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problem running CVDP

I am a first time user. I'm running on a MAC with 10.9.
I get these error messages but no output:

My namelist_byvar seems OK

Any suggestions?

Thanks,
Jerry


[8:00am] jerrys-mbp[/Users/potter/ncl]ncl driver.ncl
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running sst.indices.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 192 in file ncl_scripts/sst.indices.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running amo.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 71 in file ncl_scripts/amo.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running pdo.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 77 in file ncl_scripts/pdo.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running psl.modes_indices.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 292 in file ncl_scripts/psl.modes_indices.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running tas.trends_timeseries.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 122 in file ncl_scripts/tas.trends_timeseries.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running psl.trends.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 80 in file ncl_scripts/psl.trends.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running pr.trends_timeseries.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 123 in file ncl_scripts/pr.trends_timeseries.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running sst.mean_stddev.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 72 in file ncl_scripts/sst.mean_stddev.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running snd.trends.ncl
(0) File missing, creating blank array of data. View SNOWDP namelist for details.
(0) Error: gsn_panel: all of the plots passed to gsn_panel appear to be invalid
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running psl.mean_stddev.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 72 in file ncl_scripts/psl.mean_stddev.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running tas.mean_stddev.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 72 in file ncl_scripts/tas.mean_stddev.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running pr.mean_stddev.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 104 in file ncl_scripts/pr.mean_stddev.ncl

Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running sst.trends_timeseries.ncl
warning:stringtointeger: a bad value was passed; input strings must contain numeric digits, replacing with missing value
fatal:The result of the conditional expression yields a missing value. NCL can not determine branch, see ismissing function
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 224 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 122 in file ncl_scripts/sst.trends_timeseries.ncl

convert: memory allocation failed `/Volumes/LaCie/Work/UCDAVIS/Paleo/index_cycles/cas-cvdp.png' @ error/png.c/ReadOnePNGImage/2285.
convert: corrupt image `/Volumes/LaCie/Work/UCDAVIS/Paleo/index_cycles/cas-cvdp.png' @ error/png.c/ReadPNGImage/4056.
convert: no images defined `/Volumes/LaCie/Work/UCDAVIS/Paleo/index_cycles/cas-cvdp.png' @ error/convert.c/ConvertImageCommand/3187.
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) Running webpage.ncl
 
I forgot to point out that my each input file contains all the time values. I have used the convention you request and the data looks fine in each file. For example:TREFHT_12K.53101-55112.nc  Paleo run from year 531 to 551.
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,The CVDP (/CMIP5) file naming convention requires all file names to end in "YYYYMM-YYYYMM.nc". The file names are parsed by character by the CVDP. If there are not 6 characters that specify the start (+end) year and month ("YYYYMM") the package will fail. I would suggest renaming the file to "TREFHT_12K.053101-055112.nc". If that doesn't work please post back. Adam
 
It got farther this time. I have a question about the years. I have an incomplete year at the beginning and the end of the time series. Will this cause the following crash? Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Running sst.trends_timeseries.ncl
(0)    First requested year is incomplete
(0)    Last requested year is incomplete
(0)    Incomplete data year(s) requested for file /Users/potter/desktop/14K_extracted/TS_14K.053102-055205.nc, printing out time and creating blank array
(0)    Time requested: 531-552


Variable: time (coordinate)
Type: integer
Total Size: 1024 bytes
            256 values
Number of Dimensions: 1
Dimensions and sizes:    [time | 256]
Coordinates:
Number Of Attributes: 2
  units :    YYYYMM
  long_name :    time
(0)    53102
(1)    53103
(2)    53104
(3)    53105
...249)    55111
(250)    55112
(251)    55201
(252)    55202
(253)    55203
(254)    55204
(255)    55205
(0)    Error: gsn_panel: all of the plots passed to gsn_panel appear to be invalid
 Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Running webpage.ncl

 Thanks,Jerry 
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,Exactly, yes, incomplete years are not allowed. I highlighted it using error messages but I should definitely do the same in the README file.Try specifying 532 as the start year and 551 as the end year. Adam
 
It works now!I have not yet been able to figure out how to have mulitple models side by side. I don't see a flag in the driver.ncl file. When I run it with 2 rows in the namelist, I only get the first model diagnostics in the webpage output. From the CVDP page you have several models sis-by-side. What am I missing? Thanks,Jerry 
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,You shouldn't have to do anything beyond having multiple rows in the namelist file (with a hard return at the end of each row), like this:CESM1 (CAM5.2) LE Control |  /project/y4i/b.e11.B1850C5CN.f09_g16.005/ | 700 | 1099
CESM1 (CAM5.1) Control | /project/y4//b40_1850_1d_b08c5cn_138j/ | 120 | 319
CCSM4 Control | /project/y4/b40.1850.track1.1deg.006/ | 800 | 1199What does your namelist_byvar/namelist_ts file look like? Adam
 
Here is my namelist_byvar for tscam_b30_12K 12K #2 | /Users/potter/desktop/12K_extracted/TS_030101.032112.nc | 301 | 321

(only one model is shown)but my namelist file looks like this:cam_b30_12K 12K #2 | /Users/potter/desktop/12K_extracted/ | 0301 | 0321
cam_b30_14K 14K #1 | /Users/potter/desktop/14K_extracted/ | 0531 | 0551
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,Can you try setting your namelist to this:cam_b30_12K 12K #2 | /Users/potter/desktop/12K_extracted/ | 0301 | 0321
cam_b30_14K 14K #1 | /Users/potter/desktop/14K_extracted/ | 0531 | 0551
cam_b30_12K 12K #2 | /Users/potter/desktop/12K_extracted/ | 0301 | 0321And let me know what you get.. Thanks,Adam
 
Adam,
Something missing from the plots is PR. The global trends, time series and the zonal plots. here is the PR namelist:cam_b30_12K 12K #2 | /Users/potter/desktop/12K_extracted/*{PRECC,PRECL}*.nc | 301 | 321
cam_b30_14K 14K #1 | /Users/potter/desktop/14K_extracted/*{PRECC,PRECL}*.nc | 531 | 551

 the error message:(0)    Running pr.trends_timeseries.ncl
fatal:Plus: Dimension size, for dimension number 0, of operands does not match, can't continue

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 90 in file ncl_scripts/functions.ncl

fatal:["Execute.c":8567]:Execute: Error occurred at or near line 123 in file ncl_scripts/pr.trends_timeseries.ncl


When I was only getting one plot per page the PR was plotted preperly - zonal averages too.  ThanksJerry 
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,This looks to me like your PRECC and PRECL files have a different number of timesteps in them. The error message (in ncl_scripts/functions) points to the following lines:              c = addfiles(fils_precc,"r")
              arr = c[:]->PRECC
              c2  = addfiles(fils_precl,"r")
              arr = (/ arr+c2[:]->PRECL  /)   ; This is line 90The error message is coming from the arr array having a different number of timesteps than what c2[:]->PRECL is returning. Thus, either you have a different number of timesteps in your PRECC and PRECL files, or not all PRECC or PRECL files are being seen by the CVDP.Do a "ls /Users/potter/desktop/14K_extracted/*{PRECC,PRECL}*.nc" and make sure all the files are seen by that syntax. If they are, I would make sure that the same number of timesteps is present across all the PRECC files versus across all the PRECL files. Note: At this point in the code the CVDP has not selected the period of analysis. Thus, all files that match the "ls /Users/potter/desktop/14K_extracted/*{PRECC,PRECL}*.nc" are read in, and then the analysis time period is selected.Adam 
 
ADAM,I'm trying CVDP on the 20CR reanalysis and I get a strange error. Only psl is the problem now.I get this: (0)    Running pdo.ncl
 Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Running psl.modes_indices.ncl
fatal:Dimension sizes of left hand side do not match right hand side
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 1251 in file ncl_scripts/psl.modes_indices.ncl

 Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Running tas.trends_timeseries.ncl

  (0)    Running pdo.ncl
 Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Running psl.modes_indices.ncl
fatal:Dimension sizes of left hand side do not match right hand side
fatal:["Execute.c":8567]:Execute: Error occurred at or near line 1251 in file ncl_scripts/psl.modes_indices.ncl

 Copyright (C) 1995-2014 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.2.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Running tas.trends_timeseries.ncl

There is nothing obviously wrong with the data:My namelist_byvar looks like this:20CR_Reanalysis 20CR | /Volumes/LaCie/Work/NASA/ana4MIPs_use_case/20CR_diagnostics/psl_Amon_reanalysis_20CRv2_187101-201212.nc | 1871 | 2012All of the other variables work fine. I have openen the psl file with other software and it seems fine.  None of the operations that need psl have output. Thanks Jerry  
 
I found the problem. the 20CR PSL has slightly different dimensions than TS. I regridded PSL to conform and the plots all worked. Should this be mentioned in the README?Thanks,Jerry 
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,I'm glad you found the issue. To be clear though: The CVDP does not require observational datasets to be on the same grid. My routine CVDP observational datasets include HadISST (1 degree grid), 20th Century Reanalysis PSL (2 degree grid), MLOST air temperatures (5 degree grid) and GPCC (1 degree grid).However, for simulations listed in the namelist,  all variables for a particular simulation must be on the same grid IF you are writing the CVDP data out to netCDF files. This is because each simulation has its own netCDF file, and the CVDP does not check as to whether each variable is on a different grid before writing the data out. I will note this in the README file.  Adam 
 
I have been running CVDP successfully on my MAC (10.9) and now I am trying it on my LUNUX (Ubuntu 13.10). I have NCO and ImageMagick installed and running now and nco passes all  the tests. When I run in LINUX with exactly the same data as on the MAC only the first variable (pr) is read - the remaining variables are shown to be "missing" in the namelist_byvar for all the variables except prect.eg. for prect:20CR | /Volumes/UNIX/diagnostic_files/20CR_diagnostics/pr_Amon_reanalysis_20CRv2_187101-201212.nc | 1871 | 2012
CCSM4 | /Volumes/UNIX/diagnostic_files/CCSM4/pr_Amon_CCSM4_historical_r3i1p1_185001-200512.nc | 1850 | 2005

 for all others:20CR | missing | 1871 | 2012
CCSM4 | missing | 1850 | 2005and like I said the exact same data works fine on the Mac.
the data are in the assigned directories (except for snowdp)any suggestions?Thanks,Jerry  
 

asphilli

Adam Phillips
CVCWG Liaison
Staff member
Hi Jerry,That is quite odd. The package was developed on a Linux system and has been run on a Mac here. Frankly it shouldn't be a problem running on any system that has NCL v6.1.2 (or newer) and Image Magick installed. So if you were to take the CCSM4 path you supplied in the namelist (let's call it PATH), and type "ls PATH" in a terminal window do you see all the variable files listed? You should. Let me know. The only other possibility that I can think of is if you have an alias set for when you type "ls".. That might screw things up. Adam
 
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