# Vn13.3 AMIP suite on Archer2 **URL:** \ **Category:** Uncategorized\ **Tags:** Monsoon2, ARCHER2\ **Created:** [16 October 2024 15:10 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539 "2024-10-16T15:10:14Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [16 October 2024 15:10 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/1 "2024-10-16T15:10:14Z")
Hi, I’m trying to convert a suite, u-dk142, a copy of a Monsoon vn13.3 AMIP suite to work on Archer2 but I’m getting 2 errors I haven’t seen before: In fcm\_make\_um: [FAIL] ukca: name-spaces declared but not used [FAIL] fcm make -f /home4/home/n02-puma/jweber/cylc-run/u-dk142/work/19800411T0000Z/fcm\_make\_um/fcm-make.cfg -C /home/n02/n02/jweber/cylc-run/u-dk142/share/fcm\_make\_um -j 4 mirror.target=ln04:cylc-run/u-dk142/share/fcm\_make\_um mirror.prop{config-file.name}=2 # return-code=2 2024-10-16T15:08:35Z CRITICAL - failed/EXIT in fcm\_make\_pp [FAIL] pp/Postprocessing/platforms/transfer.py: merge results in conflict [FAIL] merge output: /home/n02/n02/jweber/cylc-run/u-dk142/share/fcm\_make\_pp/.fcm-make/extract/merge/pp/Postprocessing/platforms/transfer.py.diff [FAIL] source from location 0: svn://puma2.archer2.ac.uk/moci.xm/main/trunk/Postprocessing/platforms/transfer.py@4419 [FAIL] source from location 1: svn://puma2.archer2.ac.uk/moci.xm/main/branches/dev/annetteosprey/postproc\_2.3\_archer2/Postprocessing/platforms/transfer.py@3910 [FAIL] !!! source from location 2: svn://puma2.archer2.ac.uk/moci.xm/main/branches/dev/rosalynhatcher/postproc\_2.3\_pptransfer\_gridftp\_nopw/Postprocessing/platforms/transfer.py@4422 [FAIL] fcm make -f /home4/home/n02-puma/jweber/cylc-run/u-dk142/work/19800411T0000Z/fcm\_make\_pp/fcm-make.cfg -C /home/n02/n02/jweber/cylc-run/u-dk142/share/fcm\_make\_pp -j 4 mirror.target=ln04:cylc-run/u-dk142/share/fcm\_make\_pp mirror.prop{config-file.name}=2 # return-code=2 2024-10-16T15:08:33Z CRITICAL - failed/EXIT Do you have any advice on solving these? Thanks for your help, James ---
**Author:** ![mdalvi](https://avatars.discourse-cdn.com/v4/letter/m/ad7895/32.png) [@mdalvi](https://cms-helpdesk.ncas.ac.uk/u/mdalvi)\ **Post date:** [16 October 2024 16:33 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/2 "2024-10-16T16:33:36Z")
Hi James, I do not think the changes in fcm\_make\_pp and fcm\_make\_um (see snapshot) will work. For pp- there is [no branch](https://code.metoffice.gov.uk/trac/moci/browser/main/branches/dev/rosalynhatcher) with that name, so you might have to find out the appropriate one by looking at recent ARCHER suites. For um- the config\_revision is essential, otherwise the build will try to use code from head of the trunk and cause a mismatch with the setup. Mohit ![image](https://europe1.discourse-cdn.com/flex013/uploads/cms_support/original/1X/f2ba87c0e9dba4043a48e0db946dd075b36bc8bb.png) ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [16 October 2024 20:18 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/3 "2024-10-16T20:18:49Z")
Thanks, Mohit. I added the config\_revision back in but the fcm\_make\_um error has persisted. For the fcm\_make\_pp error, I tried with Ros’ postproc\_2.4\_archer2\_jasmin\_rewrite@5092 and also with pp\_sources blank and, on both occasions, it generated the same error as above. I haven’t found another vn13.3 Archer2 suite - I was hoping to use vn13.3 to make use of Dan Grosvenor’s updated hygroscopicity fix. The name-spaces error in fcm\_make\_um particularly confusing. Can you think of anything else to try? Cheers, James ---
**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:** [17 October 2024 07:57 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/4 "2024-10-17T07:57:25Z")
James You have ROSE\_APP\_OPT\_CONF\_KEYS = archer2 which is picking up a UM12.1 config branch. Probably just delete this line from archer2.rc Take a look at my u-dj927. Grenville ---
**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:** [17 October 2024 08:09 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/5 "2024-10-17T08:09:20Z")
should have said - that’s in this section [[UMBUILD]] [[[environment]]] CONFIG = ncas-ex-cce OPENMP= true OPTIM = safe PREBUILD = ROSE\_APP\_OPT\_CONF\_KEYS = archer2 check for other optional overrides ---
**Author:** ![Luke](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/luke/32/45_2.png) [@Luke](https://cms-helpdesk.ncas.ac.uk/u/Luke)\ **Post date:** [17 October 2024 08:15 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/6 "2024-10-17T08:15:13Z")
Hi James, The changes that Mohit and Grenville may have got your suite working. If your suite is nudged, another option could be to take a look at my suite [u-db533](https://code.metoffice.gov.uk/trac/roses-u/log/d/b/5/3/3/trunk) - this is a UM13.1 nudged UKESM1.1 AMIP suite on ARCHER2. It should be possible to upgrade this to UM13.3 and then apply the differences from your Monsoon2 suite to get a working equivalent. Best wishes, Luke ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [17 October 2024 11:07 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/7 "2024-10-17T11:07:50Z")
Thanks, Grenville. I removed the ROSE\_APP\_OPT\_CONF\_KEYS = archer2 in the UMBUILD section which in my AMIP suite is closest to your coupled suite u-dj927 but the I got the same error messages. I then removed it from the ATMOS\_RESOURCE section as well and got the same error messages. Finally I removed it from the EXTRACT\_RESOURCE section, which left the [[Environment]] subsection blank and the run failed as before. The suite.rc file also has: ROSE\_APP\_OPT\_CONF\_KEYS = {{CONFIG\_OPT}} {{BITCOMP\_NRUN\_OPT}} Should that be removed/altered too\> Thanks, Luke. I’m not planning to run nudged but could try upgrading the suite. Is there any documentation on how to do that? Thanks, James ---
**Author:** ![RosalynHatcher](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/rosalynhatcher/32/11_2.png) [@RosalynHatcher](https://cms-helpdesk.ncas.ac.uk/u/RosalynHatcher)\ **Post date:** [17 October 2024 18:37 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/8 "2024-10-17T18:37:35Z")
Hi James, The merge conflicts you are getting for `fcm_make_pp` are because you are still using postproc\_2.4 trunk with postproc\_2.3 branches which won’t work. Either remove the override file `app/fcm_make_pp/opt/rose-app-archer2.conf` or delete its contents. Then follow the instructions here for postproc\_2.4: [https://cms.ncas.ac.uk/unified-model/postproc/](https://cms.ncas.ac.uk/unified-model/postproc/) to upgrade postproc for ARCHER2. Similarly delete the contents of the `app/fcm_make_um/opt/rose-app-archer2.conf` as it is still picking up the UM12.1 config branch due to a higher level setting. Regards, Ros. ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [17 October 2024 20:47 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/9 "2024-10-17T20:47:51Z")
Thanks, Ros. I’ve worked through your advice and that on [https://cms.ncas.ac.uk/unified-model/postproc/](https://cms.ncas.ac.uk/unified-model/postproc/). I think something may have gone wrong with the ```auto cp ~um1/jdma/jdma.rc ~/roses/ cp -r ~um1/jdma/metadata/ncas_extras ~/roses//meta ``` section as I get the below error when I try to run **[FAIL]** cylc validate -o /tmp/tmp4FDt5S --strict u-dk142 # return-code=1, stderr= **[FAIL]** Jinja2Error: **[FAIL]** File “/home/n02/n02/jweber/cylc-run/u-dk142/jdma.rc”, line 1, in top-level template code **[FAIL]** {% if RUN and POSTPROC and PPTRANSFER and JDMA %} **[FAIL]** UndefinedError: ‘RUN’ is undefined I haven’t done the pp transfer tasks yet as I need to work out how and where to put the data on Jasmin. Are they required for the jdma? Cheers, James ---
**Author:** ![RosalynHatcher](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/rosalynhatcher/32/11_2.png) [@RosalynHatcher](https://cms-helpdesk.ncas.ac.uk/u/RosalynHatcher)\ **Post date:** [18 October 2024 07:44 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/10 "2024-10-18T07:44:45Z")
Hi James, The tasks are named slightly differently in your suite. In `jdma.rc` change the first line to be: `{% if TASK_RUN and TASK_POSTPROC and TASK_PPTRANSFER and JDMA %}` Then try running again. We can sort out the settings for pptransfer and jdma (if using) later once you’ve got the model running. Cheers, Ros. ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [22 October 2024 08:17 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/11 "2024-10-22T08:17:59Z")
Thanks, Ros. u-dk142 now runs but doesn’t seem to archive anything on Archer2 (I have a directory on work /work/n02/n02/jweber/archive) - can this be done separately to the pptransfer to Jasmin? I will also look to get the Jasmin transfer working. Cheers, James ---
**Author:** ![RosalynHatcher](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/rosalynhatcher/32/11_2.png) [@RosalynHatcher](https://cms-helpdesk.ncas.ac.uk/u/RosalynHatcher)\ **Post date:** [22 October 2024 12:11 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/12 "2024-10-22T12:11:25Z")
Hi James, The postproc step hasn’t run successfully yet and this is the step that puts data in the `/work/n02/n02/jweber/archive` directory. If you look in the job.err file for the postproc task you will see that it ran out memory. In site/archer2.rc in section `[[POSTPROC_RESOURCE]]` try up’ing the memory requested for this task by adding ```auto [[[directives]]] --mem = 25Gb ``` Reload the suite and retrigger the postproc task. Once we’ve got postproc working, if you’re transferring the data to JASMIN we should then configure the suite so it automatically deletes the data from ARCHER2 once it has been successfully transferred. Let me know once you’ve got postproc working ok and I’ll tell you what to do next. Regards, Ros. ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [23 October 2024 08:50 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/13 "2024-10-23T08:50:34Z")
Thanks, Ros. u-dk142 now sends output to the archive directory. I will follow the steps for setting up the transfer to Jasmin and let you know if I have any problems. Cheers, James ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [24 October 2024 08:13 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/14 "2024-10-24T08:13:44Z")
Hi Ros, u-dk142 is stuck on submit-retrying for pptransfer with the job.err message Lmod is automatically replacing “cce/15.0.0” with “gcc/11.2.0”. Due to MODULEPATH changes, the following have been reloaded: 1. cray-mpich/8.1.23 [WARN] file:atmospp.nl: skip missing optional source: namelist:moose\_arch [WARN] file:atmospp.nl: skip missing optional source: namelist:script\_arch [WARN] [SUBPROCESS]: Command: globus-url-copy -vb -cd -r -cc 4 -sync -cred /work/n02/n02/jweber/cred.jasmin /work/n02/n02/jweber/cylc-run/u-dk142/share/cycle/19800101T0000Z/u-dk142/19800101T0000Z/ gsiftp://gridftp1.jasmin.ac.uku-dk142/19800101T0000Z/ [SUBPROCESS]: Error = 1: error: Unable to check destination url for sync: gsiftp://gridftp1.jasmin.ac.uku-dk142/19800101T0000Z/ globus\_xio: Unable to connect to gridftp1.jasmin.ac.uku-dk142:2811 globus\_xio: globus\_libc\_getaddrinfo failed. globus\_common: Name or service not known [WARN] Transfer command failed: globus-url-copy -vb -cd -r -cc 4 -sync -cred /work/n02/n02/jweber/cred.jasmin /work/n02/n02/jweber/cylc-run/u-dk142/share/cycle/19800101T0000Z/u-dk142/19800101T0000Z/ gsiftp://gridftp1.jasmin.ac.uku-dk142/19800101T0000Z/ [ERROR] transfer.py: Unknown Error - Return Code=1 [FAIL] Command Terminated [FAIL] Terminating PostProc… [FAIL] transfer.py \<\<‘ **STDIN** ’ [FAIL] [FAIL] ‘ **STDIN** ’ # return-code=1 2024-10-24T05:06:55Z CRITICAL - failed/EXIT Could this be linked to upcoming retirement of the xfer-sp server on Jasmin? Cheers, James ---
**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:** [24 October 2024 08:29 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/15 "2024-10-24T08:29:46Z")
James Please confirm that you have followed these instructions [Configuring PPTransfer](https://cms.ncas.ac.uk/unified-model/pptransfer/) ? Grenville ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [24 October 2024 15:47 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/16 "2024-10-24T15:47:23Z")
Hi Grenville, I thought I had done all the changes but realised the transfer\_dir had not been defined. When I added that, u-dk142 throw an error (below) in the atmos\_main (despite completing it successfully before) so I am trying to work why that has happened. ? Error code: 58 ? Error from routine: UKCA\_CHEMISTRY\_CTL ? Error message: ERROR: Number of chemical active species /= jpctr ? Error from processor: 464 Once I have solved that, I will return to the pptransfer challenge and let you know how I get one. Thanks, James ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [25 October 2024 11:42 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/17 "2024-10-25T11:42:45Z")
Hi Grenville, I’ve switched to use u-dk384 which is a copy of u-dk142@301081 before I made the stash changes which caused the above atmos\_main error. u-dk384 has all the modification listed in the Configuring PPTransfer link, including the transfer dir and completes atmos\_main. I also checked the credential is valid. However, it is still failing on pptransfer with Lmod is automatically replacing “cce/15.0.0” with “gcc/11.2.0”. Due to MODULEPATH changes, the following have been reloaded: 1. cray-mpich/8.1.23 [WARN] file:atmospp.nl: skip missing optional source: namelist:moose\_arch [WARN] file:atmospp.nl: skip missing optional source: namelist:script\_arch [WARN] [SUBPROCESS]: Command: globus-url-copy -vb -cd -r -cc 4 -sync -cred /work/n02/n02/jweber/cred.jasmin /work/n02/n02/jweber/cylc-run/u-dk384/share/cycle/19800101T0000Z/u-dk384/19800101T0000Z/ gsiftp://gridftp1.jasmin.ac.uk/gws/nopw/j04/sheffield/jweber/archive/u-dk384/19800101T0000Z/ [SUBPROCESS]: Error = 1: error: Unable to check destination url for sync: gsiftp://gridftp1.jasmin.ac.uk/gws/nopw/j04/sheffield/jweber/archive/u-dk384/19800101T0000Z/ globus\_ftp\_client: the server responded with an error 530 530-Login incorrect. : globus\_gss\_assist: Gridmap lookup failure: Could not map /DC=uk/DC=ac/DC=jasmin/O=STFC RAL/CN=jmw240 530- 530 End. [WARN] Transfer command failed: globus-url-copy -vb -cd -r -cc 4 -sync -cred /work/n02/n02/jweber/cred.jasmin /work/n02/n02/jweber/cylc-run/u-dk384/share/cycle/19800101T0000Z/u-dk384/19800101T0000Z/ gsiftp://gridftp1.jasmin.ac.uk/gws/nopw/j04/sheffield/jweber/archive/u-dk384/19800101T0000Z/ [ERROR] transfer.py: Unknown Error - Return Code=1 [FAIL] Command Terminated [FAIL] Terminating PostProc… [FAIL] transfer.py \<\<‘ **STDIN** ’ [FAIL] [FAIL] ‘ **STDIN** ’ # return-code=1 2024-10-25T10:29:20Z CRITICAL - failed/EXIT Thanks, James ---
**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:** [25 October 2024 13:58 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/18 "2024-10-25T13:58:10Z")
James There has been a similar error reported - [https://cms-helpdesk.ncas.ac.uk/t/gridftp-transfer-from-archer2-to-jasmin/702](https://cms-helpdesk.ncas.ac.uk/t/gridftp-transfer-from-archer2-to-jasmin/702). The solution seemed to be related to not having access to hpxfer. Can you ssh to [hpxfer1.jasmin.ac.uk](http://hpxfer1.jasmin.ac.uk) from ARCHER? Does a simple list work from the Archer2 command line: `globus-url-copy -vb -cred /work/n02/n02/jweber/cred.jasmin -list gsiftp://gridftp1.jasmin.ac.uk/home/users/jmw240` Grenville ---
**Author:** ![James\_Weber](https://avatars.discourse-cdn.com/v4/letter/j/e495f1/32.png) [@James\_Weber](https://cms-helpdesk.ncas.ac.uk/u/James_Weber)\ **Post date:** [25 October 2024 14:14 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/19 "2024-10-25T14:14:56Z")
Hi Grenville, When I run jweber@ln01:~\> globus-url-copy -vb -cred /work/n02/n02/jweber/cred.jasmin -list gsiftp://gridftp1.jasmin.ac.uk/home/users/jmw240 The output is: gsiftp://gridftp1.jasmin.ac.uk/home/users/jmw240 jmw240 When I ran ssh -YAX [jmw240@hpxfer1.jasmin.ac.uk](mailto:jmw240@hpxfer1.jasmin.ac.uk) on archer2, the response was: ssh: connect to host [hpxfer1.jasmin.ac.uk](http://hpxfer1.jasmin.ac.uk) port 22: Connection refused I’ve just seen that my user role for the hpxfer server has expired. When I try to apply to extend it, I am asked for “The IP address from which you will be accessing the high-performance transfer machines. If you are not sure what to put here, please contact your local network administrator.” Would this be my reading IP address or an Archer2 address? Thanks, James ---
**Author:** ![RosalynHatcher](https://dub1.discourse-cdn.com/flex013/user_avatar/cms-helpdesk.ncas.ac.uk/rosalynhatcher/32/11_2.png) [@RosalynHatcher](https://cms-helpdesk.ncas.ac.uk/u/RosalynHatcher)\ **Post date:** [25 October 2024 14:30 UTC](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539/20 "2024-10-25T14:30:11Z")
Hi James, On that page it should give a dummy IP address you can enter if you going from ARCHER2 as they already know about it, otherwise ARCHER2 IP address is fine. Updated: The dummy address is: 130.246.130.166 Cheers, Ros [Next page](https://cms-helpdesk.ncas.ac.uk/t/vn13-3-amip-suite-on-archer2/1539.md?page=2)