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Errors during building CESM1.0 MODEL On Linux-Intel Compiler.

D

dfeijat@126_com

Member
Dear ALL CESM1.0 USERS,
When I was buiding the CESM1.0 model, something happened.

The followings are some messages about the enviroment-settings I used and the errors happened to me.

The full Errors are listed in "Attach Files-errorMessages.txt "
Because of :"The text that you have entered is too long (16029 characters). Please shorten it to 10000 characters long."

Any hints are appreciated.

Best Regards,

ZhenCai DU
From
Center for Monsoon System Research（CMSR）,
Institute of Atmospheric Physics（IAP）,
Chinese Academy of Sciences（CAS）
http://cmsr.iap.ac.cn


-------------------------------------------------------------------------
[dzc@n000 ~]$ cat .cshrc
# .cshrc
# Source global definitions
if ( -f /etc/cshrc ) then
. /etc/cshrc
endif
setenv PBS /opt/gridview/pbs/dispatcher
setenv PATH $PBS/bin:$PATH
alias pbs 'pbsnodes -l free'

setenv GRADS /disk1/soft/grads
setenv PATH $GRADS/bin:${PATH}
setenv GADDIR /disk1/soft/grads/data
setenv GASCRP /disk1/soft/grads/lib
alias grads '/disk1/soft/grads/bin/gradsc'
setenv OMP_NUM_THREADS 1

source /disk1/software/intel/Compiler/11.1/l_cprof_p_11.1.059/bin/ifortvars.csh intel64
source /disk1/software/intel/Compiler/11.1/059/bin/iccvars.csh intel64
setenv MPICH_PATH /disk1/software/mvapich2-1.4-intel/
setenv INC_MPI ${MPICH_PATH}/include
setenv LIB_MPI ${MPICH_PATH}/lib
setenv MPI /disk1/software/mvapich2-1.4-intel/
setenv MPICH /disk1/software/mvapich2-1.4-intel/
setenv PATH $MPI/bin:$PATH

setenv NCARG_ROOT /disk1/dzc/tool/ncl
setenv PATH $NCARG_ROOT/bin:$PATH

setenv NETCDF /disk1/dzc/tool/netcdf_ifort
setenv NETCDF_PATH /disk1/dzc/tool/netcdf_ifort
setenv INC_NETCDF $NETCDF/include
setenv LIB_NETCDF $NETCDF/lib
setenv PATH $NETCDF/bin:$PATH

setenv BLAS /disk1/dzc/tool/blas
setenv LAPACK /disk1/dzc/tool/lapack
# setenv WRF_LIBS /disk1/dzc/tool/WPS_LIBS
# setenv JASPERLIB $WRF_LIBS/lib
# setenv JASPERINC $WRF_LIBS/include/jasper

limit stacksize unlimited
limit coredumpsize unlimited
limit memorylocked unlimited

setenv prompt [`id -nu`@`hostname -s`]$


setenv LD_LIBRARY_PATH /disk1/software/intel/Compiler/11.1/059/lib/intel64:${LIB_MPI}:${LIB_NETCDF}:${LD_LIBRARY_PATH}
setenv P4_GLOBMEMSIZE 500000000
setenv DIN_LOC_ROOT_CSMDATA /disk1/dzc/cesm/inputdata
setenv DIN_LOC_ROOT /disk1/dzc/cesm/inputdata
setenv CCSMROOT /disk1/dzc/cesm/cesm1_0
setenv CASEROOT /disk1/dzc/cesm/test
setenv EXEROOT /disk1/dzc/cesm/exeroot
setenv RUNDIR ${EXEROOT}/run
setenv COMPSET B_1850-2000_WACCM_CN
setenv RES 1.9x2.5_gx1v6
setenv MACH generic_linux_intel
setenv CASE ${CASEROOT}/casename
setenv max_tasks_per_node 8

-------------------------------------------------------------------------
[dzc@n000 testname]$ ./testname.generic_linux_intel.build
-------------------------------------------------------------------------
CCSM BUILDNML SCRIPT STARTING
- To prestage restarts, untar a restart.tar file into /disk1/dzc/cesm/test/testname/run
- Create modelio namelist input files
RESTART_FMT=bin
CCSM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
CCSM PRESTAGE SCRIPT STARTING
- CCSM input data directory, DIN_LOC_ROOT_CSMDATA, is /disk1/dzc/cesm/inputdata
- Case input data directory, DIN_LOC_ROOT, is /disk1/dzc/cesm/inputdata
- Checking the existence of input datasets in DIN_LOC_ROOT

The following files were not found, this is informational only
Input Data List Files Found:
/disk1/dzc/cesm/test/testname/Buildconf/clm.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/cam.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/cpl.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/pop2.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/cice.input_data_list
File status unknown: b40.1850.track1.2deg.wcm.007.clm2.r.0156-01-01-00000.nc
File status unknown: b40.1850.track1.2deg.wcm.007.cam2.i.0156-01-01-00000.nc

- Prestaging REFCASE (ccsm4_init/b40.1850.track1.2deg.wcm.007/0156-01-01) to /disk1/dzc/cesm/test/testname/run
CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
CCSM BUILDEXE SCRIPT STARTING
- Build Libraries: mct pio csm_share
Wed Sep 22 10:09:46 CST 2010 /disk1/dzc/cesm/test/testname/mct/mct.bldlog.100922-100926
Wed Sep 22 10:09:46 CST 2010 /disk1/dzc/cesm/test/testname/pio/pio.bldlog.100922-100926
Wed Sep 22 10:09:46 CST 2010 /disk1/dzc/cesm/test/testname/csm_share/csm_share.bldlog.100922-100926
Wed Sep 22 10:09:47 CST 2010 /disk1/dzc/cesm/test/testname/run/cpl.bldlog.100922-100926
Wed Sep 22 10:09:47 CST 2010 /disk1/dzc/cesm/test/testname/run/atm.bldlog.100922-100926
ERROR: cam.buildexe.csh failed, see /disk1/dzc/cesm/test/testname/run/atm.bldlog.100922-100926
ERROR: cat /disk1/dzc/cesm/test/testname/run/atm.bldlog.100922-100926
[dzc@n000 testname]$ cat /disk1/dzc/cesm/test/testname/run/atm.bldlog.100922-100926
Wed Sep 22 10:09:47 CST 2010 /disk1/dzc/cesm/test/testname/run/atm.bldlog.100922-100926
mpif90 -c -I. -I/disk1/dzc/tool/netcdf_ifort/include -I/disk1/dzc/tool/netcdf_ifort/include -I/disk1/software/mvapich2-1.4-intel//include -I. -I/disk1/dzc/cesm/test/testname/SourceMods/src.cam -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/chemistry/pp_waccm_mozart -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/chemistry/mozart -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/waccm -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/chemistry/bulk_aero -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/chemistry/utils -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/dynamics/fv -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/cpl_mct -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/control -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/utils -I/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/utils/pilgrim -I/disk1/dzc/cesm/test/testname/lib/include -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=144 -DPLAT=96 -DPLEV=66 -DPCNST=65 -DPCOLS=16 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DSPMD -DWACCM_MOZART -DWACCM_PHYS -DMCT_INTERFACE -DHAVE_MPI -DCO2A -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -132 -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 /disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(76): error #5082: Syntax error, found IDENTIFIER 'CALL' when expecting one of: ( * ) :: , ; + . - % (/ [ : ] /) . ' ** / ...
call addfld( 'ufrclcl_Cu' , 'fraction', 1 , 'A' , 'Cumulus fraction at LCL' , phys_decomp )
----^
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(91): error #5082: Syntax error, found IDENTIFIER 'CALL' when expecting one of: ( * ) :: , ; + . - % (/ [ : ] /) . ' ** / ...
call addfld( 'tkeavg_Cu' , 'm2/s2' , 1 , 'A' , 'Average tke within PBL for convection scheme' , phys_decomp )&
----^
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(92): error #5082: Syntax error, found IDENTIFIER 'CALL' when expecting one of: ( * ) :: , ; + . - % (/ [ : ] /) . ' ** / ...
call addfld( 'zinv_Cu' , 'm' , 1 , 'A' , 'PBL top height' , phys_decomp )
----^
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(92): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: :
call addfld( 'zinv_Cu' , 'm' , 1 , 'A' , 'PBL top height' , phys_decomp )
-----------------------------------------------------------------------------------------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(137): error #5082: Syntax error, found IDENTIFIER 'CALL' when expecting one of: ( * ) :: , ; + . - % (/ [ : ] /) . ' ** / ...
call addfld('exit_conden_Cu' , 'no' , 1 , 'A' , 'exit_conden' , phys_decomp )&
----^
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(138): error #5082: Syntax error, found IDENTIFIER 'CALL' when expecting one of: ( * ) :: , ; + . - % (/ [ : ] /) . ' ** / ...
call addfld('exit_klclmkx_Cu' , 'no' , 1 , 'A' , 'exit_klclmkx' , phys_decomp )&
----^
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90(139): error #5082: Syntax error, found IDENTIFIER 'CALL' when expecting one of: ( * ) :: , ; + . - % (/ [ : ] /) . ' ** / ...
call addfld('exit_klfcmkx_Cu' , 'no' , 1 , 'A' , 'exit_klfcmkx' , phys_decomp )&
----^
....................
----^
compilation aborted for /disk1/dzc/cesm/cesm1_0/models/atm/cam/src/physics/cam/uwshcu.F90 (code 1)
gmake: *** [uwshcu.o] Error 1
 
E

eaton

CSEG and Liaisons
Try editing the Macros.generic_linux_intel file to remove the option "-132" from the FFLAGS macro. That is, change

FFLAGS := $(CPPDEFS) -g -132 -fp-model precise -convert big_endian -assume byterecl -ftz -traceback

to

FFLAGS := $(CPPDEFS) -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback
 
D

dfeijat@126_com

Member
Dear eaton,
I edited the Macros.generic_linux_intel file as you told me.
However, there are still many warnings and errors happened.
I attached all the errors to ask you for you further help at your convenience.
Any advices are appreciated.

The attached file (2010Sep23.errors.txt) contains the following messages.
cat /disk1/dzc/cesm/test/testname/mct/mct.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/pio/pio.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/csm_share/csm_share.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/cpl.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/atm.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/lnd.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/ice.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/ocn.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/glc.bldlog.100923-195720
cat /disk1/dzc/cesm/test/testname/run/ccsm.bldlog.100923-195720

Some warnings and errors are listed in the following:
configure: WARNING: UNKNOWN FORTRAN 90 COMPILER
configure: WARNING: UNKNOWN FORTRAN 90 COMPILER
configure: WARNING: PNETCDF_PATH not found in environment, defaulting to /usr/local/pnetcdf
configure: WARNING: pnetcdf.inc not found in PNETCDF_PATH/include disabling pnetcdf support
configure: WARNING: libpnetcdf.a not found in PNETCDF_PATH/lib disabling pnetcdf support
....
piolib_mod.F90(400): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [IODESC]
subroutine PIO_initdecomp_dof_dof(iosystem,basepiotype,dims,compdof,iodesc,iodof)
----------------------------------------------------------------------^
piolib_mod.F90(365): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [IODESC]
....
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_BaseMod.F90(672): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [TYPE]
subroutine ESMF_AttributeGetbyNumber(anytype, number, name, type, value, rc)
------------------------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_BaseMod.F90(623): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [TYPE]
subroutine ESMF_AttributeGet(anytype, name, type, value, rc)
--------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_BaseMod.F90(699): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [NAMELIST]
subroutine ESMF_AttributeGetNameList(anytype, count, namelist, rc)
-----------------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_BaseMod.F90(672): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VALUE]
subroutine ESMF_AttributeGetbyNumber(anytype, number, name, type, value, rc)
------------------------------------------------------------------------^
....
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_TimeMod.F90(297): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [YRL]
subroutine ESMF_TimeGet(time, YY, YRl, MM, DD, D, Dl, H, M, S, Sl, MS, &
----------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_TimeMod.F90(297): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [D]
subroutine ESMF_TimeGet(time, YY, YRl, MM, DD, D, Dl, H, M, S, Sl, MS, &
-----------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_TimeMod.F90(297): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [DL]
subroutine ESMF_TimeGet(time, YY, YRl, MM, DD, D, Dl, H, M, S, Sl, MS, &
--------------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_TimeMod.F90(297): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [SL]
subroutine ESMF_TimeGet(time, YY, YRl, MM, DD, D, Dl, H, M, S, Sl, MS, &
---------------------------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_TimeMod.F90(298): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [US]
US, NS, d_, h_, m_, s_, ms_, us_, ns_, Sn, Sd, &
------------------------------^
.......
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_AlarmMod.F90(904): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [RINGINTERVAL]
subroutine ESMF_AlarmWrite(alarm, RingInterval, RingTime, &
----------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_AlarmMod.F90(904): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [RINGTIME]
subroutine ESMF_AlarmWrite(alarm, RingInterval, RingTime, &
------------------------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_AlarmMod.F90(905): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [PREVRINGTIME]
PrevRingTime, StopTime, Ringing, &
----------------------------^
....
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_ClockMod.F90(1111): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [TIMESTEP]
subroutine ESMF_ClockWrite(clock, TimeStep, StartTime, StopTime, &
----------------------------------------^
/disk1/dzc/cesm/cesm1_0/models/utils/esmf_wrf_timemgr/ESMF_ClockMod.F90(1111): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [STARTTIME]
subroutine ESMF_ClockWrite(clock, TimeStep, StartTime, StopTime, &
--------------------------------------------------^
....
/disk1/dzc/cesm/cesm1_0/models/utils/timing/gptl.c(2156): warning #167: argument of type "int (*)(const char **, const char **)" is incompatible with parameter of type "__compar_fn_t"
qsort( sort[t], count[t], sizeof(char*), cmp );
/disk1/dzc/cesm/cesm1_0/models/utils/timing/gptl.c(2195): warning #167: argument of type "int (*)(const char **, const char **)" is incompatible with parameter of type "__compar_fn_t"
qsort( newtimers, num_newtimers, sizeof(char*), ncmp ); /*sorts by memory address to restore original order*/
/disk1/dzc/cesm/cesm1_0/models/utils/timing/gptl.c(2216): warning #167: argument of type "int (*)(const char **, const char **)" is incompatible with parameter of type "__compar_fn_t"
qsort( sort[0], count[0], sizeof(char*), cmp );
........
/disk1/dzc/cesm/cesm1_0/models/utils/timing/gptl.c(2377): warning #167: argument of type "int (*)(const char **, const char **)" is incompatible with parameter of type "__compar_fn_t"
qsort( newtimers, num_newtimers, sizeof(char*), ncmp ); /*sorts by memory address to get original order */
^

/disk1/dzc/cesm/cesm1_0/models/utils/timing/gptl.c(2468): warning #1011: missing return statement at end of non-void function "ncmp"
}
^
...
/disk1/dzc/cesm/cesm1_0/models/atm/cam/src/control/wrap_mpi.F90(1232): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [WIN]
subroutine mpiwincreate(base,size,comm,win)
------------------------------------------^
.../disk1/dzc/cesm/cesm1_0/models/lnd/clm/src/main/ncdio.F90(5059): warning #6384: The INTEGER(KIND=4) value is out-of-range. [O'0777610000000000000000']
cols(:) = nan
---------------------^
/disk1/dzc/cesm/cesm1_0/models/lnd/clm/src/main/ncdio.F90(5060): warning #6384: The INTEGER(KIND=4) value is out-of-range. [O'0777610000000000000000']
data_offset = nan
---------------------^
.........



Best Reguards.

ZhenCai DU
from
cmsr.iap.ac.cn
2010Sep24.
 
D

dfeijat@126_com

Member
Dear eaton,

After ignoring the avbove warnings and errors, the "testname.generic_linux_intel.build" yeild the output file ccsm.exe.
However, when I "testname.generic_linux_intel.run" ccsm.exe manually such as following steps, it abort quikly.
I don't know what's going wrong with it.
Can you give me some advices?

Best Regards.
ZhenCai DU
from
cmsr.iap.cas.cn


manual runing steps:

[dzc@n000 testname]$ limit coredumpsize 1000000
[dzc@n000 testname]$ limit stacksize unlimited
[dzc@n000 testname]$ cd /disk1/dzc/cesm/test/testname
[dzc@n000 testname]$ ./Tools/ccsm_check_lockedfiles
[dzc@n000 testname]$ source ./Tools/ccsm_getenv
[dzc@n000 testname]$ setenv LBQUERY FALSE
[dzc@n000 testname]$ setenv LBSUBMIT FALSE
[dzc@n000 testname]$ setenv LID "`date +%y%m%d-%H%M%S`"
[dzc@n000 testname]$ env | egrep '(MP_|LOADL|XLS|FPE|DSM|OMP|MPC)'
OMP_NUM_THREADS=1
COMPSET=B_1850-2000_WACCM_CN
CCSM_COMPSET=B_1850-2000_WACCM_CN (B20TRWCN)
COMP_ATM=cam
COMP_LND=clm
COMP_ICE=cice
COMP_GLC=sglc
COMP_OCN=pop2
COMP_CPL=cpl
CCSM_LCOMPSET=B_1850-2000_WACCM_CN
CCSM_SCOMPSET=B20TRWCN
COMP_INTERFACE=MCT
BUILD_COMPLETE=TRUE
SMP_BUILD=a0l0i0o0g0c0
SMP_VALUE=a0l0i0o0g0c0
POP_DECOMPTYPE=cartesian
CICE_DECOMPTYPE=cartesian
POP_AUTO_DECOMP=true
CICE_AUTO_DECOMP=true
[dzc@n000 testname]$ cd $CASEROOT
[dzc@n000 testname]$ source $CASETOOLS/ccsm_buildnml.csh
-------------------------------------------------------------------------
CCSM BUILDNML SCRIPT STARTING
- To prestage restarts, untar a restart.tar file into /disk1/dzc/cesm/test/testname/run
- Create modelio namelist input files
RESTART_FMT=bin
CCSM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
[dzc@n000 run]$ cd $CASEROOT
[dzc@n000 testname]$ source $CASETOOLS/ccsm_prestage.csh
-------------------------------------------------------------------------
CCSM PRESTAGE SCRIPT STARTING
- CCSM input data directory, DIN_LOC_ROOT_CSMDATA, is /disk1/dzc/cesm/inputdata
- Case input data directory, DIN_LOC_ROOT, is /disk1/dzc/cesm/inputdata
- Checking the existence of input datasets in DIN_LOC_ROOT

The following files were not found, this is informational only
Input Data List Files Found:
/disk1/dzc/cesm/test/testname/Buildconf/clm.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/cam.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/cpl.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/pop2.input_data_list
/disk1/dzc/cesm/test/testname/Buildconf/cice.input_data_list

- Prestaging REFCASE (ccsm4_init/b40.1850.track1.2deg.wcm.007/0156-01-01) to /disk1/dzc/cesm/test/testname/run
CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
[dzc@n000 testname]$ if !(-d $RUNDIR/timing) mkdir $RUNDIR/timing
[dzc@n000 testname]$ if !(-d $RUNDIR/timing/checkpoints) mkdir $RUNDIR/timing/checkpoints
[dzc@n000 testname]$ rm -f $RUNDIR/timing/ccsm_timing*
rm: No match.
[dzc@n000 testname]$
[dzc@n000 testname]$ set sdate = `date +"%Y-%m-%d %H:%M:%S"`
[dzc@n000 testname]$ echo "run started $sdate" >>& $CASEROOT/CaseStatus
[dzc@n000 testname]$ sleep 25
[dzc@n000 testname]$ cd $RUNDIR
[dzc@n000 run]$ echo "`date` -- CSM EXECUTION BEGINS HERE"
Fri Sep 24 01:40:51 CST 2010 -- CSM EXECUTION BEGINS HERE
[dzc@n000 run]$ setenv OMP_NUM_THREADS 1
[dzc@n000 run]$ pwd
/disk1/dzc/cesm/test/testname/run
[dzc@n000 run]$ ll

-rw-r--r-- 1 dzc dzc 9523 Sep 24 01:39 atm_in
-rw-r--r-- 1 dzc dzc 155 Sep 24 01:39 atm_modelio.nml
-rw-r--r-- 1 dzc dzc 710979300 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.h0.0155-12.nc
-rw-r--r-- 1 dzc dzc 281835568 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.h1.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 1646580108 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.h2.0155-09-23-00000.nc
-rw-r--r-- 1 dzc dzc 22081768 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.h3.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 627700 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.h4.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 497297616 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.i.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 619875176 Sep 24 01:39 b40.1850.track1.2deg.wcm.007.cam2.r.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 281839716 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.cam2.rh1.0155-05-01-00000.nc
-rw-r--r-- 1 dzc dzc 149718200 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.cam2.rh2.0155-05-01-00000.nc
-rw-r--r-- 1 dzc dzc 6972540 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.cam2.rs.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 150407684 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.cice.r.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 26072408 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.clm2.h0.0155-12.nc
-rw-r--r-- 1 dzc dzc 738707 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.clm2.r.0156-01-01-00000
-rw-r--r-- 1 dzc dzc 137752176 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.clm2.r.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 99688836 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.cpl.r.0156-01-01-00000.nc
-rw-r--r-- 1 dzc dzc 603586560 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.pop.r.0156-01-01-00000
-rw-r--r-- 1 dzc dzc 12383 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.pop.r.0156-01-01-00000.hdr
-rw-r--r-- 1 dzc dzc 85217 Sep 24 01:40 b40.1850.track1.2deg.wcm.007.pop.ro.0156-01-01-00000
-rwxr-xr-x 1 dzc dzc 123700887 Sep 23 22:11 ccsm.exe
-rw-r--r-- 1 dzc dzc 155 Sep 24 01:39 cpl_modelio.nml
-rw-r--r-- 1 dzc dzc 126 Sep 24 01:39 drv_flds_in
-rw-r--r-- 1 dzc dzc 2530 Sep 24 01:39 drv_in
-rw-r--r-- 1 dzc dzc 155 Sep 24 01:39 glc_modelio.nml
-rw-r--r-- 1 dzc dzc 2332 Sep 24 01:39 ice_in
-rw-r--r-- 1 dzc dzc 155 Sep 24 01:39 ice_modelio.nml
-rw-r--r-- 1 dzc dzc 2967 Sep 24 01:39 lnd_in
-rw-r--r-- 1 dzc dzc 155 Sep 24 01:39 lnd_modelio.nml
-rw-r--r-- 1 dzc dzc 155 Sep 24 01:39 ocn_modelio.nml
-rw-r--r-- 1 dzc dzc 15449 Sep 24 01:39 pop2_in
-rw-r--r-- 1 dzc dzc 529 Sep 24 01:40 rpointer.atm
-rw-r--r-- 1 dzc dzc 257 Sep 24 01:40 rpointer.drv
-rw-r--r-- 1 dzc dzc 257 Sep 24 01:40 rpointer.ice
-rw-r--r-- 1 dzc dzc 257 Sep 24 01:40 rpointer.lnd
-rw-r--r-- 1 dzc dzc 55 Sep 24 01:40 rpointer.ocn.ovf
-rw-r--r-- 1 dzc dzc 70 Sep 24 01:40 rpointer.ocn.restart
-rw-r--r-- 1 dzc dzc 103 Sep 24 01:40 rpointer.ocn.tavg
-rw-r--r-- 1 dzc dzc 1864 Sep 24 01:39 seq_maps.rc
drwxr-xr-x 3 dzc dzc 4096 Sep 24 01:40 timing
[dzc@n000 run]$ which mpirun
/disk1/software/mvapich2-1.4-intel//bin/mpirun
[dzc@n000 run]$ mpirun -np 8 ./ccsm.exe
(seq_comm_setcomm) initialize ID ( 7 GLOBAL ) pelist = 0 7 1 ( npes = 8) ( nthreads = 1)
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fff5e1b2a84) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fff272bcb94) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fffa6d8f694) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fffa461bf14) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fff1eb52414) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fff1fcbe594) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fff1eb52414) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
Fatal error in MPI_Group_range_incl:
Invalid argument, error stack:
MPI_Group_range_incl(170).........: MPI_Group_range_incl(group=0x88000000, n=1, ranges=0xbd6aad0, new_group=0x7fff1488a294) failed
MPIR_Group_check_valid_ranges(302): The 0th element of a range array ends at 63 but must be nonnegative and less than 8
rank 7 in job 1 n000_34297 caused collective abort of all ranks
exit status of rank 7: killed by signal 9
rank 3 in job 1 n000_34297 caused collective abort of all ranks
exit status of rank 3: killed by signal 9
rank 2 in job 1 n000_34297 caused collective abort of all ranks
exit status of rank 2: killed by signal 9
rank 1 in job 1 n000_34297 caused collective abort of all ranks
exit status of rank 1: killed by signal 9
 
E

eaton

CSEG and Liaisons
It appears that the messages from the build are all warnings and not fatal errors. So I suspect that you build is OK.

The output from trying to run the model indicates that the job is dying because by default the CESM scripts are setting things up to run using 64 tasks, but only 8 tasks are available:

[dzc@n000 run]$ mpirun -np 8 ./ccsm.exe

The mpirun command needs to use the argument "-np 64". Or if 64 cores are not available on your system then you need to edit the env_mach_pes.xml file to use fewer tasks. See the cesm user guide for more info on this.
 
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