sankal76@paran_com
New Member
Hi, All
I am trying to do a initial run using run-ibm.csh (CAM) and I have output file.
----------------------------------------------------------------
bld
camrun.cam2.h0.0000-09-01-00000.nc
camrun.clm2.h0.0000-09-01-00000.nc
core
namelist
--------------------------------------------------------------
but, this output file is broken. I don't open nc file. What's problem?
This is my run-ibm.csh file, log file and cam2.camrun.rpointer file
1) run-ibm.csh
-------------------------------------------------------------
#@ job_name = camrun
#@ job_type = parallel
#@ notification = complete
#@ notify_user = sankal76@paran.com
#@ class = large
#@ total_tasks = 2
#@ output = out.$(jobid)
#@ error = out.$(jobid)
#@ network.MPI = sn_single,shared,US,,instances=2
#@ blocking = unlimited
#@ rset = RSET_MCM_AFFINITY
#@ mcm_affinity_options = mcm_distribute mcm_sni_none
#@ resources = ConsumableCpus(1) ConsumableMemory(1500mb)
#@ wall_clock_limit = 08:00:00
#@ node_usage = shared
#@ queue
# must be set equal to (CPUs-per-node / tasks_per_node)
setenv OMP_NUM_THREADS 1
## suggestion from Jim Edwards to reintroduce XLSMPOPTS on 11/13/03
setenv XLSMPOPTS "stack=256000000"
setenv AIXTHREAD_SCOPE S
setenv MALLOCMULTIHEAP true
setenv OMP_DYNAMIC false
## Do our best to get sufficient stack memory
limit stacksize unlimited
## netCDF stuff
setenv INC_NETCDF /applic/local/include/NETCDF_64bit
setenv LIB_NETCDF /applic/local/lib
## ROOT OF CAM DISTRIBUTION - probably needs to be customized.
## Contains the source code for the CAM distribution.
## (the root directory contains the subdirectory "models")
set camroot = /gpfs1/sjkim/cam1
## ROOT OF CAM DATA DISTRIBUTION - needs to be customized unless running at NCAR.
## Contains the initial and boundary data for the CAM distribution.
## (the root directory contains the subdirectories "atm" and "lnd")
setenv CSMDATA /gpfs1/sjkim/CSMDATA
## Default namelist settings:
## $case is the case identifier for this run. It will be placed in the namelist.
## $runtype is the run type: initial, restart, or branch.
## $nelapse is the number of timesteps to integrate, or number of days if negative.
set case = camrun
set runtype = initial
set nelapse = -100
## $wrkdir is a working directory where the model will be built and run.
## $blddir is the directory where model will be compiled.
## $rundir is the directory where the model will be run.
## $cfgdir is the directory containing the CAM configuration scripts.
set wrkdir = /gpfs1/sjkim/cam
set blddir = $wrkdir/$case/bld
set rundir = $wrkdir/$case
set cfgdir = $camroot/models/atm/cam/bld
## Ensure that run and build directories exist
mkdir -p $rundir || echo "cannot create $rundir" && exit 1
mkdir -p $blddir || echo "cannot create $blddir" && exit 1
## If an executable doesn't exist, build one.
if ( ! -x $blddir/cam ) then
cd $blddir || echo "cd $blddir failed" && exit 1
$cfgdir/configure || echo "configure failed" && exit 1
echo "building CAM in $blddir ..."
rm -f Depends
gmake -j4 >&! MAKE.out || echo "CAM build failed: see $blddir/MAKE.out" && exit 1
endif
## Create the namelist
cd $blddir || echo "cd $blddir failed" && exit 1
$cfgdir/build-namelist -s -case $case -runtype $runtype -o $rundir/namelist
-namelist "&camexp nelapse=$nelapse mss_irt=0 nsrest=0 iradsw=-1 iradlw=-1 iradae=-12 itsst=72 nhtfrq=-24 nrefrq=0 dtime=1200 iyear_ad=1950 /" || echo "build-namelist failed" && exit 1
## Run CAM
cd $rundir || echo "cd $rundir failed" && exit 1
echo "running CAM in $rundir"
poe $blddir/cam < namelist || echo "CAM run failed" && exit 1
exit 0
--------------------------------------------------------------------------
2) log file
------------------------------------------------------------------------
creating /gpfs1/sjkim/cam/camrun/bld/Filepath
creating /gpfs1/sjkim/cam/camrun/bld/params.h
creating /gpfs1/sjkim/cam/camrun/bld/misc.h
creating /gpfs1/sjkim/cam/camrun/bld/preproc.h
creating /gpfs1/sjkim/cam/camrun/bld/Makefile
creating /gpfs1/sjkim/cam/camrun/bld/config_cache.xml
configure done.
building CAM in /gpfs1/sjkim/cam/camrun/bld ...
running CAM in /gpfs1/sjkim/cam/camrun
ATTENTION: 0031-408 2 tasks allocated by LoadLeveler, continuing...
t_setoption: option disabled: Usr Sys
t_setoption: option disabled: Usr Sys
2 pes participating in computation
-----------------------------------
NODE# NAME
0 gaia05
1 gaia05
------------------------------------------------------------
NCAR Community Atmospheric Model (CAM)
$Name: cam3_0_brnchT_release01 $
$Date: 2004/05/20 18:36:01 $
------------------------------------------------------------
(Online documentation is available on the CAM
home page: http://www.ccsm.ucar.edu/models/atm-cam/
License information is available as a link from above or from:
home page: http://www.ccsm.ucar.edu/models/atm-cam/license.html)
------------------------------------------------------------
DATE 10/22/08 TIME 17:06:03
------------------------------------------------------------
DYCORE is EUL
scon set to fixed value of 1367000.00000000000
Filename specifier for tape 1 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 2 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 3 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 4 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 5 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 6 = %c.cam2.h%t.%y-%m-%d-%s.nc
AEROSOL_SETOPTS: prognostic sulfur aerosols are off
AEROSOL_SETOPTS: feedback of prognostic sulfur aerosols is disabled
AEROSOL_SETOPTS: prognostic carbon aerosols are off
AEROSOL_SETOPTS: feedback of prognostic carbon aerosols is disabled
AEROSOL_SETOPTS: prognostic sea salt aerosols are off
AEROSOL_SETOPTS: feedback of prognostic sea salt aerosols is disabled
READ_NAMELIST:rest_pfile=
------------------------------------------
*** INPUT VARIABLES (CAMEXP) ***
------------------------------------------
Initial run
********** CASE = camrun **********
.....
.....
.....
COLDSST: encountered in cldfrc: 568 16 0.531001765219891730E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 319 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 319 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 569 16 0.533793285244801297E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 569 16 0.533793285244801297E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 320 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 320 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 570 16 0.539802977296172104E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 570 16 0.539802977296172104E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 571 16 0.540041210221462453E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 571 16 0.540041210221462453E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 572 16 0.543463327845589150E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 572 16 0.543463327845589150E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 573 16 0.551192877722568308E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 573 16 0.551192877722568308E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 574 16 0.563068038127461090E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 574 16 0.563068038127461090E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 575 16 0.567225335074252879E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 575 16 0.567225335074252879E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 576 16 0.583807210453221037E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 576 16 0.583807210453221037E-01 0.000000000000000000E+00
ERROR: 0031-250 task 0: Segmentation fault
ERROR: 0031-250 task 1: Segmentation fault
CAM run failed
--------------------------------------------------------------------------
3) cam2.camrun.rpointer
--------------------------------------------------------------------------
/R602KSJ/csm/camrun/atm/rest/camrun.cam2.r.0000-09-01-02400
# The following lists the other files needed for restarts (cam only reads the first line of this file).
# The files below refer to the files needed for the master restart file:/R602KSJ/csm/camrun/atm/rest/camrun.cam2.r.0000-09-01-02400
# /R602KSJ/csm/camrun/atm/rest/camrun.cam2.ra.0000-09-01-02400
# /R602KSJ/csm/camrun/atm/rest/camrun.cam2.rh0.0000-09-01-02400
------------------------------------------------------------------------
* How can I chang file path in cam2.camrun.rpointer file?
(ex. /R602KSJ/csm/camrun/atm/rest
I am trying to do a initial run using run-ibm.csh (CAM) and I have output file.
----------------------------------------------------------------
bld
camrun.cam2.h0.0000-09-01-00000.nc
camrun.clm2.h0.0000-09-01-00000.nc
core
namelist
--------------------------------------------------------------
but, this output file is broken. I don't open nc file. What's problem?
This is my run-ibm.csh file, log file and cam2.camrun.rpointer file
1) run-ibm.csh
-------------------------------------------------------------
#@ job_name = camrun
#@ job_type = parallel
#@ notification = complete
#@ notify_user = sankal76@paran.com
#@ class = large
#@ total_tasks = 2
#@ output = out.$(jobid)
#@ error = out.$(jobid)
#@ network.MPI = sn_single,shared,US,,instances=2
#@ blocking = unlimited
#@ rset = RSET_MCM_AFFINITY
#@ mcm_affinity_options = mcm_distribute mcm_sni_none
#@ resources = ConsumableCpus(1) ConsumableMemory(1500mb)
#@ wall_clock_limit = 08:00:00
#@ node_usage = shared
#@ queue
# must be set equal to (CPUs-per-node / tasks_per_node)
setenv OMP_NUM_THREADS 1
## suggestion from Jim Edwards to reintroduce XLSMPOPTS on 11/13/03
setenv XLSMPOPTS "stack=256000000"
setenv AIXTHREAD_SCOPE S
setenv MALLOCMULTIHEAP true
setenv OMP_DYNAMIC false
## Do our best to get sufficient stack memory
limit stacksize unlimited
## netCDF stuff
setenv INC_NETCDF /applic/local/include/NETCDF_64bit
setenv LIB_NETCDF /applic/local/lib
## ROOT OF CAM DISTRIBUTION - probably needs to be customized.
## Contains the source code for the CAM distribution.
## (the root directory contains the subdirectory "models")
set camroot = /gpfs1/sjkim/cam1
## ROOT OF CAM DATA DISTRIBUTION - needs to be customized unless running at NCAR.
## Contains the initial and boundary data for the CAM distribution.
## (the root directory contains the subdirectories "atm" and "lnd")
setenv CSMDATA /gpfs1/sjkim/CSMDATA
## Default namelist settings:
## $case is the case identifier for this run. It will be placed in the namelist.
## $runtype is the run type: initial, restart, or branch.
## $nelapse is the number of timesteps to integrate, or number of days if negative.
set case = camrun
set runtype = initial
set nelapse = -100
## $wrkdir is a working directory where the model will be built and run.
## $blddir is the directory where model will be compiled.
## $rundir is the directory where the model will be run.
## $cfgdir is the directory containing the CAM configuration scripts.
set wrkdir = /gpfs1/sjkim/cam
set blddir = $wrkdir/$case/bld
set rundir = $wrkdir/$case
set cfgdir = $camroot/models/atm/cam/bld
## Ensure that run and build directories exist
mkdir -p $rundir || echo "cannot create $rundir" && exit 1
mkdir -p $blddir || echo "cannot create $blddir" && exit 1
## If an executable doesn't exist, build one.
if ( ! -x $blddir/cam ) then
cd $blddir || echo "cd $blddir failed" && exit 1
$cfgdir/configure || echo "configure failed" && exit 1
echo "building CAM in $blddir ..."
rm -f Depends
gmake -j4 >&! MAKE.out || echo "CAM build failed: see $blddir/MAKE.out" && exit 1
endif
## Create the namelist
cd $blddir || echo "cd $blddir failed" && exit 1
$cfgdir/build-namelist -s -case $case -runtype $runtype -o $rundir/namelist
-namelist "&camexp nelapse=$nelapse mss_irt=0 nsrest=0 iradsw=-1 iradlw=-1 iradae=-12 itsst=72 nhtfrq=-24 nrefrq=0 dtime=1200 iyear_ad=1950 /" || echo "build-namelist failed" && exit 1
## Run CAM
cd $rundir || echo "cd $rundir failed" && exit 1
echo "running CAM in $rundir"
poe $blddir/cam < namelist || echo "CAM run failed" && exit 1
exit 0
--------------------------------------------------------------------------
2) log file
------------------------------------------------------------------------
creating /gpfs1/sjkim/cam/camrun/bld/Filepath
creating /gpfs1/sjkim/cam/camrun/bld/params.h
creating /gpfs1/sjkim/cam/camrun/bld/misc.h
creating /gpfs1/sjkim/cam/camrun/bld/preproc.h
creating /gpfs1/sjkim/cam/camrun/bld/Makefile
creating /gpfs1/sjkim/cam/camrun/bld/config_cache.xml
configure done.
building CAM in /gpfs1/sjkim/cam/camrun/bld ...
running CAM in /gpfs1/sjkim/cam/camrun
ATTENTION: 0031-408 2 tasks allocated by LoadLeveler, continuing...
t_setoption: option disabled: Usr Sys
t_setoption: option disabled: Usr Sys
2 pes participating in computation
-----------------------------------
NODE# NAME
0 gaia05
1 gaia05
------------------------------------------------------------
NCAR Community Atmospheric Model (CAM)
$Name: cam3_0_brnchT_release01 $
$Date: 2004/05/20 18:36:01 $
------------------------------------------------------------
(Online documentation is available on the CAM
home page: http://www.ccsm.ucar.edu/models/atm-cam/
License information is available as a link from above or from:
home page: http://www.ccsm.ucar.edu/models/atm-cam/license.html)
------------------------------------------------------------
DATE 10/22/08 TIME 17:06:03
------------------------------------------------------------
DYCORE is EUL
scon set to fixed value of 1367000.00000000000
Filename specifier for tape 1 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 2 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 3 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 4 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 5 = %c.cam2.h%t.%y-%m-%d-%s.nc
Filename specifier for tape 6 = %c.cam2.h%t.%y-%m-%d-%s.nc
AEROSOL_SETOPTS: prognostic sulfur aerosols are off
AEROSOL_SETOPTS: feedback of prognostic sulfur aerosols is disabled
AEROSOL_SETOPTS: prognostic carbon aerosols are off
AEROSOL_SETOPTS: feedback of prognostic carbon aerosols is disabled
AEROSOL_SETOPTS: prognostic sea salt aerosols are off
AEROSOL_SETOPTS: feedback of prognostic sea salt aerosols is disabled
READ_NAMELIST:rest_pfile=
------------------------------------------
*** INPUT VARIABLES (CAMEXP) ***
------------------------------------------
Initial run
********** CASE = camrun **********
.....
.....
.....
COLDSST: encountered in cldfrc: 568 16 0.531001765219891730E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 319 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 319 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 569 16 0.533793285244801297E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 569 16 0.533793285244801297E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 320 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 320 16 1.00000000000000000 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 570 16 0.539802977296172104E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 570 16 0.539802977296172104E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 571 16 0.540041210221462453E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 571 16 0.540041210221462453E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 572 16 0.543463327845589150E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 572 16 0.543463327845589150E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 573 16 0.551192877722568308E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 573 16 0.551192877722568308E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 574 16 0.563068038127461090E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 574 16 0.563068038127461090E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 575 16 0.567225335074252879E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 575 16 0.567225335074252879E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 576 16 0.583807210453221037E-01 0.000000000000000000E+00
COLDSST: encountered in cldfrc: 576 16 0.583807210453221037E-01 0.000000000000000000E+00
ERROR: 0031-250 task 0: Segmentation fault
ERROR: 0031-250 task 1: Segmentation fault
CAM run failed
--------------------------------------------------------------------------
3) cam2.camrun.rpointer
--------------------------------------------------------------------------
/R602KSJ/csm/camrun/atm/rest/camrun.cam2.r.0000-09-01-02400
# The following lists the other files needed for restarts (cam only reads the first line of this file).
# The files below refer to the files needed for the master restart file:/R602KSJ/csm/camrun/atm/rest/camrun.cam2.r.0000-09-01-02400
# /R602KSJ/csm/camrun/atm/rest/camrun.cam2.ra.0000-09-01-02400
# /R602KSJ/csm/camrun/atm/rest/camrun.cam2.rh0.0000-09-01-02400
------------------------------------------------------------------------
* How can I chang file path in cam2.camrun.rpointer file?
(ex. /R602KSJ/csm/camrun/atm/rest