I have made a python 3.8 virtual environment with Anaconda.
Installed singularity with conda, version 3.8.6
Installed Stimela version 1.7.9 with Conda.
I have also specified the path for the Stimela cache and temp directories.
After pulling all the images with singularity I tried to run my .yml file.
Whatever I am trying to do I am getting an error..
The error.....
INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /data/manisha/TEST_DATA/arpan/STIMELA_IMAGES/stimela_ddfacet_1.7.1.sif: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled
: exit status 1
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: /data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/bin/singularity run --workdir /data/manisha/TEST_DATA/arpan/test_caracal/.stimela_workdir-17060054084448693 --containall --userns returns error code 255
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: job failed at 2024-01-23 15:53:31.281294 after 0:00:01.924652
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: Traceback (most recent call last):
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/recipe.py", line 713, in run
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: job.run_job()
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/recipe.py", line 425, in run_job
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: self.job.run(output_wrangler=self.apply_output_wranglers)
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/singularity.py", line 128, in run
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: utils.xrun(f"{BINARY} run --workdir {self.execdir} --containall {extras}",
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/utils/xrun_poll.py", line 227, in xrun
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: raise StimelaCabRuntimeError("{} returns error code {}".format(command_name, status))
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: stimela.utils.StimelaCabRuntimeError: /data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/bin/singularity run --workdir /data/manisha/TEST_DATA/arpan/test_caracal/.stimela_workdir-17060054084448693 --containall --userns returns error code 255
2024-01-23 15:53:
From the initial inspection, it looks to me as a singularity problem. Is not conda installed singularity sufficient? Do we need a singularity with root permissions?
Let me first describe the setup.
The error.....
INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /data/manisha/TEST_DATA/arpan/STIMELA_IMAGES/stimela_ddfacet_1.7.1.sif: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled
: exit status 1
2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: /data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/bin/singularity run --workdir /data/manisha/TEST_DATA/arpan/test_caracal/.stimela_workdir-17060054084448693 --containall --userns returns error code 255 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: job failed at 2024-01-23 15:53:31.281294 after 0:00:01.924652 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: Traceback (most recent call last): 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/recipe.py", line 713, in run 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: job.run_job() 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/recipe.py", line 425, in run_job 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: self.job.run(output_wrangler=self.apply_output_wranglers) 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/singularity.py", line 128, in run 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: utils.xrun(f"{BINARY} run --workdir {self.execdir} --containall {extras}", 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: File "/data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/lib/python3.8/site-packages/stimela/utils/xrun_poll.py", line 227, in xrun 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: raise StimelaCabRuntimeError("{} returns error code {}".format(command_name, status)) 2024-01-23 15:53:31 STIMELA.image_target_1 ERROR: stimela.utils.StimelaCabRuntimeError: /data/manisha/TEST_DATA/arpan/anaconda3/envs/38data/bin/singularity run --workdir /data/manisha/TEST_DATA/arpan/test_caracal/.stimela_workdir-17060054084448693 --containall --userns returns error code 255 2024-01-23 15:53:
From the initial inspection, it looks to me as a singularity problem. Is not conda installed singularity sufficient? Do we need a singularity with root permissions?