Re: trouble installing PyNIO in home directory of hopper

Thanks for the file. I downloaded it and tried opening it with PyNIO 1.4.1 on my Mac. I didn't have any problems with it:

>>> import Nio
>>> a = Nio.open_file("cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc")
>>> print(a)

Nio file: cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc
   global attributes:
      title : CLM History file information
      comment : NOTE: None of the variables are weighted by land fraction!
      Conventions : CF-1.0
      history : created on 03/06/12 21:39:19
      source : Community Land Model CLM4.0
      hostname : hopp2
      username : cdkoven
      version :
      revision_id : $Id: histFileMod.F90 34707 2012-02-14 06:12:46Z erik $
      case_title : UNSET
      case_id : cktest_clm45sci_v2_debug1
      Surface_dataset : surfdata_1.9x2.5_simyr1850_c091108.nc
      Initial_conditions_dataset : ckexp001d_1x1_CTvsdent_CORRnitrif_newphotosy_10daynfix_RUNOFFLEACH2_spup.clm2.r.0190-01-01-00000.nc
      PFT_physiological_constants_dataset : pft-physiology.crops_rootbeta.20
. . .

What kind of system do you have where you see the problem?

   uname -a

I'm wondering if there might be an issue with your version of NetCDF. Dave might be able to suggest some debugging tips to try to narrow down the source of the problem.

--Mary

On Mar 7, 2012, at 10:30 AM, Charlie Koven wrote:

> Hi Mary,
>
> On Mar 7, 2012, at 6:57 AM, Mary Haley wrote:
>
>> Hi Charlie,
>>
>> Thanks for the typo correction in the previous email. :-)
>
> That was Michael with the typo correction, not me :) -- thanks Michael
>
>>
>> With the problem below, are you able to open this file from straight python (not IPython)? How big is the file, and how big are the ones you are able to open successfully?
>>
>
> Yes, same problem.
>
> the only two files I tried it on are a CLM history file and a CLM restart file. for some reason the restart file loads but the history file doesn't. the restart file is actually bigger, 1.2G vs. 75M for the history file. I don't think there is any issue with the file though--I can open both files on the Nio install I have working on my workstation.
>
>> What version of PyNIO are you using?
>
>>>> Nio.__version__
> '1.4.1'
>
>>
>> Finally, would you be able to provide the cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc file so we can try opening it here?
>>
>
> Sure. I just uploaded the file.
>
> Thanks,
>
> Charlie
>
>
>
>
>> ftp ftp.cgd.ucar.edu
>> anonymous
>> <use your email address for the password>
>> cd incoming
>> put cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc
>> quit
>>
>> Thanks,
>>
>> --Mary
>>
>> On Mar 6, 2012, at 5:07 PM, Charlie Koven wrote:
>>
>>> Hi,
>>>
>>> now that I've gotten PyNGL to install successfully in my home directory on hopper, I thought I should try to get PyNIO working.
>>>
>>> i set the module environment to use gcc by:
>>>
>>> module unload pgi
>>> module load gcc
>>>
>>> and the env variables I am using are:
>>>
>>> export F2CLIBS=gfortran
>>> export F2CLIBS_PREFIX=/opt/gcc/4.6.1/snos/lib/
>>> export HAS_OPENDAP=0
>>> export NETCDF_PREFIX=/opt/cray/netcdf/4.1.1.0/netcdf-gnu
>>>
>>>
>>> the library seems to build ok but when I try to load a CLM history file, I get the following error:
>>>
>>>
>>> IPython 0.12 -- An enhanced Interactive Python.
>>> ? -> Introduction and overview of IPython's features.
>>> %quickref -> Quick reference.
>>> help -> Python's own help system.
>>> object? -> Details about 'object', use 'object??' for extra details.
>>>
>>> In [1]: import Nio
>>>
>>> In [2]: file_in = Nio.open_file('cktest_clm45sci_v2_debug1.clm2.h0.0001-02.nc')
>>> Error: in routine alloca() there is a
>>> stack overflow: thread 0, max 8180KB, used 0KB, request 8B
>>>
>>>
>>> It does seem to be able to load smaller files, however. Any idea what is causing this?
>>>
>>> Thanks,
>>> Charlie
>>>
>>>
>>> _______________________________________________
>>> pyngl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
>>
>

_______________________________________________
pyngl-talk mailing list
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/pyngl-talk
Received on Thu Mar 8 10:37:51 2012