Fwd: some problems in configure the cam5

[lupeng2006@hotmail_com]

Dear all
I want to run the CAM5 in IBM aix
but when configure using run-ibm.csh* there are some thing wrong.
I attached the run-ibm.csh* in CAM3 which can run CAM3 in our computers
Who can help me change it to fit CAM5, thank you very much

#! /usr/bin/csh -f


#-----------------------------------------------------------------------
## IBM
##------------
##
## This is an example script to build and run the default CAM configuration
## on an IBM SP. The default configuration is T42L26, Eulerian dynamics,
## CLM2 land model, and CSIM4 ice model.
##
## Setting LoadLeveler options for batch queue submission.
## @ class is the queue in which to run the job.
## To see a list of available queues, type "llclass" interactively.
## @ node is the number of nodes. @tasks_per_node should be set to 1 because
## of the hybrid OpenMP/MPI configuration of CAM. The number of nodes should
## be a power of 2, up to a max of 16 for T42.
## @ output and @error are the names of file written to the directory from
## which the script is submitted containing STDOUT and STDERR respectively
## @ job_type = parallel declares that multiple nodes will be used.
## @ network.MPI: Has to do with network connection between nodes. Best to leave alone.
## @ node_usage = not_shared acquires dedicated access to nodes for the job.
## @ queue tells load leveler to submit the job

###@ class = normald
###@ node = 4
###@ tasks_per_node = 4
###@ output = out.$(jobid)
###@ error = err.$(jobid)
###@ job_type = parallel
###@ network.MPI = sn_all,shared,us
###@ node_usage = shared
###@ job_name = cam3_wm
###@ queue

## POE Environment. Set these for interactive jobs. They're ignored by LoadLeveler
## MP_NODES is the number of nodes. The number chosen should be a power of 2, up to a max of 16 for T42.
#setenv MP_NODES 2
#setenv MP_TASKS_PER_NODE 1
#setenv MP_EUILIB us
#setenv MP_RMPOOL 1
# TH: bug fix suggested by Brian Eaton 1/24/03
#unsetenv MP_PROCS

# must be set equal to (CPUs-per-node / tasks_per_node)
#setenv OMP_NUM_THREADS 4

## 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 for Q32
#setenv INC_NETCDF /opt/netcdf-3.5.1/include
#setenv LIB_NETCDF /opt/netcdf-3.5.1/lib
## netCDF stuff for Q64
setenv INC_NETCDF /u/student/soft/netcdf-3.5.1_64/include
setenv LIB_NETCDF /u/student/soft/netcdf-3.5.1_64/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 = /ngpfs/fs3/student/cam3

## 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 /ngpfs/fs3/student/cam3/inputdata

## 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 = test32
set runtype = initial
set nelapse = 150

## $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 = /ngpfs/fs3/student
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 /" || echo "build-namelist failed" && exit 1

$cfgdir/build-namelist -s -case $case -runtype $runtype
-namelist "&camexp nelapse=$nelapse /"
-namelist "&camexp archive_dir='$rundir' /"
-namelist "&camexp rest_pfile ='$rundir/cam2.rpointer' /"
-o $rundir/namelist
-infile $cfgdir/namelist_sst5120
|| echo "build-namelist failed" && exit 1


## Run BCCAM

cd $rundir || echo "cd $rundir failed" && exit 1
cp $camroot/models/atm/cam/bld/cam3.cmd .
# cp $CSMDATA/atm/cam2/inic/smmr_T42_asc.dat .
###
echo "running CAM3 in $rundir"

# poe $blddir/cam < namelist || echo "CAM run failed" && exit 1
# llsubmit cam3.cmd



exit 0

 

[lupeng2006@hotmail_com]

this is my change using CAM5 run-ibm.csh
but something is wrong
#! /usr/bin/csh -f

## extract number of tasks from batch environment
set ntasks = `4`

## should be set equal to (CPUs-per-node / tasks_per_node)
setenv OMP_NUM_THREADS 4

## suggestions from Jim Edwards 07/08
setenv XLSMPOPTS "stack=256000000"
setenv OMP_DYNAMIC false
setenv AIXTHREAD_SCOPE S
setenv MALLOCMULTIHEAP true
setenv MP_USE_BULK_XFER yes
setenv MP_LABELIO yes

## Do our best to get sufficient stack memory
limit stacksize unlimited

## netCDF stuff
setenv INC_NETCDF /u/student/soft/netcdf-3.5.1_64/include
setenv LIB_NETCDF /u/student/soft/netcdf-3.5.1_64/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 = /ngpfs/fs3/student/cesm

## 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 /ngpfs/fs3/student/cesm/inputdata

## LOGNAME - used in default settings, must be set if not available
## setenv LOGNAME
if !($?LOGNAME) then
echo "LOGNAME not available for setting of defaults - setting must be added to this script"
exit 1
endif

## Default namelist settings:
## $case is the case identifier for this run. It will be placed in the namelist.
## $runtype is the run type: startup, continue, or branch.
## $stop_n is the number of days to integrate (units depend on stop_option)
set case = camrun
set runtype = startup
set stop_n = 1

## $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 = /ngpfs/fs3/student
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 -dyn fv -hgrid 1.9x2.5 -spmd -smp -ntasks $ntasks -nthreads $OMP_NUM_THREADS || echo "configure failed" && exit 1
echo "building CAM in $blddir ..."
rm -f Depends
gmake -j8 >&! 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 $runtype
# -namelist "&camexp stop_option='ndays', stop_n=$stop_n /" || echo "build-namelist failed" && exit 1

$cfgdir/build-namelist -s -case $case -runtype $runtype
-namelist "&camexp nelapse=$nelapse /"
-namelist "&camexp archive_dir='$rundir' /"
-namelist "&camexp rest_pfile ='$rundir/cam2.rpointer' /"
-o $rundir/namelist
-infile $cfgdir/namelist_sst5120
|| echo "build-namelist failed" && exit 1


## Run CAM - use 'mpirun.lsf' on bluefire
cd $rundir || echo "cd $rundir failed" && exit 1
cp $camroot/models/atm/cam/bld/cam3.cmd .
# cp $CSMDATA/atm/cam2/inic/smmr_T42_asc.dat
echo "running CAM in $rundir"

#bluefire
#mpirun.lsf /usr/local/bin/hybrid_launch $blddir/cam || echo "CAM run failed" && exit 1

exit 0

 

[eaton]

Here are a few things I see that are wrong:

. set ntasks = `4` -- This will not set ntasks to 4. Remove the backticks which are telling the shell to execute the command 4. The system will respond with something like "4: Command not found."

. the build-namelist command should not have multiple -namelist arguments. Just use one and put all the namelist variables in it; like in the example.

. the build-namelist command is using an old argument, -o, which is no longer valid. See the user guide.

. the variables being set via the -namelist argument are no longer valid. See the namelist documentation.