Opened 4 years ago

Closed 4 years ago

#1432 closed help (fixed)

UM Training

Reported by: cereeves Owned by: um_support
Component: FCM Tutorial Keywords:
Cc: Platform: PUMA
UM Version: <select version>

Description

I am attending the UKCA training course next week, but have not done the UM training. I started trying to do some of this prior to Christmas but got stuck. I have been trying to follow the UM training course that took place on 3rd December using a copy of the handout that my PhD student Fazrin brought back having attended the course. I have been going through the Prerequisites (section one) and have successfully completed parts 2.1 to 2.6. Working through 2.7, I have successfully completed parts i to iv. However, when I get to part v, I get the error permission denied. i.e.

cereeves@puma:/home/cereeves> cp ~grenville/.ssh/ssh-setup ~/.ssh/ssh-setup
cp: cannot stat `/home/grenville/.ssh/ssh-setup': Permission denied
cereeves@puma:/home/cereeves>

Please can you help. I am not sure how important this is and whether it will stop me completing the required training before the UKCA training next week.

Regards,
Claire

Change History (11)

comment:1 Changed 4 years ago by ros

Hi Claire,

Please follow instructions number 5&6 from the from the following page to get the setup script

https://puma.nerc.ac.uk/trac/UM_TUTORIAL/wiki/sshAgent

The instructions you are trying to follow are slightly specific to when you are using the training accounts on the actual course.

If you find yourself having problems with getting the ssh-agent setup please go through all the instructions on the page above and that should sort out your problems.

I believe the most important section to do before the UKCA course is the FCM UM Tutorial as this takes you through submitting a job, using FCM to make code changes, etc which will be needed on the course next week. See https://puma.nerc.ac.uk/trac/UM_TUTORIAL

Regards,
Ros.

comment:2 Changed 4 years ago by luke

Hi Claire,

Just to confirm what Ros says above - the most important part is the FCM training, as you will need knowledge of how to make branches, making code changes etc. I won't have time in the course to cover this and do the UKCA tutorials as well.

Thanks,
Luke

comment:3 Changed 4 years ago by cereeves

Ros and Luke,

Thank you both for your help. I have managed to sort out the ssh-agent and completed section 3 of the UM training. I skipped section 4 and moved on to the FCM tutorial. I have gone through the whole of the UmTutorial?/vn8.2/RunningJobs - UM FCM Tutorial. Everything seemed to work ok, although I am not sure as I couldn't find the output files as described. I found the ext.out file on PUMA in the folder specified, where [umbase | ummodel] was umatmos. I found the comp.leave file in ARCHER but it was in $HOME/output. I could not find the .leave file. Although I have submitted the modification using the branch vn8.2_um_shell1, I don't know if it worked as I can't find the .leave file to check. What I also find mystifying is that the first 2 jobs (2599060 & 2599159) still appear when I check the queue, but the third one (2599192) has disappeared. It makes me wonder if I am doing things correctly.

I shall carry on and hope that despite these uncertainties I will have learnt enough to cope with the UKCA course come Monday.

Cheers,
Claire

comment:4 Changed 4 years ago by ros

Hi Claire,

If you can change the permissions on your ARCHER directories I can take a quick look.

chmod -R g+rX /home/n02/n02/cereeves
chmod -R g+rX /work/n02/n02/cereeves

Cheers,
Ros.

comment:5 Changed 4 years ago by cereeves

Ros,

I have just changed the permissions as suggested.

Thanks,
Claire

comment:6 Changed 4 years ago by ros

Hi Claire,

It looks like the "short" queue on ARCHER is not currently running hence why 2 of your jobs are stuck in the queue and you have no .leave file. The 3rd job would have run before these 2 as it was a compile job which is sent to a different queue (serial). I assume ARCHER will sort out the short queue next week, but if you wish to get the jobs running before then you will need to remove the hand-edit in your job. From memory go to UMUI window sub-model independent → compilations & modifications → user hand-edit files and change Y to N for the short-job hand-edit which I think is the only one in the table for this job. Resubmit the job to run and it should then go into the standard queue and run.

Cheers,
Ros.

comment:7 Changed 4 years ago by cereeves

Ros,

Thanks for looking into this. I think I'll just wait for the jobs to run during the week. At least I have gone through most of that part of the tutorial and I need to move on get through the next bit on code changes.

Thanks again,
Claire

comment:8 Changed 4 years ago by cereeves

Me again!

My latest problem is failing to create a branch in the FCM GUI. I get the error:
"Can't exec "gedit": No such file or directory at /home/um/fcm-2014-02/bin/../lib/FCM/System/CM/CommitMessage.pm line 91.

[FAIL] gedit /tmp/pV4F31IRNd # rc=-1

Claire

comment:9 Changed 4 years ago by cereeves

Now managed to create branch using the command line. This appears to be successful:
Committed revision 5301.
[info] Created: svn://puma/UM_TUTORIAL_svn/UM/branches/dev/cereeves/vn8.2_tutorial
but I can't find it within TRAC!
I have been able to checkout the URL and the a new directory is created with the branch name in my working directory.

comment:10 Changed 4 years ago by luke

Hi Claire,

Your branch is there on the UM Tutorial Trac page (and not the main UM trac pages - there are a large number of trac pages for various things, and it is easy to get lost):

https://puma.nerc.ac.uk/trac/UM_TUTORIAL/browser/UM/branches/dev/cereeves/vn8.2_tutorial

There is another ticket mentioning problems with gedit - see #1017 . I don't think that Gedit is installed on PUMA - try nedit, emacs, or vim. I would also suggest always using the command-line to create branches, rather than the GUI. Personally I just find it easier.

Thanks,
Luke

comment:11 Changed 4 years ago by annette

  • Component changed from PUMA to FCM Tutorial
  • Platform set to PUMA
  • Resolution set to fixed
  • Status changed from new to closed

Hi Claire,

I presume this answered your questions, so I'm closing the ticket.

Annette

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