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Revision Author Date Message Commit Date
0bf92a3 Merge branch 'iulian787/fortran_wrappers_imoab' into iulian787/context_migrate 15 August 2021, 03:47:48 UTC
a92f137 rename iMOAB*Fort with iMOAB*Fortran also, rename for consistency iMOAB_RegisterFortranApplication with iMOAB_RegisterApplicationFortran 14 August 2021, 21:34:15 UTC
2573151 use fortran wrappers for some iMOAB methods more exactly, all methods that have as parameters MPI_Comm* or MPI_Group* These are just int* in Fortran, and they need to be converted properly to C/C++ structures Because of that, change the actual methods for fortran to use int* in those places 13 August 2021, 16:22:36 UTC
03f5d69 fix compile error on atm / moab the method gfr_f_get_corner_latlon was not found by intel compiler on chrysalis, because the module it came from was not specified "use gllfvremap_mod, only: gfr_f_get_corner_latlon" not sure how gnu is able to find it on my laptop maybe because it is debug mode? Anyway, it needs to be specified, otherwise it should not compile 12 August 2021, 02:10:42 UTC
ef7b3d8 Update config_compilers and machines to latest master Update config_compilers and machines to be identical to master as of Aug 12, 2021, d53497edf3a. Only change is to add MOAB_PATH to bebob, chrysalis and anlworkstation. 11 August 2021, 04:16:40 UTC
261008b Merge branch 'iulian787/api_imoab_change' into sarich/use-moab-driver 10 August 2021, 20:15:28 UTC
dbd7bcf changes required for new context logic before, context_id defaulted to -1 for initial migrate now, it will show the other component id also, iMOAB_GraphCoverage changed API it has ids for components from initial migrate this should work now against the branch iulian07/context_changes_master in MOAB 03 August 2021, 16:30:11 UTC
b110f68 new bubble option (same as commit 06f89c883a6a76346b6d on sarich/use-moab-driver-rebase) 15 July 2021, 18:20:41 UTC
37e964f replace T with theta-l : vtheta_dp another solution would be to change the build options: xmlchange CAM_TARGET=preqx 15 July 2021, 18:01:22 UTC
ae75d50 more rebasing fixes 28 June 2021, 00:14:19 UTC
00e4903 splice in moab changes to mpas-source submodule to subdirectory 27 June 2021, 19:42:38 UTC
86cb2d2 update moab driver from latest mct config changes 08 June 2021, 17:11:41 UTC
f802379 Edit some of the driver-moab files that diverged from driver-mct 02 June 2021, 21:36:29 UTC
eca7c96 Rebase fixes to get mct driver to compile 02 June 2021, 21:35:24 UTC
0bc0b4c use seaice component moab id bad copy from ocean code; need to use sea ice imoab APP id [BFB] - Bit-For-Bit 02 June 2021, 21:33:22 UTC
e10fa57 add more messages mostly to know where we are, and figure out where it is stuck [BFB] - Bit-For-Bit 02 June 2021, 21:33:22 UTC
65272ed add sea ice moab instance on coupler pes add migrate mesh from sea ice comp to coupler fields are not yet added, intx not yet computed [BFB] - Bit-For-Bit 02 June 2021, 21:33:22 UTC
d6607d7 add river model *********1*********2*********3*********4*********5*********6*********7** add river model in moab, as a point cloud for a half degree river model, there are 720*360 points; all points are distributed, by default in round robin way all segments in gsmap for r model are length 1 !! add mask and partition tag so far [BFB] - Bit-For-Bit 02 June 2021, 21:33:22 UTC
c535ff6 set new moab paths for chrysalis and anvil for intel (intel 20) and intel 18 for anvil 02 June 2021, 21:33:21 UTC
f76a368 add chrysalis machine to config files 02 June 2021, 21:33:21 UTC
fc3dcee Update the MOAB driver to use deep copies of files from mct driver instead of symlinks. 02 June 2021, 21:33:21 UTC
3fa30bf add sea-ice model modify the mpas_moabmesh api, to allow sea-ice, similar to MPAS ocean [BFB] - Bit-For-Bit 02 June 2021, 21:33:21 UTC
30922a3 tagname used even without MOABDEBUG [BFB] - Bit-For-Bit 02 June 2021, 21:33:21 UTC
17ea9bf allow tri-grid and original land derived from atm it is basically decided by the samegrid_al logical flag it turns false if trim(atm_gnam) /= trim(lnd_gnam) sameg_al = samegrid_al is set in init_land_moab, and it is a global variable exported from seq_comm_mct (this is where we keep all global moab variables) we basically use the old code if sameg_al is true, and use tri-grid when sameg_al is false; there are many cases now, due to pg2 and sameg_al supported at the same time [BFB] - Bit-For-Bit 02 June 2021, 21:33:21 UTC
4c22b90 replace MergeVertices iMOAB_MergeVertices affects even ocean projection. temporarily, use full vertices, unmerged, for land mesh. need to set a global ID for the vertices too, otherwise migration does not work properly 02 June 2021, 21:33:21 UTC
d6958d6 rename variables for clarification 02 June 2021, 21:33:21 UTC
ceb92f3 define tag name proj correctly [BFB] - Bit-For-Bit 02 June 2021, 21:33:21 UTC
07d78b7 atm/lnd intx similar to atm/ocn similarity is that land is now a full mesh there is no more point cloud land [BFB] - Bit-For-Bit See confluence for a more detailed description about these tags. 02 June 2021, 21:33:20 UTC
08b11a0 consider land a full mesh, similar to ocean *********1*********2*********3*********4*********5*********6*********7** [BFB] - Bit-For-Bit 02 June 2021, 21:33:20 UTC
f800695 create the land projected tag on land component pes too 02 June 2021, 21:33:20 UTC
9c50035 remove partition tag on land mesh 02 June 2021, 21:33:20 UTC
1074a0c merge vertices in land instance *********1*********2*********3*********4*********5*********6*********7** cells created in land/domain have repeated vertices that need to be merged out Maintaining a good mesh is not easy, as vertices have to be renumbered and deleted cells removed from material sets [BFB] - Bit-For-Bit 02 June 2021, 21:33:20 UTC
e508c74 instance land domain mesh *********1*********2*********3*********4*********5*********6*********7** read xv and yv variables from fatm fraction file use pio, and allocate ni * nj * nv array of doubles on each task extract only what is needed to fill the missing data from domain (latv and lonv) use that later in lnd_comp_mct to explicit vertices [BFB] - Bit-For-Bit 02 June 2021, 21:33:20 UTC
bbef10f change options for anvil for intel18 use different modules, for which moab / hdf5 parallel works define /home/iulian/moab-blds/blues/moabs29 as the MOAB_PATH ne11 small model works for coupled system (CASES/W22a) ne30 crashes during zoltan call, with seemingly a mvapich error ? 02 June 2021, 21:33:20 UTC
94a21dd add error checking mostly in cplcomp_exchange and in prep_atm_mod [BFB] - Bit-For-Bit 02 June 2021, 21:33:20 UTC
478b62c correct tag migration pg2 ocn case For projection from atm to ocean, we need to send data from phys grid mesh towards the intersection of ocean and atm pg2 mesh; also, we will use for atm side still the T_ph16 names, as the tags are named as in the spectral case [BFB] - Bit-For-Bit 02 June 2021, 21:33:19 UTC
0d858b1 fix prep_atm_ocn_moab logic it should be executed over joint atm/coupler communicator not only over coupler intx add Only weight generation is over intx app similar error in land/coupler in prep_atm_mod.F90 [BFB] - Bit-For-Bit 02 June 2021, 21:33:19 UTC
1b456e1 pg mesh and tri-grid start prep atm is changed in 2 major ways 1) pg mesh can be active now, an it is used for data transfer / projection 2) if land is coming from atm mesh, there is no intersection or projection needed, only comm graph directly , based on global_id of phys atm and global id of land mesh on top of it (they match) 3) start land on diff mesh logic; will need to instance land mesh for this to work; right now, land mesh is just a point cloud it will need to be proper mesh; connectivity and all enchilada [BFB] - Bit-For-Bit 02 June 2021, 21:33:19 UTC
6073c09 introduce pg atm mesh to the comp exchange atm_pg_active flag is defined in seq_comm_mct, to signal if we are using pgx atm mesh maybe it will become default if active, send FV / PG mesh, not coarse it has important implications on sending/receiving tags [BFB] - Bit-For-Bit 02 June 2021, 21:33:19 UTC
4b3be68 comment out print statements 02 June 2021, 21:33:19 UTC
72fa331 use global id from gdofel not from GDOF elem()%gdof() does not have global ids only gdofel local array has them [BFB] - Bit-For-Bit 02 June 2021, 21:33:19 UTC
13ceb95 Correct connectivity for pg2 mesh connectivity is still wrong; [BFB] - Bit-For-Bit 02 June 2021, 21:33:19 UTC
2ca2b41 instance all moab atm meshes need to reuse the pg2 computed after phys grid init, not 02 June 2021, 21:33:19 UTC
fa44d46 Instance pg2 mesh *********1*********2*********3*********4*********5*********6*********7** create local mesh edges, using GraphVertex information about neighbors also, local elements are in increasing id order [BFB] - Bit-For-Bit 02 June 2021, 21:33:18 UTC
64d9a80 start PGx mesh instance in MOAB *********1*********2*********3*********4*********5*********6*********7** introduce a new PID app, for PGx mesh use coarse mesh first, but will have to use coordinates from fvgrid generated already we do not want to recompute positions of new vertices in the middle Also, the center of FV cell is already computed, will use a tag to set the center position [BFB] - Bit-For-Bit 02 June 2021, 21:33:18 UTC
703e752 add grid files for ne16pg2_r05_oQU240 these files are newer, but we still need them on the older branch [BFB] - Bit-For-Bit 02 June 2021, 21:33:18 UTC
14a3e8d changes for bebop use newer netcdf modules, that are built with hdf5 parallel also, use current moab master (as of July 2020), installed here /home/iulian/moab-blds/bebop/moab-j3 02 June 2021, 21:33:18 UTC
5e64243 revert some change from before *********1*********2*********3*********4*********5*********6*********7** coverage graph need to be called on component and coupler at the same time; we cannot skip it on component side [BFB] - Bit-For-Bit 02 June 2021, 20:58:42 UTC
369fc42 check imoab app ids for consistency *********1*********2*********3*********4*********5*********6*********7** in a simple case without mpas ocean(ne4pg2_ne4pg2 grid), we do not instantiate moab mpas app; we cannot do intersection, data transfer, etc [BFB] - Bit-For-Bit 02 June 2021, 20:58:42 UTC
298cc7d fix up cmake variables for moab 02 June 2021, 20:58:42 UTC
f4a52aa add iulian787/compute_graph changes *********1*********2*********3*********4*********5*********6*********7** * send now to intx atm oc from phys atm do not compute anymore the comm graph from phys atm to atm on coupler compute now a comm graph between phys atm and intx atm-ocn, similar to imoab_phatm_ocn_coupler.cpp on MOAB send from phys atm to intx , and project after that to ocean on coupler PEs still need to send back to the ocean comp * exercise comm between atm physics and atm on coupler * atm physics grid in moab implement it now as part of atm_mct_init method mesh is already distributed, so use ppgrid module for nlcols, lat, lon, area fraction is always 1, and mask too also, during writing of GS map moab files, use shr_CONST_PI, do not redefine it, from shr_const_mod [BFB] - Bit-For-Bit 02 June 2021, 20:58:42 UTC
0b157eb more fixes for cmake and merge. Right now manually links to stdc++ and TempestRemap libs, will have to fix later 02 June 2021, 20:58:41 UTC
77ed476 some cmake fixes 02 June 2021, 20:58:41 UTC
8ab328f remove nets and nete from list of params *********1*********2*********3*********4*********5*********6*********7** * remove nets and nete from moab api call; use nelemd * ierr defined twice in HAVE_MOAB case [BFB] - Bit-For-Bit 02 June 2021, 20:58:41 UTC
c22c745 merge mct driver updates into moab add cmake support 02 June 2021, 20:58:41 UTC
735ead9 take out some nete, nets setup so mct driver can compile 02 June 2021, 20:58:41 UTC
7e2d388 update mpas-source and revert machine files to master 02 June 2021, 20:58:41 UTC
eeb21cb forgot to release buffers when sending mesh initially 02 June 2021, 20:57:40 UTC
212ff12 remove outdated comments 02 June 2021, 20:57:40 UTC
e4ce41a build imoab land model from domain do not build it from mct data structures mct might be replaced with moab 02 June 2021, 20:57:39 UTC
6b3084a atm physics grid in moab implement it now as part of atm_mct_init method mesh is already distributed, so use ppgrid module for nlcols, lat, lon, area fraction is always 1, and mask too also, during writing of GS map moab files, use shr_CONST_PI, do not redefine it, from shr_const_mod 02 June 2021, 20:57:39 UTC
715e49b initialize iMOAB id for land it was causing a crash in a 2+2 layout also, index the moab debug files for projection on coupler (land and ocean), and after migration back to components (land and ocean) 02 June 2021, 20:57:39 UTC
e5dcc8d change of iMOAB api do not need the components ids for coverage graph and migrate tags data; comm graph is found from context now 02 June 2021, 20:57:39 UTC
33e99e8 weight id name is scalar-pc 02 June 2021, 20:57:39 UTC
545a74d land atm coupling needs moab to be built on iulian07/atm-lnd-coupl branch it has the land atm projection 02 June 2021, 20:57:39 UTC
21ce96b context argument for migrate tags and coverage mesh context is now the ocean-coupler 02 June 2021, 20:57:39 UTC
715bd8b forgotten guard for writing moab files 02 June 2021, 20:57:38 UTC
f88869a glc model is usually off, check flag before calling moab 02 June 2021, 20:57:38 UTC
b38280c understand better mct domain for components use moab h5m file to dump mct grids activated only when MOABDEBUGMCT is defined 02 June 2021, 20:57:38 UTC
3f6b4d7 projected tags need to be created in advance on ocean pes otherwise migration of the tag will fail (silently) 02 June 2021, 20:57:38 UTC
a39bd46 reset anvil to centos6 02 June 2021, 20:57:38 UTC
54e5893 Add soft keys for anlworkstation 02 June 2021, 20:57:38 UTC
d7e1405 prefer RCB to migrate RCB behaves better for intersection, later Also, it is more stable 02 June 2021, 20:57:38 UTC
af3008c set partition tag after migration for visibility of the land model after migration it was not really needed; also, need to correct the setting of the tags in iMOAB 02 June 2021, 20:57:38 UTC
a2b862e migrate land model to coupler pes also add more MOABDEBUG ifdefs when writing h5m debug files this branch needs to use moab branch iulian07/point_cloud_migrate 02 June 2021, 20:57:37 UTC
0c4880c Add anvil gnu modules for moab 02 June 2021, 20:57:37 UTC
a664e84 update anvil modules for intel mvapich stack 02 June 2021, 20:57:37 UTC
ae82bb8 remove USE_MOAB variable, since --driver moab implies this 02 June 2021, 20:57:37 UTC
1730fcd update bebop config files to use moab 02 June 2021, 20:57:37 UTC
f351b08 Add cpp to disable h5m timestep output Add a MOABDEBUG cpp around the various blocks of code that output h5m files every timestep. Off by default. 02 June 2021, 20:57:37 UTC
7d49bbe add more tags for the land mesh in moab add partition tag (special integer, because the VisIt moab plugin does not work with partition tag over set of vertices only) add frac and area tag on vertices They are obtained from the domain mct structure Also, the global id tag is obtained from the mect structure that was created Maybe later we will have to create them from the actual file Maybe later will not create the gsMap at all? The important thing is to match the atm mesh exactly including the position, and global id (GlobGridNum) 02 June 2021, 20:57:37 UTC
984b7c8 instantiate moab land model on land PEs use the land domain created earlier read lat, lon and global grid number, to set the GLOBAL_ID tag on the cloud mesh the global ID, position should match exactly the atm mesh, land portion 02 June 2021, 20:57:36 UTC
e5d1a31 comment out gs map dumping 02 June 2021, 20:57:36 UTC
fa892bf register land iMOAB app 02 June 2021, 20:57:36 UTC
e4d54b3 introduce iMOAB id for land mlnid iMOAB app id for land mesh, on land PEs mblxid iMOAB app id for land mesh, on coupler PEs (after migration) 02 June 2021, 20:57:36 UTC
290637b correct order of components in receive element tag It still communicated what we want, because we did not use order (+1/-1) after finding the ParCommGraph instance 02 June 2021, 20:57:36 UTC
f1cdb3c add HAVE_MOAB guards for moab module in dynamics/se 02 June 2021, 20:57:36 UTC
0aac418 fix anvil key 02 June 2021, 20:57:36 UTC
4919fee update for anvil keys 02 June 2021, 20:57:36 UTC
33ee3e5 change iMOAB api for weight computation add user controllable monotonicity parameter to the weight computation routine in iMOAB API; before, it was hard coded to 0 inside iMOAB method; 02 June 2021, 20:57:35 UTC
38e735e another size error 02 June 2021, 20:57:35 UTC
d6d5584 character * size in fortran tags names are concatenated, increase the size it should be increased when we will export more tags 02 June 2021, 20:57:35 UTC
0175183 export more data from spectral elements load more tags ( U and V velocities ), and set up migration and projection at the same time for all variables needs fixes on the MOAB branch too separator between tag names is ";" , semicolon It is a hard constraint, that needs to be used inside iMOAB tag migrate and iMOAB projection methods 02 June 2021, 20:57:35 UTC
cb1e596 remove debugging code was a leftover when I was trying to understand how are the chunks generated, and used in mct coupler it could be reused at some point 02 June 2021, 20:57:35 UTC
3f515e9 modified iMOAB interface for weights weights have now an identifier to be able to reuse the same intersection for multiple weights matrices the character id should uniquely identify it 02 June 2021, 20:57:35 UTC
f2e739f correct comments no code is changed 02 June 2021, 20:57:35 UTC
3c00f5e migrate projected tag back to ocean pes need to change also the prep_ocn_mod.F90 for the moab driver some semoab changes just to make it easier to debug (more consistency for allocated arrays) 02 June 2021, 20:57:34 UTC
edadded add zoltan dependency if moab is built with zoltan, use graph partitioning for migration ; use moab/MOABConfig.h to see if zoltan is available also, remove MOABConfig from semoab; it is not used there 02 June 2021, 20:57:34 UTC
aa6b39b fixes to get moab driver working (still mostly copy of mct driver) 02 June 2021, 20:55:53 UTC
75b3652 add iulian's changes 02 June 2021, 20:55:53 UTC
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