Update scripts #26
Merged
Update scripts #26
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
update Macros.cheyenne for debug options update test output and base_suite list
reusable in icepack.
|
The base suite runs to completion on Conrad. So I am marking this as approved. |
mattdturner
approved these changes
Sep 19, 2017
|
@eclare108213, are you ok if I merge these to master? These changes align the cice and icepack scripts a bit and fix some of the bugs that were found in cice and icepack thru testing. |
|
Yes, I think this is okay to merge. I haven't tested it. My one suggestion is to make sure that the documentation is up to date with what's available in the scripts. Thx! |
|
I made some minor updates to the documentation in google docs and in the README. I think it would be good to clarify how the documentation is going to be organized. Do we want both the google doc and README, should they be the same or how should they reference each other, how does the user guide align with the other documentation being put in place. I will merge this now. |
|
Documentation that is downloaded with the code for offline reference should be considered "primary", in my opinion, meaning that other other references such as the wiki point to it. The exception will be the sphinx scientific docs, which will be "primary" online with downloadable pdfs with the code. I view the google docs more for planning and background info. cc to @duvivier for further comment. |
|
My opinion is that we should move away from using both google docs and sphinx since I think it will be easy to lose track of which have been updated and could cause confusion for users/developers about where to update. It seems to me it would be pretty easy to incorporate all the info in the google doc into sphinx and just include it as an additional page in the general documentation. I'm happy to go ahead and do this if you guys think it makes sense. If we want to keep them separate I'd suggest we name the google docs version "Quick Start User's guide" vs. the sphinx docs "Scientific user's guide" or something like that. |
|
I agree that we shouldn't use both places as 'final' or 'primary' user references. I do think we should continue using google docs in general, for planning, design docs, etc but not point users to them (and label them as working or draft documents). That puts all of the "official" reference material/documentation on github. The next question is where those docs go, in our git space. In the June meeting at NCAR we agreed to use sphinx for the scientific documentation and user guides, and point to them from the wiki or readme pages. We could consider putting user guides directly in as readme or other (e.g. pdf) files. My main requirement is that the critical info is downloaded when the code is cloned. Beyond that, it's just a matter of being able to maintain it easily as things evolve. Sphinx is a bit more of a hurdle for that, I think, but we can document how to do that too... Other opinions welcome.
e
…________________________________
From: Alice DuVivier <notifications@github.com>
Sent: Wednesday, September 20, 2017 9:58 AM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Mention
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
My opinion is that we should move away from using both google docs and sphinx since I think it will be easy to lose track of which have been updated and could cause confusion for users/developers about where to update. It seems to me it would be pretty easy to incorporate all the info in the google doc into sphinx and just include it as an additional page in the general documentation. I'm happy to go ahead and do this if you guys think it makes sense.
If we want to keep them separate I'd suggest we name the google docs version "Quick Start User's guide" vs. the sphinx docs "Scientific user's guide" or something like that.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#26 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHy5nxVydOsarR_9j1XufE6ga83xsGYgks5skTYPgaJpZM4Pbn2s>.
|
|
Right now on the wiki there are these links for guides: Is there a reason the "Quick Start" and User Guide are separate? It looks to me like they cover the same sorts of materials. My feeling is they should be merged, probably into the README_v6 document so that we can track those changes easily and it would be downloaded with the code. Alternately, we could just make a separate wiki page with that info, but that wouldn't be downloaded with the code so I am not sure that's what we want. The sphinx documentation link is for the "Scientific guide" and we can link the pdf that I will create as well that will be downloaded with the code. I'm not sure how we should address the git workflow guide. I think we need all that info available, but I'm not sure we need it to be downloaded with the code. The google doc is in nice shape, but would we want to put this info on the wiki, another sphinx page? I don't have a clear solution/path but we might want a pdf version of this as well as a working copy. |
|
Yes, I agree that the user guide info that is on google docs should be moved into github. Maybe we should get rid of the README_v6 and have something called "User Guide" (or similar) instead. The README_v6 file is left over from the svn repo, where we didn't have the README.md front page. README.md should be enough to convey the basic info and point to the location of 'quick start' instructions, if not show them explicitly.
In my opinion, we could keep the git workflow guide on google docs for the time being, because we're still working on it. We should probably have a guinea pig go through everything in there and make sure it's right; the last bit about changing Icepack in CICE is especially tricky and I'm not sure we settled on the right way to do it. Also, I think we've more or less decided against using tags but that decision hasn't been finalized. Eventually the git workflow guide could go on a wiki page, not downloaded, in my opinion.
e
In
…________________________________
From: Alice DuVivier <notifications@github.com>
Sent: Wednesday, September 20, 2017 11:21 AM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Mention
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
Right now on the wiki there are these links for guides:
"Quick Start" instructions are available in README_v6.
Online and searchable documentation of the current version of CICE (links to sphinx)
CICE User Guide (links to google docs)
CICE Git and Workflow Guide (links to google docs)
Is there a reason the "Quick Start" and User Guide are separate? It looks to me like they cover the same sorts of materials. My feeling is they should be merged, probably into the README_v6 document so that we can track those changes easily and it would be downloaded with the code. Alternately, we could just make a separate wiki page with that info, but that wouldn't be downloaded with the code so I am not sure that's what we want.
The sphinx documentation link is for the "Scientific guide" and we can link the pdf that I will create as well that will be downloaded with the code.
I'm not sure how we should address the git workflow guide. I think we need all that info available, but I'm not sure we need it to be downloaded with the code. The google doc is in nice shape, but would we want to put this info on the wiki, another sphinx page? I don't have a clear solution/path but we might want a pdf version of this as well as a working copy.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#26 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHy5n0BZKan9ZtduQ2Y2foSmYKLTZCUtks5skUmMgaJpZM4Pbn2s>.
|
|
We also have README.test, which I think ought to be part of the user guide too, rather than a separate file.
…________________________________
From: Elizabeth Hunke <notifications@github.com>
Sent: Wednesday, September 20, 2017 11:49 AM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Your activity
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
Yes, I agree that the user guide info that is on google docs should be moved into github. Maybe we should get rid of the README_v6 and have something called "User Guide" (or similar) instead. The README_v6 file is left over from the svn repo, where we didn't have the README.md front page. README.md should be enough to convey the basic info and point to the location of 'quick start' instructions, if not show them explicitly.
In my opinion, we could keep the git workflow guide on google docs for the time being, because we're still working on it. We should probably have a guinea pig go through everything in there and make sure it's right; the last bit about changing Icepack in CICE is especially tricky and I'm not sure we settled on the right way to do it. Also, I think we've more or less decided against using tags but that decision hasn't been finalized. Eventually the git workflow guide could go on a wiki page, not downloaded, in my opinion.
e
In
________________________________
From: Alice DuVivier <notifications@github.com>
Sent: Wednesday, September 20, 2017 11:21 AM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Mention
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
Right now on the wiki there are these links for guides:
"Quick Start" instructions are available in README_v6.
Online and searchable documentation of the current version of CICE (links to sphinx)
CICE User Guide (links to google docs)
CICE Git and Workflow Guide (links to google docs)
Is there a reason the "Quick Start" and User Guide are separate? It looks to me like they cover the same sorts of materials. My feeling is they should be merged, probably into the README_v6 document so that we can track those changes easily and it would be downloaded with the code. Alternately, we could just make a separate wiki page with that info, but that wouldn't be downloaded with the code so I am not sure that's what we want.
The sphinx documentation link is for the "Scientific guide" and we can link the pdf that I will create as well that will be downloaded with the code.
I'm not sure how we should address the git workflow guide. I think we need all that info available, but I'm not sure we need it to be downloaded with the code. The google doc is in nice shape, but would we want to put this info on the wiki, another sphinx page? I don't have a clear solution/path but we might want a pdf version of this as well as a working copy.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#26 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHy5n0BZKan9ZtduQ2Y2foSmYKLTZCUtks5skUmMgaJpZM4Pbn2s>.
-
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub<#26 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHy5n_n1qoqxb81L308ysKO7p2LmP6X4ks5skVAcgaJpZM4Pbn2s>.
|
|
I agree with this strategy. I personally think we should have a user
guide and a science guide that's in github, in sphinx. It could also be
a single document, maybe that's actually better. the repo should
include a pdf of it/them, and the guides should be available via a clear
web link on README.md and/or github wiki. I think the git workflow
guide could remain a google doc. I think that is important to publish
but it's important only to a subset of the community. I think it could
be migrated to the wiki at some point, but almost think it's easier to
work with in google docs, at least for now. A link should be available
via the README.md and/or the wiki. We should get rid of other
references when we are ready, that is at least the README_v6 and the
google doc user guide. There is also a readme for testing that needs to
be migrated into the user guide. QuickStart could be a first chapter in
the user guide.
Anyway, I agree that we should start the consolidation process and that
the science/user guide info needs to be available via pdf and web and
sphinx seems to be the way to do that. The git workflow can remain
separate via wiki or google doc.
…On 9/20/17 10:49 AM, Elizabeth Hunke wrote:
Yes, I agree that the user guide info that is on google docs should be
moved into github. Maybe we should get rid of the README_v6 and have
something called "User Guide" (or similar) instead. The README_v6 file
is left over from the svn repo, where we didn't have the README.md
front page. README.md should be enough to convey the basic info and
point to the location of 'quick start' instructions, if not show them
explicitly.
In my opinion, we could keep the git workflow guide on google docs for
the time being, because we're still working on it. We should probably
have a guinea pig go through everything in there and make sure it's
right; the last bit about changing Icepack in CICE is especially
tricky and I'm not sure we settled on the right way to do it. Also, I
think we've more or less decided against using tags but that decision
hasn't been finalized. Eventually the git workflow guide could go on a
wiki page, not downloaded, in my opinion.
e
In
________________________________
From: Alice DuVivier ***@***.***>
Sent: Wednesday, September 20, 2017 11:21 AM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Mention
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
Right now on the wiki there are these links for guides:
"Quick Start" instructions are available in README_v6.
Online and searchable documentation of the current version of CICE
(links to sphinx)
CICE User Guide (links to google docs)
CICE Git and Workflow Guide (links to google docs)
Is there a reason the "Quick Start" and User Guide are separate? It
looks to me like they cover the same sorts of materials. My feeling is
they should be merged, probably into the README_v6 document so that we
can track those changes easily and it would be downloaded with the
code. Alternately, we could just make a separate wiki page with that
info, but that wouldn't be downloaded with the code so I am not sure
that's what we want.
The sphinx documentation link is for the "Scientific guide" and we can
link the pdf that I will create as well that will be downloaded with
the code.
I'm not sure how we should address the git workflow guide. I think we
need all that info available, but I'm not sure we need it to be
downloaded with the code. The google doc is in nice shape, but would
we want to put this info on the wiki, another sphinx page? I don't
have a clear solution/path but we might want a pdf version of this as
well as a working copy.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on
GitHub<#26 (comment)>,
or mute the
thread<https://github.com/notifications/unsubscribe-auth/AHy5n0BZKan9ZtduQ2Y2foSmYKLTZCUtks5skUmMgaJpZM4Pbn2s>.
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
<#26 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AHzcHj17TZW3ecLCC38pe_iTaryuQHAVks5skVAcgaJpZM4Pbn2s>.
|
|
That sounds like the final word to me! Let's go with it.
e
________________________________
From: Tony Craig <notifications@github.com>
Sent: Wednesday, September 20, 2017 12:06 PM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Mention
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
I agree with this strategy. I personally think we should have a user
guide and a science guide that's in github, in sphinx. It could also be
a single document, maybe that's actually better. the repo should
include a pdf of it/them, and the guides should be available via a clear
web link on README.md and/or github wiki. I think the git workflow
guide could remain a google doc. I think that is important to publish
but it's important only to a subset of the community. I think it could
be migrated to the wiki at some point, but almost think it's easier to
work with in google docs, at least for now. A link should be available
via the README.md and/or the wiki. We should get rid of other
references when we are ready, that is at least the README_v6 and the
google doc user guide. There is also a readme for testing that needs to
be migrated into the user guide. QuickStart could be a first chapter in
the user guide.
Anyway, I agree that we should start the consolidation process and that
the science/user guide info needs to be available via pdf and web and
sphinx seems to be the way to do that. The git workflow can remain
separate via wiki or google doc.
On 9/20/17 10:49 AM, Elizabeth Hunke wrote:
Yes, I agree that the user guide info that is on google docs should be
moved into github. Maybe we should get rid of the README_v6 and have
something called "User Guide" (or similar) instead. The README_v6 file
is left over from the svn repo, where we didn't have the README.md
front page. README.md should be enough to convey the basic info and
point to the location of 'quick start' instructions, if not show them
explicitly.
In my opinion, we could keep the git workflow guide on google docs for
the time being, because we're still working on it. We should probably
have a guinea pig go through everything in there and make sure it's
right; the last bit about changing Icepack in CICE is especially
tricky and I'm not sure we settled on the right way to do it. Also, I
think we've more or less decided against using tags but that decision
hasn't been finalized. Eventually the git workflow guide could go on a
wiki page, not downloaded, in my opinion.
e
In
________________________________
From: Alice DuVivier ***@***.***>
Sent: Wednesday, September 20, 2017 11:21 AM
To: CICE-Consortium/CICE
Cc: Hunke, Elizabeth Clare; Mention
Subject: Re: [CICE-Consortium/CICE] Update scripts (#26)
Right now on the wiki there are these links for guides:
"Quick Start" instructions are available in README_v6.
Online and searchable documentation of the current version of CICE
(links to sphinx)
CICE User Guide (links to google docs)
CICE Git and Workflow Guide (links to google docs)
Is there a reason the "Quick Start" and User Guide are separate? It
looks to me like they cover the same sorts of materials. My feeling is
they should be merged, probably into the README_v6 document so that we
can track those changes easily and it would be downloaded with the
code. Alternately, we could just make a separate wiki page with that
info, but that wouldn't be downloaded with the code so I am not sure
that's what we want.
The sphinx documentation link is for the "Scientific guide" and we can
link the pdf that I will create as well that will be downloaded with
the code.
I'm not sure how we should address the git workflow guide. I think we
need all that info available, but I'm not sure we need it to be
downloaded with the code. The google doc is in nice shape, but would
we want to put this info on the wiki, another sphinx page? I don't
have a clear solution/path but we might want a pdf version of this as
well as a working copy.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on
GitHub<#26 (comment)>,
or mute the
thread<https://github.com/notifications/unsubscribe-auth/AHy5n0BZKan9ZtduQ2Y2foSmYKLTZCUtks5skUmMgaJpZM4Pbn2s>.
-
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
<#26 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AHzcHj17TZW3ecLCC38pe_iTaryuQHAVks5skVAcgaJpZM4Pbn2s>.
-
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#26 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHy5n8ZTg3USQ63FZbevlLhUu5ZiZ_q4ks5skVQRgaJpZM4Pbn2s>.
|
|
Sounds good to me too. I will start consolidating the readme_v6, readme.test, and google doc into new sections in the sphinx document. I'll make sure that the Readme.md and wiki files point to that document directly as well. I am also happy to be the guinea pig for the github workflow stuff. I'm currently working on the cice testing and trying to get a gx1 grid going with some help from Dave, so that will be a good way to test this all out. |
JFLemieux73
added a commit
to JFLemieux73/CICE
that referenced
this pull request
Nov 18, 2021
* Initial coding of strain_rates_U * strain_rates_U is done * Small corrections following Philippes comments
apcraig
added a commit
that referenced
this pull request
Nov 8, 2022
* merge latest master (#4) * Isotopes for CICE (#423) Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> * updated orbital calculations needed for cesm * fixed problems in updated orbital calculations needed for cesm * update CICE6 to support coupling with UFS * put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied * Convergence on ustar for CICE. (#452) (#5) * Add atmiter_conv to CICE * Add documentation * trigger build the docs Co-authored-by: David A. Bailey <dbailey@ucar.edu> * update icepack submodule * Revert "update icepack submodule" This reverts commit e70d1ab. * update comp_ice.backend with temporary ice_timers fix * Fix threading problem in init_bgc * Fix additional OMP problems * changes for coldstart running * Move the forapps directory * remove cesmcoupled ifdefs * Fix logging issues for NUOPC * removal of many cpp-ifdefs * fix compile errors * fixes to get cesm working * fixed white space issue * Add restart_coszen namelist option * update icepack submodule * change Orion to orion in backend remove duplicate print lines from ice_transport_driver * add -link_mpi=dbg to debug flags (#8) * cice6 compile (#6) * enable debug build. fix to remove errors * fix an error in comp_ice.backend.libcice * change Orion to orion for machine identification * changes for consistency w/ current emc-cice5 (#13) Update to emc/develop fork to current CICE consortium Co-authored-by: David A. Bailey <dbailey@ucar.edu> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> * Fixcommit (#14) Align commit history between emc/develop and cice-consortium/master * Update CICE6 for integration to S2S * add wcoss_dell_p3 compiler macro * update to icepack w/ debug fix * replace SITE with MACHINE_ID * update compile scripts * Support TACC stampede (#19) * update icepack * add ice_dyn_vp module to CICE_InitMod * update gitmodules, update icepack * Update CICE to consortium master (#23) updates include: * deprecate upwind advection (#508) * add implicit VP solver (#491) * update icepack * switch icepack branches * update to icepack master but set abort flag in ITD routine to false * update icepack * Update CICE to latest Consortium master (#26) update CICE and Icepack * changes the criteria for aborting ice for thermo-conservation errors * updates the time manager * fixes two bugs in ice_therm_mushy * updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases * add cice changes for zlvs (#29) * update icepack and pointer * update icepack and revert gitmodules * Fix history features - Fix bug in history time axis when sec_init is not zero. - Fix issue with time_beg and time_end uninitialized values. - Add support for averaging with histfreq='1' by allowing histfreq_n to be any value in that case. Extend and clean up construct_filename for history files. More could be done, but wanted to preserve backwards compatibility. - Add new calendar_sec2hms to converts daily seconds to hh:mm:ss. Update the calchk calendar unit tester to check this method - Remove abort test in bcstchk, this was just causing problems in regression testing - Remove known problems documentation about problems writing when istep=1. This issue does not exist anymore with the updated time manager. - Add new tests with hist_avg = false. Add set_nml.histinst. * revert set_nml.histall * fix implementation error * update model log output in ice_init * Fix QC issues - Add netcdf ststus checks and aborts in ice_read_write.F90 - Check for end of file when reading records in ice_read_write.F90 for ice_read_nc methods - Update set_nml.qc to better specify the test, turn off leap years since we're cycling 2005 data - Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data - Add QC run to base_suite.ts to verify qc runs to completion and possibility to use those results directly for QC validation - Clean up error messages and some indentation in ice_read_write.F90 * Update testing - Add prod suite including 10 year gx1prod and qc test - Update unit test compare scripts * update documentation * reset calchk to 100000 years * update evp1d test * update icepack * update icepack * add memory profiling (#36) * add profile_memory calls to CICE cap * update icepack * fix rhoa when lowest_temp is 0.0 * provide default value for rhoa when imported temp_height_lowest (Tair) is 0.0 * resolves seg fault when frac_grid=false and do_ca=true * update icepack submodule * Update CICE for latest Consortium master (#38) * Implement advanced snow physics in icepack and CICE * Fix time-stamping of CICE history files * Fix CICE history file precision * Use CICE-Consortium/Icepack master (#40) * switch to icepack master at consortium * recreate cap update branch (#42) * add debug_model feature * add required variables and calls for tr_snow * remove 2 extraneous lines * remove two log print lines that were removed prior to merge of driver updates to consortium * duplicate gitmodule style for icepack * Update CICE to latest Consortium/main (#45) * Update CICE to Consortium/main (#48) Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics. Refactored eap puny/pi lookups to improve scalar performance Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp Update for sea bed stress calculations * fix comment, fix env for orion and hera * replace save_init with step_prep in CICE_RunMod * fixes for cgrid repro * remove added haloupdates * baselines pass with these extra halo updates removed * change F->S for ocean velocities and tilts * fix debug failure when grid_ice=C * compiling in debug mode using -init=snan,arrays requires initialization of variables * respond to review comments * remove inserted whitespace for uvelE,N and vvelE,N * Add wave-cice coupling; update to Consortium main (#51) * add wave-ice fields * initialize aicen_init, which turns up as NaN in calc of floediam export * add call to icepack_init_wave to initialize wavefreq and dwavefreq * update to latest consortium main (PR 752) * add initializationsin ice_state * initialize vsnon/vsnon_init and vicen/vicen_init Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com>
apcraig
added a commit
that referenced
this pull request
Aug 28, 2023
…856) * merge latest master (#4) * Isotopes for CICE (#423) Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> * updated orbital calculations needed for cesm * fixed problems in updated orbital calculations needed for cesm * update CICE6 to support coupling with UFS * put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied * Convergence on ustar for CICE. (#452) (#5) * Add atmiter_conv to CICE * Add documentation * trigger build the docs Co-authored-by: David A. Bailey <dbailey@ucar.edu> * update icepack submodule * Revert "update icepack submodule" This reverts commit e70d1ab. * update comp_ice.backend with temporary ice_timers fix * Fix threading problem in init_bgc * Fix additional OMP problems * changes for coldstart running * Move the forapps directory * remove cesmcoupled ifdefs * Fix logging issues for NUOPC * removal of many cpp-ifdefs * fix compile errors * fixes to get cesm working * fixed white space issue * Add restart_coszen namelist option * update icepack submodule * change Orion to orion in backend remove duplicate print lines from ice_transport_driver * add -link_mpi=dbg to debug flags (#8) * cice6 compile (#6) * enable debug build. fix to remove errors * fix an error in comp_ice.backend.libcice * change Orion to orion for machine identification * changes for consistency w/ current emc-cice5 (#13) Update to emc/develop fork to current CICE consortium Co-authored-by: David A. Bailey <dbailey@ucar.edu> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> * Fixcommit (#14) Align commit history between emc/develop and cice-consortium/master * Update CICE6 for integration to S2S * add wcoss_dell_p3 compiler macro * update to icepack w/ debug fix * replace SITE with MACHINE_ID * update compile scripts * Support TACC stampede (#19) * update icepack * add ice_dyn_vp module to CICE_InitMod * update gitmodules, update icepack * Update CICE to consortium master (#23) updates include: * deprecate upwind advection (#508) * add implicit VP solver (#491) * update icepack * switch icepack branches * update to icepack master but set abort flag in ITD routine to false * update icepack * Update CICE to latest Consortium master (#26) update CICE and Icepack * changes the criteria for aborting ice for thermo-conservation errors * updates the time manager * fixes two bugs in ice_therm_mushy * updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases * add cice changes for zlvs (#29) * update icepack and pointer * update icepack and revert gitmodules * Fix history features - Fix bug in history time axis when sec_init is not zero. - Fix issue with time_beg and time_end uninitialized values. - Add support for averaging with histfreq='1' by allowing histfreq_n to be any value in that case. Extend and clean up construct_filename for history files. More could be done, but wanted to preserve backwards compatibility. - Add new calendar_sec2hms to converts daily seconds to hh:mm:ss. Update the calchk calendar unit tester to check this method - Remove abort test in bcstchk, this was just causing problems in regression testing - Remove known problems documentation about problems writing when istep=1. This issue does not exist anymore with the updated time manager. - Add new tests with hist_avg = false. Add set_nml.histinst. * revert set_nml.histall * fix implementation error * update model log output in ice_init * Fix QC issues - Add netcdf ststus checks and aborts in ice_read_write.F90 - Check for end of file when reading records in ice_read_write.F90 for ice_read_nc methods - Update set_nml.qc to better specify the test, turn off leap years since we're cycling 2005 data - Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data - Add QC run to base_suite.ts to verify qc runs to completion and possibility to use those results directly for QC validation - Clean up error messages and some indentation in ice_read_write.F90 * Update testing - Add prod suite including 10 year gx1prod and qc test - Update unit test compare scripts * update documentation * reset calchk to 100000 years * update evp1d test * update icepack * update icepack * add memory profiling (#36) * add profile_memory calls to CICE cap * update icepack * fix rhoa when lowest_temp is 0.0 * provide default value for rhoa when imported temp_height_lowest (Tair) is 0.0 * resolves seg fault when frac_grid=false and do_ca=true * update icepack submodule * Update CICE for latest Consortium master (#38) * Implement advanced snow physics in icepack and CICE * Fix time-stamping of CICE history files * Fix CICE history file precision * Use CICE-Consortium/Icepack master (#40) * switch to icepack master at consortium * recreate cap update branch (#42) * add debug_model feature * add required variables and calls for tr_snow * remove 2 extraneous lines * remove two log print lines that were removed prior to merge of driver updates to consortium * duplicate gitmodule style for icepack * Update CICE to latest Consortium/main (#45) * Update CICE to Consortium/main (#48) Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics. Refactored eap puny/pi lookups to improve scalar performance Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp Update for sea bed stress calculations * fix comment, fix env for orion and hera * replace save_init with step_prep in CICE_RunMod * fixes for cgrid repro * remove added haloupdates * baselines pass with these extra halo updates removed * change F->S for ocean velocities and tilts * fix debug failure when grid_ice=C * compiling in debug mode using -init=snan,arrays requires initialization of variables * respond to review comments * remove inserted whitespace for uvelE,N and vvelE,N * Add wave-cice coupling; update to Consortium main (#51) * add wave-ice fields * initialize aicen_init, which turns up as NaN in calc of floediam export * add call to icepack_init_wave to initialize wavefreq and dwavefreq * update to latest consortium main (PR 752) * add initializationsin ice_state * initialize vsnon/vsnon_init and vicen/vicen_init * Update CICE (#54) * update to include recent PRs to Consortium/main * fix for nudiag_set allow nudiag_set to be available outside of cesm; may prefer to fix in coupling interface * Update CICE for latest Consortium/main (#56) * add run time info * change real(8) to real(dbl)kind) * fix syntax * fix write unit * use cice_wrapper for ufs timer functionality * add elapsed model time for logtime * tidy up the wrapper * fix case for 'time since' at the first advance * add timer and forecast log * write timer values to timer log, not nu_diag * write log.ice.fXXX * only one time is needed * modify message written for log.ice.fXXX * change info in fXXX log file * Update CICE from Consortium/main (#62) * Fix CESMCOUPLED compile issue in icepack. (#823) * Update global reduction implementation to improve performance, fix VP bug (#824) * Update VP global sum to exclude local implementation with tripole grids * Add functionality to change hist_avg for each stream (#827) * Update Icepack to #6703bc533c968 May 22, 2023 (#829) * Fix for mesh check in CESM driver (#830) * Namelist option for time axis position. (#839) * reset timer after Advance to retrieve "wait time" * add logical control for enabling runtime info * remove zsal items from cap * fix typo --------- Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> Co-authored-by: Jun.Wang <Jun.Wang@noaa.gov>
TillRasmussen
pushed a commit
to TillRasmussen/CICE
that referenced
this pull request
Sep 16, 2023
…ICE-Consortium#856) * merge latest master (#4) * Isotopes for CICE (CICE-Consortium#423) Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> * updated orbital calculations needed for cesm * fixed problems in updated orbital calculations needed for cesm * update CICE6 to support coupling with UFS * put in changes so that both ufsatm and cesm requirements for potential temperature and density are satisfied * Convergence on ustar for CICE. (CICE-Consortium#452) (#5) * Add atmiter_conv to CICE * Add documentation * trigger build the docs Co-authored-by: David A. Bailey <dbailey@ucar.edu> * update icepack submodule * Revert "update icepack submodule" This reverts commit e70d1ab. * update comp_ice.backend with temporary ice_timers fix * Fix threading problem in init_bgc * Fix additional OMP problems * changes for coldstart running * Move the forapps directory * remove cesmcoupled ifdefs * Fix logging issues for NUOPC * removal of many cpp-ifdefs * fix compile errors * fixes to get cesm working * fixed white space issue * Add restart_coszen namelist option * update icepack submodule * change Orion to orion in backend remove duplicate print lines from ice_transport_driver * add -link_mpi=dbg to debug flags (#8) * cice6 compile (#6) * enable debug build. fix to remove errors * fix an error in comp_ice.backend.libcice * change Orion to orion for machine identification * changes for consistency w/ current emc-cice5 (#13) Update to emc/develop fork to current CICE consortium Co-authored-by: David A. Bailey <dbailey@ucar.edu> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> * Fixcommit (#14) Align commit history between emc/develop and cice-consortium/master * Update CICE6 for integration to S2S * add wcoss_dell_p3 compiler macro * update to icepack w/ debug fix * replace SITE with MACHINE_ID * update compile scripts * Support TACC stampede (#19) * update icepack * add ice_dyn_vp module to CICE_InitMod * update gitmodules, update icepack * Update CICE to consortium master (CICE-Consortium#23) updates include: * deprecate upwind advection (CICE-Consortium#508) * add implicit VP solver (CICE-Consortium#491) * update icepack * switch icepack branches * update to icepack master but set abort flag in ITD routine to false * update icepack * Update CICE to latest Consortium master (CICE-Consortium#26) update CICE and Icepack * changes the criteria for aborting ice for thermo-conservation errors * updates the time manager * fixes two bugs in ice_therm_mushy * updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases * add cice changes for zlvs (CICE-Consortium#29) * update icepack and pointer * update icepack and revert gitmodules * Fix history features - Fix bug in history time axis when sec_init is not zero. - Fix issue with time_beg and time_end uninitialized values. - Add support for averaging with histfreq='1' by allowing histfreq_n to be any value in that case. Extend and clean up construct_filename for history files. More could be done, but wanted to preserve backwards compatibility. - Add new calendar_sec2hms to converts daily seconds to hh:mm:ss. Update the calchk calendar unit tester to check this method - Remove abort test in bcstchk, this was just causing problems in regression testing - Remove known problems documentation about problems writing when istep=1. This issue does not exist anymore with the updated time manager. - Add new tests with hist_avg = false. Add set_nml.histinst. * revert set_nml.histall * fix implementation error * update model log output in ice_init * Fix QC issues - Add netcdf ststus checks and aborts in ice_read_write.F90 - Check for end of file when reading records in ice_read_write.F90 for ice_read_nc methods - Update set_nml.qc to better specify the test, turn off leap years since we're cycling 2005 data - Add check in c ice.t-test.py to make sure there is at least 1825 files, 5 years of data - Add QC run to base_suite.ts to verify qc runs to completion and possibility to use those results directly for QC validation - Clean up error messages and some indentation in ice_read_write.F90 * Update testing - Add prod suite including 10 year gx1prod and qc test - Update unit test compare scripts * update documentation * reset calchk to 100000 years * update evp1d test * update icepack * update icepack * add memory profiling (CICE-Consortium#36) * add profile_memory calls to CICE cap * update icepack * fix rhoa when lowest_temp is 0.0 * provide default value for rhoa when imported temp_height_lowest (Tair) is 0.0 * resolves seg fault when frac_grid=false and do_ca=true * update icepack submodule * Update CICE for latest Consortium master (CICE-Consortium#38) * Implement advanced snow physics in icepack and CICE * Fix time-stamping of CICE history files * Fix CICE history file precision * Use CICE-Consortium/Icepack master (CICE-Consortium#40) * switch to icepack master at consortium * recreate cap update branch (CICE-Consortium#42) * add debug_model feature * add required variables and calls for tr_snow * remove 2 extraneous lines * remove two log print lines that were removed prior to merge of driver updates to consortium * duplicate gitmodule style for icepack * Update CICE to latest Consortium/main (CICE-Consortium#45) * Update CICE to Consortium/main (CICE-Consortium#48) Update OpenMP directives as needed including validation via new omp_suite. Fixed OpenMP in dynamics. Refactored eap puny/pi lookups to improve scalar performance Update Tsfc implementation to make sure land blocks don't set Tsfc to freezing temp Update for sea bed stress calculations * fix comment, fix env for orion and hera * replace save_init with step_prep in CICE_RunMod * fixes for cgrid repro * remove added haloupdates * baselines pass with these extra halo updates removed * change F->S for ocean velocities and tilts * fix debug failure when grid_ice=C * compiling in debug mode using -init=snan,arrays requires initialization of variables * respond to review comments * remove inserted whitespace for uvelE,N and vvelE,N * Add wave-cice coupling; update to Consortium main (CICE-Consortium#51) * add wave-ice fields * initialize aicen_init, which turns up as NaN in calc of floediam export * add call to icepack_init_wave to initialize wavefreq and dwavefreq * update to latest consortium main (PR 752) * add initializationsin ice_state * initialize vsnon/vsnon_init and vicen/vicen_init * Update CICE (CICE-Consortium#54) * update to include recent PRs to Consortium/main * fix for nudiag_set allow nudiag_set to be available outside of cesm; may prefer to fix in coupling interface * Update CICE for latest Consortium/main (CICE-Consortium#56) * add run time info * change real(8) to real(dbl)kind) * fix syntax * fix write unit * use cice_wrapper for ufs timer functionality * add elapsed model time for logtime * tidy up the wrapper * fix case for 'time since' at the first advance * add timer and forecast log * write timer values to timer log, not nu_diag * write log.ice.fXXX * only one time is needed * modify message written for log.ice.fXXX * change info in fXXX log file * Update CICE from Consortium/main (CICE-Consortium#62) * Fix CESMCOUPLED compile issue in icepack. (CICE-Consortium#823) * Update global reduction implementation to improve performance, fix VP bug (CICE-Consortium#824) * Update VP global sum to exclude local implementation with tripole grids * Add functionality to change hist_avg for each stream (CICE-Consortium#827) * Update Icepack to #6703bc533c968 May 22, 2023 (CICE-Consortium#829) * Fix for mesh check in CESM driver (CICE-Consortium#830) * Namelist option for time axis position. (CICE-Consortium#839) * reset timer after Advance to retrieve "wait time" * add logical control for enabling runtime info * remove zsal items from cap * fix typo --------- Co-authored-by: apcraig <anthony.p.craig@gmail.com> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: Mariana Vertenstein <mvertens@ucar.edu> Co-authored-by: Minsuk Ji <57227195+MinsukJi-NOAA@users.noreply.github.com> Co-authored-by: Tony Craig <apcraig@users.noreply.github.com> Co-authored-by: Philippe Blain <levraiphilippeblain@gmail.com> Co-authored-by: Jun.Wang <Jun.Wang@noaa.gov>
anton-seaice
pushed a commit
to anton-seaice/CICE
that referenced
this pull request
Dec 1, 2023
update CICE and Icepack * changes the criteria for aborting ice for thermo-conservation errors * updates the time manager * fixes two bugs in ice_therm_mushy * updates Icepack to Consortium master w/ flip of abort flag for troublesome IC cases
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Updated the scripts to fix a few problems and make consistent with first version of icepack scripts
Developer(s): tcraig
Updated documentation (Y/N): N
Results (bit for bit, roundoff, climate changing): bit for bit
Code review:
Other Relevant Details:
Added new pond namelist script option$status ($ ?) checks
Removed old cice5 scripts
Refactored some env variable names for better consistency and reuse with icepack scripts
Fixed
Added ICE_MACHINE_MAKE variable
Updated sed usage to make them POSIX compliant for use on OSX
Added testmachine machine option that should be usable on any platform to test scripts