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cesm1_0_3 Release Notes

cesm1_0_3

Release Notes

Contents

Release Notes

The main purpose of this release update is to provide the capability of running CESM1.0 with the CMIP5 20th Century and RCP8.5, RCP6.0, RCP4.5 and RCP2.6 scenarios (see also the Model Output Diagnostic Plots).

In addition, CESM1.0.3 also includes new component science, particularly for CAM and CLM. This includes a new CAM5.1, optional CLM crop and irrigation capabilities, and new WACCM capability to output history along satellite tracks and be driver by specified dynamics (see Notable Improvements).

This model also includes enhancements and bug fixes, as noted below and in the "Answer-Changing Features" section.

What's New

Answer-Changing Features

The following changes in the cesm1_0_3 tag will result in most cases not producing bit-for-bit results when compared with cesm1_0_2.

Known Problems

 


 


____________________________________________________________________________________________

Description: 
Date       : 
Contact    : 



 

 

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Description: The CICE history files have some incorrect history fields (albpnd, albice, albsno). These should not be used.
Date       : 2011-06-06 (originally reported 2011-05-09)
Contact    : Dave Bailey 
Information:

The counters for these albedos over ponds, ice, and snow are incorrect. These
should not be used. They are diagnostic only. A fix is currently being worked
on and will be released at a later date.




 

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Description: Gregorian calendar in CICE
Date       : 2011-06-06
Contact    : Dave Bailey
Information:

The Gregorian calendar in the sea ice model has some inconsistencies. 

This mode should be used with caution. 

Note that this affects the Gregorian calendar only in 
compsets with active or prescribed ice (B, D, E, F). 

Questions about this should be directed to dbailey --at -- ucar --dot-- edu.




 

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Description: WACCM compsets and use of ESMF library
Date       : 2011-06-06
Contact    : Francis Vitt
Information:

There is a known problem with following WACCM compsets when the ESMF time manager is
used. The problem occurs when the solar_parms_file input file contains data for leap days
(Feb 29) while the calendar is 'NOLEAP'.  A work around to this problem is to use the
following alternative datasets for solar_parms_file which do not contain leap days:

B_1850-2000_WACCM_CN
 solar_parms_file = '$DIN_LOC_ROOT/atm/waccm/solar/proxy_solar_Solomon_Richmond_1845-2008_daily_noleap_c110526.nc'


B_1955-2005_WACCM_CN
F_1955-2005_WACCM_CN
B_RCP2.6_WACCM_CN
B_RCP4.5_WACCM_CN
B_RCP8.5_WACCM_CN
 solar_parms_file = '$DIN_LOC_ROOT/atm/waccm/solar/wasolar_1948-2140_daily_noleap_c110525.nc'




 


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Description: Use non-default compiler for ne240_f02_t12 on jaguarpf or hopper
Date       : 2011-06-07
Contact    : Jim Edwards
Information:

The ne240_f02_t12 high-resolution case does not run with the default compiler 
set on jaguarpf or hopper. In both cases, ne240_f02_t12 will run by reverting
to the pgi9 compiler set.

Compiler sets are controlled via the env_machine_specific file in your $CASE
directory. 

The lines in env_mach_specific are:
  module switch pgi pgi/9.0.4 
  module swap xt-mpich2 xt-mpich2/5.1.2
  module switch xt-libsci xt-libsci/10.4.9

Due to the large task count and memory requirements of this case,
we have thus far been unable to test the problem on any other platform.

____________________________________________________________________________________________

Update: Old pgi9 compiler is no longer available
Date  : December 2011
Information:
    
The alternate compiler is no longer available.   We will look into an alternative solution.





 


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Description: D, G, and I compsets have dust wet/dry deposition mislabeled for bin 4 -- no change to answers
Date       : 2011-06-09
Contact    : erik
Bug number : 1359
Information:

Mark Flanner found the following error in the datm template for prescribed aerosol:

Index: datm.template.streams.xml
===================================================================
--- datm.template.streams.xml    (revision 28874)
+++ datm.template.streams.xml    (working copy)
@@ -1542,8 +1542,8 @@
       DSTX02DD   dstdry2         
       DSTX03WD   dstwet3         
       DSTX03DD   dstdry3 
-      DSTX04WD   dstdry4                         
-      DSTX04DD   dstwet4         
+      DSTX04WD   dstwet4                         
+      DSTX04DD   dstdry4         
    
    
       %p

This is an issue with all "D", "G" and "I" compsets in cesm1_0_3. There's
only one D compset: D_NORMAL_YEAR, and two G compsets: G_1850_ECOSYS, and
G_NORMAL_YEAR, there's 25 "I" compsets.

Mark also assures us that this has no impact on simulations:

"As far as I can tell this had zero impact because CESM1 
treats the dry and wet dust deposition identically in both SNICAR and 
the sea-ice model.  I only noticed it because I recently made a change 
to the code that does differentiate between wet and dry dust deposition."







 


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Description: List of minor issues for CLM in cesm1_0_3
Date       : 2011-06-09
Contact    : erik
Information:

There is a list of minor issues and Known limitations with CLM under the Documentation 
for CLM4 in cesm1_0_3 at

     http://www.cesm.ucar.edu/models/cesm1.0/clm/KnownBugs.CESM1.0.3
     http://www.cesm.ucar.edu/models/cesm1.0/clm/models/lnd/clm/doc/KnownLimitations





 


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Description: Scripts don't support ESMF serial code
Date       : 2011-06-09
Contact    : erik
Information:

During compilation, ESMF is trying to link in a mpi library.
On bluefire, setting ESMF_LIBDIR to /contrib/esmf_5_2_0-64-O-mpiuni
will allow you to run serial code.




 


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Description: "Claim exceeds reservation's resources" error message in ccsm.log on Crays
Date       : 2011-06-10
Contact    : Chris Fischer
Information:

On a rare occasion you can get this error message when two concurrent tasks, with different threading, are running
on the same node.  The fix for this is to change the PES layout so the concurrent tasks are on different nodes.






 


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Description: ESMF library path on bluefire points to a temproray area.
Date       : 2011-06-10
Contact    : Chris Fischer
Information:


The ESMF_LIBDIR is set to a directory on /ptmp, which is temporary storage.  It should be set to /contrib/esmf_5_2_0-64-O/lib/
in env_build.xml.  You may use the follow xmlchange command.

xmlchange -file env_build.xml -id ESMF_LIBDIR -val /contrib/esmf_5_2_0-64-O/lib/





 


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Description: Problem running I1850SPINUPCN with more than 82 years of data
Date       : 2011-06-10
Contact    : erik
Bugnumber  : 1339
Information:

In order to run with more than 82 years of CPLHIST data the file limit in shr_stream needs
to increase from 1000 to 2000 (technically 1860 would be sufficient, but might
as well bump it to 2000).

Index: shr_stream_mod.F90
===================================================================
--- shr_stream_mod.F90    (revision 28396)
+++ shr_stream_mod.F90    (working copy)
@@ -101,7 +101,7 @@
    end type shr_stream_fileType

    !--- hard-coded array dims ~ could allocate these at run time ---
-   integer(SHR_KIND_IN),parameter :: nFileMax = 1000  ! max number of files
+   integer(SHR_KIND_IN),parameter :: nFileMax = 2000  ! max number of files

    type shr_stream_streamType
       !private                                    ! no public access to internal components

We didn't put this change in as it causes a compiler error on bluefire for AIX
when compiling the dlnd component.

See the CLM KnownBugs file for more information on this...

http://www.cesm.ucar.edu/models/cesm1.0/clm/KnownBugs.CESM1.0.3





 


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Description: I1850SPINUPCN compset points to a transient case rather than a fixed 1850 case
Date       : 2011-06-10
Contact    : erik
Bugnumber  : 1354
Information:

When the I1850SPINUPCN compset is run the case that is used is:

DATM_CPL_CASE="b40.20th.track1.1deg.012"

which is a transient case rather than a fixed 1850 case.

So it should be changed to...

b40.1850.track1.1deg.006a

and the years adjusted to be within 953 and 1108.





 


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Description: On machine Lynx env_build.xml and env_run.xml references to /ptmp must be changed to /glade/scratch
Date       : 2011-06-14
Contact    : dfeddema
Information:

On machine Lynx when a user creates a new case using script create_newcase,
files env_build.xml and env_run.xml will contain references to /ptmp that
must be edited and changed to /glade/scratch. 





 


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Description: B_1850_CAM5_CN and B_1850-2000_CAM5_CN: problem with initialization datsets.
Date       : 2011-06-17
Contact    : hannay
Information:

We are aware of problems in the initialization datasets when using the compsets B_1850_CAM5_CN and B_1850-2000_CAM5_CN at the resolution f19_g16.
A new set of initialization datasets is available on the SVN repository. Users can customize the default configuration to access to these new datasets.   
The easiest way to achieve this is to modify the file env_conf.xml BEFORE invoking configure. This can be done with the commands. 
xmlchange -file env_conf.xml -id RUN_REFDATE -val '0070-01-01'
xmlchange -file env_conf.xml -id RUN_REFCASE -val 'b40_1850_2d_r07c5cn_160jp'






 


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Description: compsets: E_2000_CN_GLC, E_1850_CN_GLC, F_AMIP_CAM5_CN, F_1850_CN_GLC do NOT have CN turned on as they should!
Date       : 2011-06-29
Contact    : erik
Bugnumber  : 1366
Information:

The compsets:

E_2000_CN_GLC
E_1850_CN_GLC
F_AMIP_CAM5_CN
F_1850_CN_GLC

fail to turn CN on in CLM as they should. The scripts/ccsm_utils/Case.template/config_compsets.xml can be edited to add
the line:

  CLM_CONFIG_OPTS="-bgc cn"

Or you can set this in any case that generates with xmlchange

   ./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -append -val "-bgc cn"





 


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Description:  WACCM gravity wave breaking bug
Date       : 2011-08-31
Contact    : Michael Mills, mmills@ucar.edu
Information:

Details: Gravity waves break in the middle and upper atmosphere where molecular diffusion
coefficients become large. However, the gravity wave breaking scheme has been passed an eddy
diffusivity for heat (kvh) instead of molecular diffusivity. Hence gravity wave breaking in the upper
atmosphere is not treated correctly. In tests where this bug is fixed, very little change is seen in
calculated climate or dynamics of the middle atmosphere. This bug should be fixed with the next
public release of CESM.






 


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Description: F_1850_chem and F_2000_chem compsets should not be used
Date       : 2011-09-07
Contact    : fischer
Information:

F_1850_chem and F_2000_chem compsets should not be used





 

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Description: coupler input_data_list may be incomplete
Date       : 2011-11-11
Contact    : tcraig
Information:

The coupling input data list in the case directory file
Buildconf/cpl.input_data_list does not always generate
a complete list of needed files.  The fix is as follows,

in models/drv/bld/cpl.template, delete

======

set mapfilevarname = (map_a2of_file map_a2os_file map_o2af_file map_o2as_file \
                 map_a2lf_file map_a2ls_file map_l2af_file map_l2as_file \
                 map_r2o_file)

set i = 0
foreach mapfile (\$map_a2of_file \$map_a2os_file \$map_o2af_file \$map_o2as_file \
                 \$map_a2lf_file \$map_a2ls_file \$map_l2af_file \$map_l2as_file \
                 \$map_r2o_file)
  @ i++
  if (\$mapfile != idmap) then
    if(-r "\$DIN_LOC_ROOT/\$mapfile") then
      set \$mapfilevarname[\$i] = \$DIN_LOC_ROOT/\$mapfile
      cat >> \$CASEBUILD/cpl.input_data_list << EOF
      \$mapfilevarname[\$i] = \$DIN_LOC_ROOT/\$mapfile
EOF
    else if(-r "\$DIN_LOC_ROOT/cpl/cpl6/\$mapfile") then
      set \$mapfilevarname[\$i] = \$DIN_LOC_ROOT/cpl/cpl6/\$mapfile
      cat >> \$CASEBUILD/cpl.input_data_list << EOF
      \$mapfilevarname[\$i] = \$DIN_LOC_ROOT/cpl/cpl6/\$mapfile
EOF

    endif
  endif
end

======

and replace it with

=======

set mapfilevarname = \
                  (map_a2of_file   map_a2os_file   map_o2af_file   map_o2as_file \
                   map_a2lf_file   map_a2ls_file   map_l2af_file   map_l2as_file \
                   map_r2o_file)

set i = 0
foreach mapfile (\$map_a2of_file \$map_a2os_file \$map_o2af_file \$map_o2as_file \
                 \$map_a2lf_file \$map_a2ls_file \$map_l2af_file \$map_l2as_file \
                 \$map_r2o_file)
  @ i++                
  if (\$mapfile != idmap) then  
    if (\$mapfile =~ *cpl/gridmaps*) then
       set mapdir = ""
    else
       if (\$mapfile =~ */*) then
          echo "ERROR: unsupported mapfile path \$mapfile"
          exit -9
       endif
       set mapdir = "cpl/cpl6/"
    endif
cat >> \$CASEBUILD/cpl.input_data_list << EOF
\$mapfilevarname[\$i] = \${DIN_LOC_ROOT}/\${mapdir}\${mapfile} 
EOF
    set \$mapfilevarname[\$i] = \${DIN_LOC_ROOT}/\${mapdir}\${mapfile} 
  endif
end





 


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Description: I compsets hang at configure step with a bad user_nl_clm file that has double quotes
Date       : 2011-11-18
Contact    : erik
Bugnumber  : 1425
Information:

Charlie Koven found this issue..

If you have an input user_nl_clm namelist being parsed that has double quotes in it --
Namelist.pm gets in an infinite loop and hangs...

So something like...

hist_fincl1 =
'NET_NMIN_vr',''GROSS_NMIN_vr','POTENTIAL_IMMOB_vr','ACTUAL_IMMOB_vr','SMINN_TO_PLANT_vr'

will cause configure to hang -- until you hit control-C.

The work around is to give it a correct namelist without the double-quotes. But, you'll have to
recognize the problem yourself.





 


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Description: Problem running PST.f09_g16.I.jaguarpf
Date       : 2011-12-01
Contact    : erik
bugnumber  : 1410
Information:

Running on jaguar I get the following problem...


aprun: -N cannot exceed -n
aprun: Exiting due to errors. Application aborted

aprun looks like this..


   aprun -n 8 -N 12 -d 1 ./ccsm.exe >&! ccsm.log.$LID

and batch has...

#PBS -l size=12

every component has 8 processors except ocean which has 5, no concurrency and
no threads.

============================================================================
NOTE: This problem report applies to a very limited set of circumstances,
and is included in the cesm1_0_4 release notes because it was reported for
a previous release.

In the rare event that a user encounters a similar problem, in which
the number of processors used is less than the number of processors on
the node, the fix is to change the value for the -N option in the
aprun command to the number of processors used.
============================================================================





 


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Description: CFC initialization in POP is incorrect for 20th century branch and hybrid runs
Date       : 2013-01-28
Contact    : mlevy
Information:

To fix this problem, copy this version of
ocn.cfc.setup.csh into $CASEROOT/SourceMods/src.pop2/





 


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Description: Incorrect diagnostic output for POP2 variable RHO_VINT
Date       : 2013-02-05
Contact    : mlevy
Information:

There is a bug in the way POP2 computes the diagnostic variable RHO_VINT. Note that
this issue does not affect any of the prognostic variables in the CESM 1.0[.x]
releases.

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