[[ParentLinkage(=)]] [[BR]] [[PageOutline]] = '''Using libIGCM(v1_1) library with ORCA2_LIM''' = == A - Purposes: == [[BR]] * Document the using of libIGCM for NEMO, in configuration ORCA2_LIM [[BR]] [[BR]] == B - Quick start guide: == [[BR]] * Define the following alias to use SVN : [[BR]] {{{ alias svn_ano='svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl' alias svn_libigcm='svn co http://forge.ipsl.jussieu.fr/libigcm/svn/tags/libIGCM_v1_1 libIGCM' alias svn_nemoligcm='svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/libIGCM/ORCA2_LIM/IGCM00 IGCM00' }}} * Create and go into working directory : [[BR]] {{{ mkdir TRY ; cd TRY }}} * Extract modipsl : [[BR]] {{{ svn_ano }}} * Extract NEMO : [[BR]] {{{ cd modipsl/util ./model NEMO }}} * Extract libigcm : [[BR]] {{{ cd ../ svn_libigcm }}} * Extract card for NEMO for libIGCM : [[BR]] {{{ cd config/ORCA2_LIM svn_nemoligcm }}} * Choosing ORCA2_LIM configuration : [[BR]] {{{ cd ../../modeles/UTIL ./fait_config ORCA2_LIM }}} * Install the makefiles : [[BR]] {{{ cd ../../util ./ins_make }}} * Compile : [[BR]] {{{ cd ../config/ORCA2_LIM gmake }}} * Submit Job : [[BR]] {{{ ( Editing at this point modipsl/config/ORCA2_LIM/IGCM00/config.card ) ../../util/ins_job cd IGCM00 qsub Job_NL1 }}} [[BR]] [[BR]] == C - List of possible errors : == [[BR]] === C.1 Errors in modipsl/config/ORCA2_LIM/IGCM00/Script_Output_''!JobName'' === [[BR]] * '''Error : TERM = (vt100) ${HOME:-.}/.profile: .bashrc: not found''' * '''Error : ksh: D--------------------------------------------------------------------==: not found''' it can depends on your '''.profile''' file. To solve it:: .profile file it can be like: «# .profile (idris) [[BR]] # Fichier d environnement a charger sur la frontale TX7 unix LINUX [[BR]] # Vous pouvez mettre a jour le fichier .profile_tx [[BR]] if [ `hostname` = "brodie" -a -f $HOME/.profile_tx ]; then [[BR]] . $HOME/.profile_tx [[BR]] # Fichier d environnement a charger sur les noeuds SX8 unix SUPER-UX [[BR]] # Vous pouvez mettre a jour le fichier .profile_sx [[BR]] elif [ `hostname` != "brodie" -a -f $HOME/.profile_sx ]; then [[BR]] . $HOME/.profile_sx [[BR]] else [[BR]] echo [[BR]] fi » * '''Error : cat: cannot open ........./modipsl/config/ORCA2_LIM/IGCM00/../.resol ''' : it is due to modipsl/libIGCM/AA_job file. To solve it:: change in this way: #-- Resolution FLAG for oasis input [[BR]] #RESOL=$(cat ${SUBMIT_DIR}/../.resol) [[BR]] RESOL= go in modipsl/config/ORCA2_LIM/IGCM00 directory cancel '''run.card.init''' and '''Job_''Name''' files and then do an '''ins_job''' again. (does not still fixed in libIGCM_v1_1) * '''Error : Input files and BC for NEMO DO NOT EXIST (i.e. sst_data.nc, sss_data.nc, geothermal_heating.nc, bathy_level.nc, etc...)''' IGCM_sys_Get, ERROR : regular file ...../OCE/ORCA2_LIM/bathy_level.nc DOES NOT EXIST . To solve it:: In this moment we've still to download on gaya.idris.fr:~/!reee512/NEMO/ORCA2_LIM_nemo_v3.tar file, and to untar it into the directory: ${R_BC}/OCE/ORCA2_LIM and where ${R_BC} is a variable that can be changed in modipsl/config/ORCA2_LIM/IGCM00/config.card file. * '''Error : IGCM_debug_Exit : IGCM_config_Initialize Error !PeriodState : Fatal ''' To solve it:: change line in modipsl/config/ORCA2_LIM/IGCM00/run.card !PeriodState=Fatal [[BR]] in [[BR]] !PeriodState= or rm modipsl/config/ORCA2_LIM/IGCM00/run.card * '''Error : compiling ''' For compiling problem on mercure and platine use new mod.def, fldread.F90, fait_AA_make, BB_make [[BR]] [[BR]] == D - List of possible remarks and suggestions == [[BR]] * '''Every time that we change modipsl/config/ORCA2_LIM/IGCM00/config.card''' we have to cancel modipsl/config/ORCA2_LIM/IGCM00/run.card.init cancel modipsl/config/ORCA2_LIM/IGCM00/Job_''Name'' and run ./modipsl/util/ns_job script * '''To perform a second simulation after a run with !PeriodState=Fatal''' cancel modipsl/config/ORCA2_LIM/IGCM00/stack_error, modipsl/config/ORCA2_LIM/IGCM00/Script_Output_''!JobName'' but do not cancel modipsl/config/ORCA2_LIM/IGCM00/run.card.init file, if not run.card file is not re-created. ( File run.card.init il created with ins_job script ) * '''Does it exists a caption file for run.card.init options?''' In to run.card.init file who can we undesrtand syntax of? : !TimeSeriesRunning=n [[BR]] !TimeSeriesCompleted= [[BR]] !SeasonalRunning=n [[BR]] Is there a reference file? * '''test with trunk/libIGCM''' To use libIGCM trunk version it is necessary to add in config.card in POST Session: !RebuildFromArchive=false NOTE: We wait for !http://forge.ipsl.jussieu.fr/libigcm/browser/tags version 2 to do changes in config.card: !http://forge.ipsl.jussieu.fr/nemo/svn/branches/libIGCM/ORCA2_LIM/IGCM00/ * '''Change in nemo.card or in nemo.driver variable: ORCA_NPDT_JOUR and OPA_NPDT_JOURS''' * '''Have informations about mailing system for good jobs, on ccrt and idris''' [[BR]] [[BR]] == E - To do list == [[BR]] * run on CCRT machines (errors: config.card, in Job_NL1.e '''libIGCM/libIGCM_debug/libIGCM_debug.ksh: line 59: set: +A: invalid option''' # Declare a stack of functions calls # insert last argument of the Stack set +A IGCM_debug_Stack ${NULL_STR} set +A IGCM_debug_StackArgs ${NULL_STR} IGCM_debug_LenStack=0 ) * solve "test argument expected problem" * test mpi * test for Calendar Type, Output frequency and Restarts:[[BR]] Simulation duration = '''5 year ''' !PeriodLength = '''1Y''' timestep: rdt = '''5760''' equivalent to ORCA_NPDT_JOUR = '''15''' || || || '''Output Frequency''' || || || || '''5d''' || '''1M''' || '''1Y''' || || '''Calendar Type '''|| '''360d''' || ongoing || ongoing || to do || || '''Calendar Type '''|| '''365d''' || to do || to do || to do || || '''Calendar Type '''|| '''leap''' || to do || to do || to do || [[BR]] [[BR]] == F - Remember: files to change for NEMO == [[BR]] * '''fait_AA_make''' difference with the old one: in #- Compilation options --- echo '#-Q- sx8mercure F_O = -f2003 nocbind -size_t64 -dw -Wf\"-A dbl4\" -sx'''8''' -C vopt -Wf"-P nh" -Wf',-pvctl noassume loopcnt=10000 -L transform' -I $(MODDIR) -I $(MODDIR)/oce -I $(NCDF_INC)' ( old version: echo '#-Q- sx8mercure F_O = -f2003 nocbind '''noopt_ieee''' -size_t64 -dw -Wf\"-A dbl4\" -sx6 -C vopt -Wf"-P nh" -Wf',-pvctl noassume loopcnt=10000 -L transform' -I $(MODDIR) -I $(MODDIR)/oce -I $(NCDF_INC)' ) * '''BB_make''' * '''AA_job''' difference with the old one: [[BR]] #RESOL=$(cat ${SUBMIT_DIR}/../.resol) [[BR]] '''RESOL=''' * '''fldread.F90''' difference with the old one: [[BR]] in line 74 INTEGER jf, '''ji, jj''' ! dummy indices[[BR]] in line 94-99: '''DO jj = 1, jpj''' '''DO ji = 1, jpi''' '''sd(jf)%fdta(ji,jj,1) = sd(jf)%fdta(ji,jj,2)''' '''END DO''' '''END DO''' in lines 164-169: '''sd(jf)%fnow(:,:) = ztintb * sd(jf)%fdta(:,:,1) + ztinta * sd(jf)%fdta(:,:,2)''' [[BR]] '''DO jj = 1, jpj''' '''DO ji = 1, jpi''' '''sd(jf)%fnow(ji,jj) = ztintb * sd(jf)%fdta(ji,jj,1) + ztinta * sd(jf)%fdta(ji,jj,2)''' '''END DO'''[[BR]] '''END DO''' in lines 172-181: '''sd(jf)%fnow(:,:) = sd(jf)%fdta(:,:,2) ! piecewise constant field'''[[BR]] '''DO jj = 1, jpj''' '''DO ji = 1, jpi''' '''sd(jf)%fnow(ji,jj) = sd(jf)%fdta(ji,jj,2) ! piecewise constant field''' '''END DO''' '''END DO''' * '''mod.def''' difference with the old one: #-S- 10 svn co -r 47 !http://forge.ipsl.jussieu.fr/libigcm/svn [[BR]] #-H- NEMO_IGCM IOIPSL/src - svn - tag v2_1_'''4''' [[BR]] #-C- NEMO_IGCM IOIPSL/tags/v2_1_'''4'''/src HEAD 8 IOIPSL/src modeles [[BR]] #-C- NEMO_IGCM '''trunk'''/'''libIGCM''' '''47''' 10 libIGCM . [[BR]] #-C- NEMO_IGCM '''tags'''/'''nemo_v3_1_beta'''/NEMO HEAD 7 . modeles [[BR]] #-C- NEMO_IGCM '''tags'''/'''nemo_v3_1_beta'''/UTIL HEAD 7 . modeles [[BR]] #-C- NEMO_IGCM '''tags'''/'''nemo_v3_1_beta'''/CONFIG/GYRE_LOBSTER HEAD 7 GYRE_LOBSTER config [[BR]] #-C- NEMO_IGCM '''tags'''/'''nemo_v3_1_beta'''/CONFIG/ORCA2_LIM HEAD 7 ORCA2_LIM config [[BR]] #-C- NEMO_IGCM '''branches/libIGCM/ORCA2_LIM/IGCM00''' HEAD 7 IGCM00 config/ORCA2_LIM [[BR]] ( '''note: NEMO_IGCM branches/libIGCM/ORCA2_LIM/IGCM00 has to be the last one command, if not it is impossible to download in ORCA2_LIM directory; because it does not exists yet''') ( old version: #-S- 10 svn !http://forge.ipsl.jussieu.fr/libigcm/svn [[BR]] #-H- NEMO_IGCM IOIPSL/src - svn - tag v2_1_6 [[BR]] #-C- NEMO_IGCM IOIPSL/tags/v2_1_6/src HEAD 8 IOIPSL/src modeles [[BR]] #-C- NEMO_IGCM tags/libIGCM_v1_1 HEAD 10 libIGCM . [[BR]] #-C- NEMO_IGCM branches/libIGCM/ORCA2_LIM/IGCM00 HEAD 7 IGCM00 config/ORCA2_LIM [[BR]] #-C- NEMO_IGCM trunk/NEMO HEAD 7 . modeles [[BR]] #-C- NEMO_IGCM trunk/UTIL HEAD 7 . modeles [[BR]] #-C- NEMO_IGCM trunk/NVTK HEAD 7 . config [[BR]] #-C- NEMO_IGCM trunk/CONFIG/GYRE_LOBSTER HEAD 7 GYRE_LOBSTER config [[BR]] #-C- NEMO_IGCM trunk/CONFIG/ORCA2_LIM HEAD 7 ORCA2_LIM config [[BR]] ) [[BR]] [[BR]] Simona Flavoni last update: [[Timestamp]]