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CAM4_0.9X1.25 problem

hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
The file
/CESM_INPUT_DATA_0.9X1.25/atm/cam/chem/trop_mozart_aero/aero/aero_1.9x2.5_L26_1850-2005_c091112.nc should contain the variable: "SO4" not "sulf:SO4"
 
L

littleho_song@yahoo_com

Member

Almost identicial. Could you post the lines from your atm_in?&prescribed_aero_nl
 prescribed_aero_datapath               = '/CESM_INPUT_DATA_0.9X1.25/atm/cam/chem/trop_mozart_aero/aero'
 prescribed_aero_file           = 'aero_1.9x2.5_L26_1850-2005_c091112.nc'
 prescribed_aero_specifier              = 'sulf:SO4', 'bcar1:CB1', 'bcar2:CB2', 'ocar1:OC1', 'ocar2:OC2', 'sslt1:SSLT01', 'sslt2:SSLT02',
         'sslt3:SSLT03', 'sslt4:SSLT04', 'dust1:DST01', 'dust2:DST02', 'dust3:DST03', 'dust4:DST04'
 prescribed_aero_type           = 'INTERP_MISSING_MONTHS'
/
 
L

littleho_song@yahoo_com

Member

Almost identicial. Could you post the lines from your atm_in?&prescribed_aero_nl
 prescribed_aero_datapath               = '/CESM_INPUT_DATA_0.9X1.25/atm/cam/chem/trop_mozart_aero/aero'
 prescribed_aero_file           = 'aero_1.9x2.5_L26_1850-2005_c091112.nc'
 prescribed_aero_specifier              = 'sulf:SO4', 'bcar1:CB1', 'bcar2:CB2', 'ocar1:OC1', 'ocar2:OC2', 'sslt1:SSLT01', 'sslt2:SSLT02',
         'sslt3:SSLT03', 'sslt4:SSLT04', 'dust1:DST01', 'dust2:DST02', 'dust3:DST03', 'dust4:DST04'
 prescribed_aero_type           = 'INTERP_MISSING_MONTHS'
/
 
L

littleho_song@yahoo_com

Member
Somehow there might be a bug in the check_input_data  script, it couldn't get these files?File status unknown: b40.20th.track1.1deg.004.cam.i.1979-01-01-00000.ncFile status unknown: b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000.ncFile status unknown: b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000.nc  These 3 files are NOT in the DIN_LOC_ROOT directory for some reasons.I even run the check_input_data -inputdata $DIN_LOC_ROOT -export   
 
L

littleho_song@yahoo_com

Member
Somehow there might be a bug in the check_input_data  script, it couldn't get these files?File status unknown: b40.20th.track1.1deg.004.cam.i.1979-01-01-00000.ncFile status unknown: b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000.ncFile status unknown: b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000.nc  These 3 files are NOT in the DIN_LOC_ROOT directory for some reasons.I even run the check_input_data -inputdata $DIN_LOC_ROOT -export   
 
L

littleho_song@yahoo_com

Member
I redid everything again, now I am getting this:   So there is no b40.20th.track1.1deg.004.cam.i.1979-01-01-00000.nc?/(shr_sys_abort) ERROR: GETFIL: FAILED to get b40.20th.track1.1deg.004.cam.i.1979-01-01-00000.nc
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
MPI_Abort: error code = 1001
 
L

littleho_song@yahoo_com

Member
I redid everything again, now I am getting this:   So there is no b40.20th.track1.1deg.004.cam.i.1979-01-01-00000.nc?/(shr_sys_abort) ERROR: GETFIL: FAILED to get b40.20th.track1.1deg.004.cam.i.1979-01-01-00000.nc
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
MPI_Abort: error code = 1001
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
The lines are:
&prescribed_aero_nl
 prescribed_aero_datapath               = '/glade/p/cesmdata/cseg/inputdata/atm/cam/chem/trop_mozart_aero/aero'
 prescribed_aero_file           = 'aero_1.9x2.5_L26_1850-2005_c091112.nc'
 prescribed_aero_specifier              = 'sulf:SO4', 'bcar1:CB1', 'bcar2:CB2', 'ocar1:OC1', 'ocar2:OC2', 'sslt1:SSLT01', 'sslt2:SSLT02',
         'sslt3:SSLT03', 'sslt4:SSLT04', 'dust1:DST01', 'dust2:DST02', 'dust3:DST03', 'dust4:DST04'
 prescribed_aero_type           = 'INTERP_MISSING_MONTHS'but I don't think the problem is over there.The error your are getting implies that clim_modal_aero is  set to true.
The variable clim_modal_aero  is true only when modal aerosols are used in the climate calculation.
This is not the case in CAM4.

There is something wrong is in your setting and I am trying to figure out what.
Maybe you orginally built this case with another compset thet uses modal aersol (for instance F_AMIP_CAM5).
ANd if you didn't do a clean build, there might be something worng with your setting.

Please could you try to recreate the case from scratch (just do the sequence of CESM command using another casename).   
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
The lines are:
&prescribed_aero_nl
 prescribed_aero_datapath               = '/glade/p/cesmdata/cseg/inputdata/atm/cam/chem/trop_mozart_aero/aero'
 prescribed_aero_file           = 'aero_1.9x2.5_L26_1850-2005_c091112.nc'
 prescribed_aero_specifier              = 'sulf:SO4', 'bcar1:CB1', 'bcar2:CB2', 'ocar1:OC1', 'ocar2:OC2', 'sslt1:SSLT01', 'sslt2:SSLT02',
         'sslt3:SSLT03', 'sslt4:SSLT04', 'dust1:DST01', 'dust2:DST02', 'dust3:DST03', 'dust4:DST04'
 prescribed_aero_type           = 'INTERP_MISSING_MONTHS'but I don't think the problem is over there.The error your are getting implies that clim_modal_aero is  set to true.
The variable clim_modal_aero  is true only when modal aerosols are used in the climate calculation.
This is not the case in CAM4.

There is something wrong is in your setting and I am trying to figure out what.
Maybe you orginally built this case with another compset thet uses modal aersol (for instance F_AMIP_CAM5).
ANd if you didn't do a clean build, there might be something worng with your setting.

Please could you try to recreate the case from scratch (just do the sequence of CESM command using another casename).   
 
L

littleho_song@yahoo_com

Member
After I mannually got the cam.i and clm2.r files from the svn portal. I now met the following problems. (shr_sys_abort) ERROR: aborting in ice-pio_ropen with invalid file
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
 
L

littleho_song@yahoo_com

Member
After I mannually got the cam.i and clm2.r files from the svn portal. I now met the following problems. (shr_sys_abort) ERROR: aborting in ice-pio_ropen with invalid file
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
Did you copy over all the files present in:
inputdata/ccsm4_init/b40.20th.track1.1deg.004/1979-01-01/This is not enough to copy clm and cam files. You need:b40.20th.track1.1deg.004.cam2.h0.1978-12.nc
b40.20th.track1.1deg.004.cam2.i.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cam2.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cam2.rs.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cice.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.clm2.h0.1978-12.nc
b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000
b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cpl.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.pop.r.1979-01-01-00000
b40.20th.track1.1deg.004.pop.r.1979-01-01-00000.hdr
b40.20th.track1.1deg.004.pop.ro.1979-01-01-00000
rpointer.atm
rpointer.drv
rpointer.ice
rpointer.lnd
rpointer.ocn.ovf
rpointer.ocn.restart
rpointer.ocn.tavg


 
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
Did you copy over all the files present in:
inputdata/ccsm4_init/b40.20th.track1.1deg.004/1979-01-01/This is not enough to copy clm and cam files. You need:b40.20th.track1.1deg.004.cam2.h0.1978-12.nc
b40.20th.track1.1deg.004.cam2.i.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cam2.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cam2.rs.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cice.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.clm2.h0.1978-12.nc
b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000
b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.cpl.r.1979-01-01-00000.nc
b40.20th.track1.1deg.004.pop.r.1979-01-01-00000
b40.20th.track1.1deg.004.pop.r.1979-01-01-00000.hdr
b40.20th.track1.1deg.004.pop.ro.1979-01-01-00000
rpointer.atm
rpointer.drv
rpointer.ice
rpointer.lnd
rpointer.ocn.ovf
rpointer.ocn.restart
rpointer.ocn.tavg


 
 
L

littleho_song@yahoo_com

Member
it is strange that the check_input_data didn't do that.I guess I don't need the b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000 - could you provide a brief explanation of the h0, r, rs and ro? Thanks
 
L

littleho_song@yahoo_com

Member
it is strange that the check_input_data didn't do that.I guess I don't need the b40.20th.track1.1deg.004.clm2.r.1979-01-01-00000 - could you provide a brief explanation of the h0, r, rs and ro? Thanks
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
See: http://www.cesm.ucar.edu/models/cesm1.0/filename_conventions_cesm.html
$type = (h*,r*,i*,d*)
$type is a one-, two-, or three-character string which denotes the output file type. In the future, more characters may be required. $type must begin with h (history), r (restart), i (initial), or d (diagnostic) and may be followed by up to two optional characters
  • (a-z,0-9). Certain restart $type strings have special meanings: rs (cam surface restart), rh (restart history), and rd (restart diagnostic).
    One known exception to this is that the cice model sometimes generates history files with a $type string of unlimited length and which may include the "_" (underscore) character or other characters.
 
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
See: http://www.cesm.ucar.edu/models/cesm1.0/filename_conventions_cesm.html
$type = (h*,r*,i*,d*)
$type is a one-, two-, or three-character string which denotes the output file type. In the future, more characters may be required. $type must begin with h (history), r (restart), i (initial), or d (diagnostic) and may be followed by up to two optional characters
  • (a-z,0-9). Certain restart $type strings have special meanings: rs (cam surface restart), rh (restart history), and rd (restart diagnostic).
    One known exception to this is that the cice model sometimes generates history files with a $type string of unlimited length and which may include the "_" (underscore) character or other characters.
 
 
P

pengyf

PengYifeng
New Member
littleho_song@yahoo_com said:
Hi,I need some help on the CESM1.2 running with CAM4 (F_AMIP) with 0.9x1.25 resolution.I followed the instruction carefully and configure this on a Linux machine –(Intel(R) Xeon(R) CPU E7- 4870 @ 2.40GHz, Red Hat Enterprise Linux Server release 6.2 (Santiago))pgf90 11.10-0 64-bit target on x86-64 Linux -tp nehalem (shr_sys_abort) ERROR: Input string (sulf is not a cld borne aerosol,cannot form interstitial species name (shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping MPI_Abort: error code = 1001
Click to expand...
hello，I get the same error with "(shr_sys_abort) ERROR: Input string (sulf is not a cld borne aerosol,cannot form interstitial species name (shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping MPI_Abort: error code = 1001",.Have you solved this problem?
 
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