[ncl-talk] trouble reading .h5 file

[Rick Brownrigg]

(apologies for missing a previous email where you told me 6.2.2 before I
asked again)

That is indeed odd that 6.2.2 works well on one Linux system but not the
other. In recent years, we have been encouraging people to use the
miniconda method of downloading, mostly because it's less fuss for users
and *should* be self-contained. However, I suppose it's worth a shot trying
to download a precompiled version.

Sorry, I wish I could be of more help. Normally, I'd ask you to try and run
ncl under strace to get an idea of where things go awry, but I am no longer
in a position to effectively debug and make fixes to the code.

Rick

On Fri, Aug 21, 2020 at 3:51 PM Manisha Ganeshan <
manisha.ganeshan86 at gmail.com> wrote:

> I'd like to add that I used miniconda for installing NCL 6.6.2.
> I'm wondering if the problem will be fixed if I were to try to download
> and install the pre-compiled version of the code.
>
> On Fri, Aug 21, 2020 at 5:41 PM Manisha Ganeshan <
> manisha.ganeshan86 at gmail.com> wrote:
>
>> Would it be a good idea to try and re-install NCL perhaps?
>>
>> On Fri, Aug 21, 2020 at 4:44 PM Manisha Ganeshan <
>> manisha.ganeshan86 at gmail.com> wrote:
>>
>>> It is failing when I type addfile(), and when I type ncl_dump, with
>>> "segmentation fault".
>>>
>>> On Fri, Aug 21, 2020 at 4:43 PM Manisha Ganeshan <
>>> manisha.ganeshan86 at gmail.com> wrote:
>>>
>>>> I'm confirming that I'm in fact using version 6.6.2 (I've checked ncl
>>>> -v).
>>>> It's odd that I'm able to read the file in another linux system which
>>>> is very similar to the one I'm using. Both systems have NCL version 6.6.2.
>>>> Unfortunately, all the data are in the first linux system, and so I'm
>>>> trying to find an efficient way to solve this problem.
>>>>
>>>>
>>>> On Fri, Aug 21, 2020 at 4:39 PM Rick Brownrigg <brownrig at ucar.edu>
>>>> wrote:
>>>>
>>>>> Well I don't think the size (1.5GB) is an issue. Again, are you using
>>>>> an older version?
>>>>>
>>>>>     ncl -v
>>>>>
>>>>> Is it failing when you do a simple addfile()?  Or when you actually
>>>>> access a particular variable?
>>>>>
>>>>> On Fri, Aug 21, 2020 at 1:17 PM Manisha Ganeshan <
>>>>> manisha.ganeshan86 at gmail.com> wrote:
>>>>>
>>>>>> Is there any other reason it could be failing due to segmentation
>>>>>> fault?
>>>>>>
>>>>>> On Fri, Aug 21, 2020 at 2:57 PM Manisha Ganeshan <
>>>>>> manisha.ganeshan86 at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Rick,
>>>>>>>
>>>>>>> I'm using the same version (6.6.2). I installed using conda, and so
>>>>>>> far it has worked okay. I've read .he5 files using the same version.
>>>>>>>
>>>>>>> Nisha
>>>>>>>
>>>>>>> On Fri, Aug 21, 2020 at 1:54 PM Rick Brownrigg <brownrig at ucar.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Nisha,
>>>>>>>>
>>>>>>>> I was able to read that file just fine with ncl_filedump.  This is
>>>>>>>> on a mac using the latest version, ncl v6.6.2
>>>>>>>>
>>>>>>>> Are you using an older version of NCL?  More recent versions have
>>>>>>>> better and more complete support for HDF5.
>>>>>>>>
>>>>>>>> Hope that helps...
>>>>>>>> Rick
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Aug 21, 2020 at 11:25 AM Manisha Ganeshan via ncl-talk <
>>>>>>>> ncl-talk at mailman.ucar.edu> wrote:
>>>>>>>>
>>>>>>>>>  ATL09_20181016052938_02690101_002_01.h5
>>>>>>>>> <https://drive.google.com/file/d/1RICsYg5nwZTcVeCGJmdkvED445pQaTp6/view?usp=drive_web>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> I'm trying to read the attached hdf5 file but I get a segmentation
>>>>>>>>> fault. Is it because of the size which is roughly 1.5 gb?
>>>>>>>>> Even when I try ncl_filedump, I get the same error message.
>>>>>>>>> I'd appreciate any help or suggestions.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Nisha
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Dr. Manisha Ganeshan
>>>>>>>>> Universities Space Research Association
>>>>>>>>> Maryland, U.S.A.
>>>>>>>>> _______________________________________________
>>>>>>>>> ncl-talk mailing list
>>>>>>>>> ncl-talk at mailman.ucar.edu
>>>>>>>>> List instructions, subscriber options, unsubscribe:
>>>>>>>>> https://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Dr. Manisha Ganeshan
>>>>>>> Universities Space Research Association
>>>>>>> Maryland, U.S.A.
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Dr. Manisha Ganeshan
>>>>>> Universities Space Research Association
>>>>>> Maryland, U.S.A.
>>>>>>
>>>>>
>>>>
>>>> --
>>>> Dr. Manisha Ganeshan
>>>> Universities Space Research Association
>>>> Maryland, U.S.A.
>>>>
>>>
>>>
>>> --
>>> Dr. Manisha Ganeshan
>>> Universities Space Research Association
>>> Maryland, U.S.A.
>>>
>>
>>
>> --
>> Dr. Manisha Ganeshan
>> Universities Space Research Association
>> Maryland, U.S.A.
>>
>
>
> --
> Dr. Manisha Ganeshan
> Universities Space Research Association
> Maryland, U.S.A.
>
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