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Problem with porting CESM 1.2.0 to a new machine

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yli_ouc@...
Problem with porting CESM 1.2.0 to a new machine

Hello everyone

I am trying to port CESM1.2.0 to a local cluster. The compiler is intel compiler and openmpi, with netcdf. I managed to create a new case with resolution f45_g37 and compset X, the build process was fine, too.

However, there were problems when I run *.submit, the log file says

===============================================

Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
-------------------------------------------------------------------------
CESM BUILDNML SCRIPT STARTING
- To prestage restarts, untar a restart.tar file into /public/home/test11/liyi/root_cesm/ccsmuser/test2/run
infile is /public/home/test11/liyi/root_cesm/case/test2/Buildconf/cplconf/cesm_namelist
CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
-------------------------------------------------------------------------
CESM PRESTAGE SCRIPT STARTING
- Case input data directory, DIN_LOC_ROOT, is /public/home/test11/liyi/cesm/inputdata
- Checking the existence of input datasets in DIN_LOC_ROOT
CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
Fri Jul 26 08:55:44 CST 2013 -- CSM EXECUTION BEGINS HERE
Fri Jul 26 08:55:44 CST 2013 -- CSM EXECUTION HAS FINISHED
ls: No match.
Model did not complete - no cesm.log file present - exiting

===============================================

I had mpirun & mpiexec checked (by compiling and running fhello_world_mpi.F90), they seem work fine.

 

Thank You

jedwards

Add a -x to the first line of your run script to get a little more detail in the output.  Are you sure that mpirun or mpiexec is in the path of your submitted job?

CESM Software Engineer

yli_ouc@...

jedwards,

I added -x as you suggested, the error messages seem to be unhelpful

==================================================

cd /public/home/test11/liyi/root_cesm/ccsmuser/test2/run

echo `date` -- CSM EXECUTION BEGINS HERE

date

Fri Jul 26 22:10:26 CST 2013 -- CSM EXECUTION BEGINS HERE

setenv OMP_NUM_THREADS 1

wait

echo `date` -- CSM EXECUTION HAS FINISHED

date

Fri Jul 26 22:10:26 CST 2013 -- CSM EXECUTION HAS FINISHED

set sdate = `date +"%Y-%m-%d %H:%M:%S"`

date +%Y-%m-%d %H:%M:%S

cd /public/home/test11/liyi/root_cesm/ccsmuser/test2/run

set CESMLogFile = `ls -1t cesm.log* | head -1`

head -1

ls: No match.

if ( ==  ) then

echo Model did not complete - no cesm.log file present - exiting

Model did not complete - no cesm.log file present - exiting

exit -1

============================================Any way to test weather mpirun/mpiexec is in the path of my job? I could run fhello_world_mpi.f90 successfully without specify the path of mpirun/mpiexec cause it's in the PATH environment Thank you
Attachment: 
jedwards

 

echo `date` -- CSM EXECUTION BEGINS HERE

date

Fri Jul 26 22:10:26 CST 2013 -- CSM EXECUTION BEGINS HERE

setenv OMP_NUM_THREADS 1

wait

echo `date` -- CSM EXECUTION HAS FINISHED

 

I don't see your mpirun or mpiexec command here - probably a mistake in your mkbatch script is preventing that section of code from being copied to the run script.   Make sure that any environment variables that you use in the mkbatch script are escaped so that they are not evaluated too early.   If this isn't making sense attach your mkbatch script and I'll have a look.  

 

CESM Software Engineer

fkc000@...

Hi jedwards,

    It seems that I have the same problem with yli_ouc, which also says "Model did not complete - no cesm.log file present - exiting". I guess it might also be the mkbatch problem. Actually I just copied the default mkbatch.userdefined file. Here's the log file of runnning ./test.submit and my mkbatch file if has any help.

Best regards

    

Attachment: 
jedwards

You need to edit that mkbatch file and uncomment the mpirun command appropriate for your environment.

CESM Software Engineer

fkc000@...

Thank you for your kindly reply. 

Yet another problem arised, "mpirun: Command not found". I've passed the "helloworld" test with the command "./mpirun -np 4 helloworld.o"  and feel confused. Any suggestions?

 

jedwards

The syntax ./mpirun suggests that the mpirun command was in your current directory when you ran the helloworld program.   You need the mpirun command to be in your path when you run cesm.  You can set the path in your default environment or in the env_mach_specific file. 

CESM Software Engineer

janezhang8587@...

Dear jedwards,

I also meet the same error. So I added the -x to the first line of your run script to get a little more detaile. Seeing the detailed output as follows, I still can not know how to settle.

 

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4

./Tools/ccsm_check_lockedfiles

source ./Tools/ccsm_getenv

./Tools/xml2env

if ( 0 != 0 ) then

foreach i ( env_case.xml env_run.xml env_conf.xml env_build.xml env_mach_pes.xml )

source env_case

setenv CASE testX4

setenv CASEROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4

setenv CCSMROOT /lustre/baijingjing/Cesm/cesm1_0_4

setenv GRID 4x5_gx3v7

setenv CCSM_COMPSET X_PRESENT_DAY (X)

setenv MACH mach_a

setenv PTS_MODE FALSE

setenv CCSMUSER baijingjing

setenv CASETOOLS /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Tools

setenv CASEBUILD /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf

setenv SCRIPTSROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts

setenv UTILROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/ccsm_utils

setenv BLDROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/ccsm_utils/Build

setenv CODEROOT /lustre/baijingjing/Cesm/cesm1_0_4/models

setenv SHAREROOT /lustre/baijingjing/Cesm/cesm1_0_4/models/csm_share

setenv COMP_ATM xatm

setenv COMP_LND xlnd

setenv COMP_ICE xice

setenv COMP_GLC xglc

setenv COMP_OCN xocn

setenv COMP_CPL cpl

setenv ATM_GRID 4x5

setenv LND_GRID 4x5

setenv OCN_GRID gx3v7

setenv ICE_GRID gx3v7

setenv ATM_NX 72

setenv ATM_NY 46

setenv LND_NX 72

setenv LND_NY 46

setenv GLC_NX 72

setenv GLC_NY 46

setenv ICE_NX 100

setenv ICE_NY 116

setenv OCN_NX 100

setenv OCN_NY 116

setenv OS Linux

setenv CCSM_LCOMPSET X_PRESENT_DAY

setenv CCSM_SCOMPSET X

setenv CCSM_CCOST -6

setenv CCSM_GCOST -1

setenv CCSM_MCOST 0

setenv XMLMODE normal

if ( 0 != 0 ) then

rm env_case

if ( 0 != 0 ) then

end

source env_run

setenv CONTINUE_RUN FALSE

setenv RESUBMIT 0

setenv CCSM_REPOTAG cesm1_0_4

setenv CASESTR UNSET

setenv STOP_OPTION ndays

setenv STOP_N 5

setenv STOP_DATE -999

setenv REST_OPTION ndays

setenv REST_N 5

setenv REST_DATE -999

setenv PIO_ASYNC_INTERFACE FALSE

setenv PIO_STRIDE -1

setenv PIO_ROOT 1

setenv PIO_NUMTASKS -1

setenv PIO_TYPENAME netcdf

setenv PIO_DEBUG_LEVEL 0

setenv OCN_PIO_STRIDE -99

setenv OCN_PIO_ROOT 0

setenv OCN_PIO_NUMTASKS 1

setenv OCN_PIO_TYPENAME nothing

setenv LND_PIO_STRIDE -99

setenv LND_PIO_ROOT -99

setenv LND_PIO_NUMTASKS -99

setenv LND_PIO_TYPENAME nothing

setenv ICE_PIO_STRIDE -99

setenv ICE_PIO_ROOT -99

setenv ICE_PIO_NUMTASKS -99

setenv ICE_PIO_TYPENAME nothing

setenv ATM_PIO_STRIDE -99

setenv ATM_PIO_ROOT -99

setenv ATM_PIO_NUMTASKS -99

setenv ATM_PIO_TYPENAME nothing

setenv CPL_PIO_STRIDE -99

setenv CPL_PIO_ROOT -99

setenv CPL_PIO_NUMTASKS -99

setenv CPL_PIO_TYPENAME nothing

setenv GLC_PIO_STRIDE -99

setenv GLC_PIO_ROOT -99

setenv GLC_PIO_NUMTASKS -99

setenv GLC_PIO_TYPENAME nothing

setenv CALENDAR NO_LEAP

setenv START_TOD 0

setenv BUDGETS FALSE

setenv DRV_THREADING FALSE

setenv BFBFLAG FALSE

setenv CHECK_TIMING TRUE

setenv SAVE_TIMING FALSE

setenv INFO_DBUG 1

setenv TIMING_BARRIER FALSE

setenv TIMER_LEVEL 4

setenv COMP_RUN_BARRIERS FALSE

setenv ORBITAL_MODE fixed_year

setenv ORBITAL_YEAR 1990

setenv ORBITAL_YEAR_ALIGN 1990

setenv EPS_FRAC 1.0e-02

setenv EPS_AMASK 1.0e-13

setenv EPS_AGRID 1.0e-12

setenv EPS_AAREA 9.0e-07

setenv EPS_OMASK 1.0e-06

setenv EPS_OGRID 1.0e-02

setenv EPS_OAREA 1.0e-01

setenv SHR_MAP_DOPOLE TRUE

setenv VECT_MAP npfix

setenv AOFLUX_GRID ocn

setenv TPROF_OPTION never

setenv TPROF_N -999

setenv TPROF_DATE -999

setenv AVGHIST_OPTION never

setenv AVGHIST_N -999

setenv AVGHIST_DATE -999

setenv HISTINIT FALSE

setenv HIST_OPTION never

setenv HIST_N -999

setenv HIST_DATE -999

setenv BUDGET_INST 0

setenv BUDGET_DAILY 0

setenv BUDGET_MONTHLY 1

setenv BUDGET_ANNUAL 1

setenv BUDGET_LONGTERM_EOY 1

setenv BUDGET_LONGTERM_STOP 0

setenv OCN_TIGHT_COUPLING FALSE

setenv BATCHQUERY /opt/tsce/share/bin/qstat

setenv BATCHSUBMIT /opt/tsce/share/bin/qsub

setenv DIN_LOC_ROOT_CSMDATA /lustre/baijingjing/Cesm/inputdata

setenv DIN_LOC_ROOT_CLMQIAN /lustre/baijingjing/Cesm/inputdata/atm/datm7/atm_forcing.datm7.Qian.T62.c080727

setenv DIN_LOC_ROOT /lustre/baijingjing/Cesm/inputdata

setenv LOGDIR /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/logs

setenv DOUT_S TRUE

setenv DOUT_S_ROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/archive/testX4

setenv DOUT_S_SAVE_INT_REST_FILES FALSE

setenv DOUT_L_MS FALSE

setenv DOUT_L_MSROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/archive/csm/testX4

setenv DOUT_L_HPSS_ACCNT 00000000

setenv DOUT_L_HTAR FALSE

setenv CCSM_BASELINE /lustre/baijingjing/Cesm/cesm1_0_4/scripts/baselines

setenv CCSM_CPRNC /lustre/baijingjing/Cesm/cesm1_0_4/scripts/tools/cprnc/cprnc

setenv OCN_TAVG_TRACER_BUDGET FALSE

setenv OCN_TAVG_HIFREQ FALSE

if ( 0 != 0 ) then

rm env_run

if ( 0 != 0 ) then

end

source env_conf

setenv RUN_TYPE startup

setenv RUN_STARTDATE 0001-01-01

setenv RUN_REFCASE case.std

setenv RUN_REFDATE 0001-01-01

setenv BRNCH_RETAIN_CASENAME FALSE

setenv GET_REFCASE FALSE

setenv USE_MPISERIAL FALSE

setenv MPISERIAL_SUPPORT TRUE

setenv ATM_NCPL 48

setenv LND_NCPL 48

setenv ICE_NCPL 48

setenv OCN_NCPL 1

setenv GLC_NCPL 1

setenv MAP_A2OF_FILE map_fv4x5_to_gx3v7_aave_da_091218.nc

setenv MAP_A2OS_FILE map_fv4x5_to_gx3v7_bilin_da_091218.nc

setenv MAP_O2AF_FILE map_gx3v7_to_fv4x5_aave_da_091218.nc

setenv MAP_O2AS_FILE map_gx3v7_to_fv4x5_aave_da_091218.nc

setenv MAP_A2LF_FILE idmap

setenv MAP_A2LS_FILE idmap

setenv MAP_L2AF_FILE idmap

setenv MAP_L2AS_FILE idmap

setenv MAP_R2O_FILE_R05 map_r05_to_gx3v5_e2000r500_040209.nc

setenv MAP_R2O_FILE_R19 UNSET

setenv MAP_R2O_FILE_RX1 map_rx1_to_gx3v5_e1000r500_090319.nc

setenv CPL_EPBAL off

setenv CPL_ALBAV false

setenv CCSM_BGC none

setenv CCSM_VOC FALSE

setenv CCSM_CO2_PPMV 379.000

if ( 0 != 0 ) then

rm env_conf

if ( 0 != 0 ) then

end

source env_build

setenv EXEROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4

setenv COMP_INTERFACE MCT

setenv ESMF_LIBDIR

setenv USE_ESMF_LIB FALSE

setenv DEBUG FALSE

setenv BUILD_THREADED FALSE

setenv PIO_CONFIG_OPTS  --disable-mct --disable-timing 

setenv GLC_NEC 10

setenv GMAKE gmake

setenv GMAKE_J 8

setenv RUNDIR /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

setenv OBJROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4

setenv LIBROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib

setenv INCROOT /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib/include

setenv BUILD_COMPLETE TRUE

setenv SMP_BUILD a0l0i0o0g0c0

setenv SMP_VALUE a0l0i0o0g0c0

setenv BUILD_STATUS 0

if ( 0 != 0 ) then

rm env_build

if ( 0 != 0 ) then

end

source env_mach_pes

setenv NTASKS_ATM 16

setenv NTHRDS_ATM 1

setenv ROOTPE_ATM 0

setenv NTASKS_LND 16

setenv NTHRDS_LND 1

setenv ROOTPE_LND 0

setenv NTASKS_ICE 16

setenv NTHRDS_ICE 1

setenv ROOTPE_ICE 0

setenv NTASKS_OCN 16

setenv NTHRDS_OCN 1

setenv ROOTPE_OCN 0

setenv NTASKS_CPL 16

setenv NTHRDS_CPL 1

setenv ROOTPE_CPL 0

setenv NTASKS_GLC 16

setenv NTHRDS_GLC 1

setenv ROOTPE_GLC 0

setenv PSTRID_ATM 1

setenv PSTRID_LND 1

setenv PSTRID_ICE 1

setenv PSTRID_OCN 1

setenv PSTRID_CPL 1

setenv PSTRID_GLC 1

setenv TOTALPES 16

setenv PES_LEVEL 1c

setenv MAX_TASKS_PER_NODE 24

setenv PES_PER_NODE 24

setenv BATCH_PES 0

setenv CCSM_PCOST 1

setenv CCSM_TCOST 0

setenv CCSM_ESTCOST -6

if ( 0 != 0 ) then

rm env_mach_pes

if ( 0 != 0 ) then

end

if ( -f env_mach_specific ) source env_mach_specific

source env_mach_specific

setenv NETCDF_PATH /lustre/baijingjing/program/netcdf4.1.3

setenv INC_NETCDF /lustre/baijingjing/program/netcdf4.1.3/include

setenv LIB_NETCDF /lustre/baijingjing/program/netcdf4.1.3/lib

setenv MOD_NETCDF /lustre/baijingjing/program/netcdf4.1.3/include

setenv MPICH_PATH /lustre/baijingjing/program/mpich2

setenv INC_MPI /lustre/baijingjing/program/mpich2/include

setenv LIB_MPI /lustre/baijingjing/program/mpich2/lib

if ( FALSE == FALSE ) then

endif

setenv INTEL /opt/intel

setenv PATH /opt/intel/composer_xe_2013.3.163/bin:/opt/intel/composer_xe_2013.3.163/bin/intel64:/opt/intel/composer_xe_2013.3.163/bin/intel64_mic:/opt/intel/composer_xe_2013.3.163/mpirt/bin:/lustre/baijingjing/program/pnetcdf/bin:/lustre/baijingjing/program/netcdf4.1.3/bin:/lustre/baijingjing/program/hdf5/bin:/lustre/baijingjing/program/mpich2/bin:/opt/intel/composer_xe_2013.3.163/bin/intel64:/opt/intel/composer_xe_2013.3.163/bin/intel64:/opt/intel/composer_xe_2013.3.163/mpirt/bin/intel64:/opt/intel/composer_xe_2013.3.163/bin/intel64:/opt/intel/composer_xe_2013.3.163/bin/intel64_mic:/opt/intel/composer_xe_2013.3.163/debugger/gui/intel64:/usr/local/maui/sbin:/usr/local/maui/bin:/opt/tsce/share/bin:/opt/tsce/share/sbin:/opt/tsce/share/jdk1.6.0_10/bin:/opt/tsce/share/jdk1.6.0_10/jre/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:.:/lustre/baijingjing/bin

setenv LD_LIBRARY_PATH /opt/intel/composer_xe_2013.3.163/mpirt/lib:/opt/intel/composer_xe_2013.3.163/compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/compiler/mic:/opt/intel/composer_xe_2013.3.163/mkl/lib/intel64:/opt/intel/composer_xe_2013.3.163/mkl/lib/mic:/lustre/baijingjing/program/mpich2/lib:/opt/intel/composer_xe_2013.3.163/compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/mpirt/lib/intel64:/opt/intel/composer_xe_2013.3.163/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/ipp/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/opt/intel/composer_xe_2013.3.163/compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/mkl/lib/intel64:/opt/intel/composer_xe_2013.3.163/tbb/lib/intel64/gcc4.4

setenv P4_GLOBMEMSIZE 1000000000

set fname = env_derived

cat

source env_derived

set MODELS = ( cpl atm lnd ice ocn glc )

set COMPONENTS = ( cpl xatm xlnd xice xocn xglc )

set NTASKS = ( 16 16 16 16 16 16 )

set NTHRDS = ( 1 1 1 1 1 1 )

set ROOTPE = ( 0 0 0 0 0 0 )

set PSTRID = ( 1 1 1 1 1 1 )

cp -f env_derived LockedFiles/env_derived.locked

if ( TRUE != TRUE ) then

setenv LBQUERY TRUE

setenv LBSUBMIT TRUE

setenv LID `date +%y%m%d-%H%M%S`

date +%y%m%d-%H%M%S

env

egrep (MP_|LOADL|XLS|FPE|DSM|OMP|MPC)

CCSM_COMPSET=X_PRESENT_DAY (X)

COMP_ATM=xatm

COMP_LND=xlnd

COMP_ICE=xice

COMP_GLC=xglc

COMP_OCN=xocn

COMP_CPL=cpl

CCSM_LCOMPSET=X_PRESENT_DAY

CCSM_SCOMPSET=X

COMP_RUN_BARRIERS=FALSE

COMP_INTERFACE=MCT

BUILD_COMPLETE=TRUE

SMP_BUILD=a0l0i0o0g0c0

SMP_VALUE=a0l0i0o0g0c0

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4

source /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Tools/ccsm_buildnml.csh

echo -------------------------------------------------------------------------

-------------------------------------------------------------------------

set buildnml = TRUE

if ( 0 ) then

echo  CCSM BUILDNML SCRIPT STARTING

 CCSM BUILDNML SCRIPT STARTING

echo  - To prestage restarts, untar a restart.tar file into /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

 - To prestage restarts, untar a restart.tar file into /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

foreach DIR ( /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4 /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib/include /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4 /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run )

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4 ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4

end

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib

end

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib/include ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lib/include

end

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4 ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4

end

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

end

set rundir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

set docdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs ) then

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4

setenv COMPLIBS 

@ n = 0

foreach model ( cpl atm lnd ice ocn glc )

@ n = 0 + 1

set comp = cpl

set objdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl/obj

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl/obj ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl/obj

set libdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/cpl

/lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf/cpl.buildnml.csh

 - Create modelio namelist input files

if ( 0 != 0 ) then

end

@ n = 1 + 1

set comp = xatm

set objdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm/obj

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm/obj ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm/obj

set libdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/atm

/lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf/xatm.buildnml.csh

if ( 0 != 0 ) then

end

@ n = 2 + 1

set comp = xlnd

set objdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd/obj

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd/obj ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd/obj

set libdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/lnd

/lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf/xlnd.buildnml.csh

if ( 0 != 0 ) then

end

@ n = 3 + 1

set comp = xice

set objdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice/obj

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice/obj ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice/obj

set libdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ice

/lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf/xice.buildnml.csh

if ( 0 != 0 ) then

end

@ n = 4 + 1

set comp = xocn

set objdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn/obj

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn/obj ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn/obj

set libdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/ocn

/lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf/xocn.buildnml.csh

if ( 0 != 0 ) then

end

@ n = 5 + 1

set comp = xglc

set objdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc/obj

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc/obj ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc/obj

set libdir = /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc

if ! ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc ) mkdir -p /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/glc

/lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Buildconf/xglc.buildnml.csh

if ( 0 != 0 ) then

end

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

chmod +w /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/drv_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/README /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/seq_maps.rc /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xatm_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xglc_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xice_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xlnd_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xocn_in

cp -p drv_in xatm_in xglc_in xice_in xlnd_in xocn_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/

cp -p seq_maps.rc /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/

chmod 444 /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/drv_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/README /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/seq_maps.rc /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xatm_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xglc_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xice_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xlnd_in /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/CaseDocs/xocn_in

echo  CCSM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY

 CCSM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4

source /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4/Tools/ccsm_prestage.csh

if ( 0 ) then

echo -------------------------------------------------------------------------

-------------------------------------------------------------------------

echo  CCSM PRESTAGE SCRIPT STARTING

 CCSM PRESTAGE SCRIPT STARTING

echo  - CCSM input data directory, DIN_LOC_ROOT_CSMDATA, is /lustre/baijingjing/Cesm/inputdata

 - CCSM input data directory, DIN_LOC_ROOT_CSMDATA, is /lustre/baijingjing/Cesm/inputdata

echo  - Case input data directory, DIN_LOC_ROOT, is /lustre/baijingjing/Cesm/inputdata

 - Case input data directory, DIN_LOC_ROOT, is /lustre/baijingjing/Cesm/inputdata

echo  - Checking the existence of input datasets in DIN_LOC_ROOT

 - Checking the existence of input datasets in DIN_LOC_ROOT

if ! ( -d /lustre/baijingjing/Cesm/inputdata ) then

if ( `./check_input_data -inputdata $DIN_LOC_ROOT -check | grep "unknown" | wc -l` > 0 ) then

./check_input_data -inputdata /lustre/baijingjing/Cesm/inputdata -check

wc -l

grep unknown

if ( `./check_input_data -inputdata $DIN_LOC_ROOT -check | grep "missing" | wc -l` > 0 ) then

./check_input_data -inputdata /lustre/baijingjing/Cesm/inputdata -check

wc -l

grep missing

if ( `./check_input_data -inputdata $DIN_LOC_ROOT -check | grep "missing" | wc -l` > 0 ) then

./check_input_data -inputdata /lustre/baijingjing/Cesm/inputdata -check

wc -l

grep missing

if ( ( FALSE == TRUE ) && ( startup != startup ) && ( FALSE == FALSE ) ) then

echo  CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY

 CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY

if ( -d /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run/timing ) rm -r -f /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run/timing

rm -r -f /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run/timing

mkdir /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run/timing

mkdir /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run/timing/checkpoints

set sdate = `date +"%Y-%m-%d %H:%M:%S"`

date +%Y-%m-%d %H:%M:%S

echo run started 2015-05-14 21:06:14

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/exe/testX4/run

echo `date` -- CSM EXECUTION BEGINS HERE

date

Thu May 14 21:06:14 CST 2015 -- CSM EXECUTION BEGINS HERE

setenv OMP_NUM_THREADS 1

if ( FALSE == FALSE ) then

mpirun -np 16 ./ccsm.exe

else

wait

echo `date` -- CSM EXECUTION HAS FINISHED

date

Thu May 14 21:06:14 CST 2015 -- CSM EXECUTION HAS FINISHED

cd /lustre/baijingjing/Cesm/cesm1_0_4/scripts/testX4

./Tools/ccsm_postrun.csh

-----------------01

ls: No match.

Model did not complete - no cpl.log file present - exiting

exit 1

 

 

 

jedwards

I don't see any error in this output.   Do you have stdout and stderr?   If there is no cpl log written then the model never started and the error is probably in your mkbatch set up.  

Have you tried to run an mpi hello world program?   After you successfully run the hello world program from the command line, try running it from the mkbatch -

replace the cesm.exe in mkbatch with hello world and run an X case - does that work? 

CESM Software Engineer

yli_ouc@...

Hi jedwards,

I find I failed to specify mpirun in the mkbatch file, the compset X case finished successly.

Thank you

jhhan@...

Dear All,

Hello, everyone.

I have also same problems.

I tried all of methods that you guys comments on above to solve the problems.

but, it still say "Model did not complete - no cesm.log file present - exiting".

I also want test "Hello world MPI" for test of MPI run. 

I tried "Hello world MPI" from the manual in a webpage. But, it was not working.

Unfortunately, I'm beginner of both linux and cesm.

So, please, tell me the method for cheking of MPI run step by step ?

Thank you everyone!  

 

J. Han

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