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Update CIME to ESMCI cime5.8.4 #3010

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merged 4,125 commits into from
Jun 25, 2019
Merged

Update CIME to ESMCI cime5.8.4 #3010

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90c2f90
minor modification in directory structure
uturuncoglu Mar 14, 2019
cdc639a
Update input locations on Theia
rsdunlapiv Mar 15, 2019
3954d17
Update ESMF library on Stampede2
rsdunlapiv Mar 15, 2019
9075688
Update esmf library on Theia
rsdunlapiv Mar 18, 2019
299fc80
Check for correct restart file pointer when using NUOPC
rsdunlapiv Mar 22, 2019
60d339c
fix for latent heat and net longwave radiation
uturuncoglu Mar 26, 2019
a263510
Default PIO to version 1 on Stampede and turn off ESMF logs
rsdunlapiv Apr 8, 2019
c6f8597
fix for merging preciptiation with ice melt
uturuncoglu Apr 11, 2019
84833ac
Enable optional checkpointing of timing data during initialization
Apr 25, 2019
26795a1
Unset OMP_NUM_THREADS in MPI-only runs
amametjanov Apr 25, 2019
57e6a2e
fix for edison
jedwards4b Apr 25, 2019
edf6f84
Merge pull request #3091 from jedwards4b/edison_port
fischer-ncar Apr 25, 2019
9ab758d
Change DATM_CLMNCEP_YR_ALIGN for present-day compsets
billsacks Apr 25, 2019
66904a2
Generalize DATM_CLMNCEP_YR_ALIGN for present-day compsets
billsacks Apr 25, 2019
a13fe09
better error reporting for refcase errors
jedwards4b Apr 26, 2019
e57f162
minor fix in mediator code to merge it with FV3 branch
uturuncoglu Apr 26, 2019
a1c0e9d
Merge pull request #3095 from jedwards4b/get_refcase_errors
fischer-ncar Apr 26, 2019
158682e
Change optional checkpoint of initialization to mandatory
Apr 26, 2019
8b98f95
replace tabs with spaces in buildnml
uturuncoglu Apr 26, 2019
9152947
Update for cime5.6.15
fischer-ncar Apr 26, 2019
cb69c61
check existence of scalar fields before querying their value
uturuncoglu Apr 26, 2019
fd91ef5
Merge branch 'worleyph/cime/anvil_perfarch_update' (PR #2846)
sarich Apr 29, 2019
c12f130
Merge esmci_remote_for_split/master
jgfouca Apr 29, 2019
5c31dc0
Merge pull request #3096 from ESMCI/jgfouca/branch-for-acme-split-201…
jgfouca Apr 29, 2019
81c5d92
Update Anvil to Slurm and SoftEnv built on CentOS6
amametjanov Apr 29, 2019
303a4b3
increase wallclock time for Vnuopc_Ln9.f19_g17.X test
uturuncoglu Apr 29, 2019
30a75e5
Split NETCDF_PATH into C and Fortran paths
amametjanov Apr 29, 2019
cf100f6
add netcdf fflags
sarich Apr 29, 2019
8cb2432
Run in acme-centos6 partition on Anvil
amametjanov Apr 29, 2019
3a705ff
Merge pull request #3093 from billsacks/datm_yralign_v2
jedwards4b Apr 30, 2019
4d4872c
change anvil nodename regex for centos6 nodes
sarich Apr 30, 2019
1584669
Allow machine level customization of the run_exe
jhkennedy Apr 30, 2019
d49bf70
Add NLDAS2 datm forcing option
billsacks Apr 30, 2019
24cad68
Move custom run_exe into mpirun spec
jhkennedy Apr 30, 2019
6d92d78
COMPOSE: add COMPOSE options to namelist_*.xml; use COMPOSE in E3SM t…
ambrad Apr 29, 2019
e9a7d76
Remove lines referring to rcp compsets with nldas2 forcing
billsacks Apr 30, 2019
2f627f1
Also allow machine-mpirun level customization of the run_misc_suffix
jhkennedy Apr 30, 2019
1b6a2f9
Add more information in comment
billsacks Apr 30, 2019
e922850
C++/Kokkos: Refine a few build pieces.
ambrad Apr 30, 2019
4b90b1e
Upate env_mach_specific schema and CIME docs
jhkennedy Apr 30, 2019
b896c79
Merge pull request #3098 from billsacks/nldas_forcing_v2
fischer-ncar Apr 30, 2019
5f36ee7
Fix incorrect var refference
jhkennedy Apr 30, 2019
d7d46e1
Reset Anvil changes
jhkennedy Apr 30, 2019
f364901
Use RawConfigParser to load saved submit options
jhkennedy May 1, 2019
9057073
C++/Kokkos: Refine a few build pieces. (PR #2894)
jgfouca May 2, 2019
95fba2b
Missed a spot in wget that needed no-check-cert
jgfouca May 2, 2019
ffff255
merge to cime master hash b896c79
jedwards4b May 2, 2019
5cf618a
Merge pull request #3101 from jedwards4b/nuopc-cmeps
jgfouca May 2, 2019
638ff00
Progress on cam CMakeLists file
jgfouca May 2, 2019
9243e33
Merge remote-tracking branch 'upstream/master' into ambrad/homme/comp…
ambrad May 6, 2019
9105342
Merge pull request #3099 from ESMCI/jhkennedy/custom-run_exe-3081
jedwards4b May 7, 2019
651663a
Merge pull request #3100 from ESMCI/jhkennedy/RawConfigParser
jedwards4b May 7, 2019
464a003
Merge pull request #89 from ESMCI/jedwards/mergetob896c79
uturuncoglu May 7, 2019
2db97d1
set stampede2 default PIO 2 and pnetcdf 1.11.1, change flux max itera…
uturuncoglu May 7, 2019
6ae4bc3
fixes for running f19_f19_mg17
May 7, 2019
edb917b
add izumi to testlist
uturuncoglu May 7, 2019
4a2265d
Test with changing logic for ocn-glc coupling
jonbob May 6, 2019
431978e
dont require optional arguments
jedwards4b May 8, 2019
22b2da0
fix mpi-serial
jedwards4b May 8, 2019
29536e1
fix archive dir for stampede
jedwards4b May 8, 2019
f951cfe
Merge pull request #3103 from jedwards4b/optional_args_required
jedwards4b May 8, 2019
aa7c809
Minor cleanup to previous commit
matthewhoffman May 8, 2019
4a67f36
fix stampede2 pnetcdf module version
uturuncoglu May 8, 2019
1546442
Add FindPETSc
jgfouca May 8, 2019
37e95b1
done with raw porting, now comes debugging
jgfouca May 8, 2019
337d52d
Fixes
jgfouca May 8, 2019
eae0478
Update CIME to ESMCI cime5.8.2-2 (#2908)
jgfouca May 9, 2019
99c81e1
Merge E3SM-Project/ndk/machinefiles/cori-knl-cflag-math (PR #2878)
ndkeen May 9, 2019
0e2f124
send run two TestStatus.log to case1 log
jedwards4b May 9, 2019
7167787
Merge remote-tracking branch 'upstream/master' into ambrad/homme/comp…
ambrad May 9, 2019
688d1a4
Updates for pleiades
fvitt May 9, 2019
1e703d8
Merge pull request #3108 from fvitt/pleiades
jedwards4b May 9, 2019
b7892a9
Small upgrade to e3sm_cime_mgmt
jgfouca May 9, 2019
a018cfa
changes to get mom cap working again
Apr 17, 2019
7b8e02b
introduction of new aofluxes calculation in mediator
Apr 23, 2019
7b49507
updates to get pop/ww3 caps working
Apr 23, 2019
fdaa2ab
fixes to get GECO compset running
Apr 26, 2019
f3f1fd8
add --xml-driver to create_test
jedwards4b Apr 26, 2019
2f1b4e9
changes to git dice working with Si_ifrac_01
Apr 26, 2019
e0a1a0e
added new grid for pop forcing
Apr 30, 2019
0fc0ee2
changes to have nag working
May 1, 2019
8c42a8c
updates for merge to latest nuopc-cmeps
May 4, 2019
427261d
fixed bug in coldair outbreak setting
May 5, 2019
201c1c3
changes for new calendar functionality
May 6, 2019
c493c3c
reverted back to original version for med_phases_aofluxes_mod.F90 due…
May 6, 2019
50eb5d7
removed shr_cal references
May 10, 2019
635001c
removal of use_string_mod
May 10, 2019
f692111
Start of changes to datm to point to new CO2 and presaero CMIP6 futur…
ekluzek May 12, 2019
03f1d19
set default for PIO_REARRANGER to box rearranger
May 12, 2019
c1609b3
Change CMIP5 RCP to CMIP6 SSP
ekluzek May 13, 2019
f48977d
Correct the SSP period portion in the compset names, and get the peri…
ekluzek May 13, 2019
2426d5d
Tool for validating transition to CMake
jgfouca May 13, 2019
acc5d81
Remove no longer-used cime_model variable
matthewhoffman May 14, 2019
9c0de8d
Cleanup formatting in compute_melt_fluxes()
matthewhoffman May 14, 2019
e573fe7
Change DATM_CLMNCEP_YR_ALIGN for present-day compsets (PR #3093), app…
ekluzek May 14, 2019
d495bef
Merge pull request #3107 from jedwards4b/compare_two_status_to_origin…
jedwards4b May 14, 2019
ee02675
Fix typo
jgfouca May 14, 2019
afbe152
Add in the SSP5-8.5 presaero file
ekluzek May 14, 2019
9c02c08
Merge esmci_remote_for_split/master
jgfouca May 14, 2019
1bcc269
Change FFLAGS_NOOPT to be an append
jgfouca May 14, 2019
1ca2910
Merge pull request #91 from ESMCI/mvertens/newcalendar
uturuncoglu May 14, 2019
f43ef89
Merge pull request #3110 from ekluzek/datmsettings4PDcompsets
jedwards4b May 14, 2019
25c0d52
Merge pull request #3111 from ESMCI/jgfouca/branch-for-acme-split-201…
jgfouca May 14, 2019
e43dcd2
Correct the datasets add in the new SSP1-1.9 and SSP4-3.4 co2 files
ekluzek May 14, 2019
fd42a89
Remove the presaero SSP files that aren't there put a null file in th…
ekluzek May 14, 2019
4888a9b
Move latbnd before standard cases for CO2 tseries, set forcing align …
ekluzek May 14, 2019
e3470fe
Merge commit '4888a9b' into addSSPCO2npresaero
ekluzek May 14, 2019
59960d9
Merge pull request #3112 from ekluzek/addSSPCO2npresaero
jedwards4b May 15, 2019
29413a7
Update for cime5.6.16 tag
fischer-ncar May 15, 2019
bd7e7fd
fix README
jedwards4b May 15, 2019
5a886de
Update config_machines.xml
wadeburgess May 15, 2019
5d9d12b
Add x2g_*_from_lnd lists for use in prep_glc LND routines
matthewhoffman May 16, 2019
642c941
Progress changing cam/buildib to python
jgfouca May 16, 2019
0be6d8d
Remove Depends files for unsupported platforms
jgfouca May 16, 2019
9d7622b
Port Depends to cmake
jgfouca May 16, 2019
e45af40
changes to define and use empty groups
uturuncoglu May 17, 2019
9102e24
else statement is removed to eliminate code duplication
uturuncoglu May 17, 2019
7dd2ade
Merge branch 'fv3namelist' into nuopc-cmeps
rsdunlapiv May 17, 2019
a808912
Get cosp integration working
jgfouca May 17, 2019
328bd4f
bld_diff can run with any python
jgfouca May 20, 2019
d6205d7
Homme needs to use GMAKE_J and should do a VERBOSE build
jgfouca May 20, 2019
1586bf1
fix memleak in med_phases_prep_ocn_mod
alperaltuntas May 20, 2019
c23ea15
Provide sane default for the number of create_test parallel jobs
jhkennedy May 20, 2019
ebe3766
bld_diff should not fail so easily
jgfouca May 21, 2019
67373b9
Merge branch 'matthewhoffman/coupler/iceshelf_ocean_coupling_Fyke2_cl…
jonbob May 21, 2019
586f317
The best way to deal with the circular deps between cosp
jgfouca May 21, 2019
324e665
Merge branch 'worleyph/cime/init_profiling' into master (PR #2882)
jgfouca May 21, 2019
1093d45
bless_test_results: Be able to handle build-only tests
jgfouca May 21, 2019
b7527d2
Merge branch 'nuopc-cmeps' of https://github.com/ESMCI/cmeps-cime int…
May 22, 2019
428d528
added new runseq directory and removed all nuopc_runseq files
May 20, 2019
6111db8
bug fixes
May 22, 2019
cae6b73
Set default NTEST_PARALLEL_JOBS=MAX_MPITASKS_PER_NODE and limit E3SM …
jhkennedy May 21, 2019
0c68369
merge maint-5.6 to master, resolve conflicts
jedwards4b May 22, 2019
01ad76b
ChangeLog should be from master
jedwards4b May 22, 2019
ef59f55
Use truncated division operator in SEQ test for py2+3
jhkennedy May 22, 2019
6d8b2a3
Merge pull request #3117 from jedwards4b/maint-5.6-merge
jedwards4b May 22, 2019
ea3d1bf
Merge pull request #3118 from ESMCI/jhkennedy/seq-test-py3
jedwards4b May 22, 2019
a224635
Merge pull request #3115 from ESMCI/jhkennedy/test-concurrent-tasks
jedwards4b May 22, 2019
229d622
Update cori's cmake version
jgfouca May 22, 2019
bcb3582
fixed bugs in run sequence generation
May 22, 2019
daf0c4d
fix pylint error
May 22, 2019
ddf1e00
address pylint issues
jedwards4b May 23, 2019
7a78dbb
fix py3 lint issue
jedwards4b May 23, 2019
bace875
get the name right
jedwards4b May 23, 2019
860af52
Update CIME to ESMCI cime5.8.2-3 (PR #2938)
jgfouca May 23, 2019
3af676b
Merge pull request #93 from ESMCI/fix_memleak
uturuncoglu May 23, 2019
abe811e
Merge pull request #94 from ESMCI/mvertens/runseq
uturuncoglu May 23, 2019
404eb56
Update anvil cmake
jgfouca May 23, 2019
5c0c773
Update Livermore Computing configs
AaronDonahue May 23, 2019
513c2cb
Fixes for anvil
jgfouca May 23, 2019
ad1441d
Update theta cmake
jgfouca May 23, 2019
6a73858
remove cmeps from cime and make it external
uturuncoglu May 23, 2019
633eca5
update cheyenne intel compiler, add DOI
jedwards4b May 23, 2019
e5339c2
make it a link
jedwards4b May 23, 2019
979b021
update cime hash
uturuncoglu May 23, 2019
13c2757
Merge pull request #3120 from jedwards4b/cheyenne_compiler_and_doi
jgfouca May 23, 2019
8cfdc8f
Fix for bebop
jgfouca May 23, 2019
c425be2
addign the test
oksanaguba May 24, 2019
e1051a7
Add support for performance archiving on Compy
worleyph May 24, 2019
26b4b2a
Fix configure to work with cmake Depends files
jgfouca May 24, 2019
733e188
Fix PNETCDF for some platforms
jgfouca May 24, 2019
928a202
Another try for pnetcdf
jgfouca May 24, 2019
e7b7676
Merge remote-tracking branch 'origin/master' into jgfouca/cam/cmakify
jgfouca May 24, 2019
1438086
Merge esmci_remote_for_split/master
jgfouca May 28, 2019
7c0ea93
Remove duped line
jgfouca May 28, 2019
0855336
Fix bug in PET timestamp
jgfouca May 28, 2019
93e1b5a
Import some fixes
jgfouca May 28, 2019
481075c
Fix bug in generating baselines
jgfouca May 28, 2019
060da8a
addition uf usermods documentation
May 28, 2019
51de77f
Minor refactor of kokkos stuff in build.py
jgfouca May 28, 2019
c2b8aa6
Better handling of kokkos
jgfouca May 28, 2019
3145712
Merge branch 'oksanaguba/eam/fc-test-thetasl' into master (PR #2942)
jgfouca May 29, 2019
f8e753f
Merge branch 'jgfouca/cam/cmakify' (PR #2922)
jgfouca May 29, 2019
5a7b543
Progress
jgfouca May 28, 2019
af7399f
Adds cmake 3.11.4 module to Compy's machine files
singhbalwinder May 30, 2019
f4416ac
Merge branch 'worleyph/cime/compy_perf_arch'
bibiraju May 30, 2019
9575a8a
Fix cmake building of atm on anlworkstation
jgfouca May 30, 2019
a7d1096
Implement a more-advanced way of sharing builds within test suites
jgfouca May 30, 2019
3bf427c
Swtich build group output to debug
jgfouca May 30, 2019
f1790b9
Merge branch 'jgfouca/cime/create_test_share_upgrade' into master (PR…
jgfouca May 30, 2019
c1c4245
start over with tests
oksanaguba May 29, 2019
88b5cce
move Externals.cfg to ../Externals_cime.cfg (UFSCOMP)
jedwards4b May 31, 2019
4f20a4b
Merge pull request #3124 from ESMCI/mvertens/usermodsdoc
jedwards4b May 31, 2019
fb19ae5
Cleanup whitespace / indentation
billsacks May 31, 2019
c9b6606
make test optional
jedwards4b May 31, 2019
c19271c
Move MAP xml variables into shared config_component.xml
billsacks May 31, 2019
56cca5c
fix indentation
jedwards4b May 31, 2019
9a2b690
revert change
jedwards4b May 31, 2019
6493b34
Merge pull request #3126 from jedwards4b/nuopc-cmeps
jedwards4b May 31, 2019
ea9b84a
moving thetasl test to shared execs set
oksanaguba May 31, 2019
83063d6
Run_sub_or_cmd is not thread safe
jgfouca May 31, 2019
e218c9b
Use idmap_ignore for optional mapping files
billsacks May 31, 2019
8614f1c
Sandiatoss3 needs newer cmake
jgfouca Jun 3, 2019
5c43a15
Merge pull request #3123 from ESMCI/jgfouca/branch-for-acme-split-201…
jgfouca Jun 3, 2019
2bae7d8
fix build issues for nuopc, add dir to .gitignore
jedwards4b Jun 4, 2019
92767b7
updates for nuopc on stampede
jedwards4b Jun 4, 2019
1f86eda
Merge branch 'jgfouca/clm/cmakify' (PR #2954)
jgfouca Jun 4, 2019
59a7b56
rework nuopc build
jedwards4b Jun 4, 2019
626d122
fix nuopc K_TestCimeCase
jedwards4b Jun 4, 2019
de8d905
fix py3 issue
jedwards4b Jun 4, 2019
637c8f4
Add logic to control activation of glcshelf_c2_ice
matthewhoffman Jun 5, 2019
89fad14
Merge pull request #3085 from ESMCI/azamat/threading/dont-set-threads…
jgfouca Jun 5, 2019
0c7b60d
do not move mediator build
jedwards4b Jun 5, 2019
1b211e3
Merge branch 'master' of https://github.com/ESMCI/cime
Jun 5, 2019
daf05e9
Merge pull request #3129 from jedwards4b/nuopc_build_fixes
mvertens Jun 5, 2019
a8bf363
Merge branch 'master' of https://github.com/ESMCI/cime
Jun 5, 2019
caa0dcf
fixes for nuopc scripts_regressions_tests to work
Jun 5, 2019
52b581d
Update CIME to ESMCI cime5.8.2-3 (PR #2967)
jgfouca Jun 6, 2019
3812456
Update anvils cmake version
jgfouca Jun 6, 2019
046e63b
Merge branch 'jgfouca/cime/update_anvil_cmake' into master (PR #2977)
jgfouca Jun 6, 2019
27dcebe
fix nuopc build, update for stamepede esmf lib
jedwards4b Jun 6, 2019
28d58b1
update esmf nuopc build on cheyenne
jedwards4b Jun 6, 2019
69de0cb
change hires settings to lowres
oksanaguba Jun 6, 2019
f383ae6
Merge pull request #3137 from jedwards4b/build_fix
jedwards4b Jun 6, 2019
2b9dc42
moving tests to integration
oksanaguba Jun 6, 2019
9f39361
Add logic to control activation of glcshelf_c2_ice (#3131)
billsacks Jun 7, 2019
b51b397
Update for cime5.8.3
fischer-ncar Jun 7, 2019
02563fd
Merge branch 'oksanaguba/eam/tests-ftypes2' (PR #2955)
jgfouca Jun 10, 2019
6ed296e
Merge esmci_remote_for_split/master
jgfouca Jun 10, 2019
b0a787b
Remove duped code
jgfouca Jun 10, 2019
1878414
Revert "Merge pull request #3085 from ESMCI/azamat/threading/dont-set…
jgfouca Jun 10, 2019
180ae0d
Fix pylint error
jgfouca Jun 11, 2019
5ef0c73
change test to allow for nuopc
jedwards4b Jun 11, 2019
b0a7b75
Merge pull request #3141 from jedwards4b/nuopc_nodefail_fix
jgfouca Jun 11, 2019
54cb3fb
Cmake macro no longer relies on environment
jgfouca Jun 11, 2019
1f8d04a
Better fix for cmake macros
jgfouca Jun 11, 2019
40361f0
Typo fix
jgfouca Jun 11, 2019
ae6ee47
Another fix
jgfouca Jun 11, 2019
7366718
Fix some occurances of FFLAGS_NOOPT that now need FFLAGS
jgfouca Jun 11, 2019
45e0345
move so that var is defined
jedwards4b Jun 12, 2019
a3d36d3
Merge pull request #3139 from ESMCI/jgfouca/branch-for-acme-split-201…
jgfouca Jun 12, 2019
fc598a7
Merge pull request #3143 from jedwards4b/incflagfix
jedwards4b Jun 12, 2019
1c22a99
require ids in namelist definition files to be lower case
jedwards4b Jun 13, 2019
99d6925
Build groups need to be hashable for cesm
jgfouca Jun 13, 2019
4567384
Merge pull request #3146 from ESMCI/jgfouca/fix_test_sched_cesm
jgfouca Jun 13, 2019
338daf4
if CIME_DRIVER=nuopc add pylint check for nuopc files
jedwards4b Jun 13, 2019
3c28a33
Merge pull request #3145 from jedwards4b/downcase_namelist_definition
jedwards4b Jun 13, 2019
1a36bcd
mods for Theia slurm job scheduler
uturuncoglu Jun 13, 2019
973b767
remove comment
jedwards4b Jun 13, 2019
38b5153
Merge pull request #3147 from jedwards4b/nuopc_code_checker
jedwards4b Jun 13, 2019
6259432
fix for Theia
uturuncoglu Jun 13, 2019
41c0649
Squashed 'src/externals/pio2/' changes from 0f241db..6f0afaa
jedwards4b Jun 14, 2019
2e0bc58
update pio2 to pio2.4.4
jedwards4b Jun 14, 2019
6f1273b
fix more conflicts
jedwards4b Jun 14, 2019
439881d
Makefile cleanup for mpi-serial build
jedwards4b Jun 14, 2019
b85c408
reset default pio_version to 1
jedwards4b Jun 14, 2019
a170130
Merge pull request #3148 from jedwards4b/pio2_update
jgfouca Jun 14, 2019
5c379f8
fix linker error
jedwards4b Jun 17, 2019
8f0e3d3
Merge pull request #3150 from ESMCI/theia_to_slurm
jedwards4b Jun 18, 2019
52113d1
Merge commit '8f0e3d31f5b5fc31ec59204c874bece7d24a8a28' into jgfouca/…
jgfouca Jun 24, 2019
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3 changes: 3 additions & 0 deletions cime/.gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -17,3 +17,6 @@ scripts/Tools/JENKINS*

# Ignore anything that are produced under scripts "cases" directory
/scripts/cases/

#Ignore nuopc driver available seperatly
src/drivers/nuopc
253 changes: 253 additions & 0 deletions cime/ChangeLog
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Original file line number Diff line number Diff line change
@@ -1,5 +1,258 @@
======================================================================

Originator: Chris Fischer
Date: 6-7-2019
Tag: cime5.8.3
Answer Changes: [None, Round Off, Climate Changing]
Tests: scripts_regression_tests.py with CIME_DRIVER=nuopc,
scripts_regression_tests
Dependencies:

Brief Summary:
- Add logic to control activation of glcshelf_c2_ice.
- Fix nuopc build, update for stamepede esmf lib.
- Fixes for nuopc scripts_regressions_tests.
- Merge branch master.
- Merge branch master.
- Merge acme split 2019-5-28
- Remove the nuopc driver and mediator to a separate repository https://github.com/ESCOMP/CMEPS.git
- New documentation explaining how to invoked the --user-mods-dir option to create_newcase.
- Update cheyenne intel compiler, add DOI.
- Provide default for the number of create_test parallel jobs.
- Use truncated division operator in SEQ SystemTest for py2+3 compatibility.
- Merge maint-5.6.
- Merge acme split 2019-05-14.
- Fix typo.
- Send the case2 TestStatus.log updates to the case1 file.
- Small upgrade to e3sm_cime_mgmt.
- Optional arguments run_exe and run_misc_suffix not required.
- Fix ConfigParser fails with some saved submit_options.
- Allow custom run_exe and run_misc_suffix.
- Nuopc cmeps.
- Add NLDAS2 datm forcing option.
- Change DATM_CLMNCEP_YR_ALIGN for present-day compsets.
- Merge acme split 2019-04-29
- Fix for edison.
- Update modules cheyenne.
- Poperly link nag f90.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
9f39361 Add logic to control activation of glcshelf_c2_ice (#3131)
f383ae6 Merge pull request #3137 from jedwards4b/build_fix
caa0dcf fixes for nuopc scripts_regressions_tests to work
a8bf363 Merge branch 'master' of https://github.com/ESMCI/cime
1b211e3 Merge branch 'master' of https://github.com/ESMCI/cime
5c43a15 Merge pull request #3123 from ESMCI/jgfouca/branch-for-acme-split-2019-05-28
6493b34 Merge pull request #3126 from jedwards4b/nuopc-cmeps
4f20a4b Merge pull request #3124 from ESMCI/mvertens/usermodsdoc
13c2757 Merge pull request #3120 from jedwards4b/cheyenne_compiler_and_doi
a224635 Merge pull request #3115 from ESMCI/jhkennedy/test-concurrent-tasks
ea3d1bf Merge pull request #3118 from ESMCI/jhkennedy/seq-test-py3
6d8b2a3 Merge pull request #3117 from jedwards4b/maint-5.6-merge
25c0d52 Merge pull request #3111 from ESMCI/jgfouca/branch-for-acme-split-2019-05-14
ee02675 Fix typo
d495bef Merge pull request #3107 from jedwards4b/compare_two_status_to_original_case
b7892a9 Small upgrade to e3sm_cime_mgmt
f951cfe Merge pull request #3103 from jedwards4b/optional_args_required
651663a Merge pull request #3100 from ESMCI/jhkennedy/RawConfigParser
9105342 Merge pull request #3099 from ESMCI/jhkennedy/custom-run_exe-3081
5cf618a Merge pull request #3101 from jedwards4b/nuopc-cmeps
b896c79 Merge pull request #3098 from billsacks/nldas_forcing_v2
3a705ff Merge pull request #3093 from billsacks/datm_yralign_v2
5c31dc0 Merge pull request #3096 from ESMCI/jgfouca/branch-for-acme-split-2019-04-29
edf6f84 Merge pull request #3091 from jedwards4b/edison_port
35068d0 Merge pull request #3089 from jedwards4b/updatemodulescheyenne
f0f0b60 Merge pull request #3088 from jedwards4b/fixnagissue


Modified files: git diff --name-status [previous_tag]
M .gitignore
M README.md
M config/cesm/config_grids.xml
M config/cesm/machines/config_batch.xml
M config/cesm/machines/config_compilers.xml
M config/cesm/machines/config_machines.xml
M config/cesm/machines/config_pio.xml
M config/e3sm/allactive/config_pesall.xml
M config/e3sm/config_grids.xml
M config/e3sm/machines/config_batch.xml
M config/e3sm/machines/config_compilers.xml
M config/e3sm/machines/config_machines.xml
M config/e3sm/machines/config_pio.xml
M config/e3sm/machines/syslog.anvil
M config/e3sm/tests.py
M config/xml_schemas/config_machines.xsd
M config/xml_schemas/env_mach_specific.xsd
M doc/source/users_guide/compsets.rst
M doc/source/users_guide/create-a-case.rst
M doc/source/users_guide/machine.rst
M scripts/Tools/Makefile
M scripts/Tools/archive_metadata
M scripts/create_test
M scripts/fortran_unit_testing/run_tests.py
M scripts/lib/CIME/Servers/wget.py
M scripts/lib/CIME/SystemTests/erp.py
M scripts/lib/CIME/SystemTests/seq.py
M scripts/lib/CIME/SystemTests/system_tests_common.py
M scripts/lib/CIME/XML/env_mach_specific.py
M scripts/lib/CIME/build.py
M scripts/lib/CIME/case/case.py
M scripts/lib/CIME/case/case_run.py
M scripts/lib/CIME/case/case_submit.py
M scripts/lib/CIME/case/check_input_data.py
M scripts/lib/CIME/case/check_lockedfiles.py
M scripts/lib/CIME/code_checker.py
M scripts/lib/CIME/hist_utils.py
M scripts/lib/CIME/namelist.py
M scripts/lib/CIME/provenance.py
M scripts/lib/CIME/simple_compare.py
M scripts/lib/CIME/test_scheduler.py
M scripts/lib/CIME/test_utils.py
M scripts/lib/e3sm_cime_mgmt.py
M scripts/tests/scripts_regression_tests.py
M src/build_scripts/buildlib.csm_share
M src/build_scripts/buildlib.kokkos
M src/components/data_comps/datm/cime_config/config_component.xml
M src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M src/components/data_comps/datm/nuopc/atm_comp_nuopc.F90
M src/components/data_comps/datm/nuopc/datm_comp_mod.F90
M src/components/data_comps/datm/nuopc/datm_shr_mod.F90
M src/components/data_comps/dice/nuopc/dice_comp_mod.F90
M src/components/data_comps/dice/nuopc/dice_shr_mod.F90
M src/components/data_comps/dice/nuopc/ice_comp_nuopc.F90
M src/components/data_comps/dlnd/nuopc/dlnd_comp_mod.F90
M src/components/data_comps/dlnd/nuopc/lnd_comp_nuopc.F90
M src/components/data_comps/docn/nuopc/docn_comp_mod.F90
M src/components/data_comps/docn/nuopc/ocn_comp_nuopc.F90
M src/components/data_comps/drof/nuopc/drof_comp_mod.F90
M src/components/data_comps/drof/nuopc/drof_shr_mod.F90
M src/components/data_comps/drof/nuopc/rof_comp_nuopc.F90
A src/components/data_comps/dshr_nuopc/dshr_methods_mod.F90
M src/components/data_comps/dshr_nuopc/dshr_nuopc_mod.F90
M src/components/data_comps/dwav/nuopc/dwav_comp_mod.F90
M src/components/data_comps/dwav/nuopc/wav_comp_nuopc.F90
D src/components/stub_comps/satm/nuopc/atm_comp_nuopc.F90
D src/components/stub_comps/sglc/nuopc/glc_comp_nuopc.F90
D src/components/stub_comps/sice/nuopc/ice_comp_nuopc.F90
D src/components/stub_comps/slnd/nuopc/lnd_comp_nuopc.F90
D src/components/stub_comps/socn/nuopc/ocn_comp_nuopc.F90
D src/components/stub_comps/srof/nuopc/rof_comp_nuopc.F90
D src/components/stub_comps/swav/nuopc/wav_comp_nuopc.F90
M src/components/xcpl_comps/xatm/nuopc/atm_comp_nuopc.F90
M src/components/xcpl_comps/xglc/nuopc/glc_comp_nuopc.F90
M src/components/xcpl_comps/xice/nuopc/ice_comp_nuopc.F90
M src/components/xcpl_comps/xlnd/nuopc/lnd_comp_nuopc.F90
M src/components/xcpl_comps/xocn/nuopc/ocn_comp_nuopc.F90
M src/components/xcpl_comps/xrof/nuopc/rof_comp_nuopc.F90
M src/components/xcpl_comps/xshare/mct/dead_mod.F90
A src/components/xcpl_comps/xshare/nuopc/dead_methods_mod.F90
M src/components/xcpl_comps/xshare/nuopc/dead_nuopc_mod.F90
M src/components/xcpl_comps/xwav/nuopc/wav_comp_nuopc.F90
M src/drivers/mct/cime_config/buildnml
M src/drivers/mct/cime_config/config_component.xml
M src/drivers/mct/cime_config/config_component_cesm.xml
M src/drivers/mct/cime_config/config_component_e3sm.xml
M src/drivers/mct/cime_config/config_compsets.xml
M src/drivers/mct/cime_config/namelist_definition_drv.xml
M src/drivers/mct/main/cime_comp_mod.F90
M src/drivers/mct/main/prep_glc_mod.F90
M src/drivers/mct/main/prep_ice_mod.F90
M src/drivers/mct/main/prep_ocn_mod.F90
M src/drivers/mct/main/seq_rest_mod.F90
M src/drivers/mct/shr/seq_flds_mod.F90
M src/drivers/mct/shr/seq_infodata_mod.F90
D src/drivers/nuopc/cime_config/buildexe
D src/drivers/nuopc/cime_config/buildnml
D src/drivers/nuopc/cime_config/config_archive.xml
D src/drivers/nuopc/cime_config/config_component.xml
D src/drivers/nuopc/cime_config/config_component_cesm.xml
D src/drivers/nuopc/cime_config/config_compsets.xml
D src/drivers/nuopc/cime_config/config_pes.xml
D src/drivers/nuopc/cime_config/namelist_definition_drv.xml
D src/drivers/nuopc/cime_config/namelist_definition_drv_flds.xml
D src/drivers/nuopc/cime_config/namelist_definition_modelio.xml
D src/drivers/nuopc/cime_config/nuopc_runseq_A
D src/drivers/nuopc/cime_config/nuopc_runseq_ADLND
D src/drivers/nuopc/cime_config/nuopc_runseq_ADWAV
D src/drivers/nuopc/cime_config/nuopc_runseq_B
D src/drivers/nuopc/cime_config/nuopc_runseq_C_G_D_swav
D src/drivers/nuopc/cime_config/nuopc_runseq_C_G_D_ww3
D src/drivers/nuopc/cime_config/nuopc_runseq_C_wav
D src/drivers/nuopc/cime_config/nuopc_runseq_F
D src/drivers/nuopc/cime_config/nuopc_runseq_I
D src/drivers/nuopc/cime_config/nuopc_runseq_I_mosart
D src/drivers/nuopc/cime_config/nuopc_runseq_NEMS
D src/drivers/nuopc/cime_config/nuopc_runseq_NEMS.cold
D src/drivers/nuopc/cime_config/nuopc_runseq_NEMS.warm
D src/drivers/nuopc/cime_config/nuopc_runseq_Q
D src/drivers/nuopc/cime_config/nuopc_runseq_X
D src/drivers/nuopc/cime_config/nuopc_runseq_default
D src/drivers/nuopc/cime_config/testdefs/testlist_drv.xml
D src/drivers/nuopc/cime_config/testdefs/testmods_dirs/drv/5steps/shell_commands
D src/drivers/nuopc/cime_config/testdefs/testmods_dirs/drv/default/shell_commands
D src/drivers/nuopc/cime_config/testdefs/testmods_dirs/drv/glcnec10/include_user_mods
D src/drivers/nuopc/cime_config/testdefs/testmods_dirs/drv/glcnec10/shell_commands
D src/drivers/nuopc/cime_config/testdefs/testmods_dirs/drv/som/shell_commands
D src/drivers/nuopc/cime_config/user_nl_cpl
D src/drivers/nuopc/cime_driver/ensemble_driver.F90
D src/drivers/nuopc/cime_driver/esm.F90
D src/drivers/nuopc/cime_driver/esmApp.F90
D src/drivers/nuopc/cime_driver/t_driver_timers_mod.F90
D src/drivers/nuopc/cime_driver/util.F90
D src/drivers/nuopc/cime_flds/esmFlds.F90
D src/drivers/nuopc/cime_flds/esmFldsExchange.F90
D src/drivers/nuopc/cime_flds/fd.yaml
D src/drivers/nuopc/cime_flds_shr/glc_elevclass_mod.F90
D src/drivers/nuopc/cime_flds_shr/seq_drydep_mod.F90
D src/drivers/nuopc/cime_flds_shr/shr_carma_mod.F90
D src/drivers/nuopc/cime_flds_shr/shr_fire_emis_mod.F90
D src/drivers/nuopc/cime_flds_shr/shr_megan_mod.F90
D src/drivers/nuopc/cime_flds_shr/shr_ndep_mod.F90
D src/drivers/nuopc/mediator/ESMFConvenienceMacros.h
D src/drivers/nuopc/mediator/ESMFVersionDefine.h
D src/drivers/nuopc/mediator/med.F90
D src/drivers/nuopc/mediator/med_fraction_mod.F90
D src/drivers/nuopc/mediator/med_internalstate_mod.F90
D src/drivers/nuopc/mediator/med_io_mod.F90
D src/drivers/nuopc/mediator/med_map_mod.F90
D src/drivers/nuopc/mediator/med_merge_mod.F90
D src/drivers/nuopc/mediator/med_phases_aofluxes_mod.F90
D src/drivers/nuopc/mediator/med_phases_history_mod.F90
D src/drivers/nuopc/mediator/med_phases_ocnalb_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_atm_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_glc_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_ice_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_lnd_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_ocn_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_rof_mod.F90
D src/drivers/nuopc/mediator/med_phases_prep_wav_mod.F90
D src/drivers/nuopc/mediator/med_phases_profile_mod.F90
D src/drivers/nuopc/mediator/med_phases_restart_mod.F90
D src/drivers/nuopc/shr/CMakeLists.txt
D src/drivers/nuopc/shr/med_constants_mod.F90
D src/drivers/nuopc/shr/shr_expr_parser_mod.F90
D src/drivers/nuopc/shr/shr_nuopc_methods_mod.F90
D src/drivers/nuopc/shr/shr_nuopc_multiinst_mod.F90
D src/drivers/nuopc/shr/shr_nuopc_scalars_mod.F90
D src/drivers/nuopc/shr/shr_nuopc_time_mod.F90
D src/drivers/nuopc/shr/shr_nuopc_utils_mod.F90
A src/share/nuopc/glc_elevclass_mod.F90
A src/share/nuopc/seq_drydep_mod.F90
A src/share/nuopc/shr_carma_mod.F90
A src/share/nuopc/shr_expr_parser_mod.F90
A src/share/nuopc/shr_fire_emis_mod.F90
A src/share/nuopc/shr_megan_mod.F90
A src/share/nuopc/shr_ndep_mod.F90
M src/share/util/shr_const_mod.F90
M src/share/util/shr_pio_mod.F90
M tools/statistical_ensemble_test/README

======================================================================
======================================================================


Originator: Chris Fischer
Date: 4-23-2019
Tag: cime5.8.2
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2 changes: 1 addition & 1 deletion cime/config/cesm/machines/Depends.babbageKnc
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@@ -1,6 +1,6 @@

shr_ncread_mod.o: shr_ncread_mod.F90
$(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS_NOOPT) $<
$(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS) $(FFLAGS_NOOPT) $<

quadrature_mod.o: quadrature_mod.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -DIS_ACCELERATOR $<
2 changes: 1 addition & 1 deletion cime/config/cesm/machines/Depends.cray
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@@ -1,6 +1,6 @@
NOOPTOBJS= ice_boundary.o dyn_comp.o unicon.o

$(NOOPTOBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<


2 changes: 1 addition & 1 deletion cime/config/cesm/machines/Depends.intelmic
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Expand Up @@ -3,4 +3,4 @@
# $(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS_NOOPT) -O1 $<

shr_ncread_mod.o: shr_ncread_mod.F90
$(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS_NOOPT) $<
$(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS) $(FFLAGS_NOOPT) $<
2 changes: 1 addition & 1 deletion cime/config/cesm/machines/Depends.intelmic14
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Expand Up @@ -3,4 +3,4 @@
# $(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS_NOOPT) -O1 $<

shr_ncread_mod.o: shr_ncread_mod.F90
$(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS_NOOPT) $<
$(FC) -c $(FPPFLAGS) $(INCLDIR) $(INCS) $(FREEFLAGS) $(FFLAGS) $(FFLAGS_NOOPT) $<
4 changes: 2 additions & 2 deletions cime/config/cesm/machines/Depends.nag
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@@ -1,4 +1,4 @@
wrap_mpi.o: wrap_mpi.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
fft99.o: fft99.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FFLAGS_NOOPT) $(FREEFLAGS) $<
12 changes: 9 additions & 3 deletions cime/config/cesm/machines/config_batch.xml
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Expand Up @@ -571,12 +571,18 @@
</queues>
</batch_system>

<batch_system type="pbs" MACH="theia" >
<batch_system MACH="theia" type="slurm" >
<batch_submit>sbatch</batch_submit>
<submit_args>
<arg flag="-l procs=" name=" $TOTALPES"/>
<arg flag="--time" name="$JOB_WALLCLOCK_TIME"/>
<arg flag="-q" name="$JOB_QUEUE"/>
<arg flag="--account" name="$PROJECT"/>
</submit_args>
<directives>
<directive>--partition=theia</directive>
</directives>
<queues>
<queue walltimemax="01:00:00" nodemin="1" nodemax="35">batch</queue>
<queue walltimemax="01:00:00" nodemin="1" nodemax="171">batch</queue>
</queues>
</batch_system>

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32 changes: 0 additions & 32 deletions cime/config/cesm/machines/config_compilers.xml
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Expand Up @@ -503,38 +503,6 @@ using a fortran linker.
<TRILINOS_PATH MPILIB="mpich2">$ENV{TRILINOS_PATH}</TRILINOS_PATH>
</compiler>

<compiler MACH="athena">
<CPPDEFS>
<!-- these flags enable nano timers -->
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
</CPPDEFS>
<NETCDF_PATH>$ENV{NETCDF}</NETCDF_PATH>
<PIO_FILESYSTEM_HINTS>gpfs</PIO_FILESYSTEM_HINTS>
<PNETCDF_PATH>$ENV{PNETCDF}</PNETCDF_PATH>
<AR>xiar</AR>
<ARFLAGS>
<base>cru</base>
</ARFLAGS>
</compiler>

<compiler MACH="athena" COMPILER="intel">
<CFLAGS>
<append> -xHost </append>
</CFLAGS>
<CPPDEFS>
<append> -DINTEL_MKL -DHAVE_SSE2 </append>
</CPPDEFS>
<FFLAGS>
<append> -xHost </append>
</FFLAGS>
<MPICXX MPILIB="mpich2">mpiicpc</MPICXX>
<MPICC MPILIB="mpich2">mpiicc</MPICC>
<MPIFC MPILIB="mpich2">mpiifort</MPIFC>
<SCC>icc</SCC>
<SFC>ifort</SFC>
<TRILINOS_PATH MPILIB="mpich2">$ENV{TRILINOS_PATH}</TRILINOS_PATH>
</compiler>

<compiler MACH="bluewaters">
<CPPDEFS>
<append MODEL="gptl"> -DHAVE_PAPI </append>
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