| Version 54 (modified by flavoni, 9 years ago) (diff) |
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Using libIGCM library with ORCA2_LIM for nemo_v3_6
Purposes
Through libIGCM give an example of run of configuration ORCA1_LIM3_PISCES with :
- Climatological and Interannual (years from 1948 to 2009) forcing files COREII
- outputs:
- ocean: 1D 5D 1M 1Y
- ice: 1M
- biology: 1D 1M 1Y
- RESTARTS every year
- on Idris ADA machine
Official documentation of Libigcm is :
Quick start guide :http://www.nemo-ocean.eu/Using-NEMO/Configurations/
- Create and go into working directory :
mkdir TP-NEMO-libIGCM ; cd TP-NEMO-libIGCM
- Define the following alias to use SVN :
alias svn_ano='svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl'
- Extract modipsl (modipsl with libIGCM)
svn_ano
- Extract the model "NEMO_v6":
cd modipsl/util ** ./model NEMO_v6
verify NEMOGCM revision in modipsl/util/mod.def file: (fixed revision of NEMO: 5618 )
#-H- NEMO_v6 NEMOGCM for CMIP6 exercise
#-H- NEMO_v6 libIGCM tag libIGCM_v2.6
#-M- NEMO_v6 Christian.Ethe@…
#-C- NEMO_v6 tags/libIGCM_v2.7 HEAD 10 libIGCM .
#-C- NEMO_v6 branches/2015/nemo_v3_6_STABLE/NEMOGCM 5618 7 . modeles
#-C- NEMO_v6 trunk/ORCA1_LIM3_PISCES HEAD 17 . modeles/NEMOGCM/CONFIG
#-C- NEMO_v6 CONFIG/UNIFORM/v6/NEMO_v6 HEAD 8 NEMO_v6 config
(The OFFICIAL repository for the CONFIG ORCA1_LIM3_PISCES is the web site shaconemo: https://forge.ipsl.jussieu.fr/shaconemo/wiki/README_ORCA1_LIM3_PISCES )
NOTA BENE : ORA1_LIM3_PISCES configuration is by default (in libIGCM) run with xios_server en detached mode --> so you need to download and compile xios:
- Download XIOS (branch 1.0 revision 703)
(The documentation of xios is available here: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation )
- Compile XIOS (on ADA machine):
cd $WORKDIR svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0 XIOS -r 703 ./make_xios --arch X64_ADA (./make_xios -h for help)
- Edit NEMOGCM/CONFIG/cfg.txt file, and add the following line:
ORCA1_LIM3_PISCES OPA_SRC LIM_SRC_3 NST_SRC TOP_SRC
- Compile ORCA1_LIM3_PISCES configuration (Using ./makenemo -h to see help ( to see list of compilers availables, to see options,...))
cd ../modeles/NEMOGCM/CONFIG ./makenemo -n ORCA1_LIM3_PISCES -m X64_ADA -j8 -j8 compile with 8 proc for compilation phase -j0 option create only configuration directory but does not compile it
- Copy executable nemo.exe (and xios_server.exe if needed in detached mode) in modipsl :
cd ../../../bin ln -s ../modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/BLD/bin/nemo.exe nemo.exe (cp $WORKDIR/XIOS/bin/xios_server.exe xios_server.exe)
NOTA: YOU CAN WANT TO USE MORE THAN ONE EXECUTABLE : so you can do, for example,
ln -s ../modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca1_lim3_pisces.exe ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM3_PISCES/BLD/bin/nemo.exe nemo_orca2_lim3_pisces.exe ln -s ../modeles/NEMOGCM/CONFIG/ORCA2_LIM2_PISCES/BLD/bin/nemo.exe nemo_orca2_lim2_pisces.exeJUST BECAREFUL to use SAME executable name in config.card
- This is the structure of config in modipsl:
modipsl/config/NEMO_v6/
GENERAL
EXPERIMENTS/
ORCA1_LIM3_PISCES/
clim/
config.card
COMP/
xios.card
lim3.card
pisces.card
opa9.card
ia/
config.card
COMP/
xios.card
lim3.card
pisces.card
opa9.card
ORCA2_LIM2_PISCES/
clim/
config.card
COMP/
lim2.card
pisces.card
opa9.card
ORCA2_LIM3_PISCES/
clim/
config.card
COMP/
lim3.card
pisces.card
opa9.card
- To create submission directory you have to copy config.card file in config/NEMO-v6 directory:
cd modipsl/config/NEMO_v6 cp EXPERIMENTS/ORCA1_LIM3_PISCES/clim/config.card .
- Editing at this point modipsl/config/NEMO_v6/config.card (according to iodef.xml file) see detailed page for more informations: page description of config.card
vi config.card # Modify AT LEAST JobName=eOR1L3P
- BE CAREFUL at this point: VERIFY in namelist_ORCA1_cfg that you domain decomposition is:
- jpni = 17
- jpnij = 221
- jpnj = 13
if not NEMO makes itself its decomposition like 221 * 1 and THIS DOES NOT WORK (your ocean.output will end with : "dta_tsd: deallocte T & S arrays as they are only use to initialize the run" WITHOUT ERROR MESSAGE
- Create Job : (using ins_job in modsipl/libIGCM directory)
../../libIGCM/ins_job
ls modipsl/config/NEMO_v6
GENERAL
EXPERIMENTS
eOR1L3P #new submission directory, config card is now HERE
- LOOK AT alla parameters of the Job you've created :
By default is 1 hour (@ wall_clock_limit = 1:00:00), but for ORCA1-LIM3-PISCES is 1:45 for 1 year
vi eOR1L3P/Job_eOR1L3P # @ wall_clock_limit = 1:45:00
- Submit Job :
cd ../ (back into modipsl directory) ./util/ins_job cd ../config/ORCA2_LIM/IGCM00 llsubmit Job_Name
* SPECIAL INFORMATIONS FOR RUN ORCA2-LIM3-PISCES *
ORCA2-LIM3-PISCES does not exists between reference configurations in v3_6_STABLE NEMOGCM/CONFIGURATION so you've to:
- Create configuration ORCA2_LIM3_PISCES without compile it (with -j0):
./makenemo -n ORCA2_LIM3_PISCES -r ORCA2_LIM_PISCES -j0
- Edit cfg.txt file by changing ORCA2_LIM3_PISCES definition :
vi cfg.txt ORCA2_LIM3_PISCES OPA_SRC '''LIM_SRC_3''' NST_SRC TOP_SRC
- Clean the configuration ORCA2_LIM3_PISCES just created :
./makenemo -n ORCA2_LIM3_PISCES clean
- Change cpp keys:
vi ORCA2_LIM3_PISCES/cpp_ORCA2_LIM3_PISCES.fcm bld::tool::fppkeys key_trabbl '''key_lim3''' key_dynspg_flt key_diaeiv key_ldfslp key_traldf_c2d key_traldf_eiv key_dynldf_c3d key_zdftke key_zdfddm key_zdftmx key_top key_pisces key_iomput key_mpp_mpi
- And finally compile the ORCA2_LIM3_PISCES configuration :
./makenemo -n ORCA2_LIM3_PISCES -j 8 -m X64_ADA
If you want to switch from climatological to interannual see page description of config.card
Simona Flavoni last update: Timestamp?
