# Free running mode with vn12 nesting suite **URL:** \ **Category:** Unified Model\ **Tags:** ARCHER2, Nesting-Suite\ **Created:** [12 September 2022 08:43 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722 "2022-09-12T08:43:06Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [12 September 2022 08:43 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/1 "2022-09-12T08:43:07Z")
Hi CMS, I’m trying to submit a vn 12.0 suite in free-running mode (i.e. FREE\_RUN = true), with large-scale forcing from ERA5. However, the suite won’t submit and I get Jinja2 errors related to errors in suite-runtime/lams.rc at submission time: > [FAIL] File “/home/shakka/cylc-run/u-cq701/suite-runtime/lams.rc”, line 466, in top-level template code > [FAIL] DATADIR = {{mod[“ics”][“dir”]}} > [FAIL] UndefinedError: ‘dict object’ has no attribute ‘prev\_ics’ Looks like the code that allows each cycle to take initial conditions from the previous LAM forecast isn’t complete. Am I missing a branch/code update or revision that will allow this suite to run like this in free-running mode? Or have I hit upon a combo of incompatible settings? Thanks in advance, Ella ---
**Author:** ![grenville](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/grenville/32/29_2.png) [@grenville](https://cms-helpdesk.ncas.ac.uk/u/grenville)\ **Post date:** [13 September 2022 07:57 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/2 "2022-09-13T07:57:59Z")
Hi Ella Some changes were made 8 weeks ago to u-by395 in the fix\_ics branch - see `https://code.metoffice.gov.uk/trac/rmed/ticket/300` – I’ve not looked hard at what’s been done… Grenville ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [13 September 2022 10:14 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/3 "2022-09-13T10:14:37Z")
Grenville, you genius. I never would have found that tidbit of info - thanks! I’ve made a copy from the correct revision and it seems to be running fine. Just a note though that the latest revisions of u-by395 don’t have the option to run on archer2 (only ncas-cray-xc30) so I had to update the following files to get it to work: bin/setup\_metadata meta/rose-meta.conf opt/rose-suite-ncas.conf and made the folder /site/ncas-cray-ex/ with the suite-adds.rc and suite-vars.rc files. I’ve committed these changes in my new suite u-cq759 so it should run okay at revision 236230. Cheers! Ella ---
**Author:** ![grenville](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/grenville/32/29_2.png) [@grenville](https://cms-helpdesk.ncas.ac.uk/u/grenville)\ **Post date:** [13 September 2022 10:28 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/4 "2022-09-13T10:28:17Z")
Ella - I think not! Glad it’s working. We are working to get our ARCHER2 additions into the trunk. Grenville ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [13 September 2022 14:45 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/5 "2022-09-13T14:45:01Z")
Hmm. Have gotten to the first ec\_recon step and encountering some more failures - nothing particularly useful in the pe\_output or job.out files, even with extra diagnostic messages switched on in RCF\_PRINTSTATUS. Any idea how to extract a little more detail from this error message? The input ancillaries are the same that are working without hitch in my re-initialised run and it’s the first cycle point, so I am struggling to figure out what the input list in question could be. ??? ???!!!???!!!???!!!???!!!???!!! ERROR ???!!!???!!!???!!!???!!!???!!! ? Error code: 4001 ? Error from routine: CHECK\_IOSTAT ? Error message: ? Error reading namelist EXCEPTIONS ? IoMsg: A READ operation tried to read past the end-of-file. ? Please check input list against code. ? Error from processor: 0 ? Error number: 0 ??? ---
**Author:** ![grenville](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/grenville/32/29_2.png) [@grenville](https://cms-helpdesk.ncas.ac.uk/u/grenville)\ **Post date:** [13 September 2022 15:40 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/6 "2022-09-13T15:40:06Z")
Ella I suspect it’s read past the end of `SHARED` ```auto FILE_MANAGER: Assigned : SHARED (see FILE_MANAGER: : Unit : 11 (fortran) ???????????????????????????????????????????????????????????????????????????????? ???!!!???!!!???!!!???!!!???!!! ERROR ???!!!???!!!???!!!???!!!???!!! ? Error code: 4001 ? Error from routine: CHECK_IOSTAT ? Error message: ? Error reading namelist EXCEPTIONS ? IoMsg: A READ operation tried to read past the end-of-file. ? Please check input list against code. ? Error from processor: 0 ? Error number: 0 ???????????????????????????????????????????????????????????????????????????????? ``` which probably means there’s a mismatch between the namelist(s) created by Rose and those expected by the model. This suite is UM vn12.2 – u-co447 was UM vn12.0 (did that one work?) Grenville ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [13 September 2022 15:52 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/7 "2022-09-13T15:52:02Z")
ahaaa. u-co433 is the one that’s running (I used u-co447 to create my n2560 ancils). Currently having some issues with the Arctic suite u-cq635. But that’s by the by. cq758 and cq759 (Arctic/Antarctic free-running suites, respectively) are both 12.2 whereas the re-initialised suites are 12.0. How can I make the namelists match (or is there no quick fix for that?) ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [13 September 2022 18:12 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/8 "2022-09-13T18:12:36Z")
Got to the bottom of it: there are two extra entries in the SHARED namelist within glm\_um/rose-app.conf@L70 at vn12.2 [file:SHARED] source=(namelist:nlcfiles) namelist:nlstcall namelist:ancilcta namelist:temp\_fixes namelist:jules\_temp\_fixes namelist:carbon\_options namelist:coupling\_control namelist:model\_domain namelist:planet\_constants namelist:run\_dust namelist:run\_glomap\_aeroclim namelist:run\_ukca namelist:run\_gwd namelist:run\_vera namelist:run\_murk namelist:run\_convection **(namelist:run\_comorph)** namelist:run\_bl namelist:run\_precip namelist:run\_radiation namelist:run\_cloud namelist:run\_aerosol namelist:lam\_config namelist:run\_ozone namelist:run\_free\_tracers namelist:run\_eng\_corr namelist:gen\_phys\_inputs namelist:run\_dyn namelist:run\_dyntest namelist:easyaerosol namelist:jules\_model\_environment namelist:jules\_surface\_types namelist:jules\_surface namelist:jules\_radiation namelist:jules\_hydrology namelist:jules\_rivers (namelist:jules\_overbank) namelist:jules\_water\_resources namelist:jules\_sea\_seaice namelist:jules\_soil namelist:jules\_vegetation namelist:jules\_irrig namelist:jules\_soil\_biogeochem namelist:jules\_snow (namelist:jules\_urban) namelist:run\_stochastic namelist:run\_electric namelist:ancilcta (namelist:items(:)) **namelist:exceptions** Have amended this and it is now running. Looks like there are a few differences between vn12.0/12.2 app/um/rose-app.conf namelists too, but I’ll tackle those when I get there. Thanks for your help! E ---
**Author:** ![bassett](https://avatars.discourse-cdn.com/v4/letter/b/ed655f/32.png) [@bassett](https://cms-helpdesk.ncas.ac.uk/u/bassett)\ **Post date:** [14 September 2022 08:55 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/9 "2022-09-14T08:55:29Z")
Hi Grenville / Ella, we’re also experiencing issues when setting free running to True. Receive a mod is undefined error. ![Screenshot 2022-09-14 at 09.52.54](https://europe1.discourse-cdn.com/flex013/uploads/cms_support/original/1X/60bb1b6bd6836346c391c635c19e3028867df080.png) Ella - is it ok to take a look at your suite to see the changes you made to get it to work? Grenville - when will the archer2 fix for this be released? Much appreciated Richard ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [14 September 2022 09:09 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/10 "2022-09-14T09:09:49Z")
Hi Richard, Of course! I’m still working through a couple of fixes to the namelists, but I’ll pop a comment here to let you know when I’m done and commit the changes for you. Cheers, Ella ---
**Author:** ![bassett](https://avatars.discourse-cdn.com/v4/letter/b/ed655f/32.png) [@bassett](https://cms-helpdesk.ncas.ac.uk/u/bassett)\ **Post date:** [14 September 2022 09:19 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/11 "2022-09-14T09:19:36Z")
Amazing thank you! ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [14 September 2022 17:22 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/12 "2022-09-14T17:22:37Z")
Hi Richard, I’ve just committed a version of suite u-cq759 which is running at vn12.2 on archer2 in free-running mode. There were a lot of finnicky namelist changes to get it to run so hopefully this saves you some effort! Best wishes, Ella ---
**Author:** ![bassett](https://avatars.discourse-cdn.com/v4/letter/b/ed655f/32.png) [@bassett](https://cms-helpdesk.ncas.ac.uk/u/bassett)\ **Post date:** [15 September 2022 11:31 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/13 "2022-09-15T11:31:09Z")
Brilliant this is really great and will certainly save us considerable time! I had a quick test and it looks to be missing the /site/ncas-cray-ex/ folder, wondering if its not synced across? Can’t see it in [https://code.metoffice.gov.uk/trac/roses-u/browser/c/q/7/5/9/trunk](https://code.metoffice.gov.uk/trac/roses-u/browser/c/q/7/5/9/trunk) (apologies if I missed it) Thanks Richard ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [16 September 2022 08:05 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/14 "2022-09-16T08:05:03Z")
Woops, well spotted - forgot to fcm add it! Will correct that now… E ---
**Author:** ![shakka](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/shakka/32/111_2.png) [@shakka](https://cms-helpdesk.ncas.ac.uk/u/shakka)\ **Post date:** [16 September 2022 08:45 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/15 "2022-09-16T08:45:04Z")
Hmm. Unfortunately after 30 mins I get an error in the fcst like this: Error from routine: set\_thermodynamic Error message: A total of 25 points had negative mass in set\_thermodynamic. This indicates the pressure fields are inconsistent between different levels and the model is about to fail. @Grenville, have I missed something when copying stuff over from u-by395 do you think? I’ve clearly done something! Cheers Ella ---
**Author:** ![system](https://europe1.discourse-cdn.com/flex013/uploads/cms_support/original/1X/1fd2411499ffcbc299fe756cd5cdf26e44956558.png) [@system](https://cms-helpdesk.ncas.ac.uk/u/system)\ **Post date:** [18 September 2022 08:45 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/16 "2022-09-18T08:45:31Z")
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**Author:** ![grenville](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/grenville/32/29_2.png) [@grenville](https://cms-helpdesk.ncas.ac.uk/u/grenville)\ **Post date:** [20 September 2022 16:19 UTC](https://cms-helpdesk.ncas.ac.uk/t/free-running-mode-with-vn12-nesting-suite/722/17 "2022-09-20T16:19:33Z")
Hi Ella I don’t think this is a problem with something missing from the suite – more some numerical instability in the model. There are several queries on our old helpdesk relating to set\_thermodynamics errors, see for example [#3136 (negative mass in set\_thermodynamic) – Old CMS Website](https://pumatest.nerc.ac.uk/trac/cms_website/ticket/3136), where the problem seemed to be resolved by shortening the time step. Perhaps try that. Grenville