| cb9b02d | Balwinder Singh | 17 April 2019, 17:44:03 UTC | Removes GNU compiler entries | 17 April 2019, 17:44:03 UTC |
| b80f13b | Balwinder Singh | 17 April 2019, 16:53:35 UTC | Adds pnetcdf required by MPAS [BFB] - Bit-For-Bit | 17 April 2019, 16:53:35 UTC |
| 68ef274 | Balwinder Singh | 15 April 2019, 21:18:29 UTC | PGI works now and gnu builds fine gnu compiler builds fine but blows up during run time with following error: set_time_float_from_date: error return from ESMF_TimeSet for set_time_float_from_date ERROR: CHKRC [BFB] - Bit-For-Bit | 15 April 2019, 21:22:47 UTC |
| a87eddf | Balwinder Singh | 15 April 2019, 14:51:24 UTC | Adds machine files for Compy This PR adds first set of machine files for E3SM machine Compy. Machine files for compilers Intel, gnu and PGI are added. I have used the following test to compile and run the model: SMS.ne4_ne4.FC5AV1C-L For the above test: -Intel compiler works fine -GNU 4.8.5: Land model has a compile time error -PGI: Netcdf is not built with this compiler yet [BFB] | 15 April 2019, 21:22:47 UTC |
| 09f1a33 | Azamat Mametjanov | 14 April 2019, 21:25:40 UTC | Merge branch 'azamat/anvil/build-pnetcdf-run-netcdf' (PR #2853) Build PIO1 with pnetcdf on Anvil [BFB] | 14 April 2019, 21:25:40 UTC |
| 879bbaf | Azamat Mametjanov | 14 April 2019, 21:16:29 UTC | Build PIO1 with pnetcdf on Anvil | 14 April 2019, 21:16:29 UTC |
| 152fae6 | Azamat Mametjanov | 11 April 2019, 22:38:24 UTC | Merge branch 'azamat/anvil/backout-version-upgrades' (PR #2850) Anvil module updates. [non-BFB] - due to module version changes | 11 April 2019, 22:38:24 UTC |
| 8e69ae4 | Azamat Mametjanov | 11 April 2019, 22:27:18 UTC | Anvil module updates | 11 April 2019, 22:27:18 UTC |
| c726a77 | James Foucar | 11 April 2019, 19:19:44 UTC | Merge branch 'jgfouca/cime/improve_wget_robustness' into master (PR #2849) Improve robustness of wget Better error messages and avoid check certificates. [BFB] * jgfouca/cime/improve_wget_robustness: Improve robustness of wget Update CIME to ESMCI cime5.8.1 (PR #2842) | 11 April 2019, 19:21:30 UTC |
| d0da49e | James Foucar | 11 April 2019, 19:13:41 UTC | Improve robustness of wget Better error messages and avoid check certificates. [BFB] | 11 April 2019, 19:13:41 UTC |
| c947c07 | James Foucar | 10 April 2019, 19:08:29 UTC | Update CIME to ESMCI cime5.8.1 (PR #2842) Update CIME to ESMCI cime5.8.1 Squash merge of jgfouca/branch-for-to-acme-2019-04-08 Features: * Support optional components by filling in stub models for any missing component class * cprnc: Make FIELDLIST message more informative * cprnc: allow differences in field lists for time-constant fields Bug fixes: * The check for an rpointer.drv file did not consider multidriver mode. * Fix ./case.build --clean * PET and ERP tests were not setting compile_threaded correctly. * Fixes inconsistency between MPASCICE and MPASSI, change all occurances of the former to the latter This is non-BFB for A cases due to: ESMCI/cime#3053 [non-BFB] | 11 April 2019, 18:57:18 UTC |
| fae0a81 | Balwinder Singh | 11 April 2019, 16:19:56 UTC | Merge branch 'whannah/atm/aqua_planet_fix' (PR #2752) Restore Aquaplanet Capability Although there was a working aquaplanet compset that was sometimes used for testing, it included realistic topography that resulted in towering mountains of water. This PR adds new compsets to that are true aquaplanet configurations consistent with the Aquaplanet Experiment (APE) protocol. I adopted a different compset naming strategy instead of following the "FC5AV1" convention. The new compsets have short names like "F-EAMv1-AQP1", where the number at the end can be changed to match the SST patterns of the APE protocol (http://www.met.reading.ac.uk/~mike/APE/). The SST pattern is now controlled by "DOCN%AQP1" and set by the data ocean component in the CIME source directories. The old data ocean code in the atmosphere directories is obsolete, which is confusing, so I deleted it all. The atmosphere is set by "_CAM5%AQUA", which is very similar to the current FC5AV1C-L except that it includes the "-aquaplanet" flag that allows the domain and topography to be set internally without the need for external files. I also added a new cam.i file to the repo: cami_aquaplanet_ne30np4_L72_c15-02-2019.nc This PR resolves the following issues: Fixes #2383 Fixes #2719 Fixes #2841 Notes on regression tests: This PR replaces two existing tests (ERP_Ln9.ne4_ne4.FC5AV1C-L-AQUAP and SMS_Ld1.ne4_ne4.FC5AV1C-L-AQUAP,cam-clubb_only) with the following tests which use the new compset: ERP_Ln9.ne4_ne4.F-EAMv1-AQP1 SMS_Ld1.ne4_ne4.F-EAMv1-AQP1,cam-clubb_only Some caveats about these compsets: aerosols are still present, but the "constant droplet" mode is automatically activated. So while direct radiative impacts are still present, aerosol-cloud interactions should be effectively disabled. After doing some tests I noticed that the net TOA radiative balance was the opposite sign of what I normallly see from F-compsets. I think this is due to the combination of using different solar forcing data file and prescribed ozone. I based these choices on the current aquaplanet options in CAM6, but we may want to revisit how these things are set in the future. A new use case was added to have special default namelist settings, but orbital parameters cannot be set this way. Therefore, following the CAM6 code, I added the CAM_USER_MODS section within config_component.xml, which sets some values in the user_nl_cpl file. I wish there were a cleaner way of setting these, but this method works pretty well. [BFB] - This PR replaces two existing AQUAP tests with new ones * whannah/atm/aqua_planet_fix: Added aquaplanet check in mo_drydep.F90 Renamed compset long names to fix tests Updated ncdata default for ne4 and ne30 aquaplanet Changed aqua compsets in intergration test Fixed default ncdata file for aquaplanet Added new default aqua initial condition file Added new aqua-planet compsets Changed how aqua_mode is set Added aquaplanet to atmos configure script Added aquaplanet option to configure options modified log message in shr_strdata_mod Removed the cam_aqu and cam_dom directories Conflicts: cime/config/e3sm/tests.py components/cam/src/utils/cam_dom/ocn_comp.F90 components/cam/src/utils/cam_dom/sst_data.F90 | 11 April 2019, 16:19:56 UTC |
| a4d85f3 | jayeshkrishna | 10 April 2019, 20:34:52 UTC | Merge pull request #2840 from E3SM-Project/jayeshkrishna/suppress_pio_non_root_msgs Making sure that we print out PIO logs only from rank 0 of each component. This bug was introduced in PR #2799. Fixes #2839 [BFB] | 10 April 2019, 20:34:52 UTC |
| be9e9e7 | Junqi Yin | 09 April 2019, 21:06:38 UTC | Merge branch 'bishtgautam/lnd/emi-example' (PR #2823) Updates EMI for ELM Restructures the External Model Interface (EMI) directories and adds a demo code showing the usage of EMI. [BFB] | 09 April 2019, 21:06:38 UTC |
| 9fa4bf2 | Walter Hannah | 08 April 2019, 19:33:56 UTC | Added aquaplanet check in mo_drydep.F90 This check in get_landuse_and_soilw_from_file() avoids loading the drydep file for aquaplanet runs. modified: components/cam/src/chemistry/mozart/mo_drydep.F90 | 08 April 2019, 19:33:56 UTC |
| 37cbcfc | Min Xu | 06 April 2019, 04:06:26 UTC | Merge branch 'minxu74/machines/summit/update-ibm-compiler-wrapper' (PR #2724) Change the IBM Fortran and C wrappers from the Fortran 77 to Fortran 90 functionality and change their MPI wrappers to the common names (i.e. mpif90, mpicc, and mpicxx). | 06 April 2019, 04:06:26 UTC |
| dd99b92 | Azamat Mametjanov | 04 April 2019, 23:37:47 UTC | Merge branch 'sarich/anvil-condo-modules' (PR #2834) Update Anvil soft-env modules after the upgrade of the OS, module environment and update to SLURM. [non-BFB] - due to update of software libraries | 04 April 2019, 23:37:47 UTC |
| 8ff8ac6 | Azamat Mametjanov | 04 April 2019, 23:27:32 UTC | Update cprnc | 04 April 2019, 23:27:32 UTC |
| aecdb2c | jayeshkrishna | 04 April 2019, 22:38:08 UTC | Suppress pio logs on non-component-root processes Fixing a bug that was introduced in PR #2799 (commit : 3eebd7fe90a87f8e824989bddbd63ad053239aad ). Making sure that we print out PIO logs only from rank 0 of each component. The old code printed out logs from all ranks in each component, resulting in large log files. Fixes #2839 | 04 April 2019, 22:38:08 UTC |
| 65cde6d | Azamat Mametjanov | 04 April 2019, 17:56:00 UTC | Add pnetcdf for intel+mvapich | 04 April 2019, 17:56:00 UTC |
| 19e69db | Azamat Mametjanov | 04 April 2019, 00:27:47 UTC | Add intel+mvapich libs | 04 April 2019, 00:27:47 UTC |
| 16a8bf7 | Azamat Mametjanov | 03 April 2019, 20:41:02 UTC | Switch from mpirun/mpiexec to srun | 03 April 2019, 20:41:02 UTC |
| 326715f | Jason Sarich | 02 April 2019, 22:18:54 UTC | anvil module - avoid openmpi 3.1.3 binding bug | 02 April 2019, 22:18:54 UTC |
| 035564f | Jason Sarich | 02 April 2019, 21:21:45 UTC | revert anvil netcdf and hdf5 libraries to known working version | 02 April 2019, 21:21:45 UTC |
| 6400843 | Junqi Yin | 01 April 2019, 22:32:40 UTC | Merge branch 'bishtgautam/clm/remove-clm4-0-from-mkmapdata' (PR #2816) Remove support for clm4_0 from mkmapdata Support for clm4_0 is removed from mkmapdata script. This modification was mistakenly omitted from PR-#2777. [BFB] | 01 April 2019, 22:32:40 UTC |
| 6a5857f | James Foucar | 29 March 2019, 22:01:12 UTC | Merge branch 'oksanaguba/homme/map2-bug-issue2535' into master (PR #2824) Fix issue 2535 about map2 in homme This fixes issue #2535 about nonbfb behavior wrt # of ranks. Note that the problem is only with interpolated output (not mentioned in the issue). There is no problem with reproducibility in the dycore. One can compare std outputs from different # of ranks and the output is identical. In addition we ran native output with the same scripts and movies are identical. In case of interpolated output and map2 there is a code in interpolation_mod (in routine cube_facepoint_unstructured) that exits after the first matching element for an interpotalion point is found. In scenario when 2 elements share the same point, run with both elements on the same rank can possibly return element with lower global id as the match for this point. However, in case when both elements belong to different ranks, only element with bigger global id will 'owe' this point. The fix addresses exactly this scenario. I re-used the same scripts as in issue #2535 to test this pr with map2 for runs with meshes on 24 ranks and for runs with ne2 on 24 ranks. I did not run ne2 vs mesh comparisons. Though there is an 'exit' statement in defining local_gid for map0, I don't believe map0 has the same issue. There, global id is computed from cube face value for a particular interpolation point. Then a rank tries to find an element with such id within its element set. This logic does not seem to depend on a rank. [non-BFB] * origin/oksanaguba/homme/map2-bug-issue2535: bugfix | 01 April 2019, 21:31:37 UTC |
| c08df24 | James Foucar | 29 March 2019, 23:32:16 UTC | Merge branch 'jgfouca/cime/fix_build_threaded_casing' into master (PR #2828) Use consistent casing (all-caps) for build_threaded value Three different casing styles were being used for this value and Make does case-senstive comparisons, so it was incorrectly interpretting build_threaded to be false. Fixes #2826 [BFB] * jgfouca/cime/fix_build_threaded_casing: Use consistent casing (all-caps) for build_threaded value | 29 March 2019, 23:34:07 UTC |
| a45ed0d | James Foucar | 29 March 2019, 22:57:31 UTC | Use consistent casing (all-caps) for build_threaded value Three different casing styles were being used for this value and Make does case-senstive comparisons, so it was incorrectly interpretting build_threaded to be false. [BFB] | 29 March 2019, 22:57:31 UTC |
| f4be1a5 | Azamat Mametjanov | 29 March 2019, 21:27:12 UTC | cleanup | 29 March 2019, 21:27:12 UTC |
| da8fe7f | Oksana Guba | 28 March 2019, 20:09:12 UTC | bugfix | 28 March 2019, 20:09:12 UTC |
| 569c0d2 | Jason Sarich | 28 March 2019, 16:26:12 UTC | add fixed intel-openmpi module to new anvil build | 28 March 2019, 16:26:12 UTC |
| 9a2cd84 | Gautam Bisht | 28 March 2019, 16:05:49 UTC | Updates the Stub EM code Includes updates corresponding to data strucutre refacator in ELM | 28 March 2019, 16:05:49 UTC |
| 6e47b9f | Wuyin Lin | 28 March 2019, 15:53:21 UTC | Merge singhbalwinder/atm/rem-old-gust (PR #2720) Manually reverts gustiness changes introduced by 9bbfad5 and 2338c63. The gustiness parameterization is now implemented in eam model via 932f14c. This PR removes gustiness changes added by 9bbfad5 and 2338c63 as they are no longer needed. [BFB] - Bit-For-Bit [NML] | 28 March 2019, 15:53:21 UTC |
| 2cb9eb0 | Jason Sarich | 28 March 2019, 15:17:20 UTC | update anvil config files to use condo nodes | 28 March 2019, 15:17:20 UTC |
| 39a9fb7 | James Foucar | 26 March 2019, 22:03:33 UTC | Merge branch 'jgfouca/cime/kokkos_bld_improvements' into master (PR #2822) Add a new kokkos build-only test to e3sm_developer. Change list: * Add a new 'B' test option to indicate a build-only test * Have '--with-openmp --with-serial' be the default kokkos configuration * Add SMS_B.ne4_ne4.FC5AV1C-L-AQUAP.cam-hommexx to e3sm_developer [BFB] * jgfouca/cime/kokkos_bld_improvements: Add a new kokkos build-only test to e3sm_developer. | 27 March 2019, 19:51:05 UTC |
| d11fb8c | Gautam Bisht | 26 March 2019, 23:48:15 UTC | Adds a readme and makefile for EMI Demo code | 27 March 2019, 18:29:29 UTC |
| 15a0e4b | Gautam Bisht | 19 March 2019, 06:38:19 UTC | Minor update to the EMI demo code Prints an additional field that is returned back from Stub EM to ELM during timestepping | 27 March 2019, 18:29:22 UTC |
| 63e2f6d | Gautam Bisht | 15 March 2019, 02:55:07 UTC | Minor fix to ELM configure script | 27 March 2019, 18:29:09 UTC |
| 551fc79 | Gautam Bisht | 15 March 2019, 02:31:53 UTC | Updates ELM stub and demo code to use CNCarbonStateType | 27 March 2019, 18:28:56 UTC |
| 8c9d41f | Gautam Bisht | 15 March 2019, 02:29:11 UTC | Adds code to exchange CNCarbonStateType | 27 March 2019, 18:28:43 UTC |
| 0000ded | Gautam Bisht | 21 February 2019, 19:52:51 UTC | Minor fix | 27 March 2019, 18:28:36 UTC |
| 2baa4eb | Gautam Bisht | 21 February 2019, 19:45:25 UTC | Adds fixes to cmake Add fixes to get the code correctly compiled on Edison | 27 March 2019, 18:28:20 UTC |
| f77ae2c | Gautam Bisht | 21 February 2019, 18:54:44 UTC | Rename few cmake files | 27 March 2019, 18:28:12 UTC |
| b48b66d | Gautam Bisht | 21 February 2019, 00:35:45 UTC | Adds a demo for a Stub EM | 27 March 2019, 18:28:04 UTC |
| fa94aea | Gautam Bisht | 21 February 2019, 00:23:16 UTC | Fixes length of variable to store name of EMI data | 27 March 2019, 18:27:56 UTC |
| cca0e0b | Gautam Bisht | 21 February 2019, 00:22:41 UTC | Adds capability to print all EMI Data in a list | 27 March 2019, 18:27:49 UTC |
| beb1fe9 | Gautam Bisht | 19 February 2019, 17:41:28 UTC | Adds .gitignore files for EMI The build and local directorys created during CMake build/installation are not to be tracked by Git. | 27 March 2019, 18:27:36 UTC |
| 301acfe | Gautam Bisht | 19 February 2019, 17:40:41 UTC | Renames ExternalModelInterfaceDataMod.F90 ExternalModelInterfaceDataMod.F90 is renamed EMI_DataMod.F90 | 27 March 2019, 18:27:28 UTC |
| f0eb5b4 | Gautam Bisht | 19 February 2019, 17:34:15 UTC | Renames ExternalModelInterfaceDataDimensionMod.F90 The ExternalModelInterfaceDataDimensionMod.F90 is renamed EMI_DataDimensionMod.F90 | 27 March 2019, 18:27:19 UTC |
| 0761008 | Gautam Bisht | 19 February 2019, 17:23:54 UTC | Restructures ELM's EMI directory - Directory structure of External Model Interface (EMI) is restructured to allow adding a stub driver for ELM. CMake files are added to test EMI. - Additonally, ELM's configure script is updated to included updated EMI directory structure | 27 March 2019, 18:27:06 UTC |
| cfb7fc2 | Gautam Bisht | 27 March 2019, 14:39:39 UTC | Merge branch 'qzhu-lbl/lnd/ch4_inundation_bugfix' (PR #2814) ZWT0, F0, P3 parameters (for inundated fraction calculation) are not correctly read in add surface dataset file identifier in CH4Mod.F90 open surface dataset file for reading in ZWT0, F0, P3 Resolves #2815 [BFB] | 27 March 2019, 14:39:39 UTC |
| c59c981 | Jon Wolfe | 27 March 2019, 14:33:15 UTC | Merge branch 'darincomeau/mpaso/enable_eddystats' (PR #2821) Turn on eddy stats for oEC60to30v3 and oEC60to30v3wLI grids by default This PR turns on the ocean analysis member eddyProductVariables by default for the oEC60to30v3 and oEC60to30v3wLI MPAS-Ocean grids. This was created from the head of maint-1.2. Tested with: * ERS.T62_oEC60to30v3wLI.GMPAS-DIB-IAF-ISMF.edison_intel [BFB] [NML] - only for compsets using oEC60to30v3, oEC60to30v3wLI grids | 27 March 2019, 14:33:15 UTC |
| 3a132e4 | James Foucar | 26 March 2019, 20:20:24 UTC | Add a new kokkos build-only test to e3sm_developer. Change list: 1) Add a new 'B' test option to indicate a build-only test 2) Have '--with-openmp --with-serial' be the default kokkos configuration 3) Add SMS_B.ne4_ne4.FC5AV1C-L-AQUAP.cam-hommexx to e3sm_developer [BFB] | 26 March 2019, 20:30:03 UTC |
| c21bb46 | Darin Comeau | 26 March 2019, 17:48:59 UTC | Turn on eddy stats for oEC60to30v3 and oEC60to30v3wLI ocn grids by default | 26 March 2019, 20:22:52 UTC |
| a2dd2fc | jayeshkrishna | 26 March 2019, 16:21:33 UTC | Merge pull request #2811 from E3SM-Project/jayeshkrishna/pio2_cime_changes This PR includes CIME fixes for PIO2, * Configure/compile options for PIO2 * Some machine file changes for anlworkstation for PIO2 (Upgrades NetCDF and PnetCDF lib versions, reduces default number of tasks from 64 to 32) [BFB] | 26 March 2019, 16:21:33 UTC |
| a6fce97 | Jon Wolfe | 26 March 2019, 14:22:36 UTC | Merge branch 'mark-petersen/ocean/fix_AM_index_variable_name' (PR #2812) Fix indexing issue in ocean SurfaceAreaWeighted AM This PR updates the mpas-source submodule to fix several small issues: * Fixes indexing issue in ocean SurfaceAreaWeighted AM. It is bfb in the simulations. Output file for one ocean analysis member will change. * Spelling corrections in comments and timers * Fix snowFlow misspelling Fixes #2781 [BFB] | 26 March 2019, 14:22:36 UTC |
| 4a3194d | Balwinder Singh | 25 March 2019, 21:28:50 UTC | Merge branch 'worleyph/cam/user_defined_lbal' (PR #2784) Add option to load balance atm. physics wrt column cost estimates a) Add measurement and output per chunk of atmospheric physics cost Measurement of cost on a per chunk basis allows for a more direct evaluation of physics load balancing. This will be important as new physics capabilities are added that require new physics load balancing schemes, for example, superparameterization and elevation classes. Here this capability is added. A new logical namelist parameter, phys_chnk_cost_write, is added to enable the output of these data to a file named, for the moment, atm_chunk_costs.txt. (In the future, the name of this file may be set via the namelist.) The output is disabled by default, but the data are always collected, and the collection overhead is very low. The namelist parameter can be set to true in the user_nl_cam file. This can be added to env_run.xml in the future if desired. b) Add option to load balance atm. physics wrt column cost estimates For both superparameterization and elevation class schemes the current load balancing options addressing diurnal and seasonal cycles and land/ocean differences may not address the major atmospheric physics load imbalances. One approach being investigated is to provide as input computational cost estimates for each column, and then assign columns to chunks to approximately load-balance the chunks with respect to these cost estimates. Here this capability is introduced, but if all columns cost estimates are identical (default is a value of 1.0), then the current algorithm is used. Using column cost estimates is implemented in the same logical structure as the current algorithm, being restricted to load balancing within a virtual SMP with the option of pairing each column assignment with its latitude-longitude "twin". Support for supplying column cost estimates is limited to the SE dycore first, and even this is just a dummy entry as the data must then be provided by the SE dycore via an optional parameter in the get_horiz_grid_d routine. [BFB] Fixes #2766 * worleyph/cam/user_defined_lbal: Remove another 'size' variable Lower case to match existing style Reenable support for mpiserial Rename 'size' variable so that can use 'size' fortran intrinsic Add cost_d_out to dyn_grid.F90 for EUL dycore Fix comment citing source of algorithm used in adjust_heap Fix typo in bound on how small cost_gsum can be Add option to load balance atm. physics wrt column cost estimates Add measurement and output per chunk of atmospheric physics cost | 25 March 2019, 21:33:31 UTC |
| f2f2048 | James Foucar | 25 March 2019, 20:32:19 UTC | Merge branch 'jgfouca/cime/fix_kokkos_bld' into master (PR #2819) Fix Kokkos build [BFB] * jgfouca/cime/fix_kokkos_bld: Fix boolean with wrong case Fix addition of kokkos flags Fix Kokkos build | 25 March 2019, 20:33:05 UTC |
| 686b110 | James Foucar | 25 March 2019, 20:30:48 UTC | Fix boolean with wrong case | 25 March 2019, 20:30:48 UTC |
| 12e9152 | James Foucar | 25 March 2019, 19:28:14 UTC | Fix addition of kokkos flags Has to come after include of macros file | 25 March 2019, 19:28:14 UTC |
| 874c92a | James Foucar | 25 March 2019, 18:48:51 UTC | Fix Kokkos build The most recent CIME update broke how buildlib.kokkos was probing for KOKKOS_OPTIONS. [BFB] | 25 March 2019, 18:48:53 UTC |
| ef3530e | Benjamin Hillman | 07 March 2019, 17:30:49 UTC | Remove support for clm4_0 | 25 March 2019, 16:14:01 UTC |
| ec99b1c | QING ZHU | 24 March 2019, 15:41:14 UTC | - fix ch4 inundatation parameter read in bug | 24 March 2019, 15:41:14 UTC |
| 554104c | Patrick Worley | 22 March 2019, 15:04:51 UTC | Remove another 'size' variable A formal variable in get_block_gcol_d is named 'size'. This is renamed to 'cnt' to avoid future conflicts with the fortran intrinsic 'size'. Also, array size error checking logic in get_horiz_grid_d is modified to be internally consistent. [BFB] | 22 March 2019, 15:04:51 UTC |
| a148fa5 | Patrick Worley | 22 March 2019, 03:28:54 UTC | Lower case to match existing style When importing some code from another part of E3SM, did not change style to match destimation code. Correcting this. [BFB] | 22 March 2019, 03:28:54 UTC |
| 63bc38f | Patrick Worley | 22 March 2019, 03:19:22 UTC | Reenable support for mpiserial MPI logic was added without being surrounded by 'ifdef SPMD' logic. Here newly introduced calls to MPI_WTIME are replaced with calls to system_clock (via shr_sys_irtc) and the necessary CPP logic is introduced around other new MPI calls to reenable mpiserial support. [BFB] | 22 March 2019, 03:19:22 UTC |
| 1908b4f | Patrick Worley | 21 March 2019, 18:20:01 UTC | Rename 'size' variable so that can use 'size' fortran intrinsic A formal parameter in the routine get_horiz_grid_d in dynamics/eul/dyn_grid.F90 is named 'size', which conflicts with the use of the 'size' intrinsic to return array size. Here the 'size' parameter is renamed 'nxy', as is used in dynamics/se/dyn_grid.F90 [BFB] | 21 March 2019, 18:20:01 UTC |
| c77161b | Patrick Worley | 21 March 2019, 15:58:35 UTC | Add cost_d_out to dyn_grid.F90 for EUL dycore The EUL dycore is still used for SCM and other E3SM options, and the optional parameter cost_d_out needs to be added to the get_horiz_grid_d routine in dynamics/se/dyn_grid.F90 as well. [BFB] | 21 March 2019, 15:58:35 UTC |
| 4bfc96d | mark-petersen | 21 March 2019, 15:34:29 UTC | Update MPAS source - Fixes indexing issue in SurfaceAreaWeighted AM - Spelling corrections in comments and timers - Fix snowFlow misspelling | 21 March 2019, 15:34:29 UTC |
| ad75578 | Gautam Bisht | 21 March 2019, 13:53:43 UTC | Merge branch 'brhillman/clm/update-mkmapdata' (PR #2777) Update the mkmapdata script to add additional optional arguments to allow better control of execution of underlying `ESMF_RegridWeightGen` command. Previously, this required setting environment variables before calling the script to specify the ESMF path, inputdata location, MPI command and/or number of MPI tasks. Optional arguments are added for each of these (`--esmf-path`, `--inputdata-path`, `--mpiexec`, `--ntasks`). An additional argument is added (`--output-filetype`) to override the netcdf format of the output maps. This was needed to force ESMF to write large files in 64bit-offset format instead of netcdf3, and so this can now be handled without individual customized scripts to override the default file type. Some logic was also cleaned up in the script, and some consistent formatting applied (consistent 4-space indent level as opposed to the mix of 3 and 4 that existed before). Documentation has also been updated for consistency with the changes, and clarified somewhat. Note that this script contains some hard-coded in support for certain platforms. I imagine a lot of this is outdated and not maintained, so we should probably remove it at some point and require users to correctly specify paths and MPI commands as command line options, but we can save that for a future PR if there is consensus on that. [BFB] | 21 March 2019, 13:53:43 UTC |
| 6175cb7 | Jon Wolfe | 20 March 2019, 14:46:42 UTC | Merge branch 'xylar/mpaso/fix_jigsaw_in_compass' (PR #2797) Update MPAS source for fixes to V2 mesh generation in MPAS-O (COMPASS) This pull request fixes two issues with generating E3SM V2 meshes in MPAS's COMPASS testing suite: * The meshes are now reproducible because we use the same random seed each time * Cells are no longer culled based on a bathymetry needed only for coastal test case. [BFB] | 20 March 2019, 14:46:42 UTC |
| 446913f | Gautam Bisht | 20 March 2019, 14:05:35 UTC | Merge branch 'rgknox/lnd/fates-api-7' (PR #2754) This updates the interface with FATES to match is most recent api release. Major API changes were needed to accommodate hydraulics in dynamic plants. [non-BFB] | 20 March 2019, 14:05:35 UTC |
| 34ad908 | Jayesh Krishna | 07 January 2019, 18:13:39 UTC | Fix mpi-serial + PIO2 builds Adding PIO2 configuration options required for mpi-serial. | 19 March 2019, 16:47:11 UTC |
| 2b7fc66 | Jayesh Krishna | 08 November 2018, 15:59:54 UTC | Using C++ compiler/linker for PIO2 For PIO2 we now use C++ compiler/linker. | 19 March 2019, 16:46:45 UTC |
| 0b1b6d9 | dqwu | 12 October 2018, 05:53:47 UTC | Adding HDF5_PATH to CMAKE_OPTS to build PIO | 19 March 2019, 16:45:08 UTC |
| e9dfb57 | dqwu | 12 October 2018, 05:18:56 UTC | Defining environment variable HDF5_PATH for anlworkstation | 19 March 2019, 16:44:30 UTC |
| c31d285 | dqwu | 12 October 2018, 05:02:54 UTC | Upgrading netcdf to 4.4.1 (from 4.3.3.1) for anlworkstation | 19 March 2019, 16:43:59 UTC |
| 5661c32 | dqwu | 24 March 2018, 03:43:55 UTC | Changing max tasks per node to 32 (from 64) for anlworkstation Although anlworkstation/compute001 has 64 cores it is a shared machines and we don't want to run cases on all the cores. Reducing the max tasks per node from 64 to 32. | 19 March 2019, 16:43:01 UTC |
| 0ff780a | dqwu | 24 March 2018, 03:36:58 UTC | Upgrading pnetcdf to 1.8.1 (from 1.6.1) for anlworkstation One reason we need this new version is because pnetcdf used to define NF_MAX_NAME and NC_MAX_NAME as different resulting in memory corruption in PIO (when copying data inside PIO, using NC_MAX_NAME, to strings from Fortran code, using NF_MAX_NAME). | 19 March 2019, 16:40:30 UTC |
| 6dc7e3c | dqwu | 23 March 2018, 20:27:53 UTC | Turning on PIO_USE_MALLOC option | 19 March 2019, 16:38:26 UTC |
| 4db256d | James Foucar | 19 March 2019, 15:59:12 UTC | Merge branch 'jgfouca/cime/fix_input_issues' into master (PR #2808) Fix some issues with downloading input files We (e3sm) don't have chksum files set up yet. Also, remove old input data server from XML. [BFB] * jgfouca/cime/fix_input_issues: Remove dupe Fix some issues with downloading input files Update CIME to ESMCI cime5.8.0 (#2799) | 19 March 2019, 16:00:42 UTC |
| d11ddfc | James Foucar | 19 March 2019, 15:53:09 UTC | Remove dupe | 19 March 2019, 15:53:09 UTC |
| 162b323 | James Foucar | 19 March 2019, 15:39:34 UTC | Fix some issues with downloading input files We (e3sm) don't have chksum files set up yet. Also, remove old input data server from XML. [BFB] | 19 March 2019, 15:39:34 UTC |
| 3eebd7f | James Foucar | 19 March 2019, 14:26:21 UTC | Update CIME to ESMCI cime5.8.0 (#2799) Update CIME to ESMCI cime5.8.0 Squash merge of jgfouca/branch-for-to-acme-2019-03-12 Features: * Better handling of file permissions when copying files * Minor JRA & CORE2 DATM forcing changes * Modifications to allow for E3SM developer tests for the SE SCM * Report missing variables in cprnc * Merge to latest pio2 version * update NYF CORE2 DROF data stream file. (non-BFB) * Refactor communication between build.py and Makefile: use cmd-line args instead of environment vars. * Implement share field for e3sm test suites * Implement support for checksums when download input data Bug fixes: * Fixes #2800 [non-BFB] | 19 March 2019, 14:26:21 UTC |
| 4c4aeff | jayeshkrishna | 18 March 2019, 21:09:08 UTC | Merge pull request #2772 from E3SM-Project/jayeshkrishna/pio2_clm_mosart_fixes This PR includes some fixes in CLM and Mosart required for PIO2. Although these fixes are not specific to PIO2, they showed up during testing with PIO2. Fixes #2778 [BFB] | 18 March 2019, 21:09:08 UTC |
| 97fe01a | James Foucar | 15 March 2019, 20:02:19 UTC | Merge branch 'jgfouca/cime/sandiatoss3_multiqueue' into master (PR #2804) Support multiqueueing for sandiatoss3 Any job that could run on our 'short' queue could also run on our 'batch' queue. If the short queue is full and the batch one isn't, it would make sense to run the job in the batch queue. [BFB] * jgfouca/cime/sandiatoss3_multiqueue: Support multiqueueing for sandiatoss3 | 15 March 2019, 20:03:06 UTC |
| 0ed3cc1 | James Foucar | 15 March 2019, 19:53:32 UTC | Support multiqueueing for sandiatoss3 Any job that could run on our 'short' queue could also run on our 'batch' queue. If the short queue is full and the batch one isn't, it would make sense to run the job in the batch queue. [BFB] | 15 March 2019, 19:53:32 UTC |
| 1fa556a | Wuyin Lin | 14 March 2019, 22:01:53 UTC | Merge singhbalwinder/atm/v2compset (PR #2789) Implements remaining changes for gustiness feature for EAMv2 This PR completes the gustiness feature in EAM by implementing all the right namelist settings for gustiness. A new use case file 2000_cam5_av1c-04p2_gust.xml has all the namelist values for invoking this feature using FC5AV1C-L compset. Several new namelist variables required for this feature will now appear in the namelist (atm_in). A test mod directory is also created to add a test for this feature in the nightly testing. [BFB] [NML] | 14 March 2019, 22:01:53 UTC |
| ed919b2 | Xylar Asay-Davis | 12 March 2019, 17:24:51 UTC | Update mpas-source Add changes to COMPASS to fix serveral issues with JIGSAW. These include lack of reproducibility and culling of incorrect land cells from the wrong bathymetry file. | 14 March 2019, 16:20:01 UTC |
| b7149dd | Jon Wolfe | 14 March 2019, 15:32:03 UTC | Merge branch 'xylar/add_standalone_mpaso_wind_pressure_forcing' (PR #2788) Update MPAS source for standalone time-varying forcing This pull request ibrings in a new mpas-source submodule, which adds capability for stand-alone MPAS-Ocean to include time varying wind and pressure forcing. The added code is not called during E3SM simulations and should not impact any tested configurations. It also includes associated COMPASS files for testing. [BFB] | 14 March 2019, 15:32:03 UTC |
| 751d2f5 | Balwinder Singh | 13 March 2019, 23:23:23 UTC | Applies a simpler solution using added parentheses to fix nbfb issue [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 13 March 2019, 23:23:23 UTC |
| dfedcd2 | Balwinder Singh | 13 March 2019, 21:40:10 UTC | Fixes cam_export subroutine such that this PR stays BFB [BFB] - Bit-For-Bit [NML] - Namelist Changing See confluence for a more detailed description about these tags. | 13 March 2019, 21:40:10 UTC |
| 4e1f399 | jayeshkrishna | 13 March 2019, 15:35:08 UTC | Merge pull request #2773 from E3SM-Project/jayeshkrishna/pio2_cice_fixes This PR includes a minor fix in CICE required for PIO2. Although this fix is not specific to PIO2, it showed up during testing with PIO2. [BFB] | 13 March 2019, 15:35:08 UTC |
| 79087fe | jayeshkrishna | 13 March 2019, 15:34:30 UTC | Merge pull request #2771 from E3SM-Project/jayeshkrishna/pio2_cam_fixes This PR includes some fixes in CAM required for PIO2 and adds the build script required to build HOMME on anlworkstation. Although these fixes are not specific to PIO2, they showed up during testing with PIO2. [BFB] | 13 March 2019, 15:34:30 UTC |
| 9a68348 | Min Xu | 12 March 2019, 21:05:46 UTC | Merge branch 'minxu74/machines/summit/add_netcdff_4MPAS' (PR #2796) Add the NETCDFF environment for MPAS on Summit | 12 March 2019, 21:05:46 UTC |
| 7c705c2 | Wuyin Lin | 12 March 2019, 20:45:10 UTC | Merge wlin/atm/cosp-modis-tau-fix (PR #2770) Bug fix for optical thickness calculation in COSP-MODIS Addition of optical thickness due to stratiform snow incorrectly used the values from convective cloud. Fixes #2782 [BFB] except for cosp modis diagnostics output | 12 March 2019, 20:45:10 UTC |
| 1bf22e3 | Junqi Yin | 12 March 2019, 17:17:36 UTC | Merge branch 'thorntonpe/lnd/archv2_cols' (PR #2742) Implement ELM v2 data architecture for mass and energy state and flux variables Migrates mass and energy state and flux variables from CLM4.5 data structures, which mixed variables at multiple subgrid levels, to ELM v2 data structures, which separate the variables according to subgrid level. For example, carbon state variables are moved from a single type into three distinct types, one for gridcell-level, one for column-level, and one for vegetation (patch)-level variables. Methods acting on these types are also defined independently for each subgrid level. Migrates all energy, water, carbon, nitrogen, and phosphorus state and flux variables and data-type methods. Leaves open the issue of how to structure subroutine calling interfaces. The original code uses a variety of methods. Here, an example is provided for the module biogeochem/CNCStateUpdate1Mod.F90 and all its upstream calls, based on explicit references to data type instances at the clm_driver() level, and passed references at all lower levels. Branch tests bit-for-bit against the E3SM land developer test suite. [BFB] | 12 March 2019, 17:17:36 UTC |
| b61be29 | Xylar Asay-Davis | 08 March 2019, 21:23:21 UTC | update mpas-source This pull request adds capability for stand-alone MPAS-Ocean to include time varying wind and pressure forcing. The added code is not called during E3SM simulations. Also adds associated COMPASS files for testing. bfb | 12 March 2019, 03:43:11 UTC |
| 33ccf67 | Junqi Yin | 11 March 2019, 16:23:57 UTC | Initialize qflx_lateral to 0.0 | 11 March 2019, 19:57:38 UTC |
| 9cea565 | Junqi Yin | 07 March 2019, 20:48:36 UTC | Minor fix for build error with dynSubgridAdjustmentsMod.F90 | 11 March 2019, 19:56:10 UTC |
