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46b3c79 hsiangheleellnl 20 June 2019, 21:05:06 UTC remap scheme modification for FIVE 20 June 2019, 21:05:06 UTC
743276a hsiangheleellnl 06 June 2019, 21:43:49 UTC Large scale vertical advection - bug fixed 06 June 2019, 21:43:49 UTC
1151e29 hsiangheleellnl 06 June 2019, 18:22:56 UTC Large scale vertical advection test version added 06 June 2019, 18:22:56 UTC
316892c Peter Bogenschutz 15 May 2019, 18:35:59 UTC fix issue with defining pverp_five when five is not used 15 May 2019, 18:35:59 UTC
13e1db9 Peter Bogenschutz 15 May 2019, 18:15:58 UTC update submodule error 15 May 2019, 18:15:58 UTC
6d98764 Peter Bogenschutz 15 May 2019, 17:20:31 UTC merge with master 15 May 2019, 17:20:31 UTC
aa05392 Peter Bogenschutz 15 May 2019, 16:57:49 UTC undo a kludgy fix for SE dycore to prep for merge with master 15 May 2019, 16:57:49 UTC
83ad80d Oksana Guba 15 May 2019, 14:45:18 UTC Merge branch 'ambrad/ambrad/homme/compose-theta-l' into master (PR #2896) Bring COMPOSE semi-Lagrangian tracer transport code into HOMME and E3SM. [non-BFB] for HOMME suite for 1 test, baroCamMoistSL and [NML] in the same test. Includes the following: Changes to E3SM model build system to permit SL in theta-l (only). Nontrivial changes to the HOMME standalone build system to use E3SM Kokkos submodule automatically. A cosmetic issue was changing things to move away from associating Kokkos specifically with the HOMMEXX work. If HOMME_ENABLE_COMPOSE=OFF and BUILD_HOMME_PREQX_KOKKOS=OFF, then all the Kokkos-related code is skipped. A trivial new target for testing. Will eventually expand to make a convergence test in the standalone test suite. removal of old sl_advection.F90 Add the new libcompose target. It builds COMPOSE C++ code, which is expensive relative to Fortran, just once. Then any target that wants SL links against this library. If HOMME_ENABLE_COMPOSE=OFF, this is not built. Since this is a separate lib, the files are in share/compose rather than just share. Add Fortran interfaces to libcompose. These files must be included in the list of sources for a target and so are in the share directory. They are fast to compile, like all short Fortran files. If HOMME_ENABLE_COMPOSE=OFF, code is appropriately ifdefed out, so it is innocuous to include these in the target's file list. Add a hook for a nice COMPOSE testing capability and one test. Miscellaneous changes: Remove some old code for the previous version of SL transport. Little things to support the new SL code. dcmip16_mu_s -> dcmip16_mu_s for scalars in the dynamics and dcmip16_mu_q. This is an orthogonal change we discussed a while ago. It permits SL not to do dissipation on tracers in a dcmip test as an option. Namelist and control changes for SL. [BFB] for E3SM [BFB] for all HOMME standalone tests except [non-BFB] baroCamMoistSL. 15 May 2019, 14:45:18 UTC
9e80581 hsiangheleellnl 13 May 2019, 18:51:16 UTC bugs fixed in radiation.F90 13 May 2019, 18:51:16 UTC
2bfc51a Gautam Bisht 10 May 2019, 17:28:35 UTC Merge branch 'jinyuntang/lnd/fix_float_error' (PR #2886) Fixed a number of initialization issues related to the logical switch of crop model and dynamic land use. Fixes #2832 [BFB] 10 May 2019, 17:28:35 UTC
a282f13 Andrew M. Bradley 10 May 2019, 01:38:02 UTC COMPOSE: Fix the scope of the share_kokkos_ut standalone unit tests. 10 May 2019, 01:38:02 UTC
6cc632d Andrew M. Bradley 09 May 2019, 19:26:50 UTC Merge remote-tracking branch 'upstream/master' into ambrad/homme/compose-theta-l Conflicts: components/homme/CMakeLists.txt components/homme/src/preqx_kokkos/CMakeLists.txt 09 May 2019, 19:26:50 UTC
6c1de58 James Foucar 09 May 2019, 18:52:52 UTC Merge branch 'luca/homme_cmake_subdir' (PR #2831) This PR allows to build HOMME with cmake from within another cmake project. This is needed by scream (in fact, this has already be done in the scream fork, but I want it to get in E3SM as well, so I can take care of merging E3SM master into the scream fork, taking care of the homme conflicts). The logic is simple: if there's a cmake project defined already, do not define it, do not build execs/tests, just let the host cmake project drive everything. This PR should have zero impact on standalone homme cmake build, and zero impact on cime-base builds. Note: I added a bunch of reviewers that have to do with any combination of homme, cime, and cmake. [BFB] * luca/homme_cmake_subdir: Homme: modifying cmake logic, to allow inclusion of homme with add_subdirectory 09 May 2019, 18:52:52 UTC
6a9553a noel 09 May 2019, 16:58:03 UTC Merge E3SM-Project/ndk/machinefiles/cori-knl-cflag-math (PR #2878) Fix the calculation to give the best cflag value for cori-knl 09 May 2019, 16:58:03 UTC
2b67e3b James Foucar 09 May 2019, 16:32:06 UTC Update CIME to ESMCI cime5.8.2-2 (#2908) Update CIME to ESMCI cime5.8.2-2 Squash merge of jgfouca/branch-for-to-acme-2019-05-06 Features * Nuopc update * nldas_forcing_v2: This is a regional, 0.125 degree data set over the U.S., for use in forcing CTSM. * Change DATM_CLMNCEP_YR_ALIGN for present-day compsets: Make DATM_CLMNCEP_YR_ALIGN match DATM_CLMNCEP_YR_START. This will make the model year align with the forcing year. For example, if RUN_STARTDATE is set to 2000-01-01, then the model will use year-2000 atmospheric forcing data in the first year, etc. non-BFB for any present-day compsets using datm (mostly I-cases and G-cases). Bug fix: * Fixes to NAG flags in scripts/Tools/Makefile [non-BFB] (datm) 09 May 2019, 16:32:06 UTC
143b62a Wuyin Lin 08 May 2019, 17:12:16 UTC Merge wlin/atm/trim_perl_config (PR #2888) Trim CAM's perl based configure script by removing unused or unlikely used codes in preparation for migration to using Python and CMake. The following codes are removed cice setup, as it is now controlled by CIME. codes to configure for tests. Control block in the main program for configuring test and check required modules and libraries Subroutines supporting the setup for the test that are invoked by the main programs. This include get_gmake, write_tests_filepath, check_fc, check_netcdf, check_mpi, check_esmf, run_test [BFB] 08 May 2019, 17:12:16 UTC
098c852 Junqi Yin 07 May 2019, 16:57:43 UTC Merge branch 'bishtgautam/lnd/update-land-ic' (PR #2893) Updates land initial conditions for ne0np4 Updates the land initial condition for ne0np4 resolution. The new initial conditions contain additional topounit dimension. Fixes #2890 Fixes #2891 [BFB] 07 May 2019, 16:57:43 UTC
4b1a49f Jon Wolfe 07 May 2019, 14:44:34 UTC Merge branch 'mark-petersen/ocean/addTimeSeriesMaxMin' (PR #2884) Add ocean ability to output max and min quantities in timeSeriesMonthly This PR adds the ability to output maximum and minimum observed quantities for each month. It utilizes the current timeseries AM functionality. [BFB] [NML] 07 May 2019, 14:44:34 UTC
68297f4 Mark Taylor 07 May 2019, 12:59:37 UTC Merge branch 'mt5555/refstates' (PR #2907) switch to analytic formula for hypervis dp_ref [BFB] except for HOMME tests 07 May 2019, 12:59:37 UTC
60a10b7 Mark Taylor 07 May 2019, 12:56:31 UTC Merge ranch 'origin/asteyer/imex_methods' (PR #2801) update imex schemes with new versions with improved stability [BFB] 07 May 2019, 12:56:31 UTC
04b17d3 Andrew M. Bradley 06 May 2019, 21:11:20 UTC Merge remote-tracking branch 'upstream/master' into ambrad/homme/compose-theta-l 06 May 2019, 21:11:20 UTC
fbb8b81 Mark Taylor 06 May 2019, 16:43:12 UTC Merge branch 'mt5555/supercell-x1' (PR #2906) several minor changes implemented during high-res testing added I/O output options updated superscel namelists precl output bug fix. better Newton failure diagnostics clean up EOS naming convention [BFB] 06 May 2019, 16:43:12 UTC
3424e22 Mark Taylor 05 May 2019, 14:20:34 UTC Merge remote-tracking branch 'origin/master' into supercell-x1 supercell-x1 changed the EOS interface, while on master new routines were added which used the old interface. to address this, merging master into supercell-x1 so new routines can be updated to the new interface on the branch 05 May 2019, 14:20:34 UTC
9ea7580 Mark Taylor 05 May 2019, 13:44:12 UTC tweaks to prevert merge conflicts with master 05 May 2019, 13:44:12 UTC
7df269e Mark Taylor 04 May 2019, 22:54:14 UTC added omega500 and omega850 to HS diagnostics 04 May 2019, 22:54:14 UTC
74855c0 Mark Taylor 04 May 2019, 21:49:39 UTC fix typo 04 May 2019, 21:49:39 UTC
dc700f9 Jinyun Tang 04 May 2019, 21:21:42 UTC relocate col_plant_pdemand_vr from nf to pf Now col_plant_pdemand_vr is contained as a variable in the type of phosphorus flux. Also removed some unnecessary varaibles added in last commit, and added back plant_pdemand_vr into the related value reset subroutine. Code passed the test suite e3sm_developer. 04 May 2019, 21:21:42 UTC
bc39fa4 Mark Taylor 04 May 2019, 19:58:51 UTC switch to analytic formula for hypervis dp_ref 04 May 2019, 19:58:51 UTC
a24d05f Mark Taylor 04 May 2019, 19:19:43 UTC cleaned up EOS interface 04 May 2019, 19:19:43 UTC
f5080a4 Peter Andrew Bogenschutz 03 May 2019, 21:11:43 UTC fix merge conflicts to update branch 03 May 2019, 21:11:43 UTC
2b5b1b5 Peter Andrew Bogenschutz 03 May 2019, 19:56:09 UTC modifications to allow FIVE levels to be computed on the fly, rather than having to be predetermined 03 May 2019, 19:56:09 UTC
0cd0685 Junqi Yin 03 May 2019, 18:08:07 UTC Merge branch 'bishtgautam/lnd/fixes-for-emi' (PR #2859) Fixes the definition type in EMI Changes definition of few member variables from type to class. Fixes #2855 [BFB] 03 May 2019, 18:08:07 UTC
4001fac hsiangheleellnl 02 May 2019, 21:10:22 UTC LW AOD fix in radiation.F90 02 May 2019, 21:10:22 UTC
52af695 hsiangheleellnl 02 May 2019, 20:02:57 UTC AOD fix in radiation.F90 02 May 2019, 20:02:57 UTC
b3ebebb Jon Wolfe 02 May 2019, 19:52:20 UTC Fix default settings for new variables from the ones in Registry 02 May 2019, 19:52:20 UTC
b02412d James Foucar 02 May 2019, 19:38:12 UTC Merge branch 'jgfouca/cime/wget_no_cert' into master (PR #2901) Missed a spot in wget that needed no-check-cert [BFB] * jgfouca/cime/wget_no_cert: Missed a spot in wget that needed no-check-cert change anvil nodename regex for centos6 nodes Run in acme-centos6 partition on Anvil add netcdf fflags Split NETCDF_PATH into C and Fortran paths Update Anvil to Slurm and SoftEnv built on CentOS6 02 May 2019, 19:41:47 UTC
bfdf406 James Foucar 02 May 2019, 19:37:03 UTC Missed a spot in wget that needed no-check-cert [BFB] 02 May 2019, 19:37:03 UTC
b117120 James Foucar 02 May 2019, 19:19:07 UTC C++/Kokkos: Refine a few build pieces. (PR #2894) 1. Add KOKOS_CXXFLAGS to CXXFLAGS. 2. Add CPPDEFS to CXXFLAGS. 3. Do not add CFLAGS to CXXFLAGS. 4. For default build (i.e., no KOKKOS_OPTIONS provided), build Kokkos --with-openmp only if case.get_build_threaded(). [BFB] 02 May 2019, 19:19:07 UTC
6140487 Junqi Yin 01 May 2019, 21:26:40 UTC Merge branch 'bishtgautam/lnd/add-future-luh2-dataset' (PR #2857) Adds support for LUH2 dataset Replaces the support of LUH1 dataset within the land mksrufdata tool by LUH2 dataset for historical (1850-2014) and future (2015-2100) time period. The LUH2 dataset for the future corresponds to SSP5-RCP8.5 scenario. [BFB] 01 May 2019, 21:26:40 UTC
492c434 Mark Taylor 01 May 2019, 20:01:40 UTC better dp3d refstate for hypervis 01 May 2019, 20:01:40 UTC
bb3db83 Andrew M. Bradley 01 May 2019, 19:49:52 UTC COMPOSE: Add a missing cleanup mod. 01 May 2019, 19:49:52 UTC
8c7b2ac Jon Wolfe 01 May 2019, 19:21:57 UTC Add missing groups to build-namelist script 01 May 2019, 19:21:57 UTC
e3d24a5 Andrew M. Bradley 01 May 2019, 19:04:51 UTC COMPOSE: More cleanup. In particular, remove unnecessary diffs. 01 May 2019, 19:04:51 UTC
d3f11ed Andrew M. Bradley 01 May 2019, 02:01:26 UTC COMPOSE: Clean up a few things. 01 May 2019, 02:01:26 UTC
80c5a31 Andrew M. Bradley 30 April 2019, 23:01:15 UTC COMPOSE: Make baroCamMoist-SL test run COMPOSE SL. Also remove only SL options. 30 April 2019, 23:01:15 UTC
e91e31c hsiangheleellnl 30 April 2019, 21:58:38 UTC t updated in radiation 30 April 2019, 21:58:38 UTC
0c318b3 Andrew M. Bradley 30 April 2019, 21:13:26 UTC Support building Kokkos from E3SM submodule in standalone HOMME. If the user does not provide KOKKOS_PATH, then externals/kokkos is built as part of the standalone HOMME build. 30 April 2019, 21:13:26 UTC
45db9a9 Jon Wolfe 30 April 2019, 21:01:27 UTC Add new streams to script that builds the streams.ocean file 30 April 2019, 21:01:27 UTC
2c810d7 Andrew M. Bradley 30 April 2019, 20:19:15 UTC COMPOSE: Fix some CMake issues that conflicted between HOMMEXX and COMPOSE. 30 April 2019, 20:19:15 UTC
db95f89 Andrew M. Bradley 30 April 2019, 19:06:46 UTC C++/Kokkos: Refine a few build pieces. 1. Add KOKOS_CXXFLAGS to CXXFLAGS. 2. Add CPPDEFS to CXXFLAGS. 3. Do not add CFLAGS to CXXFLAGS. 4. For default build (i.e., no KOKKOS_OPTIONS provided), build Kokkos --with-openmp only if case.get_build_threaded(). [BFB] 30 April 2019, 19:08:09 UTC
b5aaa6b Gautam Bisht 30 April 2019, 18:41:26 UTC Merge branch 'singhbalwinder/clm/missing-isnan-use' (PR #2863) Includes the missing isnan via use statement Fixes #2838 [BFB] 30 April 2019, 18:41:26 UTC
5999763 Balwinder Singh 30 April 2019, 18:03:54 UTC Merge branch 'brhillman/atm/make-rrtmgp-submodule'(PR #2805) … Make RRTMGP a submodule Make external RRTMGP code a submodule. This will allow us to more easily pull in changes to the RRTMGP code as that codebase continues to evolve. This code is developed external to E3SM, so making this a submodule to track the RRTMGP repository seems to make the most sense. This PR also pulls in the latest version of RRTMGP, which is NOT bit-for-bit with the version in master currently. Non-RRTMGP test cases should still be BFB (the only baseline comparison fail should be that for ERS_Ld5.ne4_ne4.FC5AV1C-L.cam-rrtmgp in the e3sm_atm_integration suite). This appears to be due to small differences in the values used for physical constants within the RRTMGP code, as well as a change in how the dry column molecular amounts are calculated within the RRTMGP code. These affect on the solution is small, however. Shown here are net shortwave and longwave clear-sky fluxes at the top of the atmosphere for two simulations at ne4np4 resolution, one with current master and one with these changes (with -rad rrtmgp selected for both): Grey lines indicate the column difference, with a separate scale indicated on the right axis. Note that the differences are on the order of a few $W/m^2$, while the magnitude of the column values are hundreds of W/m^2. Slight changes are needed in the E3SM code that interfaces with RRTMGP to accommodate a change in data structures in RRTMGP (ty_gas_optics is now abstract, and we access via ty_gas_optics _rrtmgp). This change is made in radiation.F90 and in cam_optics.F90. Fixes #2798 [NBFB] * brhillman/atm/make-rrtmgp-submodule: Change space to tab for consistency Set RRTMGP submodule to track master Edits for new RRTMGP interface Add RRTMGP external repo as a submodule Remove existing RRTMGP external code 30 April 2019, 18:03:54 UTC
8441833 Andrew M. Bradley 29 April 2019, 20:43:18 UTC COMPOSE: add COMPOSE options to namelist_*.xml; use COMPOSE in E3SM theta-l. Update E3SM namelist files with COMPOSE options. Make the theta-l E3SM target build with COMPOSE. 30 April 2019, 17:47:33 UTC
3e6165e Andrew M. Bradley 30 April 2019, 17:46:24 UTC Merge remote-tracking branch 'upstream/master' into composebuild3 30 April 2019, 17:46:24 UTC
248224e Gautam Bisht 30 April 2019, 17:39:45 UTC Updates land initial conditions for ne0np4 Updates the land initial condition for ne0np4 resolution. The new initial conditions contain additional `topounit` dimension. Fixes #2890 Fixes #2891 [BFB] 30 April 2019, 17:43:27 UTC
4a6be24 Andrew M. Bradley 24 April 2019, 18:57:09 UTC COMPOSE: Prepare COMPOSE for full integration. Remove unused code. Library-ize compose: 1. Move C++ SL files to src/share/compose. 2. Build the C++ files, which do not require config.h-based array sizes, as the library libcompose. This means these files get built just once, and then any exe can link against libcompose. 3. Because the F90 files depend on config.h-based array sizes, these must remain be built with each exe. But they are small files, just interfaces to the much larger C++ files. Use the define HOMME_ENABLE_COMPOSE to isolate C++-dependent code. It is TRUE by default in the standalone build. If it is set to FALSE, then HOMME Fortran targets build without building libcompose, and thus do not need Kokkos. 30 April 2019, 17:17:24 UTC
d611157 Jason Sarich 30 April 2019, 17:03:02 UTC change anvil nodename regex for centos6 nodes 30 April 2019, 17:03:02 UTC
fb4ccf0 Jon Wolfe 30 April 2019, 17:00:51 UTC Update mpas-ocean bld scripts to match Registry changes 30 April 2019, 17:00:51 UTC
9bf89b0 Azamat Mametjanov 29 April 2019, 23:06:12 UTC Run in acme-centos6 partition on Anvil 29 April 2019, 23:06:12 UTC
141aa0b Wuyin Lin 29 April 2019, 22:02:24 UTC Clean up a config reference to cice_cppdef 29 April 2019, 22:02:24 UTC
ab52999 Jason Sarich 29 April 2019, 21:46:49 UTC add netcdf fflags 29 April 2019, 21:46:49 UTC
e4b8cd8 Azamat Mametjanov 29 April 2019, 20:47:56 UTC Split NETCDF_PATH into C and Fortran paths 29 April 2019, 20:47:56 UTC
fe44e19 Wuyin Lin 29 April 2019, 20:39:33 UTC Trim cam's perl configure script step 1 Trim CAM's perl based configure script by removing unused codes in preparation for migration to using Python and CMake. In this step, the following codes are remove 1. cice setup, as it is now controlled by CIME. 2. codes to configure for tests. - Control block in the main program for configuring test and check required modules and libraries - Subroutines supporting the setup for the test that are invoked by the main programs. This include get_gmake, write_tests_filepath, check_fc, check_netcdf, check_mpi, check_esmf, run_test [BFB] 29 April 2019, 20:39:33 UTC
1327c41 Azamat Mametjanov 29 April 2019, 19:32:36 UTC Update Anvil to Slurm and SoftEnv built on CentOS6 29 April 2019, 19:32:36 UTC
55b61f6 hsiangheleellnl 29 April 2019, 18:55:33 UTC add convective cloud water for radiation 29 April 2019, 18:55:33 UTC
e952a6c Jason Sarich 29 April 2019, 15:21:30 UTC Merge branch 'worleyph/cime/anvil_perfarch_update' (PR #2846) Anvil recently moved from PBS to SLURM. This requires changes to syslog.anvil and provenance.py to replace calls to PBS inquiry functions with calls to SLURM inquiry functions, to document job provenance and to capture job progress tracking data. [BFB] 29 April 2019, 15:21:30 UTC
cd76dfc Mark Taylor 27 April 2019, 15:02:31 UTC Merge branch 'mt5555/homme_arkode_interface_update' (PR #2881) merge of the HOMME-ARKode interface. This should be BFB in that it only modifies code within an ifdef block that is disabled by default. [BFB] 27 April 2019, 15:02:31 UTC
42f0335 Mark Taylor 27 April 2019, 15:01:36 UTC Merge branch 'mt5555/nggps-nh-update' (PR #2874) updates to namelists used for some benchmarks. no impact on any E3SM tests. [BFB] 27 April 2019, 15:01:36 UTC
96b1746 Mark Taylor 27 April 2019, 15:00:32 UTC Merge branch 'origin/oksanaguba/eam/restart-thetal-nh' (PR #2775) Adds restart to runs with cam_target=theta-l with hydrostatic_mode=.false. . Required reading/writing 2 dynamic variables on interfaces, w_i and phinh_i . [BFB] 27 April 2019, 15:00:32 UTC
8ba2638 Mark Taylor 27 April 2019, 14:59:50 UTC Merge branch 'origin/oksanaguba/eam/restart-thetal' (PR #2885) Fixing restart for theta-l EAM target. The conversation including testing is in PR #2763 (which was opened to wrong base branch). * origin/oksanaguba/eam/restart-thetal: inserted if statements for restart, writing vtheta instead of t for thetal. 27 April 2019, 14:59:50 UTC
d24815b Mark Taylor 26 April 2019, 22:22:02 UTC jobscript tweaks for skybridge 26 April 2019, 22:22:02 UTC
405bf15 Mark Taylor 26 April 2019, 20:52:56 UTC jobscript: compute correct number of cores per node 26 April 2019, 20:52:56 UTC
c7c18dc Jinyun Tang 26 April 2019, 20:19:22 UTC fix an initialization bug for dynamic landuse In computing the seed amount, the variable my_pool_seed was not initalized for non-veg soil. This fix corrected the failure of ERS_D_PMx1.f19_f19.I20TRCLM45CN.cori-knl_intel.20190425_154849_q0cs0. 26 April 2019, 20:19:22 UTC
d96356d Mark Taylor 26 April 2019, 15:56:33 UTC Merge branch nonhydro/homme/integration2 (PR #2729) This PR uses one subroutine applycamforcing_tracers() to adjust tracers and to convert dynamics forcing (the crucial one is theta_dp forcing). The idea is that tracers update and recompute of forcing for theta_dp should be done at the same time. Now both stepon and standalone homme call this routine. To make it bfb with ftype2 we use a flag to interpret FQ as tendencies or adjustment. Restart routines have calls to endrun() to prevent restart in theta-l. This is not the best solution since restart is called by default at the end of the run, so, model with cam_target=theta-l crashes at the end if restart date is not pushed further. Restart for theta-l will be fixed later. Also, ftype3 code is removed. Theta-c code (which is not tested) is now broken because code in set_thermostate and tests_finalize is disabled. [BFB] 26 April 2019, 15:56:33 UTC
e5fe543 Mark Taylor 26 April 2019, 15:52:21 UTC tweak run script for updated Anvil system 26 April 2019, 15:52:21 UTC
b8ea153 mark-petersen 26 April 2019, 14:27:19 UTC Update mpas-source for addTimeSeriesMaxMin 26 April 2019, 14:27:19 UTC
8e0209f Jinyun Tang 25 April 2019, 21:26:05 UTC fixe the float invalid error When DEBUG=TRUE, the code crashes with float invalid error. It appeared that a few variables were not initialized with computable value when crop mode is off. Now these varaibles are alaways initialized, which fixes the error. No answer change is expected. 25 April 2019, 21:26:05 UTC
90a2bc1 hsiangheleellnl 25 April 2019, 18:16:01 UTC bug fixed in clubb, five and micro 25 April 2019, 18:16:01 UTC
bd399bd Jon Wolfe 25 April 2019, 14:33:23 UTC Merge branch 'mark-petersen/mpas/makefile_update' (PR #2843) MPAS Makefile and framework update This PR updates the MPAS Makefile and the MPAS framework. The changes to the MPAS framework include: * rename Makefile.in.ACME to Makefile.in.E3SM (MPAS-Dev/MPAS-Model #195); * change Makefile.in.E3SM to standard CESM formatting with TRUE in caps (MPAS-Dev/MPAS-Model #191i, Issue #2879); * add -Uvector to Makefile.in.E3SM to ignore the word 'vector' in comments when using GEN_F90=TRUE (MPAS-Dev/MPAS-Model #200, Issue #2725); * fix memory leak due to double allocate in RK4 time stepping, which is not used in E3SM runs (MPAS-Dev/MPAS-Model #185); * changes to atmosphere directories are not used by E3SM; * COMPASS testing updates, not used by E3SM, including python 3 updates; and * fix typos that cause warnings on some compilers (MPAS-Dev/MPAS-Model #196, #197, #198, #199) Necessary E3SM changes to support the new Makefile: * change calls from Makefile.in.ACME to Makefile.in.E3SM; and * additional renaming of ACME to E3SM in comments, xml descriptions, and strings Fixes #2725 Fixes #2879 [BFB] 25 April 2019, 14:33:23 UTC
746db90 Chris Vogl 24 April 2019, 23:16:36 UTC This will fix a naming mismatch that occurred during the original merge of the HOMME-ARKode interface. This should be BFB in that it only modifies code within an ifdef block that is disabled by default. 24 April 2019, 23:16:36 UTC
0b38cd3 mark-petersen 09 April 2019, 17:46:27 UTC Change ACME to E3SM in other places. Update submodule 24 April 2019, 19:38:32 UTC
c72cbaf mark-petersen 09 April 2019, 13:58:57 UTC Change ACME to E3SM in Makefile call name 24 April 2019, 18:35:30 UTC
ada6b5f Aaron Donahue 24 April 2019, 17:11:42 UTC Merge branch 'aarondonahue/cime/apr19_lc_updates' (PR #2851) Changes the config files in CIME to reflect recent changes in Livermore Computing resources: Update syrah and quartz machine config entries to explicitly load mvapich2/2.2 which is the only mvapich version on LC that grants access to pnetcdf/1.9.0. These changes reflect a change in the default module loads on LC machines. In addition, there is a change to the run_script to purge all mention of the machines cab and sierra (which have been taken down) and to add a warning message to the build section warning of the sensitivity of CIME to double slashes (//) in the case directory path. [BFB] - Bit-For-Bit 24 April 2019, 17:11:42 UTC
b594205 James Foucar 24 April 2019, 16:47:09 UTC Merge branch 'wlin/atm/cosp_radar_dep' (PR #2835) Resolving random compilation failure due to missing cosp module Nightly test of cosplite_nhtfrq5 on sandiatoss3 failed from time to time complaining error in opening a compiled module file during compilation of quickbeam/radar_simulator.f90. The missing module is scale_LUTs_io. It turns out there was no rule explicitly setting the object of radar_simulator.o to be dependent of module scale_LUTs_io, which may cause the compilation of radar_simultor.f90 to be started before scale_LUTs_io.f90 is compiled, hence unable to open the required module. This update explicitly enforces it in cam/src/physics/cosp/Makefile.cospinline.in [BFB] * origin/wlin/atm/cosp_radar_dep: Resolving random compilation failure due to missing cosp module 24 April 2019, 16:47:09 UTC
716b084 James Foucar 24 April 2019, 16:45:31 UTC Merge branch 'jgfouca/cime/minor_compiler_fixes' (PR #2864) Minor build fixes Need consistent case for USE_CXX in Makefile (Restores cxxlib flag for PIO2). Intel should not add qopenmp unless compile_threaded is TRUE. Fixes #2858 [BFB] * origin/jgfouca/cime/minor_compiler_fixes: Minor build fixes 24 April 2019, 16:45:44 UTC
4e519a8 James Foucar 24 April 2019, 16:43:50 UTC Update CIME to ESMCI cime5.8.2 (#2876) Update CIME to ESMCI cime5.8.2 Squash merge of jgfouca/branch-for-to-acme-2019-04-22 Features: * Adds a stub for Integrated Assessment Component (IAC) * Allow specific tests to ignore field list differences Bug fixes: * Minor [BFB] 24 April 2019, 16:43:50 UTC
26aa1d6 noel 23 April 2019, 21:06:42 UTC Fix the calculation to give the best cflag value (the integer passed to srun via -c) for KNL. [bfb] 23 April 2019, 21:06:42 UTC
8eb6019 Balwinder Singh 23 April 2019, 15:07:47 UTC Merge branch 'kaizhangpnl/atm/ieflx_cleanup2' (PR #2730) remove l_ieflx_fix removed l_ieflx_fix in - components/cam/bld/namelist_files/namelist_definition.xml - components/cam/src/physics/cam/phys_control.F90 - use_cases namelist files (under components/cam/bld/... ...namelist_files/use_cases) [BFB] Fixes #2731 * kaizhangpnl/atm/ieflx_cleanup2: delete l_ieflx_fix in use_cases namelist files remove l_ieflx_fix 23 April 2019, 15:07:47 UTC
9534408 asteyer 22 April 2019, 22:48:22 UTC 1 1 2 22 April 2019, 22:48:22 UTC
662009d asteyer 22 April 2019, 20:47:09 UTC adding the imkg232 method for Mark's PR 22 April 2019, 20:47:09 UTC
5cdf492 jayeshkrishna 22 April 2019, 17:24:03 UTC Merge pull request #2856 from E3SM-Project/jayeshkrishna/summit_module_fixes Upgrading the summit cmake, essl and MPI modules. Also updating the ROMIO version to prevent OOM errors. Fixes #2847 [BFB] 22 April 2019, 17:24:03 UTC
02b293b Junqi Yin 22 April 2019, 17:20:30 UTC Merge branch 'bishtgautam/lnd/fixes-for-ptm' (PR #2806) Fixes the PETSc-based thermal model in ELM Updates the MPP submodule to fix the PETSc-based thermal model [BFB] 22 April 2019, 17:20:30 UTC
b57d606 Jayesh Krishna 22 April 2019, 16:36:54 UTC Setting summit env for OOM errors OLCF recommends setting "OMPI_MCA_io" env variable to "romio314" to prevent out of memory issues with the code. In our testing we have found that setting this env gets rid of OOM errors with certain E3SM simulations (ECP simulation runs). However also note that setting this environment variable reduces the performance of parallel HDF5 (when using NetCDF4P PIO iotype to write data). See Issue #2856 22 April 2019, 16:36:54 UTC
2b5cd8e Gautam Bisht 22 April 2019, 14:23:25 UTC Merge branch 'jinyuntang/lnd/hr_fix' (PR #2722) Now hr_col is updated at the correct location. The change is smaller than round off error after a 300 years simulations. Fixes #2717 [non-BFB] 22 April 2019, 14:23:25 UTC
1b820ac Mark Taylor 21 April 2019, 22:14:06 UTC tweak cmake for upgraded anvil 21 April 2019, 22:14:06 UTC
8b1952a Mark Taylor 21 April 2019, 20:51:12 UTC fix comment in namelist 21 April 2019, 20:51:12 UTC
87c4107 Mark Taylor 05 April 2019, 16:02:51 UTC fix bug with native grid precl output 21 April 2019, 15:57:07 UTC
472d88b Mark Taylor 25 February 2019, 20:55:29 UTC need to run cmake when rebuilding 21 April 2019, 15:57:07 UTC
9b8a9a7 Mark Taylor 23 February 2019, 05:00:22 UTC use rearth from namelist, instead of hardcoding X=120 21 April 2019, 15:57:07 UTC
b636a03 Mark Taylor 19 February 2019, 19:31:36 UTC fix output of 'geo' for native grid 21 April 2019, 15:57:07 UTC
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