matching tags


20:21 Changeset [11116] by nicolasmartin

Removing of unnecessary entries

20:17 Ticket #2298 (Bug fixes to OBS and ASM found when reviewing the documentation) created by djlea
BE CAREFUL !!! Due to dynamic behaviour of this ticket creation page, it …
20:13 Ticket #2297 (Updates to ASM and OBS documentation) created by djlea
==== Context The documentation for OBS and ASM needs reviewing as it is …
19:25 Changeset [11115] by nicolasmartin

Fixed version with unused references

16:51 Changeset [11114] by cetlod

trunk:small bug fix in the previous bug correction, ticket #2296

16:49 Changeset [11113] by aumont

small bug fix in the previous bug correction

15:57 Changeset [11112] by mocavero

Update the chapter on reference configurations for 4.0 release, see #2216

15:55 Changeset [11111] by laurent

LB: skin temperature now used by ECMWF bulk algorithm, and can be xios-ed ; new module "SBC/sbcblk_skin.F90" ; all physical constants defined in SBC now moved to "DOM/phycst.F90"; all air-properties and other ABL functions gathered in a new module: "SBC/sbcblk_phymbl.F90".

15:43 Changeset [11110] by davestorkey

UKMO/NEMO_4.0_GO8_package branch: Enable product diagnostics uT, vT, wS etc. (as in GO6 package branch).

13:57 Changeset [11109] by cetlod

trunk:bug fix of the ticket #2296

13:41 Ticket #2296 (Bug in the computation of the degradation rate of GOC) closed by aumont
13:41 Changeset [11108] by aumont

bug fix of the ticket #2296

13:36 Ticket #2296 (Bug in the computation of the degradation rate of GOC) created by aumont
==== Context In the new version of PISCES available with NEMO4.0, a new …
11:50 Changeset [11107] by frrh

Commit changes from Dan Copsey's sea ice heat coupling
flux fixes in branch:
revisions 11028:11088.


20:54 Changeset [11106] by nicolasmartin

Push a second review of NEMO manual from side-by-side edition of 2 previous versions (r11051 & r11052)
I will made a final review with the first upload of the new version (r11075) and will reduce significantly it as almost the half of the references are not used.
Would have save time by checking the unused entries before…

18:20 Changeset [11105] by dancopsey

Merged in changes from dev_merge_2017_GC_couple_pkg branch except for zotx1 and zoty1 changes in sbccpl.F90.

15:21 Changeset [11104] by dancopsey

Make coupling package branch


20:05 Ticket #1922 (Uninitialized variable in sbcapr.F90) closed by smueller
duplicate: This ticket has been superseded by ticket #2295.
19:44 Ticket #1922 (Uninitialized variable in sbcapr.F90) reopened by smueller
While the reported bug has been fixed in the release-3.6 version of the …
19:28 Ticket #2295 (Subroutine bdy_dta uses an uninitialised namelist parameter unless ...) created by smueller
==== Context The bug reported in ticket #2235 is also present in the …
19:09 Ticket #2294 (Missing rewind on reference namelist for nambdy_tides) created by mdunphy
==== Context When we have >1 open boundary, and when using …
18:06 Changeset [11103] by agn

Added new code to branch

16:38 Changeset [11102] by davestorkey

dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : revert change committed by mistake.

16:10 Changeset [11101] by frrh

Merge changes from Met Office GMED ticket 450 to reduce unnecessary
text output from NEMO.
This output, which is typically not switchable, is rarely of interest
in normal (non-debugging) runs and simply redunantley consumes extra
file space.
Further, the presence of this text output has been shown to
significantly degrade performance of models which are run during
Met Office HPC RAID (disk) checks.
The new code introduces switches which are configurable via the
changes made in the associated Met Office MOCI ticket 399.

16:07 Changeset [11100] by agn

Properly undid premature check into release-4.0

15:59 Changeset [11099] by davestorkey

dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Updates and bug fixes. This version still doesn't pass all SETTE tests.

15:17 Changeset [11098] by agn

Undid premature check into release-4.0

14:59 Changeset [11097] by agn

corrected . or. byg in diahth.F90

14:59 Changeset [11096] by agn

diahth outputs now controlled only by xml

14:58 Changeset [11095] by agn

use ln_diahth in step_c1d.F90

14:58 Changeset [11094] by agn

complete merge of diahth.F90

14:58 Changeset [11093] by agn

original lot of changes to diahth.F90

14:58 Changeset [11092] by agn

modified namelist_ref to include ln_diahtth key

14:58 Changeset [11091] by agn

new diahth to work without key_diahth: changes in diahth.F90

14:58 Changeset [11090] by agn

original lot of changes to diahth.F90

14:36 Changeset [11089] by agn

Modernized diahth


17:37 Changeset [11088] by dancopsey

Set namelist entry to be false by default.

17:36 Changeset [11087] by dancopsey

Allow false value for namelist entry to be the default

16:55 Ticket #2293 (agn) created by agn
==== Context The dia_hth routine in diahth.F90 still only works with a …


13:41 Changeset [11086] by laurent

LB: initial commit from trunk at r11085


12:59 Ticket #2292 (Bugs with adaptive vertical advection: 3) Courant number computation) created by jchanut
==== Context Adaptive (based on courant number) vertical advection, …


17:39 Changeset [11085] by rrenshaw

code fixes

17:22 New reply on Beginner created by giuliabonino
[ref-cfg] Intel build (with key_agrif) based on ORCA2_LIM seg faults
16:30 Changeset [11084] by davestorkey

UKMO/NEMO_4.0_old_tidal_mixing : Update to be relative to rev 11081 of NEMO_4.0_mirror.

16:29 Changeset [11083] by davestorkey

UKMO/NEMO_4.0_GO6_mixing : Update to be relative to rev 11081 of NEMO_4.0_mirror.

16:21 Changeset [11082] by davestorkey

UKMO/NEMO_4.0_GO8_package : update to be relative to 11081 of NEMO_4.0_mirror.

16:11 Changeset [11081] by davestorkey

UKMO/NEMO_4.0_mirror : update to be a copy of rev 11079 of release-4.0.

15:32 Changeset [11080] by jcastill

Latest changes from Jason


17:16 Ticket #2291 (Bugs with adaptive vertical advection: 2) Interaction with time splitting) created by jchanut
==== Context Adaptive (based on courant number) vertical advection, …
16:48 Ticket #2290 (Bugs with adaptive vertical advection: 1) dynzdf.F90) created by jchanut
==== Context Adaptive (based on courant number) vertical advection, …
16:18 Changeset [11079] by jchanut
16:17 Changeset [11078] by jchanut
16:14 Ticket #2289 (Edge bathymetry values are wrong in the OVERFLOW test case (at U-points)) closed by jchanut
16:13 Changeset [11077] by jchanut

Correct bathymetry at U-points, #2289

16:11 Changeset [11076] by jchanut

Correct bathymetry at U-points, #2289

16:07 Ticket #2289 (Edge bathymetry values are wrong in the OVERFLOW test case (at U-points)) created by jchanut
==== Context Trivial bug in OVERFLOW test case: bathymetry computation at …
09:40 Ticket #2288 (BDY is not compatible with high order schemes) created by smasson
==== Context BDY is not compatible with high order schemes (bilaplacien, …


18:16 Changeset [11075] by nicolasmartin

Submission of an intermediate version of NEMO bibliography
Manual merge of 2 existing BibTeX entries per each reference in order not to lose a field
It remains to make a check from the diff view under Trac or a diff tool and a final cleaning for indentation and new citations keys

17:47 Ticket #2287 (Bug in bdy with flather) closed by girrmann
17:46 Changeset [11074] by girrmann

dev_r10984_HPC-13 : bug fix and cleaning of flather, see #2287 and #2285

17:09 Developers/Good Practices/Usual Commands edited by nicolasmartin
16:58 Developers/SVN Quick Reference created by nicolasmartin
16:48 Developers/Good Practices edited by nicolasmartin
16:46 Developers/Good Practices edited by nicolasmartin
15:16 Changeset [11073] by girrmann

v4 : fix bug in flather for bdy, see #2287

15:14 Changeset [11072] by girrmann

trunk : fix bug in flather for bdy, see #2287

15:07 Ticket #2287 (Bug in bdy with flather) created by girrmann
==== Context For eastern and northern boundaries (flagu = -1 and flagv = …
14:58 Changeset [11071] by girrmann

dev_r10984_HPC-13 : step 2, remove unneeded communications, see #2285


15:04 Changeset [11070] by rrenshaw

code fixes

12:23 Changeset [11069] by andmirek

ticket #2197 glob sum for parallel architecture

11:36 2019WP/HPC-12_Mocavero_mpi3 edited by andmirek
11:35 2019WP/HPC-12_Mocavero_mpi3 edited by andmirek


15:20 Changeset [11068] by dford

Branch for changes required for inclusion of spectral optics model (coupled via FABM).

11:34 Changeset [11067] by girrmann

dev_r10984_HPC-13 : new implementation of lbc_bdy_lnk in prevision of step 2, regroup communications, see #2285


18:00 Changeset [11066] by rrenshaw

changes to add regional means output and correction for section transports

16:54 Changeset [11065] by rrenshaw

new branch for changes to branch for AMM7/AMM15 3.6 suite

13:10 Changeset [11064] by dford

Deleting branch as changes merged back.

13:08 Changeset [11063] by dford

Add missing lbc_lnk and option to relax chlorophyll to climatology. See Met Office utils ticket 216.

13:06 Changeset [11062] by dancopsey

Fix compile issues for when I am running GO6+MEDUSA.

12:52 Changeset [11061] by dancopsey

Fix compile issues for when I am running GO6+MEDUSA.


15:20 Changeset [11060] by nicolasmartin

Backup a merged bibliography with duplicates commented
Bib Tool? determines double entries from successive identical citation keys so
the procedure was in 2 steps

  1. Process r11051 & r11052 versions of NEMO_manual.bib to have the same pattern for citation key
  2. Merge the 2 versions with Bib Tool? configured for duplicate checking:
    bibtool -d -- preserve.keys=on -- sort=on input_files -o output_file

It remains to clean the bibliography by deleting the doubles.

13:34 Ticket #2286 (Passive tracer vertical diffusivity in trazdf.F90 (PISCES offline)) created by mgali
==== Context When running PISCES offline simulations in 1D, I noticed …
13:05 Changeset [11059] by girrmann

dev_r10984_HPC-13 : simplify bdyini.F90 following extension of bdy detection, see #2285


21:41 Changeset [11058] by nicolasmartin

Add a configuration file as resource for Bib Tool? to define standard format for our bibliographies
After the import of several new versions of references, I found some discrepancies that it was easy to address with Bib Tool?

  • Set a common pattern for citation key: author1[_authors2[_ea]]_journalyear
  • Suppress a good bunch of trivial fields to reduce the size of the biblio in the different exports address chapter institution isbn issn issue keywords language note number organisation pages pdf series school type volume Open to discussion but to me a DOI entry is sufficient if someone wants more information
  • Prevent the use of tab for fields indentation, better readability for the bib file on Trac browser or in the output of SVN diff
  • Apply the following order of fields for every entry author # title # booktitle # journal # publisher # editor # year # month # doi # url

To apply the rules to a Bib Tex? file, run

bibtool -r bibtool.rsc input_file -o output_file
17:36 Changeset [11057] by davestorkey

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Rewrite time filtering of tracers and SSH. This version now bit compares with the base code for ORCA1 starting from a restart.
To do:

  1. Check that it bit compares with an Euler timestep.
  2. Full SETTE tests.
  3. Check that it compiles with C1D.
  4. Check that TOP works (see 1).
15:52 Changeset [11056] by girrmann

dev_r10984_HPC-13 : Bugfix following [11048], see #2285

14:57 Changeset [11055] by dancopsey

Put the switch back in again.

14:54 Changeset [11054] by dancopsey

Put the switch back in again.

12:53 Changeset [11053] by davestorkey

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Merge in latest changes from main branch and finish conversion of "h" variables. NB. This version still doesn't work!

12:05 Changeset [11052] by nicolasmartin

Upload draft version for new NEMO biblio
This is the result of the publications collecting on Cross Ref?.
By mistake, previous commit was supposed to be the one but it was just a small edition.

11:50 Changeset [11051] by nicolasmartin

Backup intermediate version before further minor modifications

10:27 Changeset [11050] by davestorkey

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps_rewrite_time_filterswap : Rewrite dynnxt.F90 and rename dynatf.F90 with time level swapping in stp. This doesn't work yet but committing for the record before I merge in Andrew's changes to the main branch.

10:22 Changeset [11049] by girrmann

dev_r10984_HPC-13 : CYCLE instruction is not systematic anymore, computation is done on the halo whenever possible and overwritten by lbc_bdy instruction, see #2285


18:36 Changeset [11048] by girrmann

dev_r10984_HPC-13 : Step 1, boundary is now detected all over the local domain, this does not change the result. Improve bdy treatment for bdy_rnf in bdytra.F90, this changes the result when keyword runoff is specified in namelist

18:26 Changeset [11047] by acc

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : Add missing initialisation of time-level indices for the AGRIF zooms. This enables AGRF SETTE tests to be reactivated but initial tests suggest minor reproducibility and restartability issues. These tests have always been sensitive to optimisation levels on the NOC cluster though so need an independent test on another system

18:02 Changeset [11046] by dancopsey

Take the switch back out again. It was decided not that this is a bug so should be automatically picked up.

17:58 Changeset [11045] by dancopsey

Take the switch back out again. It was decided not that this is a bug so should be automatically picked up.

17:13 Changeset [11044] by girrmann

dev_r10984_HPC-13 : missing part of [11024], see #2285

15:51 Changeset [11043] by nicolasmartin

Several fixes for the LaTeX compilation of the manuals

15:46 Changeset [11042] by girrmann

dev_r10984_HPC-13 : update with trunk at revision 11041

14:28 Changeset [11041] by clem

debug corner points for ice bdy

14:27 Changeset [11040] by clem

debug corner points for ice bdy

09:38 Changeset [11039] by rrenshaw

code fix


22:44 Changeset [11038] by rrenshaw

code fixes

21:03 Changeset [11037] by nicolasmartin

Review entries of TOP bibliography
Continuation of the work to complete the BibTeX entries with the help of
DOI resolver for the retrieval and Cross Ref? API for the identification.

Add byrd-co2-2008.txt & edc-co2.txt for information which give the original
references for using particular CO2 data set from NOAA-NCEI

15:44 Changeset [11036] by acc

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : Remove now redundant TARGET qualifiers from oce and dom_oce arrays

15:10 Changeset [11035] by frrh

Apply changes from UKMO GMED ticket 453 to fix OOB bugs in
the calculation of diagnostic tnpeo and to apply the correct calculation
as per the current NEMO vn4.0 and 3.6_STABLE code bases, in place of the
existing incorrect formula. Thus, tnpeo diagnostic values will change
following this update.
Model prognostics and eveolution are unaffected.


22:42 Changeset [11034] by nicolasmartin

Add a simple shell script to build the user guide
It checks Python deps, cleans the previous build and exports the guide in HTML format

22:36 Changeset [11033] by nicolasmartin

Modify the shell code in order to run as expected on different OS (Linux or MacOS)

22:34 Changeset [11032] by nicolasmartin

Fix few issues in TOP bibliography

21:41 Changeset [11031] by nicolasmartin

Update the chapters following the new keys for BibTeX entries

20:42 Changeset [11030] by nicolasmartin

Reconstruction of SI3 bibliography in bib format
Use of biblio Emacs package to retrieve BibTeX entries from

  • existing DOIs in the bbl file
  • DOIs identified by searching from Cross Ref? API
  • classical request on web search engine (few)

2 references are missing (+ one paper is submitted): TEOS-10 and MaykutThorndike73 and the file was then processed with bibtool for reformatting.
I plan to reproduce this procedure for reviewing the other bibliographies (NEMO & TOP) and the references in the user guide.

18:03 Changeset [11029] by dancopsey

Upgraded previous version of this branch.

17:55 Changeset [11028] by dancopsey

Branch off the teh GO6 package branch at revision 10681

17:33 Changeset [11027] by acc

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : Final renaming conversions and removal of temporary pointers. All non-AGRIF SETTE tests are passing (including test cases). AGRIF tests compile and link but segment on first call to Agrif_Regrid. NST changes are therefore a work in progress but nothing is broken that was not broken before

16:54 Changeset [11026] by nicolasmartin

Apply previous for SI3 specific namelists

16:51 Changeset [11025] by nicolasmartin

Set mime-type to text/x-fortran to all namelists

16:07 Changeset [11024] by girrmann

dev_r10984_HPC-13 : imrpove bdy treatment ssh and neumann, see #2285

12:21 Changeset [11023] by nicolasmartin

Fix typos with comma followed by 'and' in author entries

11:49 Changeset [11022] by nicolasmartin

Fix the relative path for the bibliography style file to apply it globally

09:54 Changeset [11021] by davestorkey

Branch of a branch to rewrite time filtering and swapping as part of KERNEL-02 action. Branch of a branch so as not to break bit comparison tests in main branch. Will merge back when happy.


22:26 Changeset [11020] by nicolasmartin

Apply svn:ignore property on TOP subfolders from ./doc/.svnignore file
Cmd to run globally: svn pset -R svn:ignore -F .svnignore latex

22:21 Changeset [11019] by nicolasmartin

Apply more or less same modifications on TOP as for SI3 for compliance
Despite remaining issues with references, TOP manual can be build like NEMO & SI3 with ./build_manual.sh TOP
For the record, the building of the 3 manuals can be launched with ./manual_build.sh all

21:25 Changeset [11018] by nicolasmartin

Update pdf version, conversion seems to be better from png

21:24 Changeset [11017] by nicolasmartin

Remove useless upper path level + Add eps & pdf format to fix inclusion issues

21:03 Changeset [11016] by nicolasmartin

Move figures of TOP manual to global location

20:57 Changeset [11015] by nicolasmartin

Modification of the content to be in line with the NEMO manual
SI3 manual can now be build like the NEMO manual with ./manual_build.sh SI3

  • Mimick the directory organisation with main and subfiles folders.
  • Regarding the particular case of namelists
    • Remove the duplicates already contained in the global namelists folder at 1st level of ./doc
    • Keep the namelists sub-folder only for namdyn_adv & namsbc which already exist in ocean namelists
  • Rewriting of SI3_manual.tex with NEMO_manual.tex as template to easily highlight differences
  • Updating of several paths for figures/namelists inclusion or LaTeX files referencing
  • LaTeX source:
    • Replacement of \forfile command for namelists with pre-configured \nlst alias
    • " "" \bm with \mathbf (save installation of an extra package)
19:05 Changeset [11014] by nicolasmartin

Add eps & pdf format for figures to fix inclusion issues

18:32 Changeset [11013] by nicolasmartin

Add explicit option for latexmk to ensure PDF export

18:18 Changeset [11012] by jchanut

#1791, report domvvl change in VORTEX test case. Modification of domvvl there should be removed.

17:39 Changeset [11011] by nicolasmartin

Remove useless upper path level

17:30 Changeset [11010] by nicolasmartin

Move figures of SI3 manual to global location

17:07 Changeset [11009] by frrh

Updates following review.

17:07 Changeset [11008] by nicolasmartin

Fix execution rights on new scripts

16:58 Changeset [11007] by nicolasmartin

Edit NEMO_manual LaTeX files to comply with previous path modification

16:56 Changeset [11006] by nicolasmartin

Reorganisation of the directory for upcoming addition of SI3/TOP figures

16:53 Changeset [11005] by nicolasmartin

Updating of the namelists

16:51 Changeset [11004] by nicolasmartin

Review of main building script

  • Exportig Python package checking to external script check_pkg.py for sharing it with the verification of deps for the user guide (sphinx, extension and theme)
  • Renaming to explicit manual_build.sh
  • Addition of basic checking for LaTeX installation (latexmk binary)
  • Implementation of loop and argument reading in order to use the same script for the 3 manuals
  • Improvment of code commentary
15:47 Changeset [11003] by girrmann

dev_r10984_HPC-13 : create developpement branch

15:43 Ticket #2285 (Optimization of the communications in BDY) created by girrmann
==== Summary ||=Action || HPC-13_IRRMANN_BDY_optimization
14:53 Changeset [11002] by jchanut

vvl interp, #1791: 1) Add resting depth at F-points. 2) Rewrite dom_vvl_interpol with 2 aditionnal methods for horizontal interpolation at U-V-F points (nmet=0,1,2 in subroutine header). Set nmet=1, i.e. interpolate interfaces instead of scale factors anomaly. 3) Changes in the rest of the code: consider input array in dom_vvl_interpol at T point for F scale factors interpolation.

14:19 Changeset [11001] by davestorkey

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : C1D and step.F90. Passes SETTE. Compiles with key_c1d.

13:20 Changeset [11000] by dancopsey

Relabel name of the switch that turns on the fix.

12:24 Changeset [10999] by jchanut

Fix for ticket #1791

10:27 Changeset [10998] by davestorkey

2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps : ICE changes. Passess non-AGRIF sette tests apart from ORCA2_SAS_ICE which doesn't seem to work for me at the moment.


00:05 HPC-WG_28_jul_17_Silvia.pdf attached to Working Groups/HPC/Mins_2017_07_28 by mocavero
Hybrid parallelisation


23:10 Documentation edited by nicolasmartin
23:10 Tag change on Documentation by nicolasmartin
Tags Documentation added; DOC, SIREN, bibliography removed
23:04 Literature created by nicolasmartin
18:16 Changeset [10997] by girrmann

v4 : Report commit from bugfix #2283 fixed in the trunk

18:02 Ticket #2283 (Reproductibility issue in dynkeg.F90 if(ln_bdy)) closed by girrmann
fixed: fixed, see [10996]
18:02 Changeset [10996] by girrmann

trunk : fixed reproductibility issue in dynkeg.F90 with bdy, see #2283

16:43 Changeset [10995] by dancopsey

Put fixes in a switch so that we don't change answers in GC3 but we still want to apply them to GC4.

15:08 Changeset [10994] by clem

couple of commits to 1) deal with ice concentration reaching 1 (so, no more limitations in the max ice concentration imposed in the namelist), 2) deal with very small negative values that can occur due to roundoff errors

15:07 Changeset [10993] by clem

couple of commits to 1) deal with ice concentration reaching 1 (so, no more limitations in the max ice concentration imposed in the namelist), 2) deal with very small negative values that can occur due to roundoff errors

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