Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Porting of master (120) to lawrencium LR2 partition. #2

Closed
wants to merge 2 commits into from

Conversation

rgknox
Copy link
Contributor

@rgknox rgknox commented Jan 11, 2016

Configuration and machine files were added to lawrencium-lr2.
Some extra changes were required beyond what had been established with ACME, as cime-gptl
build were having trouble identifying if the sys/time.h library was available to provide
machine time. It was also having trouble printing errors correctly, this was enabled by
passing c-compiler directives in config_compilers.xml. The bug fix in EDInitMod.F90
placed a filter on the initd values read in from the pft parameter file, thus preventing
the model from trying to initialize cohorts from pfts with zero initial density
(this prevents div0's).

Test suite: aux_clm45
Test baseline: none
Test namelist changes: none
Test status: [bit for bit, roundoff, climate changing]

DONE SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
--- Test Functionality: ---
PASS SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
PASS SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
--- Test time is 46 seconds ---

DONE ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
--- Test Functionality ---:
/global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.clm2.h0.nc : test compare clm2.h0 (.base and .rest files)
/global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.cpl.hi.nc : test compare cpl.hi (.base and .rest files)
FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest : test functionality summary (ERS_test)
PASS ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
--- Test time is 59 seconds ---

DONE SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
--- Test Functionality: ---
PASS SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
PASS SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
--- Test time is 34 seconds ---

RUN ERS_D_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest.160110-203643

DONE SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
--- Test Functionality: ---
PASS SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
PASS SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
--- Test time is 47 seconds ---

Fixes: Addresses teamwork task: "Develop consolidated codebase from which to start":

https://ngeetropics.teamwork.com/tasks/5048570

User interface changes?: machine files are intended to be buffered from the user.

Code review: self

… EDInitMod.F90.

Configuration and machine files were added to lawrencium-lr2.
Some extra changes were required beyond what had been established with ACME, as cime-gptl
build were having trouble identifying if the sys/time.h library was available to provide
machine time. It was also having trouble printing errors correctly, this was enabled by
passing c-compiler directives in config_compilers.xml.  The bug fix in EDInitMod.F90
placed a filter on the initd values read in from the pft parameter file, thus preventing
the model from trying to initialize cohorts from pfts with zero initial density
(this prevents div0's).

Test suite: aux_clm45
Test baseline: none
Test namelist changes: none
Test status: [bit for bit, roundoff, climate changing]

DONE SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 46 seconds ---

DONE ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
     --- Test Functionality  ---:
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.clm2.h0.nc : test compare clm2.h0 (.base and .rest files)
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.cpl.hi.nc : test compare cpl.hi (.base and .rest files)
    FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest : test functionality summary (ERS_test)
    PASS ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 59 seconds ---

DONE SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 34 seconds ---

RUN ERS_D_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest.160110-203643

DONE SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 47 seconds ---

Fixes: Addresses teamwork task: "Develop consolidated codebase from which to start":

    https://ngeetropics.teamwork.com/tasks/5048570

User interface changes?: machine files are intended to be buffered from the user.

Code review: self
@@ -705,6 +705,7 @@
<machine compiler="ed" testtype="ed" testmods="clm/edTest">ed</machine>
<machine compiler="gnu" testtype="aux_clm45" testmods="clm/edTest">yellowstone</machine>
<machine compiler="intel" testtype="aux_clm45" testmods="clm/edTest">yellowstone</machine>
<machine compiler="intel" testtype="aux_clm45" testmods="clm/edTest">lawrencium-lr2</machine>
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

For ed-clm development, we want to run all ed related tests on all supported machine and compiler combinations. For simplicity and consistency, it's best to use the 'ed' test suite instead of modifying aux_clm45. Please remove the lawrencium-lr2 tests.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It looks like there is a whitespace difference between this line and the previous one. This file isn't intended to be modified by hand, but should be modified with the manage_testlist utility in cime/scripts. If you want to modify it by hand, then you need to run manage_testlist -cleanup to sort the entries and update the whitespace. If this isn't done, it will cause unnecessary conflicts when trying to merge with other edits.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

OK. will remove the lawrencium-lr2 entries and will use the utility.

This commit addresses pull request comments by bandre. lawrencium-lr2
references were removed from the testlist, and a cleanxml call was
executed to ensure whitespaces were removed.

Test suite: ed
Test baseline: none
Test namelist changes: none
Test status: smoke tests appear to be successfull across the board
ERS and ERI's are not expected to pass until S Muszala's fixes
are applied in later subbmissions.

Fixes: See teamwork issue: https://ngeetropics.teamwork.com/tasks/5048570

User interface changes?: changes were applied to the lawrencium relevant
machine files

Code review: rgknox (self), bandre-ucar

Test Generation (non-baseline test):

./create_test \
-xml_category ed \
-xml_compiler ed \
-xml_mach ed \
-mach lawrencium-lr2 \
-compiler intel \
-testroot ${TESTROOT} \
-nobuild off \
-autosubmit on

Test Results:

DONE ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
     --- Test Functionality  ---:
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.clm2.h0.nc : test compare clm2.h0 (.base and .rest files)
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.cpl.hi.nc : test compare cpl.hi (.base and .rest files)
    FAIL ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest : test functionality summary (ERS_test)
    PASS ERS_D_Mmpi-serial_Ld5.1x1_brazil.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 56 seconds ---

DONE SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_Ld5.f19_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 47 seconds ---

RUN ERS_D_Ld5.f45_g37.ICLM45ED.lawrencium-lr2_intel.clm-edTest.160112-135757

DONE SMS_D_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_D_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_D_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 75 seconds ---

DONE SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_D_Mmpi-serial_Ld5.5x5_amazon.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 46 seconds ---

DONE SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : (test finished, successful coupler log)
      --- Test Functionality: ---
    PASS SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest : successful coupler log
    PASS SMS_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest.memleak
    --- Test time is 44 seconds ---

RUN ERS_D_Ld5.f09_g16.ICLM45ED.lawrencium-lr2_intel.clm-edTest.160112-135757

RUN ERS_D_Ld5.f10_f10.ICLM45ED.lawrencium-lr2_intel.clm-edTest.160112-135757

DONE ERI_D_Ld9.f09_g16.ICLM45BGC.lawrencium-lr2_intel.clm-default : (test finished, successful coupler log)
     --- Test Functionality  ---:
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERI_D_Ld9.f09_g16.ICLM45BGC.lawrencium-lr2_intel.clm-default.clm2.h0.nc : test compare clm2.h0 (.base and .hybrid files)
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERI_D_Ld9.f09_g16.ICLM45BGC.lawrencium-lr2_intel.clm-default.clm2.h1.nc : test compare clm2.h1 (.base and .hybrid files)
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERI_D_Ld9.f09_g16.ICLM45BGC.lawrencium-lr2_intel.clm-default.cpl.hi.nc : test compare cpl.hi (.base and .hybrid files)
    FAIL ERI_D_Ld9.f09_g16.ICLM45BGC.lawrencium-lr2_intel.clm-default : test functionality summary (hybrid test  .base and .hybrid files)
    /global/home/users/rgknox/Models/ed-clm-lcport2/cime/scripts/Tools/component_compare.sh: line 318: //global/scratch/rgknox/tools/cprnc/cprnc: No such file or directory
    FAIL ERI_D_Ld9.f09_g16.ICLM45BGC.lawre
@bandre-ucar
Copy link
Contributor

I ran the ed test suite on yellowstone_{intel | gnu | pgi}. After quick glance at the results it looks like everything at least compiled and started running, which is the only real concern about this pull request. I'm ok bringing this to master.

@bandre-ucar
Copy link
Contributor

Merged directly into master with commit: eff944c

@rgknox rgknox deleted the rgknox/cime/lport120 branch February 1, 2016 23:29
rgknox pushed a commit that referenced this pull request Apr 5, 2016
Modified clm_driver call sequence: ed_drver, EDBGCDyn, EDBGCDynSummary
bandre-ucar added a commit that referenced this pull request Jun 28, 2016
a5a3c95 Get SPL working
790d13c Merge tag 'cime4.5.14' into gswp3drvflds
b631529 Merge remote-tracking branch 'upstream/master'
f4c90e5 Merge pull request #447 from billsacks/vertical_gradient_matrix_solve
50a06a7 Merge pull request #449 from fischer-ncar/usermods_inputdata
8d812c5 Merge remote-tracking branch 'upstream/master' into usermods_inputdata
42696c9 Removed inputdata files that referenced glade from usermods.
7e01d2b Merge branch 'gswp3drvflds' of https://github.com/ekluzek/cime into gswp3drvflds
e76f958 Add SPL test
490e221 Merge branch 'gswp3drvflds' of https://github.com/ekluzek/cime into gswp3drvflds
c177e80 WW3 description
3286612 Add ability to handle WW3 DATM
b6d38ad Correct options for flux_epbal to off,ocn
5ad0fe2 Merge pull request #446 from bertinia/update_st_archive
380eb15 Minor fix to st_archive to exclude removing rpointer files
743836c update to st_archive to correctly check if interim restart file duplicates should be removed
2db6710 Add README file
9c32895 Merge pull request #443 from jedwards4b/esp_assignment_fix
7800cc7 fix issue with esp_present on restart
5396091 Merge remote-tracking branch 'upstream/master'
00ca59b Merge pull request #441 from fischer-ncar/remove_logan
2ff3b12 Merge pull request #440 from jedwards4b/jedwards/nersc_update
684431a Merge pull request #438 from mnlevy1981/mlevy/compare_namelist
00a572b Merge pull request #437 from jedwards4b/shr_orb_mod
aab40b3 Remove reference to logan from config_compilers
6cb731f fix a bug or two
775ddea Add a comment
cef70eb Back out changes related to vertical_gradient_calculator_continuous
6bd1820 Merge tag 'cime4.6.0' into gswp3drvflds
9147cb9 Don't remove existing drv_flds_in with the driver merging the versions from the components that doesn't need to happen
bb9c2a9 Add in ESP component
3f832c1 Merge tag 'cime4.5.9' into gswp3drvflds
29d1b17 Merge branch 'master' into mlevy/compare_namelist
3cb7c2a re add #118 correction to shr_orb_cosz
68bcf07 Merge branch 'master' into gswp3drvflds
8ff70f4 Merge remote-tracking branch 'upstream/master'
0d7f4f3 Merge pull request #436 from fischer-ncar/revert_Intel
2b7bbfd Reverting Intel compiler version on Yellowstone.
1d5c94f Merge remote-tracking branch 'upstream/master' into revert_Intel
7239f97 Add a bunch of tests with real output
2087fb7 Go back to setting y range ourselves
c928198 Output initial guess, unlimited and limited for each test
cb4f44b Move tests that do output to their own file
78ea018 Clean up plots
a0ab8f0 Make routine public
14173df Use factory method, call print method
0ab8f0f Print various statistics
ad6bb83 Refactor limit_gradients
eb6149f Specify initial guess and limit gradients
5caac60 Change the stub calculator to allow specifying any gradients
58b8535 Separate computation stage of gradient calculators
25bcadb Move stuff out of vertical_gradient_test_utils
f5c1ce8 Simplify vertical_gradient_calculator_continuous constructor
93c1920 Simplify vertical_gradient_calculator_2nd_order constructor
f65b5cb Remove need to pass in nelev
b827905 Remove unnecessary ability to specify min_elevation_class
8eb4a3c Add start of create_vertical_gradient_calculator_2nd_order
be9126f Begin work on factory to create gradient calculators
6d901d8 Add place-holder for limiting gradients
2be8d78 Add more tests for plotting, and tweak plotter
9484ff6 Merge pull request #434 from fischer-ncar/SSP_testreporter_fix
3571f14 Merge remote-tracking branch 'upstream/master' into SSP_testreporter_fix
7d94209 Merge pull request #433 from jedwards4b/jedwards/tuning
78099a2 Merge pull request #432 from gold2718/PGIbugfix
b976c24 Add test functionality report to SSP test
3601e78 For problematic topo values, set gradient to 0 rather than NaN
351fb92 Handle topo values out of bounds
5a0c561 Add assertion for expected gradients
0a0f504 update intel compiler on yellowstone
7979df5 Switch production code to use new gradient calculator
f647995 Output gradients to file
bcc5167 Remove unused variables
281bb95 Add a basic smoke test of the new calculator
d280f3b Move some shared test utility functions to a new file
8a63e33 Add vertical_gradient_calculator_continuous
d828818 Add a script to plot gradients
706e52b Change tridiagonal inverse test to have more unique values
8d0ed86 tune b1850 f09_g16 default
0fb6c67 Workaround for seq_infodata_mod PGI compiler bug
369d3bd Add a function to invert a tridiagonal matrix
1f444f1 Merge remote-tracking branch 'upstream/master' into shr_frz_mod_fix
27155d4 Merge pull request #428 from gold2718/ESPbugfix
fc51d10 Fixed ESP errors found in prealpha testing
535181f Change CLM_ACCELERATED_SPINUP for CLM SSP test. Add merge of drv_flds_in namelists from different components. Add die_on_conflict option to Namelist.pm merge_nl
a3d25af fix bug in string statement, load balance B1850 f19_g16
c4bda40 Add merge of component drv_flds_in into driver, and also add a die_on_conflict option to Namelist.pm merge_nl
2287638 Fixed max_alarms parameter
c6c4979 Wav clock offset fix
ea2279e Merge pull request #426 from fischer-ncar/wav_clock_fix
e3c1fcf Fix wav clock offset in the driver.
ede0eda Esp compset description fix
c5721bd Merge pull request #425 from jedwards4b/esp_compset_description_fix
0bec14e Ensure that elevation class bounds are monotonically increasing
d30f22c Comment out call to check_topo
e9e7e70 Add a test demonstrating non-monotonicity
0cd0cde Revert "Demonstrate that it works to have topo going high to low"
f93e16a Demonstrate that it works to have topo going high to low
5867dbc Add multi-point test, and a comment in production code
9950ba0 Tweak ECbottom unit test
25fe31d Add code to limit the gradient, and associated unit tests
fda0e5a Add more tests that should almost (but not quite) trigger the limiter
4f82e95 Rename tests
685515e Add a test where gradient is almost limited
6f692a8 Make a parameterized test method
4538e74 Refactor: change where statement to loop with conditional
a24c07e Finish changes for adding elevation class bounds to gradient calculator
823b635 Add elevation class bounds to vertical gradient calculator
bf715bb Remove dependence of vertical_gradient_calculator on glc_elevclass_mod
3a3ac1c Add a routine to glc_elevclass_mod: glc_all_elevclass_strings
039673e a workaround but not a fix
b307ac9 fix esp compset description to match on no compset provided
9f075fd Turn off diurnal flux, and other fixes.
f32e2fe Merge pull request #424 from fischer-ncar/diurnalfluxoff
2f7dbcd Merge pull request #423 from jedwards4b/configcompsetfixagain
4ba7f8e Fix Intel module name for corip1, should be 16.0.2.181 instead of 2016.0.2.181
7cbe05f remove blank line ;
16fcbd6 remove comment line
7a7ae4e Turn off diurnal flux, fix B1850Cw compset, move SMS_D.f19_g16.B1850 to yellowstone, update cori Intel compiler.
c0a99da another fix for compset logic
8a8be68 Merge remote-tracking branch 'upstream/master'
7de299f Merge branch 'apcraig-diurnal_fix1'
b0b2008 Merge branch 'diurnal_fix1' of https://github.com/apcraig/cime into apcraig-diurnal_fix1
8a80287 fix shr_flux_atmocn_diurnal restart problem related to cold start initialization logic
fa75de9 Merge remote-tracking branch 'mydev/user_compset_fix2' merge pr
8e4252d Merge branch 'gold2718-DART'
d54e632 Merge branch 'DART' of https://github.com/gold2718/cime into gold2718-DART merge to master
c44bacd Added comment in component_run for ESP model use
77a0d0a need an additional fix for user compsets that do not match any defined alias
3fc6a38 Merge pull request #419 from fischer-ncar/fixes
024d973 For the B1850s compsets that are based off or the B1850 compsets, same versions of CAM,CLM,POP,CICE....  The CROP option was removed, and %ECO and BGC%BDRD was added.  This was done to make the B1850 compsets more consistent.
032abf2 Added ESP component and SESP (stub ESP model).
29e0582 Merge remote-tracking branch 'upstream/master' into fixes
2fe1ac3 Set flux_diurnal to true, update debug smoke test for B1850
270de50 Set the default flux_diurnal to true in the driver.  Changed the smoke debug test for B1850 to f19_g16.
bfe2f44 Merge remote-tracking branch 'upstream/master' into fixes
4812f7f Merge pull request #415 from fischer-ncar/fixes
aa3167c Merge pull request #414 from bertinia/st_archive_fix
96446da Merge pull request #413 from fischer-ncar/test_dev
24d94d1 Merge pull request #411 from billsacks/glc_mapping_files
36d31d4 Merge pull request #410 from jedwards4b/user_compset_nextstep
5f463fa Merge pull request #406 from billsacks/jg_compset
8866fee Merge pull request #405 from fvitt/waccm_cime4.4.9
5a0080f Removed ic ice_ic from the usermods, this is now being set as the defualt. Add Hb=min(Hb,0.0) in shr_flx_mod to ensure Hb is <=0.0.  If Hb is > 0.0 there is a floating point error.
89a13fc Update st_archive to fix CIME issue #412
e2e4189 Add 5 day debug prebeta smoke test for f09_g16 B1850
2883636 Change RTM tests to MOSART,fix long line,
b03d7cc Add mapping files for new glc-lnd grid combinations
a23c7bc Define new grids that include an active glc grid
49679bb allows user_compset and alias compset to get same result
97ed005 add usage message for -keepexe flag in create_clone
dec0d59 Merge pull request #404 from billsacks/pr_template
7430725 Rename compset alias "BW1850" as "B1850Cw"
728eb9d Revert "Revert my commits on master"
579b4b6 Merge pull request #407 from jedwards4b/user_compset_fix
0a1e76b no warning if user provides compset
de7b8c6 Revert "Validate the drv namelist"
3d47d92 Validate the drv namelist
2184961 fix issue with user_compset option
1f1eca7 Add some comments pointing to open issues
98307f8 Add WACCM compset BW1850.  Remove "CCMI" B compsets (C2R).
315e717 Add a J compset test to the prebeta test suite
cb918ec Add note about CPL_ALBAV
7bec46c Add pull request template
f2262ab Change some comments in driver's config_component.xml
4fb2923 Merge remote-tracking branch 'origin/jg_compset' into jg_compset
4e967f4 Change J compset layout to be reasonably load balanced
45f47d9 Make compset match more specific for ROF_NCPL
122732f Change config_pes block so that it matches
b05f748 Make compset match less greedy for PE layout matching BGC
dc78ff7 Add a new J compset: all active except data atmosphere
e460c93 Merge pull request #399 from fischer-ncar/test_dev
5cfc0d0 Merge pull request #398 from billsacks/pelayout_b1850_x
dd5e256 Change "X" PE layout for B1850-f09 on yellowstone
5acd97b add user_nl files for b1850 usermods
0bc39f9 add user_mods for b1850
bacf592 redefine B1850
13e7bd5 add hybrid start info for B1850
eb13a18 Merge remote-tracking branch 'upstream/master' into test_dev
7e18dc0 Fix testreporter.pl status, use defaultio testing
57b0150 Merge branch 'pySECTupdate' update to pyCECT 2.0.2
8599ce1 fix merge conflicts
1acd234 bring in pyCECT 2.0.2 from cisl
3e74c29 remove old pyCECT
a02f110 Merge branch 'salinity-temp'
3eed7c6 Merge branch 'salt' of https://github.com/dabail10/cime into salinity-temp
48c17dd Merge branch 'clean_build_comment' of https://github.com/billsacks/cime into salinity-temp
6cb2d71 Revert my commits on master
e48aee0 Revert "Add setting of BARRIER for I compsets"
f59d63a Add only clauses.
3028024 Add setting of BARRIER for I compsets
0f3323e Merge branch 'master' of https://github.com/ekluzek/cime
a2ca7a5 Fix syntax error.
b0c94a5 Merge branch 'master' of https://github.com/CESM-Development/cime
f82337f Add in drv_flds namelist definition
1556bfd Add a comment about why we don't clean the shared clm library in a test
4e4c39c Merge pull request #392 from jedwards4b/RESUBMIT_SETS_CONTINUE_RUN
17a0263 Merge pull request #391 from bertinia/testreporter_fix
c18d16a Merge pull request #388 from jedwards4b/Makefilecleanup
d75ba3f fix testreporter.pl, SMS and PFS test output, cori queue settings
8917e74 address issue #386 with this new variable
34e9111 correct syntax in clean_build
908c619 do not clean shared land library in a test
6d2accc Merge pull request #60 from NCAR/ejh_23
88a6eb6 shortened lines so that NAG compiler will not complain
7c39f57 correct comparison error
bf72eec More cleanup.
1e26343 fix clean build issue in Makefile bug in xmlchange
50cad45 Cleaning up freezing point function.
6e3fecb Updated freezing point module.
f06007d Merge remote-tracking branch 'cesm-master/master'
e02e632 Change name of Solar for GSWP3 data
b5956b9 Updated freezing point code.
2b67a27 Merge pull request #383 from jedwards4b/documentCOMP_RUN_BARRIERS
ebd5c62 Merge pull request #59 from NCAR/ejh_21
762c0b0 improve documentation of COMP_RUN_BARRIERS variable
10be4d1 improve documentation of COMP_RUN_BARRIERS variable
46785d0 Add a comment.
b9ba8a1 Add some bounds on the calculation of the freezing point.
70e680a fixed handling of errors in set_chunk_cache functions
9751a59 fixed handling of errors in set_chunk_cache functions
c0f2990 Merge pull request #381 from jedwards4b/buildchanges
015fa98 Merge pull request #377 from bertinia/tests_update
f00b753 Merge pull request #376 from Katetc/master
e9dc09b new treatment of user_compset, bug fix for make clean
2fd4a49 fixes based on Jim's comments to pull request
f738fad fixes based on Jim's comments to pull request
6d398bf removed printf statement
9904cfc New csm_share moduled to compute the freezing point of salt water.
7e0ea19 using PIO_Offset instead of size_t in API
578919c got tests working with var and file chunk caches.
8edfbf5 more fixes for chunk cache functions
2437220 further development of fortran set_chunk_cache tests
d8a042f further development of fortran set_chunk_cache tests
b3b4e08 minor update for testing
ccc56c4 Breaking up four long lines into 8 shorter ones to statisfy Nag compiler requirements.
77ebc2b Merge pull request #1 from CESM-Development/master
d0191ec Modify DOCN and DICE to use salinity dependent freezing point.
8e2f9c3 Merge remote-tracking branch 'origin'
d1bf8cc Merge branch 'master' of https://github.com/CESM-Development/cime
727cffb [ 50 character, one line summary ]
cd9f1f2 Merge remote-tracking branch 'cesm-master/master'
eb4ad98 Merge pull request #374 from apcraig/cplhisthgt
416e9b3 Modify seq_io_mod.F90 so an avect field named "hgt" is never written to the history file.  This is a temporary workaround until models initialize the hgt field in the domain datatype. The exact restart test was failing in cases where hgt was not initialized (and not used) simply because it appeared on the coupler history file and was not defined uniquely in those cases.
0426d0d Merge pull request #369 from brian-eaton/grid_mod
657335a Merge pull request #370 from bertinia/remove-expectedFails
42ebbc4 Merge pull request #372 from bertinia/batch_update
43fbb2a Merge pull request #373 from bertinia/hobart_pes_update
d60b543 rest of nc4 functions in fortran API
3a98a06 more testing
854eb87 more testing
1a1c246 more tests for nc4 performance functions
0326776 update hobart pe layout for all active f19_g16
db73024 Merge pull request #58 from NCAR/ejh_20
cd1c596 set chunk cache function now working
0d1f692 further testing, other variations of fortran functions
04165b5 update config_batch.xml to remove pbs directives
d979112 test cleanup
4af979f Add correct value of ATM_NCPL for T42 grid.
791d9d1 fixed fletcher32 filter inq and documentation
1d15d18 fixed fletcher32 filter inq and documentation
21b3940 Merge pull request #57 from NCAR/ejh_18
9410243 test cleanup
929a091 fixed test output
93c8375 fixed bug in inq_var_deflate, got fortran version and tests working
be8e885 Remove ExpectedFails.xml file from CIME and update testreporter.pl
c70d96e added inq_szip fortran function
0056ace fixed name of inq_var_deflate in fortran API
452fd3a more tests for nc4 functions
f839012 fortran tests for def_var_deflate turned back on
1ada5bd add T85_T85 to config_grids.xml
191d036 Merge branch 'master' of https://github.com/Katetc/cime Fixes output issues with check_input_data
dbd94c4 Merge branch 'constance' of https://github.com/apcraig/cime Update Machine constance
f3cfb20 This branch is called mlevy/southern_ocean in the apcraig fork. There are two tags, southern_ocean_n01 which is just the streams4d update and southern_ocean_n02 which adds the stream open/close and the BARRIER_OPTION features. These changes add support for reading 4d stream data (3d space + time) and single column data, both which were tested in POP. The stream open/close feature reduces the number of open and closes done on stream input files to improve performance. The BARRIER_OPTION adds a new alarm to the driver to synchronize all tasks at a frequency specified by the BARRIER_OPTION/BARRIER_N setting. This is needed in some concurrent cases (datm/clm) where the datm model can advance in time asychronously from the rest of the model and cause MPI memory issues as data is waiting to be received.
157d136 Merge branch 'southern-ocean' merging to master
5b7af03 Merge branch 'mlevy/southern_ocean' of https://github.com/apcraig/cime into southern-ocean Merging to cime master
25aad26 Changed logger calls to prints in check_input_data to make sure the output capture in checkinputdata actually works, and missing files are appropriately downloaded.
89e1b54 add BARRIER_OPTION to driver and new logic for opening and closing files in the streams input to improve performance.
d6aeb17 fixed comment
b45360c Merge pull request #56 from NCAR/ejh_17
778a243 fixed potential memory leak in error condition, other error handling code
a7e2b4d fixed other nc4 inq functions so now result is bcast
748f357 even better handling of null pointers
d28ef0b better handling of null pointers
e649334 removed print statement
785cd2a added c99 flags to unit test directory
912c392 removed redundant broadcast
29f0abd removed unneeded test program
f09d69b fixed some nc4 code
ce3e95f fixing def_var_deflate issues
65df1e8 Merge pull request #54 from NCAR/ejh_15
6ff466c moved name null-terminator fixes to perl code which generates pio_nc.c
1259f43 Update compsets and grids for single column pop capability.
f2691ba test and fixes for name null terminator problem in processors not rank=0
70c007b getting test_names ready
93d4305 avoid fill pass with netcdf4p
260864d fix pio_inq_unlimdimid and add a test
8cf3d63 Merge pull request #52 from NCAR/ejh_14
45fb0f7 fixed compile problem when timing turned off
e2db73b clean up debug write
81deb7b Merge remote-tracking branch 'origin/master' into mlevy/southern_ocean
a3e7501 update cime for pop single column and strm4d capabilities.
ae4829f Minor updates to the testlist_allactive.xml
1b79608 Update machines files for constance.
b751502 Revert pull request  cf010df146114aa88ba772bfc5953b5573783999
1405acf Merge remote-tracking branch 'cesm-master/master'
524496f Merge branch 'jedwards4b-constance'
d0f655c Merge branch 'constance' of https://github.com/jedwards4b/cime into jedwards4b-constance
94e2837 Merge branch 'bertinia-machine_updates'
b86840c Merge branch 'machine_updates' of https://github.com/bertinia/cime into bertinia-machine_updates
a8ec7d7 Merge branch 'cacraigucar-geotrace_branch_cime' - added first file from geotracer branch
8bac184 modified: driver_cpl/bld/build-namelist - added first file from geotracer branch
f396cce batchredirect default should be empty rather than UNSET
592dec0 update constance machine setup
1e21ecc update to config_machines.xml for bluewaters upgrade; update testlist_allactive.xml
3c93918 Merge branch 'jedwards4b-pioduet' Add pio1 and pio2 subdirectories and change build to support both.
66c5321 changes so that PIO_REARRANGER setting works
2e9dfc8 Merge commit 'd95f3bed85738b7834262204b9ad19fb39f8fca7' into pioduet practice pull from subtree
d95f3be Squashed 'externals/pio2/' changes from 0cf9924..dc374a1
dc374a1 latest changes from cesm dev
e405d8e Add 'externals/pio1/' from commit 'f713b941947be742b2f7c159517e7810b24b6f95'
1d335c9 Add 'externals/pio2/' from commit '0cf9924548b5ac4b3c785985bef4e535af788610'
896f495 remove pio directory
8994b91 modify build to handle two pio libraries
4a4b5d5 Fix gnu mpi-serial compiler error and mpi-serial pio defaults
ea2b9fe improve pio performance with netcdf
0cf9924 minor bug fix
f60c4a7 separate serial and parallel in pio_darray
647e71f allocate requests in chunks
dd39a87 Merge branch 'jedwards4b-piofixesforalpha05' Merge to trunk for testing
1953598 Merge branch 'cism_nag_port' of https://github.com/billsacks/cime into jedwards4b-piofixesforalpha05 Merge branches for testing
d5758ad Revert "Remove no-longer-needed CISM_GNU CMake option"
f547459 get the option set correctly
ab851ad align cime with latest pio, including fixes for alpha05a testing
3de3528 Add pio_rearr_box to stub pio to get cime unit tests to pass
8cf46fe Merge pull request #355 from CESM-Development/revert-354-cime4.2.3_cntlexp
a9f8f02 Revert "Cime4.2.3 cntlexp"
0617ff1 Merge pull request #354 from cecilehannay/cime4.2.3_cntlexp
a6a748c fix typo in refcase name
27afe34 Merge remote-tracking branch 'cesm-master/master'
0871843 Updates for pio and archiving
466819f update archive xml to include mosart
e207dcc Merge branch 'st_archive_update' of https://github.com/bertinia/cime into bertinia-st_archive_update merge in archiver changes
9669053 Merge branch 'jedwards4b-open_mpi_pio_workaround' merge in pio changes
e2dd525 openmpi workaround pio defaults fix
dd02a91 correct a bug in settng pio defaults
6daa145 rework workaround
b2e0025 works around MPI_DATATYPE_NULL issue in openmpi
4f99653 branch for winter workshop control experiment
872e46b Change intent(out) to intent(inout) for a pointer
8078281 update st_archive, supporting files and XML schemas
9410f8a Merge pull request #49 from Katetc/master
3878373 A couple more tweaks to get output just right.
69d9ee3 remove unneeded include
e232d1c pio netcdf serial file sync issue, cimeteststatus, G compset coupling
b6f2dbd pio/netcdf serial issue / unused xml cleanup / cimeteststatus
dcd02a0 Merge branch 'ncpl' of https://github.com/dabail10/cime into cime_merge Merge for precommit testing.
f85ec1b Merge branch 'piosyncfix' of https://github.com/jedwards4b/cime into cime_merge merge branches for testing.
3146313 Remove no-longer-needed CISM_GNU CMake option
c59b447 remove unused xml fix timer issue in coupler
5aa4bd1 Changes to performance test output to make it a bit easier to parse for plots and analysis.
5cdd5cc Reverting runcdash-nersc-cray to the main repo form. Debugging paused.
e5c73d3 Merge pull request #3 from NCAR/master
7622c83 fix a sync issue with serial netcdf io
eb441c4 Merge branch 'master' of https://github.com/NCAR/ParallelIO Fix the sync operation so that the iobuf is freed for all libraries not just pnetcdf
435868e need to flush for all not just pnetcdf
db53954 Changes required to get examples to build on Yellowstone.
fce4639 Cori queue/walltime change, PFS test fix
ee28d29 Merge pull request #348 from jedwards4b/edison_port
a72f97d Merge remote-tracking branch 'cesm-master/master'
c3a9c74 port to edison slurm
b61460a Merge pull request #48 from NCAR/ejh_12
07e9e10 fixed memory leak
afc2cb3 Changes to test nightly building on cori
3c0859b Merge pull request #2 from NCAR/master
93b5f1a Merge branch 'master' into ejh_12
826c7c4 added emacs temp files
9d709f3 correct path for ctest on cori
f41aa0e try salloc
5304311 another cori test change
9e4d6e9 update for slurm
ce46244 another nersc test update
00b4802 updating ctest on cori
01173f3 update nersc ctest
685bf50 update nersc ctest
a44eaa0 add code to support serial version of the test
2c47019 update nersc batch to slurm
54b28ff updates for nersc
2616613 mpimod test should be tried even if include path is not found
d11eeed update pgi compiler version on yellowstone
98a5543 update gnu compiler version on yellowstone
7e1a644 more work on netCDF-4 functions
8eef91d remove c99 style from tests, updates from cesm testing
ff0b899 more work on netCDF-4 code and tests
e009bec more work on netCDF-4 functions
ed20df5 adding and testing netCDF-4 functions
3093bab adding and testing netCDF-4 functions
6c6c8b3 more testing for netCDF-4 functions
d11b265 Merge branch 'master' of https://github.com/PARALLELIO/ParallelIO merge to trunk for testing
666f4d8 Merge pull request #47 from NCAR/ejh_11
2ec9a52 fix issue with string padding in fortran
c0d1220 fixed c99 issues
a09fe44 removed by version of nc_inq_var_fil()
3feb775 merged master
4244cb5 adding memcheck test
85b9447 Merge pull request #45 from jedwards4b/docupdate
29e1e17 fix some documentation in pio_nc.c
14416c5 updates documentation in pio_nc
6ce1ff2 remove debug print statements
8a36ae5 unlimdim in dof seems to be working now
0e23b35 fixed test code
6e8b33d fixing problems with test_nc4 on non-netcdf-4 builds
b40221e removed MPI error handler setting which caused errors on some platforms
ce6a5bc fix issue in inq_unlimdim
43f5043 adding support for unlimdimindof
17634e9 starting to isolate some memory leak issues
f8daed1 Merge pull request #44 from Katetc/master
7f852c3 Updated MPI Serial to stub in a call to MPI_Errhandler_set. Rebuilt library and pointed nightly mpiserial tests on yellowstone to the new MPI-serial library.
01afba2 feedbacks from cesm
5f583c1 Merge pull request #43 from Katetc/master
9bfcf05 Removed for loop variable declarations so we don't have to muck with CMakeList compiler options.
6b6f179 Merge pull request #1 from NCAR/master
b79bb73 added test for inq_var_deflate
43178dd more nc4 function work
dae0d82 starting to add other netcdf-4 functions
80b7ee8 Merge pull request #42 from NCAR/ejh_10
2804de3 added tests for def_var_chunking/inq_var_chunking
26a5736 Merge remote-tracking branch 'cesm-master/master'
983a450 Work on CLMGSWP3, and remove drv_flds_in in preview_namelist
78c96aa adding test of nc4 chunking functions
dc46914 Revert "adding unit tests for def/inq chunking function"
318a1c6 adding unit tests for def/inq chunking function
6599e88 added inq function
3d12ca7 added function to define chunksizes
b562100 now using chunksizes for netCDF-4 files
0393927 Merge pull request #41 from NCAR/ejh_8
3a69130 build file fix
4fc5c97 more documentation changes
0d7ea52 doc cleanups, more work on example2
70313c0 added use of mpe logging to example2
6903e74 more work on example2
e494c22 Change the default coupling interval for G compsets.
c44afe1 more development of example2
0f10186 fixing MPI leaks
d13a119 further development of example2
7aaee0a further development of example2
6b3edf9 working on example2
f8513df Merge pull request #40 from NCAR/ejh_7
3eb3252 example now uses all four output flavors, and plain old netcdf to check the result files
89107ea fixed some doxygen warnings
ba6976c continued development of example1.c
2df0d8d clean up repo
73dd592 Merge branch 'master' of https://github.com/PARALLELIO/ParallelIO pull then push
f1ace47 update version
2697c9c Merge pull request #39 from jedwards4b/fillval_test_fix
54a124d precount outstanding requests so that request and status are sized properly
431ea2b Merge remote-tracking branch 'cesm-master/master'
6d28fa9 Merge pull request #38 from NCAR/ejh_doc3
0071d69 more discussion of examples in documentation
1bd9b3b testing memory issues
f902f0b fix for leaking MPI_Groups
7d5ebf8 fixing memory leaks and uninitialized value identified by valgrind
6e865b0 added config.h
ecef0f8 Revert "added config.h file, added PIO_USE_MALLOC to it, added resulting config.h to c files that needed it."
b770fc9 added config.h file, added PIO_USE_MALLOC to it, added resulting config.h to c files that needed it.
8f4361b added example1, improved docs, finalized timing library to please valgrind.
41f4570 adding beginning of example1.c
d202032 Merge branch 'master' of https://github.com/CESM-Development/cime
15ed685 updates from cesm testing
5325fc5 adding to documentation
4e82091 adding documentation
2f1a6f8 Merge pull request #37 from NCAR/ejh_doc2
df59de4 fixed version number
80aa58e documentation fixes
901632d Merge pull request #36 from jedwards4b/put_requests_fix
85eee34 fix an issue with put requests
bb0094c Merge pull request #35 from Katetc/master
7de57b0 Removed duplicate definition of loop counter (i) that gave the nag compiler fits.
a82aed3 Merge remote-tracking branch 'cesm-master/master'
93b26cb improving documentation, C example now checks for correct number of processors
6810404 Merge pull request #34 from NCAR/ejh_doc
809f3bf updated documentation
5c4bc27 removed unneeded includes
f946bdb added verbose option, also now check data after read
3df8a6e fixed bug in compdof array, added more documentation
08e1a27 further work on documentation
fa69758 added documentation to C example code
c88521b Add in GSWP3 for CLM
41d8486 Merge pull request #33 from NCAR/ejh_examples
3c24efe added examples to documented build targets
417a2ae fixed bug
9335536 turned on example build, initialized GPTL in C example
4d72cad updated build instructions a bit
918706d clean up and add a little documentation
f397173 add gptl init to tests, fix issues with last commit
c34292a Merge pull request #32 from jedwards4b/request_redo
16cfbea rework request list as allocatable to reduce mem usage
1ece5b2 Merge pull request #31 from jedwards4b/master
092216a increase PIO_MAX_REQUESTS and add a test to make sure it isnt exceeded
4e0e98c Merge pull request #10 from NCAR/master
f3d0f74 Merge pull request #30 from NCAR/ejh_adding_build_docs
3af2ef4 updated modified date
088f0fc added build instructions for Linux, from source code
e9e999b update pnetcdf library and compiler versions on yellowstone
680701f Merge pull request #28 from jedwards4b/cmakegptl_fix
0334df1 change HINTS to PATHS in find_path
b9a2357 Merge pull request #27 from jedwards4b/cmakegptl_fix
7936fa7 need to mv check for gptl library
68d0e8e add a little documentation
6f363e4 Merge pull request #26 from Katetc/master
3dd101a Added ifdefs around the MPIAlltoall call in the case of OPENMPI which doesn't seem to like one of the MPI types used. This allows all of the nightly tests on Hobart to complete.
15a2f4e Merge pull request #25 from Katetc/master
9691ee2 Changed runcdash back to correct URL for nightly tests.
77ab8bc Fixes to get the nightly tests to run through on Caldera with serial MPI. Better handling of bad task configurations at init time, plus added logic to the test that prevents asking for bad configurations when running serially.
d683d34 Changing checkout url so I can test problems with nightlies on Caldera
7471a1f Updated comments to support doxygen.
077ef28 Merge pull request #9 from NCAR/master
48ade07 Updated URL in README.md to point to correct location under the new NCAR domain.
a744be9 Merge pull request #24 from NCAR/katesdocbranch
5acd796 Updates to doxygen comments to fix the API/User Interface documentation on the website.
d71a484 Merge pull request #8 from NCAR/master
6506d65 Merge pull request #23 from Katetc/master
628dd8c Added code to attempt to open files with regular NetCDF if Parallel-NetCDF or NetCDF4 fails.
d81c899 Added documentation hooks to help the doxygen api page pick up on darray functions.
d3cbe86 forgot a file in previous commit
b62188b Merge pull request #21 from jedwards4b/errstrfix
5c7d994 make errstr in pio_nc.c allocatable and minimal
935d2cd Merge pull request #20 from Katetc/master
8996a50 Going to test out nightlies with the main repo.
9a7c3c3 Hobart nightly debugging. still.
9371ca0 Merge branch 'master' of https://github.com/Katetc/ParallelIO
46b95ea Testing a git issue for nightlies on Hobart
d423a7a Merge pull request #7 from PARALLELIO/master
9fce2d1 Merge pull request #19 from Katetc/master
e8b29cf Rebuilt pio_nc.c with pnetcdf 1.6.0 which is what is used on most machines now.
1ca6def split 6-hourly SOFS streams into multiple files
f742ae1 split daily SOFS streams into multiple files
3c76036 split NCEP streams into multiple files
e314c1f one last gitignore update
b04f58a didn't mean to commit .gitignore at cime/ level
4f518aa update .gitignore in mapping tools
58b5fb1 Updating ncparser.pl and pio_nc.c to support a newer version of the pnetcdf libraries.
46ca777 Added the full path to qsub and qstat on Hobart and removed the extra PIO_DASHBOARD_SITE export call in runctest-cgd.sh
3fae34e Updating Edison documentation to reflect changes in the cce module.
17ed7e8 Merge pull request #18 from Katetc/master
d51e5fb NERSC removed the cce/8.4.0.219 module we were using and replaced it with cce/8.4.0.223. I updated runcdash-nersc-cray.sh so our nightly tests will build and run again.
9044637 Merge pull request #17 from Katetc/master
f385846 Finished debugging! Cdash should work for Hobart now. Changed paths back to original locations for the git repo and Jim's dashboard directory.
d9455ff lowercase cgd
4abbae7 Still debugging
afe0cfe I think I'm almost done debugging.
04a69f1 More debugging
513aaa1 more debugging
6a66167 More debugging
879ff76 More debugging
40ed8af More debugging
2fd1f2e More debugging Hobart
0e11285 Reverting to regular CTestScript so I can merge to the main branch.
132f4a7 More debugging
c64cd46 More debugging
9e38451 more debugging
e3d42f5 more debugging
86d5cb0 More hobart debugging.
283885b more debugging
fff902e More Hobart ctest debugging.
d4b60bd More hobart ctest debugging.
26aca80 More hobart ctest debugging.
4ec1fc3 Debugging changes to Hobart tests.
4f92e91 Merge branch 'master' of https://github.com/Katetc/ParallelIO
ffe2c30 Testing changes for overnight tests on Hobart.
8660f6d Merge pull request #6 from PARALLELIO/master
a2354e4 Generating pio_nc.c with a newer parallel-netcdf library broke the build. I am checking in the previous version of the file temporarily until we get a more permanent fix in place.
2c53a65 Merge pull request #5 from PARALLELIO/master
f630c6e Updates to ncparser.pl to add a more specific link to the NetCDF documentation for the doxygen documentation of each of the wrapped functions in pio_nc.c
c7acf2c Updated documentation for building with PGI on Blue Waters.
6cfc67e Merge pull request #16 from PARALLELIO/templatingTarget
75fc329 Simplifying (doesn't appear to work, yet)
2ee7196 No SOURCES tag in add_custom_command
4f61f3f Changing to add_custom_command to fix dependencies
64d807b Attempting to change 'execute_process' to 'add_custom_target'
d922581 More things to work on testing on hobart.
81e85ec Trying stuff for the hobart nightly tests
1ae09c7 Pull source from my branch for testing for now.
72d0e5f Testing out changes to get the hobart cdash tests running.
14364ed Merge pull request #4 from PARALLELIO/master
58c6211 Removed -x from the script.
7f13253 Added a runctest file for Hobart. Hopefully this helps the nightly tests run through... though needs testing.
cf12369 Bug fix for compare_namelist.pl
53f5ad7 Merge branch 'master' of https://github.com/PARALLELIO/ParallelIO
207d705 Changes to cmake and ctest to run tests on Blue Waters. Updates to machine walkthrough documentation for Blue Waters (updated netcdf modules required to run ctest).
20ebb23 Added a link to the cdash site for nightly tests
7e59004 Added build instructions for Intel compiler on Blue Waters.
a8cc829 iframe is really, truely no longer ALLOWED by github. Will have to find a different way?
69ac68d Trying again to add an iframe to embed the nightly test results on the GitHub page.
855ff8f Trying to add an iframe to embed the nightly test results on the GitHub page.
6a63311 Added a better handler for NAG compiler -mismatch_all
27214fc update to use $ENV
ddbbe33 add hobart to supported test systems
171aa70 add ctest scripts for hobart
8c5b4ea Merge pull request #15 from Katetc/master
9365829 Cleaning up files to get ready to push bug fix changes.
5d8aa2d Debugging and fixing problem with more indexes than number of elements in the array. One test case now works, but the original one still explodes.
e3e770e Merge pull request #13 from Katetc/master
3a04958 Improved output and added DEBUG flags
0dff92d Added and improved some doxygen documentation for fortran support functions.
9a0870d Patch to allow RESUBMIT to work
af95400 Update C1DIAF streams
6f49384 Merge pull request #9 from Katetc/master
09c3132 Added link to new github.io website and doxygen documentation to main page.
b7071c8 A few last minute changes to mach-walkthrough
bd28794 Added Install walk-throughs for several super computers.
719a448 needed to build without timing
e016b30 Deleting commented-out code
777bbba Setting return variables in parent scope (instead of caching)
c4aaf21 Reverting last change (uncommenting PKGCOMP_FOUND check)
cf053f9 Removing check on PKGCOMP_FOUND
985f6f2 Changing NAG checks to STREQUAL (instead of MATCHES) just to be sure
4207106 Making compile options private
78eae8c Adding new function to initialize search paths from include/lib lists
5e4f0f4 Merge pull request #3 from PARALLELIO/master
347892e Formatting only.
3cd06f3 Allowing for all-caps MPI.mod when searching for Fortran module
b965a21 Bumping back up to cce version 8.4.0.219 to fix compile errors
0766adb Moving back to default mpich and bumping down cce version to 8.3.12
06df635 Bumping up version of mpich
3818db0 Updating cray compiler to most recent version
42d570e Allowing mpif.h for Fortran component of mpi-serial
135bd1f MPISERIAL enabling variable misnamed
31c2f3e Adding dashboard runscript for MPISERIAL build
edf8130 Removing unnecessary GNU run script
e4541b5 Typo fix.  Need prefix path, not lib path.
94dcf85 Locking software versions and cleaning environment on ALCF
1fbe81d Manually setting environment variables for ALCF IBM compiler
643f228 Adding .project (Eclipse project file) to ignores
f5f047b Merge pull request #8 from Katetc/master
1e21cfd Changes to CMakeLists for NAG compiler and shortening a line in pioperformance.F90 for NAG.
05160cd Merge pull request #7 from Katetc/master
ae84e0f Shortened two lines to make the Nag compiler happy.
880cbff Merge branch 'master' of https://github.com/katetc/ParallelIO
695877e Merge remote-tracking branch 'piomain/master'
8efad12 Merge remote-tracking branch 'ktfork/master'
06f0d74 Fix for MPI_Fortran includes in checks
133d24a Fixing bug when getting gnu compiler version
45394bc Disabling add_mpi_test when using mpi-serial
396cdcb Removing debugging statements.
ccda7e6 Debugging statements.
791b5f7 Bugfix.  Need endforeach (not endif).
3723d51 Adding MPISERIAL find package
d6c842f Adding new find package capabilities to support MPISERIAL
8ed1096 Changing comments when disabling PnetCDF
b7d7a3b Updating Introduction and Install documentation.
5400fdb Wrapping CheckMPIreturn method with NO_MPIMOD checks.
81f6409 Removing MPI_OFFSET definition from pio_kinds (just don't use module)
8d2bea2 Setting system and compiler directives.
6254b53 Adding includes/libraries for MPI only when using mpi-serial
e503ad3 Defining MPI_OFFSET for modules that do not define it
0ba152d Making NO_COMM_F2C private
8062688 Better checks on MPI to test/enable builds with mpi-serial
9a9e66d Merge branch 'master' of https://github.com/PARALLELIO/ParallelIO.git
c889bec put pnetcdf specific code in ifdef block
e9b6263 Move checkfunctionexists include to top-level
e5a35d3 Adding checks for PAPI, gettimeofday and MPI_Comm_f2c
ea720dc Defining preprocessor directives for system/compiler names
537d11f Adding a FindPAPI module for the internal GPTL
6a28ac5 .gitignore html/ folder (contains gh-pages branch)
80cdddc Merge branch 'master' of https://github.com/katetc/ParallelIO
ef790f0 Merge branch 'master' of github.com:PARALLELIO/ParallelIO updating local
385eeb2 remove debug print statement
f713b94 add support for optional old error handle
8e597f5 Adding initial ALCF IBM-compiler dashboard run script
b134aea Adding specific environment setting for ALCF
f8f3a90 Automatically getting compiler version on Edison.
87e06fb Adding build group/model (Nightly, Experimental, etc) to build dir name
d2f97b3 Getting compiler version automatically on Yellowstone
d942dba Simplify the dashboard run process.  Guarantee build/tests jobs same.
d8f87dc Adding CDash run script for Cray compiler at NERSC
00f7e48 Adding "nid*" hostnames to NERSC identifiers
0ded31f Adding GNU CDash run script for NERSC
43285b5 Adding more basic NERSC modules
1ebdef9 Need to load MPI
6dc107a Adding initial CDash run script for NERSC
22d93b2 Fix for NO_MPI_MOD --> NO_MPIMOD
0a261a9 Properly read environment variables
e613366 Setting environment for NERSC runs.
d4749d4 Adding NERSC environment and ctest run scripts.
2329452 Passing compiler ID to parallel job environment
22b86f0 Reading Dashboard model name from command line
cd5326b Adding CDash test scripts for NWSC/Yellowstone
244187c Adding pronghorn to NWSC name designations
e681f38 Removing test-run output redirect
78783a6 Re-enabling submission.
d299ffc Removing debug output.
6626b34 More debugging output.
d70e2d9 More debugging output.
5722156 Minor change to compiler info in build name.
7bfcb98 Disabling submission.  Adding debug output.
b20cc7f Bugfix.  Wrong prefix variable for options.
867b383 Don't need PREFER_STATIC on Yellowstone.  Removing.
1d742ca Adding PATHS options to the find_package func (searched after hints)
79812dd Adding debug statements
9080fb1 Removing debug lines
c96f2b8 Adding debugging output.
463e22e Removing debug output.
9164459 Debugging output.  Making execute_process command a string.
96fccd9 Testing PREFER_STATIC with Yellowstone GNU
71d9899 Allowing compiler ID to be sent to CTest via env variable
67e4061 Executing tests from binary directory
d94bbe0 Bugfix.  Using "--envs" with runjob, not "--env"
fb20503 Setting dashboard root environment variable on ALCF
ffc90e8 Set PREFER_STATIC to TRUE
246fae5 Trying PREFER_STATIC instead
15eeadf Explicitly setting HDF5_PATH for ALCF
91f0029 Preferring static on ALCF
47569d5 Removing debug statement
895897a Adding debug statement
918cdce Nope. Prepending doesn't change behavior.  Going back to append.
20bc020 Need to prepend to module path to over-ride existing Find* modules
18aa3a2 Quick datm update for 01col IAF
a615399 Bugfix.  Need to pipe extra commands to runctest script.
1d83ce0 Adding ALCF test scripts
75c70ea Need to APPEND to tag, after all
63efe69 Simplifying binary dir location to make portable
5c374d0 Using improved site-name
a7a0d7d Improved site-name format
4540983 Add C1DIAF compset / update datm streams
f55b07c Updating NWSC dashboard scripts
3e12c33 Updating NWSC run script to match new model
e518ab8 Removing limit on number of tests
10232cf Bugfix to prevent 2 submissions when attempting only 1.
b62fba8 Bugfix.  Changed test script name.
16b8579 Creating a common header-script for inclusion in main and test scripts
7ece6f6 Normal ctest_test command in Appendix script
16d3d0d Need to run appendix script from source directory
1c8a7b4 Try to append tests to same dashboard tag
d1e7368 For testing, just enable tests 5-8
c0f61d5 Try to just run ctest
4e19c06 Try to use the CTestScript for testing only...
e4d511d Renaming, again, and requiring PIO_DASHBOARD_ROOT variable for control
ae92705 Assuming source exists and all ENV variables are set before ctest
e5e0e53 Adding scripts to run on Yellowstone
4b821ef Bugfix.  Can't use Bourne-shell commands in CMake!
7d3e91b Enabling dashboard submission
0008917 Adding script-driven CTest running
775a045 Setting up configure/build system for nightly tests.
a9e4446 Adding environment setting script for default machines
990a8e0 Renaming and turning off submission for testing purposes.
ed6034f Testing
fb0b65d Starting to general the CTest dashboard script
29ed55c Re-enabling git update step, now that bugfixes are in place
88c79eb Using add_definitions to set the directory-level compile options
e3e2431 If GNU Fortran, setting tests to free-format line length
3c742c2 BUGFIX: Incorrect check for Fortran_CSIZEOF
f57b4fb BUGFIX: Incorrect global find/replace fixed!
fc1f5a8 Merge pull request #1 from PARALLELIO/master
2a22680 Adding first attempt at CTest Dashboard scripting
75d1f81 Adding installation instructions (and other info) to README
0f5f3af Adding the ability to install PIO in CMAKE_INSTALL_PREFIX location
7f65ed9 Merge pull request #4 from PARALLELIO/gptlExternal
e4af78c More updates to the README
f4619ab Adding options for backward compatibility (see below)
e496345 Fixing more references to *netCDF_DIR (should be *netCDF_PATH)
814e82c Adding messages about GPTL during build
4caf864 Properly handling QUIET and REQUIRED arguments to find_package
e2d40b3 Merge remote-tracking branch 'origin/master' into gptlExternal
d4a8f82 Adding link to external/internal GPTL if set and found
9612eb1 Changing the name of the component to Fortran_Perf
e1ab44b Removing unnecessary CPP directive
f58ee83 Adding a component for perf_mod.mod
e60327c Switch back to gptl.mod.  The perf_mod has nothing to do with gptl.
a5423dc Switch back to perf_mod.mod include file.
55d9750 Reverting to previous revision.  Unnecessary.
545c9eb Updating the Fortran interface to external/internal GPTL versions
4a0bf6d Adding find_package check for GPTL and setting CPP directives
cc0eb76 Adding find_package check for GPTL dependency
063c81c Adding a new Find module for GPTL.
d6c78e9 typo in LND_DOMAIN_FILE for 01col
21af6df Update datm defaults
eb23669 Reverting needless variable name change (back to USER_CMAKE_MODULE_PATH)
3cb6107 Create first pass at README
fd09d4f A few tweaks needed to run 01col grid
4df82aa Adding component-specific environment variables to find_package searches
80afe02 Merge pull request #3 from kmpaul/simpleCMake
6106433 Formatting only.
c53a7fc Adding INQ_VAR_FILL and DEF_VAR_FILL enum values
ec09bf0 Renaming template-generation flag to PIO_GENERATE_SOURCES_FROM_TEMPLATES
a8533fc A little execute_process cleanup
3fd011b Adding template source generation to pioc CMakeLists
3a756a1 Moving template source back into src.  Just makes more sense
6999389 Adding environment variable definitions to ALCF mpiexec command
d86bf72 Moving nc*parser.pl scripts into templates directory, too
283fb30 Moving templates into their own directory
f0b72eb Moving santos.c into _UNUSED_ until I know better where it goes
7a48e36 Moving prune_decomps.pl into top-level scripts directory
25edc19 Adding "tests" and separate "check" targets to control testing
4c282cd Doxygen cleanup.
69b6662 A little doxygen cleanup.
db451fb Moving output up one directory
47d84ec Adding "check" target to emulate autotools "make check"
2e42142 Remove unnecessary file
26dc48f Bumping up CMake minimum version to 2.8.12 and adding doc sourcedir
4bb8cee Excluding all tests from ALL
03ef90d Moving testpio example into examples directory
f0f82bd Moving all doc source into doc directory (and restructuring)
bf5a839 Finished changing _DIR variables into _PATH variables
94b6f10 Removing version files since try_run cannot be used
b0d153a Fixed check_version function to NOT try_run
2ce5199 Setting compiler options in pioperf specifically.
15db8dd Making compile options private.  May need to add to tests individually.
0fcdddf Moving back to 2.8.12 syntax
8a09383 Update factorfn default for 01col grid
8eca84c Including external macro not so easy...
1afa8fe Adding option to include an external macro script (e.g., from cime)
52dfee1 Fixed naming problems
05aabee Changing name of unit test, too
35a024a Changing name of performance test target
4d8bd8b Removing more debugging statements
7976cc6 Removing debugging statements
7983240 BUGFIX: Forgot to update add_mpi_test syntax in unit tests
5687bfc Debugging statements
6b0c666 On LSF, need to move number of tasks to end of command
721cf09 BUGFIX: Need to specify "unknown" for other platforms
0fde4cd Changing add_mpi_test to take separate ARGUMENTS and use platform execs
6cb90ad Use single column datm forcing for 1D_1D res
19a4b8a BUGFIX: Typo (num_proc -> num_procs)
e2e35d4 Adding basic CTestConfig.cmake file for CDash submissions
f1f419f BUGFIX: Need elseif statements, not if
401ff9d Creating MPI launch commands assuming running from interactive session
566998f Much faster to run CTest from within an interactive session
1bba202 Simplifying UCAR/NCAR test runs.
f67f089 Remove check_file function (not needed if using NetCDF 4.3.3+)
756b273 Changing _DIR's to _PATH's for convenience
fbd3209 Fixed platform name function
5328d3b Adding check for PREFER_STATIC (in addition to PREFER_SHARED)
a8785dd Adding check for file (instead of a direct CPP macro check)
e227f72 Fix for MPIEXEC on all other platforms
a6da680 Adding platform determining function
e054c4e Removing SOURCES keyword for CMake 2.8 syntax
4e19a39 Fix for UCAR MPIEXEC command
8cd74ec Fixed transition to CMake 2.8.
4e3d036 Update to support 01col grid
3bf8ce7 Moving to CMake 2.8 syntax.
952d48a Switching to CMake version 2.8.11- syntax
7577418 Reverting changes and bumbing CMake required to 2.8.12
3db0f0a Test out lower version of CMake
d4d9732 Bumping down to 2.8.11
7bded5a Bumping up required version for target_ commands
3dcdbff Missed GPTL
76031cf Change version in all libs
c0b5e41 Lowering CMake required version further
bd3fb50 Try reducing required CMake version
0ef8c3d BUGFIX: Need scoping for try variables
8eeb37e Adding HDF5 check for optional SZIP
1b89a53 Renaming check_package to check_property...makes more sense
adb4c68 Cleanup.  Moving mpi-related functions into LibMPI
be839f0 Simplifying check_* calls with LibCheck library functions
7e280ac Renaming LibFind for helper functions for Find* macros
ec83bfc Fix case in TryMPIMod.f90 file name
8a07afa Fixing bug with MPIEXEC not found
abb0e02 Enabling CTests (except for performance test)
d3ad6c9 First pass at enabling tests
5963c2b Adding MPI Fortran module check
532de83 Using CMake_Fortran_utils for testing purposes
50b5029 Removing required specification for NetCDF C
f0d55a4 Enabling performance test build
aec7cd4 Adding Fortran compiler checks and made compiler options public
33a5f9e Making NetCDF_C required
e12ff5e Adding big endian test
d662558 Renaming directory (to be consistent)
1594879 Adding unit test directory to build
a8c043e Formatting only
5c95933 Adding automated GenF90 download, if GENF90_DIR not set
bc60418 Checking cache variables for "if defined" instead of just "if"
8f7c7c7 Fixing version checking (one version per package)
3be528e Including check on shared libraries
56ac227 Including PnetCDF fortran libraries
80dccaa Attempting to find appends
3b2a736 Appending PnetCDF to NetCDF_Fortran, too, if needed
8237d5b Bugfix
ae373d3 Adding PnetCDF to NetCDF if required
ffec202 Removing include for CheckHDF5 module
392a45a No need for CheckHDF5 module
e9158fe Moving package checks to separate modules
19562b5 Debugging output
891187d Bugfix: extra endif removed
b78e05f Looking for all components before doing dependencies and checks
531ca7e Adding all include dirs for Fortran version checking via tryCompile
a8f76a9 Updating version requirements
374c1d5 Adding PnetCDF version checking
f2bb41b Checking NetCDF Fortran version
1a0b326 Renaming variables to ensure scoping is safe
e3e3b43 Removed debug checks.  NetCDF_Fortran version check works on mac.
3b76f49 Adding PNETCDF support check and debugging output
f5d386c Output in case version could not be found.
e8e60c3 Get NetCDF Fortran version string
a4c1ccc Removing debug statements
e564fe2 Adding NetCDF version checking analysis
741ee52 Adding version checking for NetCDF
9c9bc76 Fix for is_shared_library function
b8cef51 No up-front declaration of prefer shared or static variables
0959575 Use default find_library first, then search for shared if necessary
56dfdd8 Turning PREFER_SHARED on by default
98a1865 For testing purposes, adding tests back to all
b5b94d8 Removing old CMakeLists file
c3da0be Fixing MPI includes/libraries for HDF5 HL and Fortran_HL searches
b924600 Removing unnecessary inputs to find_package_component function
ccb16d3 Modifying find_package_component to assume variables pre-defined
41bb342 Fixed other foreach loop bugs.
ffa9e27 Removing debug statements.  Fixed foreach loop bug.
7cc4151 debug output
b4b1bc3 Debug output
ad2b73f Debugging output.
9c0a760 Updating find modules to use new helper functions
27dc859 Adding define_package_component and find_valid_components functions
6a8489b Adding find_valid_components function.
993bc8c Moving includes (removing redundant includes)
022b6c1 Removed unnecessary finds after already found
51d58b1 Manually adding libdl to NetCDF libraries when static
4dc561b Fixes to try_compile source files to check macro values are 1
91e5882 Debugging output
584f7c7 Debugging output
fea5a12 Debugging output
cbf6b17 Debugging output
59257c2 Adding tests for DAP support and Parallel support
da67f4d Adding modules for HDF5 and LIBZ by hand
25eea60 Changed NetCDF Fortran dependency
d9a371e Changing dependency of NetCDF Fortran to HDF5 Fortran
e2ebf0e Disable static libraries
c134cec Cleaner include/library hints
ec5515a Appending EXTRAs to the end of each target
8ef5ffe Using static libraries in HDF5 if set globally
3b31b01 Fix GNU compiler options
ce3c78d Correcting target and variable names in piof
f5193e2 Adding the ability to pass in extra includes, libraries, etc
8dc6d6f Removing CURL dependency.  Only needed with DAP support.
ac40e1a Use static libraries variable
0e4dff4 Remove scoping from used shared libraries variable
7c9f491 Renaming variables to provide PIO scope
7051cc6 Remove blank line
25b36d8 Removing REQUIRED from NetCDF-C dependencies
1906a44 Fixes for find_package_component macro
4a78f3d Adding new macro function to search for includes/libraries
0349b93 Starting to move common find functionality to library macro
582b108 Typos.
3a67912 Checking MPI wrapper for Fortran includes/libraries
7f45e43 BUGFIX: Removed extra endif
7ab8e4b First attempt to check MPI includes/libraries from wrapper first
45d871a BUGFIX: Typo in name of PnetCDF Fortran library
d752f73 Debugging statements.
609cb39 Using component-based find modules
d39c6db Forgot to include component-based find module for PnetCDF
2af042d Component-based versions of find modules in place
bc6102c Adding component-based NetCDF find module
e2af06a Including explicit checks for shared libraries first.
f47818e Removing PnetCDF explicit dependency on MPI
3eb6a54 Removing commented out code.
f211199 Re-publicizing NetCDF and PnetCDF link libraries
7560b46 Removing debug statement
a025a65 Debugging output
5580c3e More code cleanup
3fd1068 Removing commented out code.
2f37d25 More debugging.  Re-enabling "plural" include/link variables
13ab96c Debugging: Using single include/library from NetCDF and PnetCDF
0d50a19 Debugging: Commenting out unnecessary link to GPTL in tests
4981bf9 Debugging.  Commented out explicit MPI link and includes
b53c086 For testing purposes, making linked libraries private
69022b5 Fixed target libraries as PUBLIC
0f26432 Adding additional support to detect static libraries
cdad8e0 Look for shared variable and do not append options for dependencies
78b2d00 BUGFIX: Corrected library name
1597ba9 Changing PnetCDF module name to include language
8575a34 Adding SHARED variables to netCDF modules
4d614d3 Comments only
0f47be3 Splitting the PnetCDF module into separate languages.
772617a Re-enabling builds of tests
373a2dd Pulling out unnecessary compiler flags
92e5602 Moving VARN check into target specs, out of PnetCDF module
3bc5719 Removing separate PnetCDF_<lang> modules
25aaf33 Another fix to make only 1 library variable
1d3bf55 BUGFIX: Should only be 1 library
099ae58 Using common PnetCDF module
24fae32 Removing debug statements, adding common PnetCDF module
f5942c8 Removing debug statements
c05bf3d BUGFIX: Hack for bug in CMake v3.0; manually set normal-case found var
88ca52f More debug statements.
2560491 Look for shared as well as static in LIBM
d0dcd71 Debugging statements
469aee1 Debugging statements
770ccd6 Remove unnecessary -D from compiler definitions
adb82f1 Debugging statements.
c8e3175 Forgot to include CheckFunctionExists
724e0f5 Updating new find_package modules
cc3ddd5 Updating to use new find_package modules
30827bc No need to remove duplicates.
ddd80d0 Removing duplicates in lists.  Fixing check on environment variables.
1d9fbf5 Adding C library find_package modules
25f544d First test of new find_package modules
8f06cac Disabling tests for work with new find_package modules
7b00877 Adding most-recent LibFindMacros-based find_package modules
80804a5 Formatting only.
5c440b6 Enabling tests
71b560d "Privatizing" options and definitions (not include directories)
46c84d7 Whoops!  Actually do need the pioc library for Fortran tests
62f02ec Adding binary directory to public include directories for piof
7c22a12 Removing pioc dependency in Fortran tests
0615d19 Enabling Fortran language in tests
2b9dd0b Adding first tests to CMake
e224000 Moving (apparently) unused source out of the way
63c823e BUGFIX: Removed PUBLIC keyword from target_link_libraries
168ec68 BUGFIX: PUBLIC keyword doesn't belong in target_link_libraries
29627cd NetCDF and PnetCDF dependencies use environment variables
f22942e Adding comments
0bd858d Adding gitiginores
1de1fda New CMake build structure.
f8ff531 Restructuring the CMake build, using more subdirectories.
9afbdda Some debugging output
21c91e6 Changing library links from names to absolute paths
169010c Adding current source dir to include path
6df09af Bugfix: Need PRIVATE/PUBLIC/INTERFACE descriptor
0bdf02f Attempting CMake 3 target-specific definitions
775c1ea Cleaning out old CMakeLists and starting very simple
141f6da Merge pull request #3 from PARALLELIO/master
a337c92 add idealized block and roundrobin decomps
69222aa fixed issue with missing data in doml_mask at 900 tasks by reversing iobuf and missing data writes
11cfd54 add some documentation and improve timers.
76b6651 Merge pull request #1 from PARALLELIO/master
e21308e another rework of the request handling mechanism
121cef1 adress an issue with writing partial not decomposed fields and saving requests
abb2d76 Merge branch 'master' of github.com:PARALLELIO/ParallelIO update to latest
42a86f0 fix issue in flush_output_buffer
2fa9e88 Merge branch 'master' of github.com:PARALLELIO/ParallelIO merge in changes from cetus development
e1e5b3c remove CXX check as not needed
2ad54b7 Merge branch 'master' of github.com:PARALLELIO/ParallelIO pull in changes from alcf development
f9773af mv list alloc from malloc to bget
916918c rework of memory management for iput
9389cba fix rate estimate in pioperformance.F90 improve hole algorythm
f7b491e fix logic in mpio_onesided clause
dab77bb options for wait_all call
5c6ceb2 use PIO_REQ_NULL to maintain sync between io tasks
e592aae Merge branch 'cetusdebug3' bring in mpio_onesided optimzation
c68843a remove debug statements, force flush on record change
0561c91 add back MPIO_ONESIDED code, bug was found in pnetcdf
c1cdccf no map of 0 length required
6a217f3 still debuggin
7dd4626 improved handling of _FillValue
d20bfe2 acknowledge Worley contribution2
2c1fc72 acknowledge Worley contribution
143b545 add a check for fill values
083eaa9 Merge branch 'master' of github.com:PARALLELIO/ParallelIO into jedwards/perftune trying to get this on master and probably doing it wrong.
fd8d3d0 more extensive testing
df1a52b add PIO_CNBUFFER_LIMIT to supported environment variables, value should be a positive integer optional followed by M or K which multiple by 1000000 or 1000 respectivly
56742a7 add environment variable to control swapm settings, PIO_SWAPM expects a : seperated list of three values nreqs:handshake:isend where nreqs is an integer and handshake and isend are boolean values
9866ce2 update timers to conform to newly established standard for cesm update author name
9834318 conflict resolved
a758d32 conflict resolved
53bb021 remove debug print statement
bda85e1 remove crusty mpiserial code
4b0ceb5 reduce print statements
7cb87ff merge changes from master
ef426e4 clean up
67c6971 remove mpiserial test, no longer needed with mpiserial update
81c9c21 Merge branch 'jedwards/perftune' of github.com:PARALLELIO/ParallelIO into jedwards/perftune
b19e9c3 dont test nreqs=1
a10082a hand mrge
a1e2322 remove cmake test for mpi-serial
c7bee49 Merge branch 'master' of github.com:PARALLELIO/ParallelIO
95a8c91 remove MPISERIAL cpp flags, no longer needed
d93c410 Merge branch 'jedwards/perftune' of github.com:PARALLELIO/ParallelIO into jedwards/perftune fix the conflict
a68b9f4 Merge branch 'master' of github.com:PARALLELIO/ParallelIO into jedwards/perftune is this really what I wanted?
96040db redo perf check to avoid slow configurations
597d71a fix include path for gptl.h add headers for gptl and math correct call to io2comp
815aec3 add performance tuning
c764740 fixed an issue with size of rindex in box rearranger code
1e24916 move tests to common subdirectory to prevent tests building in cesm
ebf0519 Need to always write non-decomposed fields from io task 0 instead of rotating through tasks
b6b400d look for NETCDF_C_DIR or NETCDF_DIR
f3d6aef remove debug print statement
b431d8e add a workaround so that BGQ machines will link correctly
ae26ae8 remove some debug print statements
7a2d36d update nightly build script to use git repo
658bd07 no need to sync readonly files
3c9819a add bectl call and allow for direct use of malloc with PIO_USE_MALLOC cpp flag, fix double free issue
34ceebe Making sure that we print the failure output from rank 0 only when comparing float/double arrays. This check is already there for checking int arrays
4296efe undo last
e252797 try removing purge on goldbach
50927cc try turning of experimental part
f5ee4fb cleaned up code
ac4b542 fix for no data issues
bad9aa7 update for mira build
3d59ca7 initialize holegridsize
ae07fba fix nightly build issues
4556501 port to bluewaters
4182177 Fix an issue with identifying NETCDF NETCDF4
7c1bea1 Fix an issue with identifying NETCDF
b3a2fa1 try yellowstone again ;
03e5dd2 nominally working on cetus
216df9a onesided mpiio flags for mira
a4a94e9 try new macros file
406daf9 mail results of cetus testing
2c79831 fine tuning cetus testing
6b8f14f tests are working on cetus now
c85c9cf fix flush command for netcdf4p, netcdf4c
dd7ad9f try again on cetus
d80aa03 port to cce compiler
bd384b6 update externals
6c61a1b more cmake work
0778e5b fix typo
e937cde policy was a bad idea
6617cb3 add support for netcdf c and fortran libraries installed seperatly
e010df3 update build flags for mira
0143589 Adding some fillvalue tests for reads. These are similar to the write tests added in r1485 and r1488
6194e3f Remove debug prints and re-introduce deletion of test output files - added in r1489
42aad2a fixed fillval test
f31b63e Fixing bug in the fillvalue tests. Making sure that we read the complete data before checking the results. The previous versions used the same iodesc for read and write, so the explicit or implicit holes in the write iodesc (write compdof) were also present in the read iodesc (read compdof). Hence the reads were not reading the complete array
e337fb3  make wbuf allocatable
4f7119b Adding a test for writing data with fillvalues where the data holes are implicitly specified (rather than filling the compdof with 0s for the invalid data values, the compdof for invalid values is not specified). The old test where data holes were explicitly specified (by filling corresponding compdofs with 0s) is now renamed appropriately
0ce01f7 fix issue in netcdf4p interface
9daa924 fix for openmpi: MPI_Datatype is not an integer and cannot be used in switch statements
518547a Adding a write test with fillvalues. The compdof is defined with holes (0s) and the user specifies the fillvalue (-2) explicitly during the write.
f332eb6 work around for xlc bug?
be44462 need to find maxregions across all iotasks
9930a99 merge in fillval branch
2e88734 fixes from mira
c7a2818 try this on cetus
110bee2 not working yet, but close
68eb5cf fillvalue experiment branch
43f46c3 remove an unneeded use statement
9194276 a little cleanup
ae40fdc remove restriction on filename string length
acdb1b5 use 64bit data for pnetcdf
94568d2 nothin special
d13161f netcdf4 works
b38167e reduce number of flushes
4efd607 fix for fill in box
abae181 bug fixes in mpi type declaration
536f2c8 fix an issue with netcdf4p open test
7b4997f back to mira
da07fc1 fix membug issue
b0ad555 work around nf90_def_var_fill missing
0b534dc need to increase search size for mpas
a076839 try this
2872185 modify mpi_allreduce to work on ibm?
488dc6b still trying to handle memory issues
54dea03 try again
0c774fe revert nag compiler for goldbach build
a443cce bug fixes found in cice5 port
d21ca1c more memory management
d7c4e56 more mem management fixes
2355c73 initialize compute buffer in init call
d58c83c add memory managment
4a5b75a fix an out of bounds error
e5e6f59 fix an out of bounds error
a0abba9 updates to nightly build stuff
420a78f updates to nightly build stuff
14e41a0 updates to nightly build stuff
4b8d438 fix a cmake issue
a210d76 improved handling of halo regions on read
e67e5ae improved handling of halo regions on read
cd25733 fix some cmake issues
40f7a9c more error information for get_att
b730203 try this
43d4210 fix build issue with openmpi (basetype not integer)
7cfbc49 add fill value support for incomplete field write
62cad14 more bug fixes
c443d51 need to set PIO_WRITE flag on files opened with create
250f4d9 fix failing unittest by adding check for file in read only mode
47af1c7 more debugging
4a7c6f4 fix unittests
b5ad175 correct cpp
da17b49 fix issues in unit tests
e479dc0 replace mpi_request with int
1e6be53 MPI_Request is wrong - should be int
3fce73c more multi bug fixes
9b4db9f buffered writes
d1f510c fix a character read issue
bdb3de4 another multi …
bandre-ucar pushed a commit that referenced this pull request Dec 1, 2016
bandre-ucar pushed a commit that referenced this pull request Mar 10, 2017
Swapped indices on terminated_nindivs array, bugfix
bandre-ucar pushed a commit that referenced this pull request Mar 28, 2017
resolution of conflicts take 2
@jkshuman jkshuman mentioned this pull request Sep 11, 2017
rgknox referenced this pull request in rgknox/fates-old Oct 18, 2017
Shorten lines so can compile with nag compiler on hobart
ckoven pushed a commit that referenced this pull request Jan 19, 2018

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
added execution permission on pftindexswapper and added silent mode on modify_paramfile.
rgknox pushed a commit that referenced this pull request Feb 13, 2018
bring in recent updates in NGEET/fates master
rgknox added a commit that referenced this pull request Feb 16, 2018

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Jaholm freezing stress
@bandre-ucar bandre-ucar removed their assignment Apr 6, 2018
rgknox pushed a commit that referenced this pull request Apr 17, 2018

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Syntax updates and merge resolution
rgknox pushed a commit that referenced this pull request Jul 26, 2018

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
modularization - variable name updates
rgknox pushed a commit that referenced this pull request Oct 31, 2018

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
convert from logical to initial spread options
rgknox referenced this pull request in rgknox/fates Jan 8, 2019

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
conflict resolutions and fixes to canopy layer diagnostics
rgknox referenced this pull request in rgknox/fates Feb 28, 2019

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
…ster

integrate minor updates to crown-conservation
rgknox added a commit that referenced this pull request May 30, 2019

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
minor fixes to the hydro updates
glemieux pushed a commit that referenced this pull request Jun 5, 2020

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Deconflict PR 632 with FATES master (commit 8abef14)
glemieux pushed a commit that referenced this pull request Jul 29, 2020

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
update my fork with original
rgknox pushed a commit that referenced this pull request Oct 13, 2021

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Dynamic roots md bugfix rkupdates
rgknox pushed a commit that referenced this pull request Feb 22, 2022

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
merge root density disagregation
rgknox pushed a commit that referenced this pull request Jun 27, 2022

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Fatesluc merged
@sshu88 sshu88 mentioned this pull request Oct 26, 2022
4 tasks
glemieux pushed a commit that referenced this pull request Jun 30, 2023

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Adding the fates_rad_model to the parameter file
rgknox pushed a commit that referenced this pull request Jul 21, 2023

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
memory and restart updates to TRS
rgknox pushed a commit that referenced this pull request Sep 29, 2023

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Small quality of life update to cohort age in create_cohort
glemieux pushed a commit that referenced this pull request Oct 20, 2023

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
Update to `sci.1.57.2_api.23.0.0` and add distance utilities
glemieux pushed a commit that referenced this pull request May 10, 2024

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature.
migrating unit testing to folder unit_testing
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants