Reorganize Users Guide part 1 and 2 content #2407
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Add machines and pes-threads sections and move content to them.
remove adding-cases section and move its content, which was only about adding grids, to the new grids section.
Remove case-basics and move content to the compsets section and create-a-case section. Had previously moved grid info to the grid section.
Add new timers section and fill it with content from the old optimizing layouts section. Main content about load balancing moved to pe-threads section.
Set table of content depth back to 2 for users guide.
Move details aboug machine, batch, compiler xml files from porting to the machine section.
Move cime config dir info from part 2 to part 1
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Still working on this but wanted to put it up for people to see. Just check out this branch and build the docs on it. |
Split up the "Customizing a case" material in to several files and combine it with "Use cases" material. Move it all to part 1 and call it "Modifying a Case". Move the pelayout material to part 2 in the pes and threads section. Move the mpi example to the Porting section in part 2.
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@mvertens this is ready for review. |
mvertens
approved these changes
Apr 3, 2018
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@mvertens approved it so I'll merge it. |
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I did not intentionally remove anything and I am happy to add it back in if
we did. What was there? We have added a lot of extra documentation over the
last two weeks.
…On Thu, May 31, 2018 at 9:47 PM, Robert Jacob ***@***.***> wrote:
@mvertens <https://github.com/mvertens> and @bertinia
<https://github.com/bertinia> the "Modifying a Case" section that I added
in this PR is no longer around. Was that intentional?
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We also restructured things a bit for more clarity. Lets talk tomorrow so
that I can understand what is no longer there.
On Thu, May 31, 2018 at 9:54 PM, Mariana Vertenstein <mvertens@ucar.edu>
wrote:
… I did not intentionally remove anything and I am happy to add it back in
if we did. What was there? We have added a lot of extra documentation over
the last two weeks.
On Thu, May 31, 2018 at 9:47 PM, Robert Jacob ***@***.***>
wrote:
> @mvertens <https://github.com/mvertens> and @bertinia
> <https://github.com/bertinia> the "Modifying a Case" section that I
> added in this PR is no longer around. Was that intentional?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#2407 (comment)>, or mute
> the thread
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> .
>
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I see it. Its now called "Customizing your input variables" and the .rst files were moved out of the subdirectory they were in. I'll take a closer look tomorrow. |
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I'm trying to redo those changes I lost a few weeks ago. I have a local html build saved but not the .rst files. |
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I'd like to move the multi-year and branch-hybrid run examples from the quick start to "Customizing your input variables". They're just more examples of customizing and shouldn't be in the quick start material. |
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Sounds fine. Lets wait until Jim's PR to bring the release branch back to
master before we do this. Would this be the right way to proceed?
We should discuss how we want to do this moving forwards.
…On Thu, Jun 7, 2018 at 11:28 PM, Robert Jacob ***@***.***> wrote:
I'd like to move the multi-year and branch-hybrid run examples from the
quick start to "Customizing your input variables". They're just more
examples of customizing and shouldn't be in the quick start material.
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That PR is complete and closed.
…On Fri, Jun 8, 2018 at 9:09 AM, mvertens ***@***.***> wrote:
Sounds fine. Lets wait until Jim's PR to bring the release branch back to
master before we do this. Would this be the right way to proceed?
We should discuss how we want to do this moving forwards.
On Thu, Jun 7, 2018 at 11:28 PM, Robert Jacob ***@***.***>
wrote:
> I'd like to move the multi-year and branch-hybrid run examples from the
> quick start to "Customizing your input variables". They're just more
> examples of customizing and shouldn't be in the quick start material.
>
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Jim Edwards
CESM Software Engineer
National Center for Atmospheric Research
Boulder, CO
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Great. So should we make the changes in cime master right now and bring
those into the release branch? What's the best workflow moving forwards?
…On Fri, Jun 8, 2018 at 9:15 AM, jedwards4b ***@***.***> wrote:
That PR is complete and closed.
On Fri, Jun 8, 2018 at 9:09 AM, mvertens ***@***.***> wrote:
> Sounds fine. Lets wait until Jim's PR to bring the release branch back to
> master before we do this. Would this be the right way to proceed?
> We should discuss how we want to do this moving forwards.
>
> On Thu, Jun 7, 2018 at 11:28 PM, Robert Jacob ***@***.***>
> wrote:
>
> > I'd like to move the multi-year and branch-hybrid run examples from the
> > quick start to "Customizing your input variables". They're just more
> > examples of customizing and shouldn't be in the quick start material.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
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> > .
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National Center for Atmospheric Research
Boulder, CO
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You should continue to make changes that you want to appear on maint-5.6 on the maint-5.6 branch. We will continue to periodically merge that branch into master until it is no longer appropriate to do so. |
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Sounds good. So @rjacob should bring in his documentation changes in
maint-5.6?
…On Fri, Jun 8, 2018 at 9:19 AM, jedwards4b ***@***.***> wrote:
You should continue to make changes that you want to appear on maint-5.6
on the maint-5.6 branch. We will continue to periodically merge that branch
into master until it is no longer appropriate to do so.
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Yes I was planning to put them on the maint-5.6 branch. |
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Yes, I think so. |
jgfouca
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Aug 8, 2018
a) Use shr_reprosum_calc in seq_diag_avect_mct When BFBFLAG is set to true and when INFO_DBUG > 1, the routine seq_diag_avect_mct uses a reproducible sum algorithm that is not as accurate as the algorithm implemented in shr_reprosum_calc. In particular, when summing a vector of INFs, the current algorithm returns zero. Here we replace the existing algorithm with a call to shr_reprosum_calc. This change is BFB for standard usage (INFO_DBUG == 1). It is not BFB with respect to the associated diagnostic, written to cpl.log, when INFO_DBUG > 1. However, these diagnostics are not used in the simulation, and simulation results will BFB. b) Add option to allow INF or NaN summands in shr_reprosum_calc shr_reprosum_calc aborts if input summands include INF or NaN values. For debugging purposes, it can be useful to allow INF or NaN values, returning the IEEE standard results for such a situation (either NaN, positive INF, or negative INF, depending on the situation). An optional logical parameter, allow_infnan, is being added to the shr_reprosum_calc. When set to .true. the routine determines whether summands for an existing field contain NaN or INF values and returns the appropriate value without going through the reproducible sum algorithm (which is very slow and requires signficant memory when summing these special values). Other fields in a multiple field call to shr_reprosum_calc will be computed in the usual fashion. When allow_infnan == .false. or when the parameter is omitted, then the routine aborts with an informative error message when the input contain INF or NaN values, as is done currently. The default can be changed (from allow_infnan=.false. to allow_infnan=.true.) via a new optional parameter, repro_sum_allow_infnan_in, in shr_reprosum_setopts. A new drv_in namelist parameter, reprosum_allow_infnan, has also been added that will be passed to shr_reprosum_setopts to set the default. This can be set in user_nl_cpl. Since the default is not being changed, this change is BFB. If allow_infnan is set to .true., then runs that failed because of INFs or NaNs would now continue to run (longer), but jobs that did not fail with the original default will be BFB even with the default changed. [BFB] * worleyph/cime/repro_in_cpldiag: Minor cleanup Add option to allow INF or NaN summands in shr_reprosum_calc use shr_reprosum_calc in seq_diag_avect_mct
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Reorganize Users Guide part 1 and 2 content
Split up the CIME-Internals in to several sections and pull in material from Porting and other sections. Also move some material from part 2 to part 1.
Combine the "Use Cases" and "Customizing a Case" material in to a new "Modifying a Case" section in part 1. Move pe-layout example to part 2.
Test suite: built docs locally.
BFB
Address ESCME/cime#2390
User interface changes?: N
Update gh-pages html (Y/N)?: Y