| 14 | | === historical, pre-industrial control |
| 15 | | |
| 16 | | There are two fully coupled UKESM1 configurations which each make use of all model components: one with science settings for a historical experiment, and one with settings for a pre-industrial control experiment. |
| 17 | | |
| 18 | | ||=''UM version''=||=''historical''=||=''pre-industrial control''=|| |
| 19 | | ||=vn11.2=||=[https://code.metoffice.gov.uk/trac/roses-u/browser/b/c/6/1/3/trunk u-bc613]=||=[https://code.metoffice.gov.uk/trac/roses-u/browser/b/c/9/6/4/trunk u-bc964]=|| |
| 20 | | |
| 21 | | === abrupt4xCO2, 1%CO2 |
| 22 | | |
| 23 | | Configurations for abrupt4xCO2 and 1%CO2 experiments can be created using the pre-industrial control experiment as a starting point. |
| 24 | | |
| 25 | | To create a suite for the abrupt4xCO2 experiment, first make a copy of the [https://code.metoffice.gov.uk/trac/roses-u/browser/b/c/9/6/4/trunk pre-industrial control suite], then in `um -> namelist -> UM Science Settings -> Section 01-02 - Radation -> GAS MMRs`, set `co2_mmr=1.72728e-03`. |
| 26 | | |
| 27 | | To create a suite for the 1xCO2 experiment, first make a copy of the [https://code.metoffice.gov.uk/trac/roses-u/browser/b/c/9/6/4/trunk pre-industrial control suite], then in `um -> namelist -> UM Science Settings -> Section 01-02 - Radation -> GAS MMRs -> Varying gas MMRs`, set `l_clmchfcg=.true.` to enable time-varying GHGs. Finally, in the sub-panel `Varying CO2 MMRs`, set |
| 28 | | |
| 29 | | {{{ |
| 30 | | clim_fcg_levls_co2=4.3182e-04 |
| 31 | | clim_fcg_nyears_co2=1 |
| 32 | | clim_fcg_rates_co2=1.0 |
| 33 | | clim_fcg_years_co2=1849 |
| 34 | | }}} |
| 35 | | |
| 36 | | |
| 37 | | See [#Sciencenotes below] for more on the science settings of the model. |
| 38 | | |
| 39 | | == Options for running the model |
| 40 | | |
| 41 | | By default, each UKESM1 suite is set up to run the model on the Met Office HPC. The suite offers several options for specifying how the model is to be run, including: |
| 42 | | |
| 43 | | * login node to be used for submission to Met Office HPC: `suite conf -> Machine Options -> MetO Cray login node` |
| 44 | | * Met Office queue to which jobs will be submitted: `suite conf -> Machine Options -> HPC queue` |
| 45 | | |
| 46 | | Options for specifying the account under which jobs will be run are available in `suite conf -> Project Accounting`: |
| 47 | | |
| 48 | | * Select `Use default account` to use the default account for your department. |
| 49 | | * If this is set to `false`, then choose an option from the `Account` menu. |
| 50 | | * If the option is `other`, then enter the account explicitly in `'Other' user account`. |
| 51 | | |
| 52 | | === Running on other machines |
| 53 | | |
| 54 | | The model may be run on other (i.e. non-Met Office) machines. See [wiki:UKESM/UKESM1intro#Backgroundandprerequisites here] for more on available resources and how to access them. More specific instructions for suite settings for different machines are given in the following subsections. |
| 55 | | |
| 56 | | ==== Monsoon |
| 57 | | |
| 58 | | To run on Monsoon, the Met Office / NERC collaborative platform, set `suite conf -> Machine Options -> Site at which model is being run` to `MONSooN`. |
| 59 | | |
| 60 | | Output files created by the suite running on Monsoon may be archived via the Met Office Operational Storage Environment (MOOSE). The options for requesting this can be found under the `postproc -> Post Processing - common settings` control panel. Set `archive_command` to `Moose` and provide (or check) values for further options in the subpanel `Moose Archiving`. See [#Archivingofduplexeddata below] for more on the `non_duplexed_set` option. |
| 61 | | |
| 62 | | Note that you must have a MOOSE account before archiving can work - see [#Support below] for help. |
| 63 | | |
| 64 | | ==== NEXCS |
| 65 | | |
| 66 | | To use NEXCS, the NERC-only share of Monsoon, set `suite conf -> Machine Options -> Site at which model is being run` to `MONSooN` and select a NEXCS account for running jobs (see [#Optionsforrunningthemodel above]). |
| 67 | | |
| 68 | | Output files created by the suite running on NEXCS may be archived to disk. The options for requesting this can be found under the `postproc -> Post Processing - common settings` control panel. Set `archive_command` to `NEXCS` and provide values for `archive_root_path` and `archive_name` in the subpanel `Archer Archiving` (sic) to specify the location of the archived files on NEXCS. |
| 69 | | |
| 70 | | Following archiving, the files may be optionally transferred to a remote machine such as JASMIN. Provide values for `remote_host` (the address of the remote machine) and `transfer_dir` (the location of the archived files on the remote machine) in the subpanel `JASMIN Transfer`. In addition, transferring must be turned on by setting `suite conf -> Build and Run -> PP Transfer` to `true`. |
| 71 | | |
| 72 | | Note that, before transfer from NEXCS to JASMIN can work, some setup of communications is required - see [wiki:Docs/PostProcessingAppNexcsSetup#sshjasmin here] for more details. |
| 73 | | |
| 74 | | ==== Archer |
| 75 | | |
| 76 | | To run on Archer, the NERC platform, set `suite conf -> Machine Options -> Site at which model is being run` to `Archer` and set these other `Machine Options`: |
| 77 | | |
| 78 | | * `Use Environment Modules` to `Custom module files` |
| 79 | | * `Science Configuration Module Name` to `GC3-PrgEnv/2.0/90386` |
| 80 | | * `Module file location` to `/work/y07/y07/umshared/moci/modules/modules` |
| 81 | | |
| 82 | | In addition, the following tests (see [#Testsinthesuite below]) ''must'' be turned off when running on Archer: |
| 83 | | |
| 84 | | * `Test restartability` |
| 85 | | * `Test rigorous compiler option` |
| 86 | | * `Test PE decomposition change` |
| 87 | | * `Archive integrity` |
| 88 | | * `CPMIP Analysis -> CPMIP load balancing analysis` |
| 89 | | |
| 90 | | Output files created by the suite running on Archer may be archived to disk. The options for requesting this can be found under the `postproc -> Post Processing - common settings` control panel. Set `archive_command` to `Archer` and provide values for `archive_root_path` and `archive_name` in the subpanel `Archer Archiving` to specify the location of the archived files on Archer. |
| 91 | | |
| 92 | | Following archiving, the files may be optionally transferred to a remote machine such as JASMIN. Provide values for `remote_host` (the address of the remote machine) and `transfer_dir` (the location of the archived files on the remote machine) in the subpanel `JASMIN Transfer`. In addition, transferring must be turned on by setting `suite conf -> Build and Run -> PP Transfer` to `true`. |
| 93 | | |
| 94 | | Note that, before transfer from Archer to JASMIN can work, some setup of communications (specifically, ''both'' [wiki:Docs/PostProcessingAppArcherSetup#sshpumatodtn between PUMA and Archer data transfer node], ''and'' [wiki:Docs/PostProcessingAppArcherSetup#sshdtntojasmin between Archer data transfer node and JASMIN]) is required. |
| 95 | | |
| 96 | | == Using the model in a CMIP6 production run |
| 97 | | |
| 98 | | Using the model in a CMIP6 production run requires the provision of extra information (for example, the MIP and the experiment to which the run is contributing). This information must be specified in the suite, and the suite will check its validity. See [https://code.metoffice.gov.uk/trac/ukcmip6/wiki/CMIP6/RoseSuiteMetadata here on the MOSRS] for more details about this information. |
| 99 | | |
| 100 | | By default, the suite is ''not'' set up to run in full CMIP6 production mode, so this information is not required. To change this, set `suite info -> project` to `u-cmip6` (which will expose the interface in `suite info` for collecting this information) and set `suite conf -> Project Accounting -> CMIP6 Experiment` to `true` (which will turn on the validation of the information). More information on setting up a CMIP6 experiment is available [https://code.metoffice.gov.uk/trac/ukcmip6/wiki/ExperimentGuidance here on the MOSRS]. |
| 101 | | |
| 102 | | == Archiving of duplexed data |
| 103 | | |
| 104 | | When running on Met Office machines (including Monsoon), the suite will, by default, archive ''a single copy'' of its data to MOOSE. For critical model runs, this setting may be changed to archive two copies of the data (i.e. duplex) by switching `non_duplexed_set` in `postproc -> Post Processing-common settings -> Moose Archiving` to `false`. Further guidance on when to choose this option is available at http://www-twiki/Main/MassNonDuplexPolicy (note that this link only works from within the Met Office). |
| 105 | | |
| 106 | | == Compute resource usage |
| 107 | | |
| 108 | | The compute resources used by the suite can be set via parameters on the `Machine Options` and `Domain Decomposition` control panels under `suite conf`. The following discussion is specific to the Met Office HPC for the most part, but may still be helpful for users of other machines. |
| 109 | | |
| 110 | | The type of compute node can be set via `suite conf -> Machine Options -> XC40 core type`: a `Haswell` node has 32 cores, while `Broadwell` has 36. |
| 111 | | |
| 112 | | The suite is currently set up in `suite conf -> Domain Decomposition` to use 36 nodes (see [#Calculationofnodecount below] for more details on how this is calculated). An alternative setup uses 19 nodes. Parameter settings for both setups are: |
| 113 | | |
| 114 | | ||=''Parameter''=||=''36 node suite''=||=''19 node suite''=|| |
| 115 | | ||=Atmosphere: Processes East-West=||=32=||=32=|| |
| 116 | | ||=Atmosphere: Processes North-South=||=18=||=18=|| |
| 117 | | ||=IO Server Processes=||=0=||=0=|| |
| 118 | | ||=OpenMP threads for the atmosphere=||=2=||=1=|| |
| 119 | | ||=NEMO: Number of processes East-West=||=12=||=9=|| |
| 120 | | ||=NEMO: Number of processes North-South=||=9=||=8=|| |
| 121 | | ||=NEMO: Number of processes in XIOS server=||=6=||=6=|| |
| 122 | | ||=OpenMP threads for the ocean=||=1=||=1=|| |
| 123 | | |
| 124 | | Note that the ocean must be rebuilt (by setting `suite conf -> Build and Run -> Build Ocean` to `true`) whenever the NEMO parameters in the table are changed during a run. |
| 125 | | |
| 126 | | Setting these parameters to other values may require load balancing to ensure that HPC resources are being used in the most efficient fashion. |
| 127 | | |
| 128 | | === Calculation of node count |
| 129 | | |
| 130 | | On `Domain Decomposition -> Atmosphere`, the number of processes used by the UM can be set via `Atmosphere: Processes East-West` and `Atmosphere: Processes North-South`; additional processes for the IO Server may be requested using `IO Server Processes`. Finally, `OpenMP threads for the atmosphere` sets the number of threads for each process; multiplying this by the number of processes gives the number of compute tasks. |
| 131 | | |
| 132 | | Using the parameter values for the ''36 node suite'', the number of tasks used by the UM is `(32 * 18 + 0) * 2 = 1152`. Dividing by the number of cores per node (in this case `36`) and rounding up (because different executables cannot run on the same node) gives `32` compute nodes used by the atmosphere. |
| 133 | | |
| 134 | | A similar calculation may be performed for the settings on `Domain Decomposition -> Ocean` using `NEMO: Number of processes East-West`, `NEMO: Number of processes North-South` and `OpenMP threads for the ocean` to give `12 * 9 * 1 = 108` tasks, or `3` compute nodes used by the ocean. |
| 135 | | |
| 136 | | Finally, on the same control panel, `NEMO: Number of processes in XIOS server` is set to `6`, which equates to `1` compute node used by XIOS. |
| 137 | | |
| 138 | | Thus, the total number of nodes used by the suite is `32 + 3 + 1 = 36`. |
| 139 | | |
| 140 | | == Tests in the suite |
| 141 | | |
| 142 | | The suite contains options for testing different aspects of the model including reproducible restarting, changes in processor decomposition, comparison to known good output and integrity of archived files. Some of these tests may be of more interest to developers than general users of the model; they can be turned on or off via the `suite conf -> Testing` control panel. |
| 143 | | |
| 144 | | === Testing for PE decomposition change |
| 145 | | |
| 146 | | Changing the PE decomposition will change the results of the model because of the behaviour of the chemistry solver within the UM. Thus, by default, the `Test PE decomposition change` test (see `suite conf -> Testing`) will fail, and so this test has been turned off. There is a version of the chemistry solver which does not change results; this can be selected by setting `l_ukca_asad_columns=.true.` in `app/um/rose-app.conf`. With this option selected, the PE decomposition change test should pass. |
| 147 | | |
| 148 | | Note that we do not select this version of the chemistry solver by default because it has a performance overhead; specifically, it causes an atmosphere-only job to run about 10% slower than when running with `l_ukca_asad_columns=.false.`. |
| 149 | | |
| 150 | | It should be noted that changing the PE decomposition for the ocean in UKESM will also change results because this changes results for both the iceberg code in NEMO and for the CICE code. This behaviour cannot be rectified by setting a single variable (that is, there is no analogue of `l_ukca_asad_columns` for NEMO and CICE). |
| 151 | | |
| 152 | | == Science notes |
| 153 | | |
| 154 | | The historical release job differs from the first member of the CMIP6 historical ensemble (`u-bb075`) in the following ways: |
| 155 | | * The anthropogenic SO2 emission ancillaries were produced using different methodologies. The resulting SO2 emission in the model is nearly identical but has differences at the bit level. |
| 156 | | * It includes a fix for the aerosol plume scavenging diagnostic 38900-38932 to ensure that they bit-compare across differing processor decompositions. The difference appears at only a small number of points where the value is very close to zero. |
| 157 | | |
| 158 | | The piControl release job differs from the CMIP6 piControl run (`u-aw310`) in the following ways: |
| 159 | | * The anthropogenic emission height is different. In the release job all anthropogenic SO2 is emitted at the surface, consistent with the model's treatment of other anthropogenic emissions (except NOx emissions from aircraft which are supplied with a vertical emission profile). In the CMIP6 piControl, around 30% of anthropogenic emissions were released at 500m. Because the 1850 anthropogenic emissions are tiny relative to natural emissions from volcanoes and the ocean, this difference in emission height makes no meaningful difference to the SO2 burden or the aerosol simulation. |
| 160 | | * The release job includes several diagnostic fixes which were not included in the CMIP6 piControl run. These include: |
| 161 | | a. The fix to plume scavenging diagnostics described above |
| 162 | | b. Corrections to diagnostics 30312, 30313, 30298 which were corrupted in the CMIP6 piControl |
| 163 | | c. Addition of some other diagnostics to CMIP6 PP streams |
| 164 | | |
| 165 | | == Known issues |
| 166 | | |
| 167 | | (none) |
| | 17 | A full description of how to access and run the AMIP configuration is [wiki:UKESM/RelNotes1.0/AMIP here], whilst [wiki:UKESM/RelNotes1.0/Coupled this page] contains the instructions for accessing and running the coupled configurations. |
