Reproducibility problem with clm4_5_10_r187 -- 30% of the time randomly dies with a methane error #143
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closed: wontfix
We won't fix this issue, because it would be too difficult and/or isn't important enough to fix
type: bug
something is working incorrectly
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Erik Kluzek < erik > - 2016-08-08 13:17:17 -0600 Rosie tried similar submissions with r185 and r186 and didn't see runs that died with the same problem for 8 submissions. Hence we think this came in with r187. |
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Erik Kluzek < erik > - 2016-08-08 13:19:30 -0600 This is for a sequential layout without threading... env_mach_pes.xml: NTASKS_ATM 15 and with daily barriers... env_run.xml: BARRIER_N 1 |
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Erik Kluzek < erik > - 2016-08-08 15:01:27 -0600 We think this problem is just because Rosie's param file doesn't have rootprof_beta as a 2D variable. So the 2nd dimension (for Carbon) isn't getting initialized to anything (and set to garbage) hence the problem. so this file has rootprof_beta as a 1D variable rather than 2D. /glade/u/home/rfisher/Matlab/pft_files/FUNparams/TRY_default_c160708_hydr1.5.nc so this problem shouldn't occur for the default code where the standard params file is being used -- just for cases where a params file doesn't have rootprof_beta as a 2D variable. As a separate issue we should fix the code so it doesn't allow such a thing to happen. |
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Erik Kluzek < erik > - 2016-08-22 16:33:43 -0600 This does also occur on hobart_intel and with both PIO1 and PIO2. |
ekluzek
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closed: wontfix
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I think this issue should have been closed before since the comments indicate it had to do with a params file that didn't have a variable with the right dimension. We don't seem to be running into this problem of late, so I'm going to close it. |
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39ad53263 Merge pull request ESCOMP#150 from gold2718/fix_combo_config 75f8f02f5 Merge pull request ESCOMP#152 from jedwards4b/sort_by_local_path 42687bd53 remove commented code 29e26af81 fix pylint issues 7c9f3c613 add a test for nested repo checkout 75c5353d2 fix spacing 24a3726a1 improve sorting, checkout externals with each comp 29f45b086 remove py2 test and fix super call 880a4e765 remove decode 1c53be854 no need for set call 36c56dbac simplier fix for issue dc67cc682 simpler solution b32c6fca9 fix to allow submodule name different from path 5b5e1c2b0 Merge pull request ESCOMP#144 from billsacks/improve_errmsg c983863c4 Add another option for dealing with modified externals 59ce252cf Add some details to the error message when externals are modified be5a1a4d7 Merge pull request ESCOMP#143 from jedwards4b/add_exclude 2aa014a1b fix lint issue 49cd5e890 fix lint issues 418173ffd Added tests for ExternalsDescriptionDict afab352c8 fix lint issue be85b7d1b fix the test a580a570b push test d43710864 add a test 21affe33c fix formatting issue 72e6b64ae add an exclude option git-subtree-dir: manage_externals git-subtree-split: 39ad532636944b8e759ad9e56ef5f453aaea81f0
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0f884bfec Merge pull request #205 from jedwards4b/sunset_svn_git_access 82a5edf79 merge in billsacks:svn_testing_no_github 17532c160 Use a local svn repo for testing 9c904341a different method to determine if in tests 539952ebd remove debug print statement cc5434fa7 fix submodule testing 1d7f28840 remove broken tests 04e94a519 provide a meaningful error message 38bcc0a8c Merge pull request #201 from jedwards4b/partial_match b4466a5aa remove debug print statement c3cf3ec35 fix issue with partial branch match 7b6d92ef6 Merge pull request #198 from johnpaulalex/gitdir 927ce3a98 Merge pull request #197 from johnpaulalex/testpath a04f1148f Merge pull request #196 from johnpaulalex/readmod d9c14bf25 Change the rest of the methods to use -C. Still some usage of getcwd in test_unit_repository_git. 332b10640 Fix incorrect logged path of checkout_externals in test_sys_checkout: it was basically the parent of the current directory, which varies throughout the test. (it called abspath with '{0}/../../', which adds arbitrary and not-interpolated subdir '{0}' to the path, then removes it and removes one more level). 932a7499b Remove printlog from read_gitmodules_file since read_externals_description_file() already has a nearly-the-same printlog (but add it to the other caller). 5d13719ed Merge pull request #195 from johnpaulalex/check_repo 423395449 Update utest to mock _git_remote_verbose in a new way, since it is now called via the GitRepository class rather than on the specific GitRepository instance. d7a42ae96 Check that desired repo was actually checked out. 71596bbc1 Merge pull request #194 from johnpaulalex/manic2 4c96e824e Make the MANIC_TEST_BARE_REPO_ROOT env var special - give it a constant for easy tracking, and automatically tear it down after each test. 259bfc04d test_sys_checkout: use actual paths in on-the-fly configs rather than MANIC_TEST_BARE_REPO_ROOT env var. This will make it easier to test (in the near future) that checkout_externals actually checked out the desired repo dir. 557bbd6eb Merge pull request #193 from johnpaulalex/manic 5314eede1 Remove MANIC_TEST_TMP_REPO_ROOT environment variable in favor of module-level variable. 345fc1e14 Merge pull request #191 from johnpaulalex/test_doc12 2117b843c test_sys_checkout: verify that basic by-tag/branch/hash tests actually take us to the correct git tag/branch/hash. 94d6e5f2b Merge pull request #190 from johnpaulalex/test_doc11 3ff33a6a8 Inline local-path-creation methods 47dea7f64 Merge pull request #189 from johnpaulalex/test_doc10 9ea75cbf8 Grab-bag of renamings: Remove redundant _NAME from repo constants, and consistently add _REPO suffix (This causes the majority of diffs). c0c847ec8 Merge pull request #188 from johnpaulalex/test_doc9 2dd5ce0f7 test_sys_checkout.py: only check for correct 'required' or 'optional' state in the test that exercises required vs optional behavior. Removed a lot of boilerplate. eb3085984 Merge pull request #187 from johnpaulalex/test_doc8 1832e1f84 test_sys_checkout: Simplify many tests to only use a single external. 8689d61ec Merge pull request #186 from johnpaulalex/test_doc7 fbee4253e Grab bag of test_sys_checkout cleanups: Doc inside of each test more clearly/consistently. TestSysCheckoutSVN didn’t get the inlining-of-helper-methods treatment, now it has that. Move various standalone repo helper methods (like create_branch) into a RepoUtils class. README.md was missing newlines when rendered as markdown. Doc the return value of checkout.main Fix test_container_exclude_component - it was looking for the wrong key (which is never present); now it looks for the correct key. f0ed44a6e Merge pull request #185 from johnpaulalex/test_doc6 a3d59f5f2 Merge pull request #184 from johnpaulalex/test_doc5 5329c8ba7 test_sys_checkout: Inline config generation functions that are only called once. 464f2c7a7 test_sys_checkout: Inline another layer (per-config-file checks). Rename the 4 methods that are used multiple times, to reflect what they do rather than what they're called. 8872c0df6 Merge pull request #183 from johnpaulalex/doc_test4 c045335f6 Merge pull request #182 from johnpaulalex/doc_test3 c583b956e Merge pull request #181 from johnpaulalex/doc_test2 e01cfe278 test_sys_checkout: less confusing handling of return values from checkout_externals. Specifically, when doing a checkout, don't return tree_status from _before_ the checkout. Make a new wrapper to call checkout_externals a second time, to calculate the new status after a checkout (very frequent pattern). 23286818c test_sys_checkout: Remove another layer (which generates test component names) c3717b6bc Merge pull request #180 from johnpaulalex/doc_test 36d7a4434 test_sys_checkout.py: remove one layer of functions (that check for local status enums). No-op. 2c4584bf7 More documentation about tests: * contents of test repositories (n a new README.md) * various constants in test_sys_checkout.py that point to those contents, and terminology like container/simple/mixed. * in each test method, the scenarios being tested. * The coupling between test methods. 55e74bd0a Merge pull request #179 from johnpaulalex/circ 66be84290 Remove circular dependency by making _External stop doing tricky things with sourcetrees. 82d3b247f Merge pull request #178 from johnpaulalex/test_doc 3223f49ea Additional documentation of system tests - global variables, method descriptions. 45b7c01c3 Merge pull request #177 from jedwards4b/git_workflow ace90b2c2 try setting credentials this way f4d6aa933 try setting credentials this way 1d61a6944 use this to set git credentials 7f9d330e1 use this to set git credentials 5ac731b85 add tmate code 836847be7 get git workflow working dcd462d71 Merge pull request #176 from jedwards4b/add_github_testing 2d2479e9d Merge pull request #175 from johnpaulalex/fix 711a53fdf add github testing of prs and automatic tagging of main cfe0f888a fix typos 5665d6140 Fix broken checkout behavior introduced by PR #172. 27909e255 Merge pull request #173 from johnpaulalex/readall 00ad0440b Further tiny refactorings and docs of checkout API (no-op). Remove unused load_all param in _External.checkout(). Rename _External.checkout_externals() to checkout_subexternals(), to remove the ambiguity about whether the main external pointed to by the _External is itelf checked out (it is not) Clarify load_all documentation - it’s always recursive, but applies different criteria at each level. Rename variables in checkout.py (e.g. ext_description) to match the equivalent code in sourcetree.py. 2ea3d1a3a Merge pull request #172 from johnpaulalex/fixit 43bf8092c Merge pull request #171 from johnpaulalex/docstatus e6aa7d21e Merge pull request #170 from johnpaulalex/printdir adbd71557 On checkout, refresh locally installed optional packages regardless of whether -o is passed in. add074593 Comment tweaks, and fix 'ppath' typo 696527cb8 Document the format of various status dictionaries, and the various paths and path components within an _External. c677b9403 When processing an external, print out its path in addition to the base filename (to disambiguate all the externals.cfg's) 975d7fd5a Merge pull request #169 from johnpaulalex/docfix_branch 09709e36d Document _Externals.status(). The original comment was apparently copy-pasted from checkout(). 1d880e090 Merge pull request #167 from billsacks/fix_svn_on_windows 3510da848 Tweak a unit test to improve coverage eb7fc1368 Handle the possibility that the URL already ends with '/' 02ea87e3d Fix svn URLs on Windows b1c02ab54 Merge pull request #165 from gold2718/doc_fix 9f4be8c7b Add documentation about externals = None feature a3b3a0373 Merge pull request #162 from ESMCI/fischer/python3 d4f1b1e8d Change shebang lines to python3 2fd941abc Merge pull request #158 from billsacks/modified_solution de08dc2ee Add another option for when an external is in a modified state e954582d0 Merge pull request #156 from billsacks/onbranch_show_hash 952e44d51 Change output: put tag/hash before branch name 10288430f Fix pre-existing pylint issues 01b13f78f When on a branch, show tag/hash, too 39ad53263 Merge pull request #150 from gold2718/fix_combo_config 75f8f02f5 Merge pull request #152 from jedwards4b/sort_by_local_path 42687bd53 remove commented code 29e26af81 fix pylint issues 7c9f3c613 add a test for nested repo checkout 75c5353d2 fix spacing 24a3726a1 improve sorting, checkout externals with each comp 29f45b086 remove py2 test and fix super call 880a4e765 remove decode 1c53be854 no need for set call 36c56dbac simplier fix for issue dc67cc682 simpler solution b32c6fca9 fix to allow submodule name different from path 5b5e1c2b0 Merge pull request #144 from billsacks/improve_errmsg c983863c4 Add another option for dealing with modified externals 59ce252cf Add some details to the error message when externals are modified be5a1a4d7 Merge pull request #143 from jedwards4b/add_exclude 2aa014a1b fix lint issue 49cd5e890 fix lint issues 418173ffd Added tests for ExternalsDescriptionDict afab352c8 fix lint issue be85b7d1b fix the test a580a570b push test d43710864 add a test 21affe33c fix formatting issue 72e6b64ae add an exclude option git-subtree-dir: manage_externals git-subtree-split: 0f884bfec8e43d0c02261de858d6ec3f6d855e51
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Erik Kluzek < erik > - 2016-08-08 13:16:05 -0600
Bugzilla Id: 2344
Bugzilla Depends: 2345,
Bugzilla CC: andre, dlawren, dll, mvertens, oleson, rfisher, sacks,
A reproducibility issue came in with clm4_5_10_r187 where about 30% of the time the following case will die with a methane error, and other times run to completion. I think simpler cases will die as well, but the simpler tests I did were successful before I realized it wasn't reproducible.
create_newcase -case clm4_5_10_r187_SP_4x5_ADspin -mach yellowstone_intel -res f45_f45 -user_compset 1850_DATM%CRU_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV -user_pes_setby clm
./xmlchange CLM_ACCELERATED_SPINUP="on",STOP_N=19,STOP_OPTION="nmonths",CLM_FORCE_COLDSTART="on",DATM_CLMNCEP_YR_ALIGN=1901
./xmlchange DATM_CLMNCEP_YR_END=1905,DATM_CLMNCEP_YR_START=1901,DATM_MODE=CLMGSWP3
user_nl_clm
paramfile='/glade/u/home/rfisher/Matlab/pft_files/FUNparams/TRY_default_c160708_hydr1.5.nc'
fsurdat='/glade/p/cesm/sdwg_dev/lawrence/surfdata/surfdata_4x5_16pftsmidarctic_simyr2000_c160419.nc'
use_hydrstress=.true.
use_luna=.true.
SourceMods/src.datm/namelist_defaults_datm.xml
<namelist_defaults>
CLMGSWP3.Solar,CLMGSWP3.Precip,CLMGSWP3.TPQW,CLMCRUNCEP_V5.TPQW
<strm_datvar stream="CLMCRUNCEP_V5.TPQW">
TBOT tbot
QBOT shum
</strm_datvar>
<strm_datvar stream="CLMGSWP3.TPQW">
WIND wind
PSRF pbot
FLDS lwdn
</strm_datvar>
</namelist_defaults>
An example error message in cesm.log is...
41: Negative conc. in ch4tran. c,j,deficit (mol): 3512 1
41: 8.843302222960208E-003
0: memory_write: model date = 10623 0 memory = 104.44 MB (highwater) 1946.05 MB (usage) (pe= 0 comps= ATM ICE OCN WAV ESP)
65: Methane demands exceed methane available. Error in methane competition (mol/m^3
65: /s), c,j: -2.755768946371973E-010 6818 2
65: Latdeg,Londeg= -30.0000000000000 35.0000000000000
65: ENDRUN:
65: ERROR: Methane demands exceed methane available.ERROR in ch4Mod.F90 at line 33
65: 90
65:
65:
65:
65:
65:
65:
65: ERROR: Unknown error submitted to shr_sys_abort.
65:Image PC Routine Line Source
65:cesm.exe 000000000153ABA8 Unknown Unknown Unknown
65:cesm.exe 0000000000E43893 shr_sys_mod_mp_sh 401 shr_sys_mod.F90
65:cesm.exe 0000000000509058 abortutils_mp_end 43 abortutils.F90
65:cesm.exe 0000000000A4352D ch4mod_mp_ch4_tra 3389 ch4Mod.F90
65:cesm.exe 0000000000A377CD ch4mod_mp_ch4_ 1980 ch4Mod.F90
65:cesm.exe 0000000000511D82 clm_driver_mp_clm 835 clm_driver.F90
65:cesm.exe 00000000004FDC49 lnd_comp_mct_mp_l 437 lnd_comp_mct.F90
65:cesm.exe 000000000042EDFB component_mod_mp_ 1079 component_mod.F90
65:cesm.exe 0000000000419FB2 cesm_comp_mod_mp_ 2509 cesm_comp_mod.F90
65:cesm.exe 000000000042EB92 MAIN__ 93 cesm_driver.F90
65:cesm.exe 0000000000417B7E Unknown Unknown Unknown
65:libc.so.6 00002ACAABC8FD5D Unknown Unknown Unknown
65:cesm.exe 0000000000417A89 Unknown Unknown Unknown
a precursor to the problem seems to be these ch4tran warnings....
grep ch4tran cesm.log.160806-113740
36: Negative conc. in ch4tran. c,j,deficit (mol): 2842 1
98: Negative conc. in ch4tran. c,j,deficit (mol): 11343 1
24: Negative conc. in ch4tran. c,j,deficit (mol): 1205 1
34: Negative conc. in ch4tran. c,j,deficit (mol): 2561 1
141: Negative conc. in ch4tran. c,j,deficit (mol): 17127 1
53: Negative conc. in ch4tran. c,j,deficit (mol): 5161 1
73: Negative conc. in ch4tran. c,j,deficit (mol): 7928 1
37: Negative conc. in ch4tran. c,j,deficit (mol): 2964 1
40: Negative conc. in ch4tran. c,j,deficit (mol): 3375 1
93: Negative conc. in ch4tran. c,j,deficit (mol): 10667 1
The ch4tran warnings don't occur in the simulations that were successful.
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