1. NCAS Unified Model Introduction Part 1b: Running the UM University of Reading, 3-5 December 2014

2. Contents The UM User Interface (UMUI) Running a UM job UM output 2

3. UM User Interface The UMUI is a graphical window-based interface to the UM. It is available via the PUMA service, which provides: – All the latest UMUI changes – Centralised access to local files (hand-edits etc) – A common job database for all academic and MONSooN users The UMUI allows users to select the code version, scientific configuration and run-time options. The UMUI then creates the scripts which control the UM run. – Further changes to these scripts can be made via hand-edits. It also assigns values to namelists that are read in by the UM at runtime. 3

4. Creating a UM job Choose a UM job from UKMO, NCAS or a colleague that is close to what you wish to run. –Either copy the job into your own job if they are in the same local database, –or upload (import) a basis file (the full description of a UM job which has come from another UMUI database) into your own job. NCAS standard jobs should be available under the umui owner. Basis files can be downloaded (exported) from the UMUI and emailed. – Note that additional UMUI files (hand-edits, STASHmasters etc) and data files may also need to be copied to the target system. 4

5. Experiments: e.g. xxab A grouping of UM jobs Identified by a description in the UMUI Only your experiments are displayed by the UMUI, unless otherwise requested Experiments can be created, copied and deleted Jobs: e.g. xxabc Up to 26 jobs can be grouped in an experiment Jobs can be created, copied and deleted 2 jobs can be differenced (if using the same UM version) Within a job: Navigation window > input windows (Note that these can very between UM versions.) UMUI vocabulary 5

6. 6

7. How UM jobs are defined UM jobs are defined by: A UM version (e.g. vn8.2) Specific UMUI settings (and hand-edits which alter these) A particular horizontal and vertical resolution A list of changes to the main code base, in the form of FCM branches. A defined set of input files: start files, ancillary files and lateral boundary conditions. Modelling systems such as HadGEM3 or UKV span different UM versions and have specific “standard jobs” as they develop over time. 7

8. The UM User Interface (UMUI) Running a UM job UM output 8

9. Submitting a job The UM uses namelists for setting parameters at runtime; these are set in the UMUI. 9 scripts namelists code What do you need to know about the system where the UM is installed? directory structure and disk space setup job submission mechanism and queue structures input files available e.g. start files, ancillary files PUMAHPC (MONSooN/Archer) UM run process UMUI submit

10. Stage 1: Compilation The compilation is handled by the Flexible Configuration Management (FCM) system which: manages code components; creates Makefiles for compilation and loading; compiles and links the code according to options selected; creates an executable. UMUI settings: Compilation and Run Options -> Compile and run options for Atmosphere and Reconfiguration – “Compile Model executable” – “Run the model” – “Directory for the Model executable” : Usually $DATAW/bin – “Filename for the Model executable” : Often $RUNID.exe 10

11. Stage 2: Reconfiguration The reconfiguration is a stand-alone program which modifies UM atmosphere start files (and ocean files for UM 6.6.3 and earlier). Compiled with FCM Runs as a parallel application Produces a new start file UMUI settings: Compilation and Run Options -> Compile and run options for Atmosphere and Reconfiguration – “Compile Reconfiguration executable” – “Run the reconfiguration” – “Directory for the Reconfiguration executable” : Usually $DATAW/bin – “Filename for the Reconfiguration executable” : Often qxreconf 11

12. Stage 3: Running UMUI settings: Input/Output Control and Resources -> Start Date and Run Length Options – “Specify the date and time of the start dumps” – “Target run length” For a given run length, the number of processors and length of time to request depend on the queue structure of the machine and the performance of the job. 12

13. Stage 3: Running User Information and Submit Method -> Job submission method – “Define submission method” ‘qsub’ for PBS Pro : Cray XC30 (Archer) Loadleveler : IBMs (MONSooN) Linux ‘at’ : Local PCs and workstation – “Number of processes for ATMOS East-West” – “Number of processes for ATMOS North-South” User Information and Submit Method -> Job submission method -> Qsub – “Job time limit” 13

14. The UM User Interface (UMUI) Running a UM job UM output 14

15. STASH Spatial and Temporal Averaging and Storage Handling 1) Select diagnostic from Load New Diagnostic section 2) Time profilewhen diagnostic will be output (start and end time and frequency) whether time processing required (accumulation, mean, time series) 3) Domain profile vertical (specify which levels) horizontal (limited area, meaning [zonal, vertical, meridional, horizontal], weighting) 4) Usage profile select output unit for the diagnostic 15

16. 16

17. STASH in the UMUI The UMUI windows for STASH are different from model windows. Diagnostics -> load new diagnostics -> (double click on the section) Available diagnostics are organised in sections. Some diagnostics have HELP information, a lot don’t! Just because a diagnostic is available doesn’t mean it works! 17

18. Verify diagnostics (Ctrl+V) Package switched onPackage switched off 18

19. STASHmaster file Contains information on all the atmosphere diagnostics available 19 H1| SUBMODEL_NUMBER=1 H2| SUBMODEL_NAME=ATMOS H3| UM_VERSION=8.4 # #|Model |Sectn | Item |Name | #|Space |Point | Time | Grid |LevelT|LevelF|LevelL|PseudT|PseudF|PseudL|LevCom| #| Option Codes | Version Mask | Halo | #|DataT |DumpP | PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PCA | #|Rotate| PPF | USER | LBVC | BLEV | TLEV |RBLEVV| CFLL | CFFF | # #=============================================================================== # 1| 1 | 0 | 2 |U COMPNT OF WIND AFTER TIMESTEP | 2| 2 | 0 | 1 | 18 | 1 | 1 | 2 | 0 | 0 | 0 | 0 | 3| 000000000000010000000000000000 | 00000000000000000001 | 1 | 4| 1 | 2 | -3 -3 -3 -3 -12 20 -99 -99 -99 -99 | 5| 0 | 56 | 0 | 65 | 0 | 0 | 0 | 0 | 5 | # On puma: /home/umui/umui/umui2.0/ /variables/STASH_master_A

20. Adding new diagnostics Users can add new diagnostics Advice via the CMS website (STASH user guide) Users must provide a STASHmaster file to the UMUI: Atmosphere -> STASH -> User-STASHmaster files. Users can copy the diagnostics settings from one UM job to another using: copy_stash This script takes as input two UM basis files. The two jobs must be at the same UM version. 20

21. UM output listing Text output from the UM is written to a.leave file: e.g. xagmc000.xagmc.o98342.t14136.leave Stored in: $HOME/output Output listing options controlled by UMUI Input/Output Control and Resources -> Output Choices The output listing can be quite large and confusing. Check output listing for Timings reported at the end of the listing file Key words like ERROR, ABORT, "file not found" Check presence of key files such as: executable after compilation start file after reconfiguration output files after model run 21