[Ncep.list.nems.announce] NEMS Ticket #174 : There are a sycronic upcoming commits to the NEMS, GSM, NMM, phys, NEMSmodulefiles and chem trunks

Eugene Mirvis - NOAA Affiliate eugene.mirvis at noaa.gov
Tue Jul 12 15:48:54 UTC 2016 

==
NEMS TRAC Ticket #174:New NEMS features: the standalone integrated
pre-builds of  Phys and Chem libraries. ==

----

1. The current set of the upcoming  commits for the NEMS trac ticket #174
provides a standalone capabilities for NEMS isolated physics and chemistry
separately.

2. The phys and chem library sources and build system will be located now
as the sub-projects of nceplibs in EMC repository, inheriting all NEMS
development history as a regular nceplibs sub-projects, contain branches,
tags and the trunks, tagged currently as v10.0.10, accordingly of the NEMS
restructuring history.

3. Both: phys and chem are using the same configuration NEMS procedure,
therefore, each has NEMS conf directory as the external links to the nems
conf disrectory for now. That secures consistency of configurations between
phys, chem, and NEMS framework.

4. A dual built capability is provided for the both phys and chem
libraries:1) as the stand-alone installations 2) the builts within a
traditional NEMS structure for phys and chem development process.

5. That selection is provided via the two external parameters: $PHYS_MODE
and $CHEM_MODE.
If these parameters are set as “compile ”the built system assumes full
compilation if such library. In this case a directory chem source should
have an external link to chem at the “src” while the phys dir an external
link at src/atmos level, defined at the subversion properties at NEMSLegacy
externals. By default, both will be set to “compile” by now, as currently
agreed with component code manager and will be assigned and are located in
configuration files in conf directory for Theia and WCOSS.

6. If these options are set to use of the pre-built libraries on
operational and R&D EMC machines are needed to be exercised, $ PHYS_MODE
and/or $CHEM_MODE the value of these parameters must be changed to any
other than “compile”. In this case, NEMS’s makefile will be acting
accordingly to use pre-built libraries on each machine and the source code
within NEMS structure is not necessary to be checked out.

7. The pre-built PHYS and CHEM libraries locations :


The pre-built libraries are available on  Theia & WCOSS at the following
locations:
On Theia:
/scratch3/NSEPDEV/nceplibs/dev/
      phys, chem, phys_full and chem_full
The builds of phys and chem contain the pre-builds with an option of
GOCART_MODE=stub while phys_full and chem_full contain pre-builds with the
GOCART_MODE=full.

On WCOSS, the locations of the similar builts are at:
/usrx/local/mceplibs/dev/
      phys, chem, phys_full and chem_full consecutively.

You can link against each of these libraries directly but you have to
change the values of PHYS_MODE and CHEM_MODE from the “compile” to, perhaps
"prebuild" in the NEMS conf/configure.nems.Theia* and
conf/configure.nems.WCOSS* files. That will automatically assume in the
NEMS makefile the pre-built location paths are activated on each site
.
8. The chem and phys modulefiles______________________
In order to conveniently manipulate with different options of use, for
installation procedure and for regression testing; and also to support the
NCEPLIBS computing environment flexibility and version standards, phys and
chem modulefiles have been created. These modulefiles are also residing
under EMC repositiory as the NEMSmodulefiles sub-project of the nceplibs
project and are also available on Theia and WCOSS currently under:
/scratch3/NCEPDEV/nceplibs/dev/NEMS modulefiles,
and
/usrx/local/nceplibs/dev/NEMS modulefiles, consecutively, until an
operational implementation of the phys and chem @ nwprod will occure
Also at the repository :
https://svnemc.ncep.noaa.gov/projects/nceplibs/Modules/NEMSmodulefiles/

9. Phys and Chem installation and version control
procedures________________________
The installation of the phys and chem are simplified to :
a) Checking out need version, dev branch, tag or the phys trunk of the
development
b) gmake clean
c) running ./Install script
Commit procedure to the phys and chem trunks should be address to the phys
and chem code manager.

10. Expected file changes in reintegration:
10.1. CHEM:
[Eugene.Mirvis at t14a1 chem_trunk]$ svn merge --dry-run --reintegrate
https://svnemc.ncep.noaa.gov/projects/nceplibs/chem/branches/Euge/nemstrunk_NEMSLegacyMD
--- Merging differences between repository URLs into '.':
A    ESMFVersionDefine_ESMF_NUOPC.h
A    configure
A    Compile_theia.log
A    ESMFConvenienceMacros.h
A    InstallM
A    Modulefiles_chem
A    Modulefiles_chem/Modulefiles_phys
A    Modulefiles_chem/chem
A    Modulefiles_chem/chem/10.0.7
A    Modulefiles_chem/chem/10.0.1
A    Modulefiles_chem/chem/10.0.10
A    Modulefiles_chem/chem/build10.0.10
A    Modulefiles_chem/chem/10.0.2
A    Compile_wcoss.log
A    Install
A    detect_machine1.sh
A    clean.h
A    makefile_std1
A    makefile_std2
U    makefile
 U   .
No textual conflicts are expected

10.2 PHYS reintegration_____________________________:

Phys directory contains 2 externals for now (that reflects what was
insisted by the MESO group and accepted by M.Iredell for now)
[Eugene.Mirvis at t14a1 phys]$ svn propget svn:externals
conf
https://svnemc.ncep.noaa.gov/projects/nems/branches/euge/nemstrunk_NEMSLegacyMD/src/conf
nmmbphys https://svnemc.ncep.noaa.gov/projects/nmmb/trunk/nmmbphys

Reintegration:
[Eugene.Mirvis at t14a1 phys_trunk]$ svn merge --dry-run --reintegrate
https://svnemc.ncep.noaa.gov/projects/nceplibs/phys/branches/Euge/ncepphys_trunk_NEMSLegacy_1physMD
--- Merging differences between repository URLs into '.':
A    nmmbphys_Cln
A    share
A    share/mkDepends.pl
A    Install
A    ESMFVersionDefine_ESMF_NUOPC.h
A    Compile_theia.log
A    include
A    include/ESMFVersionDefine_ESMF_NUOPC.h
A    include/ESMFVersionDefine.h
A    include/configure.nems_univ
A    include/ESMFVersionLogic.h
A    include/NCEP_base.mk
A    include/ESMFVersionDefine_ESMF_6.3.0rp1API.h
A    include/NUOPC.inc
A    include/ESMFVersionDefine_ESMF_3.h
A    include/kind.inc
A    Compile_wcoss.log
A    Install0
A    nmmbphys_Get
U    makefile
A    configure
A    detect_machine1.sh
A    makefile_TODO
A    mersenne_twister.f
A    makefile_std1
A    idea_composition.f
A    Install_gsm
A    Install_nmm
 U   .

No textual conflicts are expected

10.3 NEMS_reintegration:
[Eugene.Mirvis at t14a1 nems_trunk]$ svn merge --dry-run --reintegrate
https://svnemc.ncep.noaa.gov/projects/nems/branches/euge/nemstrunk_NEMSLegacyMD
--- Merging differences between repository URLs into '.':
U    tests/Compile_theia.log
U    tests/rt.conf
U    tests/RegressionTests_theia.log
U    src/configure
U    src/atmos/share/makefile
D    src/chem
D    src/atmos/share/idea_composition.f
D    src/atmos/phys
D    src/atmos/share/mersenne_twister.f
U    src/atmos/makefile
U    src/conf/modules.nems.Wcoss_ESMF_700_nmmb
U    src/conf/configure.nems.Theia.intel
U    src/conf/configure.nems.Theia.intel_gsm
U    src/conf/configure.nems.Theia.intel_nmmb
U    src/conf/configure.nems.Wcoss.intel_gsm
U    src/conf/configure.nems.Wcoss.intel_nmmb
A    src/conf/modules.nems.Theia_ESMF_700_gsm
A    src/conf/modules.nems.Theia_ESMF_700_nmmb
U    src/conf/modules.nems.Wcoss_ESMF_700_gsm
D    src/conf/modules.nems.Theia_ESMF_7_gsm
D    src/conf/modules.nems.Theia_ESMF_7_nmmb
A    src/detect_machine1.sh
A    src/detect_machine.sh
U    src/makefile
 U   src
 U   .

No textual or tree conflicts
10.4 GSM_reintegration
[Eugene.Mirvis at t14a1 gsm_trunk]$ svn merge --dry-run --reintegrate
https://svnemc.ncep.noaa.gov/projects/gsm/branches/Euge/gfs_NEMSLegacy1physMD
--- Merging differences between repository URLs into '.':
 U   module_GFS_GRID_COMP_stub.F90
 U   module_GFS_INTEGRATE.F90
U    phys/makefile
 U   phys
U    libutil/makefile
 U   libutil
 U   module_GFS_GRID_COMP.F90
 U   module_GOCART_ROUTINES_stub.F90
 U   module_GFS_CORE_SETUP.F90
 U   module_GOCART_ROUTINES.F90
 U   dyn/gfs_dynamics_initialize_slg_mod.f
U    dyn/makefile
 U   dyn
UU   makefile
 U   module_GFS_INTERNAL_STATE.F90
 U   .No text conflicts are expected or result change

10. 5
[Eugene.Mirvis at t14a1 nmmb_trunk_reint]$ svn merge --dry-run --reintegrate
https://svnemc.ncep.noaa.gov/projects/nems/branches/euge/nmmbtrunk_MD
--- Merging differences between repository URLs into '.':
U    nmmbphys/makefile
U    makefile
No text conflicts expected

After that, src/atmos/phys and src/chem. Are going to be deleted from NEMS
and introduced on NEMSLegacy level as the subversion external properties as
the following:


[Eugene.Mirvis at t14a1 NEMSLegacy_1physT_MDg]$ svn propget svn:externals
NEMS
https://svnemc.ncep.noaa.gov/projects/nems/branches/euge/nemstrunk_NEMSLegacyMD
NEMS/src/atmos/gsm
https://svnemc.ncep.noaa.gov/projects/gsm/branches/Euge/gfs_NEMSLegacy1physMD
NEMS/src/atmos/nmm
https://svnemc.ncep.noaa.gov/projects/nems/branches/euge/nmmbtrunk_MD
NEMS/src/atmos/phys
https://svnemc.ncep.noaa.gov/projects/nceplibs/phys/branches/Euge/ncepphys_trunk_NEMSLegacy_1physMD
NEMS/src/chem
https://svnemc.ncep.noaa.gov/projects/nceplibs/chem/branches/Euge/nemstrunk_NEMSLegacyMD

For now
Or after the commit:
NEMS                  https://svnemc.ncep.noaa.gov/projects/nems/trunk
NEMS/src/atmos/gsm    https://svnemc.ncep.noaa.gov/projects/gsm
NEMS/src/atmos/nmm    https://svnemc.ncep.noaa.gov/projects/nems/trunk
NEMS/src/atmos/phys
https://svnemc.ncep.noaa.gov/projects/nceplibs/phys/trunk
NEMS/src/chem         https://svnemc.ncep.noaa.gov/projects/nceplibs/chem/

With associated revisions on the head of the trunks

11. Working (tested) directories
All 4 full sets of the 45 regression tests have been PASSED now.
There are 2 working directories have been tested on each machines, tested
with the options a) to compile phys and chem within traditional structure
$PHYS_MODE=compile, $CHEM_MODE=compile ( are default for now) and
b) tested with the pre-build phys, chem., phys_full and chem._full
libraries :
With the phys and chem. prebuild options PHYS_MODE=compile
CHEM_MODE=compile:
      On Theia:
PHYS_MODE=compile
CHEM_MODE=compile

/scratch4/NCEPDEV/nems/noscrub/Eugene.Mirvis/NEMSLegacy_1physT_MDg

On WCOSS __________:
PHYS_MODE=compile
CHEM_MODE=compile
/gpfs/td1/emc/global/noscrub/Eugene.Mirvis/NEMS/NEMSLegacy_1physT_MDg

With the phys and chem. prebuild options:
PHYS_MODE=prebuild
CHEM_MODE=prebuild:
On Theia:
/scratch4/NCEPDEV/nems/noscrub/Eugene.Mirvis/NEMSLegacy_1physT_MD_prebld
On WCOSS :
/gpfs/td1/emc/global/noscrub/Eugene.Mirvis/NEMS/NEMSLegacy_1physT_MDg_prebld
All full regression tests have been passed in all 4 directories. No results
changes.

GSM , NMMB code manages and NEMS team please observe upcoming changes in 24
hrs and contact me if you have any questions

Thank you,

-Eugene

---
Eugene Mirvis, *Tech Lead,*
Senior Computational Scientist, IMSG @ EMC
National Centers for Environmental Prediction,
National Oceanic and Atmospheric Administration
5830 University Research Ct., NCWCP rm 2183
College Park, MD 20740
Ph. 301.683.3809
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