Opened 4 years ago
Closed 4 years ago
#1941 closed help (fixed)
Setting up UM environment variables on ARCHER (need permission)
Reported by: | tcowan | Owned by: | willie |
---|---|---|---|
Component: | ARCHER | Keywords: | UM environment variables |
Cc: | Platform: | ARCHER | |
UM Version: | 8.2 |
Description
Hi,
I'm a new UM user and I'm trying to get environment variables set in my .profile file on ARCHER (as per http://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/UmTutorial/SettingUp).
I'm getting a permission denied when trying to access 8.2. Could I please be added permission?
Regards,
Tim
Change History (13)
comment:1 Changed 4 years ago by willie
- Owner changed from um_support to willie
- Status changed from new to accepted
comment:2 Changed 4 years ago by tcowan
Hi Willie,
I don't actually get any error messages when logging onto to ARCHER. I was receiving the message when I was submitting my model run on PUMA. I assumed it had to do with permissions when trying to access /work/n02/n02/hum/vn8.2/ — But I realise now I'm using vn8.5 and I've set that as my $UMDIR. So perhaps that is not why my job isn't running on ARCHER??
Is there a .log file that can help me find where my job is falling over? I have checked $HOME/output/ — but nothing is there.
When I submitted my latest job it stated:
Your job directory on host login.archer.ac.uk is: /home/n02/n02/tcowan/umui_runs/xmvqa-222145829
Cray PrgEnv? already loaded
craype-network-aries
cce/8.3.7
cray-libsci/13.0.1
PrgEnv?-cray/5.2.56
craype-ivybridge
cray-mpich/7.1.1
gcc/5.1.0
Total PEs requested: 96
NOTE: The following has been selected for running on the CRAY XC30
96 MPI task(s)
8 node(s)
12 MPI task(s) per node
2 OpenMP thread(s) per task
How can tell if it's running? I tried a qstat -u tcowan — but nothing came up.
Cheers,
Tim
comment:3 Changed 4 years ago by willie
Hi Tim,
The hand edit
/home/simon.tett/umui_jobs/hand_edits/vn8.5/l_solvar2
only has permission for Simon to execute. You can see this in the file umui_jobs/xmvqa/EXT_SCRIPT_LOG on PUMA.
You need to take a copy of this file and make it executable (chmod +x <file>) and change the UMUI entry to your version. Or maybe get Simon to chmod g+rx the file.
Generally errors are presented on screen somewhere. Logs can be found on PUMA in ext.out files for the job (find ~ -name ext.out), also in the umui_jobs directory and on ARCHER in the output directory. You have nothing there, but if you look in the umui_runs on ARCHER you can see each failed attempt.
Regards
Willie
comment:4 Changed 4 years ago by tcowan
Hi Willie,
He's now changed the permissions, however I think the problem may lie with at the bottom of my ext.out file:
Permission denied (publickey,keyboard-interactive).
# Time taken: 1 s⇒ ssh -n -oBatchMode=yes login.archer.ac.uk mkdir -p /home/n02/n02/stett2/build/xmvqa/baserepos/UMATMOS/cfg
[FAIL] ssh -n -oBatchMode=yes login.archer.ac.uk mkdir -p /home/n02/n02/stett2/build/xmvqa/baserepos/UMATMOS/cfg failed (255) at /home/fcm/fcm-2016.02.0/bin/../lib/FCM1/Dest.pm line 755.
Do I have to change this to my directory?
Thanks for all your help so far. It's much appreciated.
Cheers,
Tim
comment:5 Changed 4 years ago by willie
Hi Tim,
The job set up is fine. I think this is a problem with your SSH setup. Please make sure that you have followed the instructions at http://cms.ncas.ac.uk/wiki/ArcherSshAgent.
On PUMA you will need to
ssh-add
and enter your pass phrase before submitting jobs from the UMUI. What does
ssh-add -l
give you?
Regards
Willie
comment:6 Changed 4 years ago by tcowan
Hi Willie,
ssh-add -l gives me:
2048 SHA256:rY/H4/4R3F0klnAUAq7/lU4wp45aGHWvBKCKbOpNtnM /home/tcowan/.ssh/id_rsa (RSA)
I followed the SSH setup yesterday, so I think that part is fine.
Tim
comment:7 Changed 4 years ago by tcowan
Hi Willie,
I think I've fixed the ssh problem now so now my ext.out file shows that everything has been extracted to /$HOME/build/… — however the job is still not submitting to the queue on ARCHER.
Any suggestions?
Cheers,
Tim
comment:8 Changed 4 years ago by willie
Hi Tim,
That's great. It seems that you have no budget in the account n02-TITAN. Can you let us know what account you'll be using?
Regards
Willie
comment:9 Changed 4 years ago by tcowan
Hi Willie,
Okay. I think I'll be using n02-titan. I should have joined the n02-titan and n02-cssp groups. Does that not automatically happen when you join n02? How do I go about determining what my budget is?
Tim
comment:10 Changed 4 years ago by tcowan
Hi Willie,
I was just emailing Simon Tett (I'm using his code) and he thinks you can add me to n02-titan. I tried to get Grenville Lister (from Reading) but I'm not if it's been done. If you need authorisation please contact Simon Tett (simon.tett@…).
Cheers,
Tim
comment:11 Changed 4 years ago by willie
Hi Tim,
You should now have access to that account. Try your job again.
Regards
Willie
comment:12 Changed 4 years ago by tcowan
Hi Willie,
Sorry for delayed response — had a meeting to attend to. It's now running fine. Thanks for all your help. Appreciate it.
Cheers,
Tim
comment:13 Changed 4 years ago by willie
- Resolution set to fixed
- Status changed from accepted to closed
Hi Tim,
Regards
Willie