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Permissions for Input Data on Cori

jlturner

jlturner

Jason Torchinsky
New Member
Hello,

I will include code information, etc., after the issue description.

I am currently attempting to follow the quickstart tutorial to perform a test run on the Cori machine at NERSC. Here are the steps I have performed:

1. Downloaded CESM from the Github repository to a directory called CESM.
2. Created a new case with the following command
./create_newcase --case /global/project/projectdirs/m3698/CESM_simulations/B1850.f19_g17.test --compset B1850 --res f19_g17 --machine cori-knl --project m3698 --walltime 02:00:00 --queue regular
which appears to have worked successfully.
3. In the case directory (/global/project/projectdirs/m3698/CESM_simulations/B1850.f19_g17.test), I invoked the ./case.setup and ./case.build commands. I then modified the runtime settings with the following command
./xmlquery STOP_OPTION=nmonths,STOP_N=12
4. Upon submitting the job to the batch queue using the ./case.submit command, I receive the following error:
OSError: [Errno 13] Permission denied: '/project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01'

Upon further inspection, it appears that there are no public read, write, or execute permissions for the /project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020 directory, specifically the ls -l /project/projectdirs/ccsm1/inputdata/cesm2_init/ command returns

total 25
drwsrwsr-x 3 jedwards ccsm1 4096 Oct 11 2017 b.e11.B1850C5CN.f09_g16.005_yr402_cesm2_v2
drwsrwsr-x 3 jedwards ccsm1 4096 Apr 17 2018 b.e11.B1850C5CN.f09_g16.005_yr402_cesm2_v3
drwsrwsr-x 3 cfischer ccsm1 4096 May 22 2018 b.e11.B1850C5CN.f09_g16.005_yr402_cesm2_v4
drwsrwsr-x 3 jedwards ccsm1 4096 Jun 11 2018 b.e20.B1850.f09_g17.pi_control.all.297
drwsrwsr-x 3 yunhe ccsm1 4096 Jun 29 2018 b.e20.B1850.f09_g17.pi_control.all.297_transient_v2
drwxrwsr-- 3 jedwards ccsm1 4096 Nov 30 2018 b.e20.B1850.f09_g17.pi_control.all.299_merge_v2
drwxrwsr-x 4 cfischer ccsm1 4096 Jul 15 2019 b.e20.B1850.f09_g17.pi_control.all.299_merge_v3
drwxrws--- 3 cfischer ccsm1 4096 Sep 22 08:42 b.e20.B1850.f19_g17.release_cesm2_1_0.020
drwxrwsr-- 3 jedwards ccsm1 4096 Oct 5 2018 b.e20.BHIST.f09_g17.20thC.297_01_v2
drwxr-s--- 5 nanr ccsm1 4096 Apr 16 2020 b.e21.B1850.f09_g17.CMIP6-piControl.001
drwxr-s--- 2 nanr ccsm1 4096 May 8 2020 b.e21.B1850.f09_g17.CMIP6-piControl.002
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.001
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.002
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.003
drwxr-s--- 3 nanr ccsm1 4096 Apr 25 2019 b.e21.BHIST.f09_g17.CMIP6-historical.004
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.005
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.006
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.007
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.008
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.009
drwxr-s--- 4 nanr ccsm1 4096 Apr 22 2019 b.e21.BHIST.f09_g17.CMIP6-historical.010
drwxrwsr-x 3 cfischer ccsm1 4096 Apr 16 2019 b.e21.BHIST.f09_g17.CMIP6-historical.010_v2
drwxr-s--- 3 nanr ccsm1 4096 Apr 19 2019 b.e21.BHIST.f09_g17.CMIP6-historical.011
drwxrwsr-x 3 cfischer ccsm1 4096 Apr 16 2019 f.e20.FHIST.f09_f09.cesm2_1.001_v2
drwxr-s--- 3 nanr ccsm1 4096 Jul 11 2019 glade

I was wondering if it would be possible to use a different set of input data (e.g., b.e20.B1850.f09_g17.pi_control.all.299_merge_v3) which has global read permissions, or to set the global read permissions of the specified input data to open, or some other way to get the input data?

If there is another forum I should post this issue to, please let me know and I will be happy to ask there as well.

Additional Information

Code version: See version_info.txt.

No changes have been made to files in the source tree outside of those described above.

All steps to reproduce this issue have been included above.
 

Attachments

  • version_info.txt
    6.3 KB · Views: 3
F

fischer

CSEG and Liaisons
Staff member
Hi Jason,

I can fix the permissions for that directory when cori comes back up.

Chris
 
F

fischer

CSEG and Liaisons
Staff member
I've fixed the permissions for

/project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020

Chris
 
jlturner

jlturner

Jason Torchinsky
New Member
Thank you Chris! I have followed the same procedure as above, and have received the same error:
OSError: [Errno 13] Permission denied: '/project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01'

The ls -l /project/projectdirs/ccsm1/inputdata/cesm2_init/ returns

total 25
drwsrwsr-x 3 jedwards ccsm1 4096 Oct 11 2017 b.e11.B1850C5CN.f09_g16.005_yr402_cesm2_v2
drwsrwsr-x 3 jedwards ccsm1 4096 Apr 17 2018 b.e11.B1850C5CN.f09_g16.005_yr402_cesm2_v3
d-ws-wsrwx 3 cfischer ccsm1 4096 May 22 2018 b.e11.B1850C5CN.f09_g16.005_yr402_cesm2_v4
drwsrwsr-x 3 jedwards ccsm1 4096 Jun 11 2018 b.e20.B1850.f09_g17.pi_control.all.297
drwsrwsr-x 3 yunhe ccsm1 4096 Jun 29 2018 b.e20.B1850.f09_g17.pi_control.all.297_transient_v2
drwxrwsr-- 3 jedwards ccsm1 4096 Nov 30 2018 b.e20.B1850.f09_g17.pi_control.all.299_merge_v2
d-wx-wsrwx 4 cfischer ccsm1 4096 Jul 15 2019 b.e20.B1850.f09_g17.pi_control.all.299_merge_v3
d-wx-wsrw- 3 cfischer ccsm1 4096 Sep 22 08:42 b.e20.B1850.f19_g17.release_cesm2_1_0.020
drwxrwsr-- 3 jedwards ccsm1 4096 Oct 5 2018 b.e20.BHIST.f09_g17.20thC.297_01_v2
drwxr-s--- 5 nanr ccsm1 4096 Apr 16 2020 b.e21.B1850.f09_g17.CMIP6-piControl.001
drwxr-s--- 2 nanr ccsm1 4096 May 8 2020 b.e21.B1850.f09_g17.CMIP6-piControl.002
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.001
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.002
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.003
drwxr-s--- 3 nanr ccsm1 4096 Apr 25 2019 b.e21.BHIST.f09_g17.CMIP6-historical.004
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.005
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.006
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.007
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.008
drwxr-s--- 3 nanr ccsm1 4096 Jul 12 2019 b.e21.BHIST.f09_g17.CMIP6-historical.009
drwxr-s--- 4 nanr ccsm1 4096 Apr 22 2019 b.e21.BHIST.f09_g17.CMIP6-historical.010
d-wx-wsrwx 3 cfischer ccsm1 4096 Apr 16 2019 b.e21.BHIST.f09_g17.CMIP6-historical.010_v2
drwxr-s--- 3 nanr ccsm1 4096 Apr 19 2019 b.e21.BHIST.f09_g17.CMIP6-historical.011
d-wx-wsrwx 3 cfischer ccsm1 4096 Apr 16 2019 f.e20.FHIST.f09_f09.cesm2_1.001_v2
drwxr-s--- 3 nanr ccsm1 4096 Jul 11 2019 glade

which appears as I would expect. However, the ls -l /project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020 returns a permission error

ls: cannot access '/project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01': Permission denied
total 0
d????????? ? ? ? ? ? 0301-01-01
 
jlturner

jlturner

Jason Torchinsky
New Member
fischer said:
I've fixed the permissions for

/project/projectdirs/ccsm1/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020

Chris
Click to expand...
Hey Chris,

Please see my previous comment about further file permission issues. Thanks again for your time and effort!
 
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