Re: wrf_user_getvar segfault - for cape_2d

Hi Mary,

I'm running ncl 6.0.0 and my uname is

Linux 2.6.32.54-0.3-default #1 SMP 2012-01-27 17:38:56 +0100 x86_64
x86_64 x86_64 GNU/Linux

It's strange that it *does* work on copy of the file in which every
alternate lat/lon point has been removed (eg ncks -O -d Time,0,1 -d
west_east,,,2 -d south_north,,,2 -d south_north_stag,,,2 -d
west_east_stag,,,2 wrfout_d03_2009-05-18_12:00:00.nc WRF_TST.nc). I'd
be surprised if it's a memory/virtual memory problem though, as I'm on
a cluster and giving it plenty of resources. Perhaps I should ask the
cluster admins if it's a build problem they can fix?

Will.

On 14 March 2012 07:38, Mary Haley <haley@ucar.edu> wrote:
> Hi Will,
>
> I was unable to reproduce the problem using NCL V6.0.0 and the WRF_DEBUG.nc file.
>
> What version of NCL do you have?
>
> --Mary
>
> On Mar 9, 2012, at 2:58 PM, Will Thurston wrote:
>
>> Hi again,
>>
>> I've uploaded a 2 timestep version of the file (on which getting cape
>> segfaults for me) to the ftp site (put into incoming) created with
>>
>> ncks -O -d Time,0,1 wrfout_d03_2009-05-18_12:00:00 WRF_DEBUG.nc
>>
>> I'm running ncl 6.0.0 and my uname is
>>
>> Linux 2.6.32.54-0.3-default #1 SMP 2012-01-27 17:38:56 +0100 x86_64
>> x86_64 x86_64 GNU/Linux
>>
>> Cheers,
>> Will.
>>
>> On 3 March 2012 19:06, Will Thurston <willthurston@gmail.com> wrote:
>>> Hi Dennis,
>>>
>>> I tried the script with a 2 timestep version of the wrfout file and it
>>> still segfaulted when getting cape_2d. I also tried your ncks
>>> "thinned-out" version (with just two timesteps and with all 24
>>> timesteps) and both worked fine.
>>>
>>> It also works OK if I try it on a d01 or d02 file, so it seems like
>>> the problem is to do with the number of points in the domain. I'd be
>>> surprised if lack of memory was the problem though, I'm running on a
>>> cluster and throwing plenty of mem/vmem at it.
>>>
>>> Cheers,
>>> Will.
>>>
>>> On 3 March 2012 09:29, Dennis Shea <shea@ucar.edu> wrote:
>>>> The original code was from wrfhelp [cc'd here].
>>>>
>>>> I ran you script with a standard WRF output file.
>>>> I did add two printVarSummary statements.
>>>> No problems. The output follows
>>>>
>>>>
>>>> %> ncl cape_tst.ncl
>>>>
>>>>  NCAR Command Language Version 6.0.0
>>>>
>>>> (0)     Get dbz
>>>>
>>>> Variable: dbz
>>>> Type: float
>>>> Total Size: 1018464 bytes
>>>>            254616 values
>>>> Number of Dimensions: 3
>>>> Dimensions and sizes:   [Time | 24] x [south_north | 103] x [west_east |
>>>> 103]
>>>> Coordinates:
>>>> Number Of Attributes: 6
>>>>  description : Max Reflectivity
>>>>  units :       dBZ
>>>>  FieldType :   104
>>>>  MemoryOrder : XYZ
>>>>  stagger :
>>>>  coordinates : XLONG XLAT
>>>> (0)     Get CAPE
>>>>
>>>> Variable: cape
>>>> Type: float
>>>> Total Size: 4073856 bytes
>>>>            1018464 values
>>>> Number of Dimensions: 4
>>>> Dimensions and sizes:   [mcape_mcin_lcl_lfc | 4] x [Time | 24] x
>>>> [south_north | 103] x [west_east | 103]
>>>> Coordinates:
>>>> Number Of Attributes: 5
>>>>  MemoryOrder : XY
>>>>  description : mcape ; mcin ; lcl ; lfc
>>>>  FieldType :   104
>>>>  stagger :
>>>>  coordinates : XLONG XLAT
>>>>
>>>> Try your script with (say) 2 time steps.
>>>>
>>>> Also, for debugging you may wish to do something like the following
>>>>
>>>> $> ncks -O -d Time,0,1 -d west_east,,,2 -d south_north,,,2 -d
>>>> south_north_stag,,,2 -d west_east_stag,,,2 wrfout_d03_2009-05-18_12:00:00.nc
>>>> WRF_TST.nc
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 03/02/2012 02:07 PM, Will Thurston wrote:
>>>>>
>>>>> Hi there,
>>>>>
>>>>> I've had problems with ncl seg faulting when using wrf_user_getvar to
>>>>> calculate/get cape from some wrfout files, attached is a pared down
>>>>> script.
>>>>>
>>>>> I've put the get dbz and print statements in to show (myself) that ncl
>>>>> can calculate other diagnostic from 3D fields, and it is the cape part
>>>>> it falls over on.
>>>>>
>>>>> The input file is about 22 Gb and has dimensions of 24 x 27 x 723 x
>>>>> 732. This guess this is quite large so I also tried getting cape for
>>>>> just 1 timestep, rather than the whole file at once, but it still seg
>>>>> faults.
>>>>>
>>>>> ncl -V
>>>>> 6.0.0
>>>>>
>>>>> Cheers,
>>>>> Will.
>>>>>
>>>>>
>>>>>
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>>>>
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Received on Mon Mar 19 19:53:07 2012