[cam-users] CGD Forums

Tue Nov 16 09:00:00 MST 2004

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<<  How to get heating variable in CCM3?, http://bb.cgd.ucar.edu//viewtopic.php?t=62 >>

PosterjmccaaPostedMon Nov 15, 2004 6:58 pm MST, http://bb.cgd.ucar.edu//viewtopic.php?p=195#195
Message: 
 1) there may be a term associated with the conversion from kinetic energy dissipation to thermal energy that is not reflected in the above equation.
 
 
 The heating due to kinetic energy dissipation in the solution for vertical diffusion is included in the DTV term, so should not be a problem. I don't know if a dissipation heating term appears elsewhere in the model.
 
 Jim

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<<  how to resubmit the job automatically, http://bb.cgd.ucar.edu//viewtopic.php?t=51 >>

Postertz0616PostedTue Nov 16, 2004 12:15 am MST, http://bb.cgd.ucar.edu//viewtopic.php?p=196#196
Message: Thanks for your reply. My original "run-cam.csh" file is listed below.
 Hope to hear from you, thanks.
 
 
 
 #! /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 wr!
itten 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 = com_reg
 #@ account_no = XXXXXX
 #@ node = 2
 #@ tasks_per_node = 1
 #@ output = out.$(jobid)
 #@ error = out.$(jobid)
 #@ job_type = parallel
 #@ network.MPI = csss,not_shared,us
 #@ node_usage = not_shared
 #@ wall_clock_limit = 21600
 #@ 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 o!

<br />f 16 for T42.
<br />setenv MP_NODES 2
<br />setenv MP_!
 TASKS_PE
R_NODE 1
<br />setenv MP_EUILIB us
<br />setenv MP_RMPOOL 1
<br /># TH:  bug fix suggested by Brian Eaton  1/24/03
<br />unsetenv MP_PROCS
<br />
<br /># must be set equal to (CPUs-per-node / tasks_per_node)
<br />setenv OMP_NUM_THREADS 4
<br />
<br />## suggestion from Jim Edwards to reintroduce XLSMPOPTS on 11/13/03
<br />setenv XLSMPOPTS "stack=256000000"
<br />setenv AIXTHREAD_SCOPE S
<br />setenv MALLOCMULTIHEAP true
<br />setenv OMP_DYNAMIC false
<br />## Do our best to get sufficient stack memory
<br />limit stacksize unlimited
<br />
<br />## netCDF stuff
<br />setenv INC_NETCDF /usr/local/include
<br />setenv LIB_NETCDF /usr/local/lib64/r4i4
<br />
<br />## ROOT OF CAM DISTRIBUTION - probably needs to be customized.
<br />## Contains the source code for the CAM distribution.
<br />## (the root directory contains the subdirectory "models")
<br />#set camroot      = /fs/cgd/data0/$LOGNAME/cam2_0
<br />set camroot      = /home/blackforest/taoz/cam3.0/cam1
<br />
<br />!
## ROOT OF CAM DATA DISTRIBUTION - needs to be customized unless running at NCAR.
<br />## Contains the initial and boundary data for the CAM distribution.
<br />## (the root directory contains the subdirectories "atm" and "lnd")
<br />#setenv CSMDATA    /fs/cgd/csm/inputdata
<br />setenv CSMDATA    /home/blackforest/taoz/cam3.0/inputdata
<br />
<br />## Set compile options
<br /># $dycore is the dynamical core: sld, eul, or fv.
<br /># $resolution: for sld or eul: 128x256, 64x128,32x64,or 8x16; for fv: 2x2.5, 4x5, or 10x15
<br /># $usr_src specifies location of user-modified files: 'none', or valid directory.
<br /># $caseid if for notes to myself - keep it short!!!
<br />#set dycore       = sld
<br />#set dycore       = fv
<br />set dycore       = eul
<br />#set usr_src      = /fs/cgd/data0/$LOGNAME/t31_icealbedos
<br />#set usr_src      = /fs/cgd/home0/$LOGNAME/empty
<br />set usr_src      = /home/blackforest/taoz/cam3.0/empty
<br />#set caseid       = ialb
<br />set case!
id       = test1
<br />
<br />##zt added
<br />## Default nam!
 elist se
ttings:
<br />## $case is the case identifier for this run. It will be placed in the namelist.
<br />## $nelapse is the number of timesteps to integrate, or number of days if negative.
<br />if ( $dycore == 'fv' ) then
<br />    set resolution   = 2x2.5
<br />#    set resolution   = 1x1.25
<br />#    set resolution = 4x5
<br />    set nelapse      = -490
<br />#    set nelapse      = -578
<br />#     set nelapse      = -245
<br />else
<br />    set resolution   = 64x128
<br />#    set resolution   = 128x256
<br />#    set resolution   = 48x96
<br />##zt
<br />#    set nelapse      = -490
<br />##zt
<br />    set nelapse      = -1095
<br />
<br />endif
<br />set nlev         = 26
<br />set case         = ${dycore}${resolution}_$caseid
<br />#
<br />## Default namelist settings:
<br />## $case is the case identifier for this run. It will be placed in the namelist.
<br />## $runtype is the run type: initial, restart, or branch.
<br />## $nelapse is the number of timesteps to in!
tegrate, or number of days if negative.
<br />#set case         = camrun
<br />#set runtype      = initial
<br />#set nelapse      = -1
<br />#
<br />##zt added
<br />
<br />## $wrkdir is a working directory where the model will be built and run.
<br />## $blddir is the directory where model will be compiled.
<br />## $rundir is the directory where the model will be run.
<br />## $cfgdir is the directory containing the CAM configuration scripts.
<br />set wrkdir       = /ptmp/$LOGNAME
<br />set blddir       = $wrkdir/$case/bld
<br />set rundir       = $wrkdir/$case
<br />set cfgdir       = $camroot/models/atm/cam/bld
<br />
<br />## Ensure that run and build directories exist
<br />mkdir -p $rundir                || echo "cannot create $rundir" &amp;&amp; exit 1
<br />mkdir -p $blddir                || echo "cannot create $blddir" &amp;&amp; exit 1
<br />
<br />## If an executable doesn't exist, build one.
<br />if ( ! -x $blddir/cam ) then
<br />    cd $blddir              !
    || echo "cd $blddir failed" &amp;&amp; exit 1
<br />
<br !
 />## Con
trol case
<br />     $cfgdir/configure \
<br />       -dyn $dycore \
<br />       -res $resolution \
<br />       -usr_src $usr_src \
<br />       -nlev $nlev \
<br />    || echo "configure failed" &amp;&amp; exit 1
<br />
<br />#    $cfgdir/configure           || echo "configure failed" &amp;&amp; exit 1
<br />#
<br />    echo "building CAM in $blddir ..."
<br />    rm -f Depends
<br />    gmake -j4 &gt;&amp;! MAKE.out      || echo "CAM build failed: see $blddir/MAKE.out" &amp;&amp; exit 1
<br />else
<br />    echo Found $blddir/cam - not building a new one.
<br />endif
<br />
<br />## Create the namelist
<br />cd $blddir                      || echo "cd $blddir failed" &amp;&amp; exit 1
<br />echo "Building the namelist."
<br />##zt
<br />#$cfgdir/build-namelist -s -case $case -runtype $runtype -o $rundir/namelist \
<br /># -namelist "&amp;camexp nelapse=$nelapse /"  || echo "build-namelist failed" &amp;&amp; exit 1
<br />#
<br />$cfgdir/build-namelist -s \
<br />    -case!
 $case \
<br />    -runtype initial \
<br />    -o $rundir/namelist \
<br />    -namelist "&amp;camexp nelapse=$nelapse,mss_irt=0 /" \
<br />    || echo "build-namelist failed" &amp;&amp; exit 1
<br />
<br />##zt
<br />
<br />## Run CAM
<br />#cd $rundir                      || echo "cd $rundir failed" &amp;&amp; exit 1
<br />#echo "running CAM in $rundir"
<br />#poe $blddir/cam &lt; namelist      || echo "CAM run failed" &amp;&amp; exit 1
<br />#exit 0
<br />#
<br />## Run CAM
<br />cd $rundir
<br />touch output.txt
<br />echo "Beg:: "\`date\` \`perl -e 'print time();'\` &gt;&gt; output.txt
<br />poe time $blddir/cam &lt; namelist &gt;&gt;&amp; output.txt
<br />set year = \`grep restart\ file output.txt | tail -1 | sed s/^.\*.r.// | sed s/-.\*\\\$//\`
<br />#cat namelist | sed s/nsrest.\*=.\*0/nsrest\ =\ 1/ &gt; temp.namelist
<br />#\mv temp.namelist namelist
<br />##zt
<br />#if ( \$year &lt; 200 ) then
<br />if ( \$year &lt; 5 ) then
<br />##zt
<br />   echo Year is \${ye!
ar}, resubmitting.
<br />   llsubmit run-cam.csh
<br />else
<!
 br />   
touch $case.done
<br />#   setenv CASE $case
<br />#   /fs/cgd/home0/jmccaa/scripts/mkclimo.csh
<br />endif
<br />echo "End:: "\`date\` \`perl -e 'print time();'\` &gt;&gt; output.txt
<br />chmod +x $rundir/run-cam.csh
<br />exit 0

------------------------------
PosterpjrPostedTue Nov 16, 2004 2:44 am MST, http://bb.cgd.ucar.edu//viewtopic.php?p=197#197
Message: No!
<br />
<br />I dont want to see the script. I want to see the output from the script. 
<br />This will be stored in the "log" file (probably called "out.xxxxxx" where xxxxx is some random sequence) that contains results from the run
<br />after it is complete. It should tell us why the resubmit failed.
<br />
<br />Phil

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