

Thanks a lot for your help.

Best,
Mamy

Answer 3 · 2020-07-24T16:30:49.000Z

Singularity seems to have a lot of permission issues when people are converting the docker...

Are you able to run ulimit -s unlimited at the command line? Can you run it in the singularity container?

Answer 4 · 2020-07-24T17:09:41.000Z

I'm not allowed to run ulimit -s unlimited because of permission restriction.
If the issue is due to the conversion, could you please create yourself a singularity image of the tool? Is this possible for you?
I think this can be helpfull for people who cannot run docker.

Best,
Mamy

Answer 5 · 2020-07-24T17:24:13.000Z

You can't run ulimit in the container? I don't know what the issue is with singularity, but it might be more complicated than the conversion. Did you try the nix version as you are using linux?

Answer 6 · 2020-07-24T17:35:10.000Z

The problem is that I launch the job on the server (I cannot launch it locally because of memory limitation) and I can't be root on the server.

Answer 7 · 2020-07-24T17:49:47.000Z

Nix does not require root after the initial installation (just like singularity). Did you try increasing ulimit in the container?

Answer 8 · 2020-07-24T17:52:28.000Z

Also, what version of singularity are you using? Might be related: apptainer/singularity#4701

Answer 9 · 2020-08-03T13:08:15.000Z

Dear Gregory,

Sorry for my late response (I was on hollyday).
As you suggested, I will ask our system manager to install nix in the server and use it instead of singularity.
I will let you know.

Thanks a lot for your help.

Best,
Mamy

PS: For information, I was using singularity version 3.5.2 which is the only one installed in our system.

Answer 10 · 2020-08-03T13:57:04.000Z

Thanks for the update! We'll see how it goes...

Answer 11 · 2021-11-22T14:16:21.000Z

As I cannot reproduce, I am closing this issue. Please let me know if it persists.