Opened 7 months ago

Closed 6 weeks ago

Last modified 5 weeks ago

#3207 closed help (fixed)

Problem running Suite u-al752 on JASMIN

Reported by: fo196883 Owned by: pmcguire
Cc: Platform: JASMIN
UM Version:


Hello Patrick,

I have tried to run suite al-752 on JASMIN unsuccessfully. I have attached a screenshot of the status of the run.
I followed the instructions here:

I have been able to run a different suite (u-br823) successfully on JASMIN [but I am having problems running suite u-al52].

Could you please advise on what I may be doing wrong?


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Screenshot from 2020-02-20 11-18-53.png (262.8 KB) - added by pmcguire 7 months ago.

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Change History (17)

Changed 7 months ago by pmcguire

comment:1 Changed 7 months ago by pmcguire

Hi Frederick
I'd be happy to help.
Are you new to JASMIN?
Which queue are you using? The short-serial queue? Or the new_users queue?
Can you change the permissions of your home directory so that I can see your log files?
Right now your permissions are:

drwx------ 1 fo196883 users 0 Feb 20 09:47 /home/users/fo196883

But they should be: drwxr-xr--
Do you have a cms_helpdesk account? We try to support people at the helpdesk.
If you don't have a cms_helpdesk account, can we create one for you?
Patrick McGuire

comment:2 Changed 7 months ago by pmcguire

Hello Patrick,

I am new to JASMIN. I am using the new_users queue.

I have changed the permissions on my home directory.

I have a helpdesk account but just wanted to check with you directly since you trained us on u-al752.


comment:3 Changed 7 months ago by pmcguire

  • Status changed from new to accepted

comment:4 Changed 7 months ago by pmcguire

Hi Frederick
What is your helpdesk account username?
If you don't want to create a ticket on the helpdesk, I can do that for you.
All the tickets with the component as JULES and Land Surface Modelling go directly to me first,

Thanks for changing your permissions. I will look.

I looked at your u-br823 suite, and it uses the par-single queue.
Since that works for you, maybe you'r not considered to be a new_user anymore,
and the short-serial queue could work for you with u-al752.

Also, I would just try to retrigger the JULES app by right-mouse clicking on the JULES app in the cylc GUI,
and selecting the retrigger option.

comment:5 Changed 7 months ago by pmcguire

Hi Frederick
According to this log file of yours:


it says that the new_users queue doesn't exist anymore.
Maybe you can try changing to short-serial?
I will update the documentation.

comment:6 Changed 7 months ago by pmcguire

Hello Patrick,

It is running now. Thanks very much for the help.


comment:7 Changed 7 months ago by pmcguire

what is your CMS Helpdesk username?
I will add a ticket there on your behalf.

comment:8 Changed 7 months ago by pmcguire

Hello Patrick,

Yes I changed the queue to short-serial.

Could you please create a username for me then.


comment:9 Changed 7 months ago by pmcguire

Hello Patrick,

The main run is now complete but the plots failed to run.

I will try re-running to see if I can get the plots as well. Otherwise, I will copy the outputs and make plots.


comment:10 Changed 7 months ago by pmcguire

Hi Frederick:
Did you look at your .err and .out files deep in the ~/cylc-run/u-al752/log directory?
Do those show why the plotting failed?

comment:11 Changed 7 months ago by pmcguire

Hello Patrick

I don't have .err or .out files in my log directory.


comment:12 Changed 7 months ago by pmcguire

Hi Frederick
Yes, there are no .err and .out files now, since you reran JULES since you previously ran JULES and you had created them.
The log files for the previous run of JULES are now all tarred and zipped in to a .tar.gz file:


If you untar and unzip that .tar.gz file, you will see these files:


The second file (the .out file) suggests that the plotting failed for GPP for the one of the Brazil sites (LBA_PDG).
Maybe you can temporarily disabled either that LBA_PDG site or all the LBA sites, to try to get the plotting working?

I think it's very important to get the plotting working. It's one of the most important aspects of this u-al752 suite,
to run JULES on a bunch of sites and then compare the models to the observations for all the variables with the plots.


comment:13 Changed 7 months ago by pmcguire

Hello Patrick,

I have now run the peg subset successfully including the plots.

Thanks very much for the help. I will now explore the suite and let you know if there are any challenges.


comment:14 Changed 7 months ago by pmcguire

Hi Fred
I just created this ticket for this help. These tickets are searchable, so if you or anybody else has similar problems in the future, they can be found with a search engine like Google.

How is the u-al752 suite coming along? Did your exploration of the suite uncover any issues that you need help with?

comment:15 Changed 6 weeks ago by pmcguire

  • Resolution set to fixed
  • Status changed from accepted to closed

Hi Fred:
I am closing this ticket now.

comment:16 Changed 5 weeks ago by pmcguire

  • Cc fo196883 removed
  • Reporter changed from pmcguire to fo196883
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