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[netCDF #MRA-585540]: Write a netcdf4classic file

Wei,

I'd like to download the file and check it here.  I have space for a 35 GB
file, but you'd need to make it available for ftp or http access, as I
don't have easy access to files on glade currently.  Is that possible?

--Russ


On Fri, Sep 26, 2014 at 11:37 AM, Wei Huang <address@hidden
> wrote:

> New Client Reply: Write a netcdf4classic file
>
> Joe,
>
> Here is NCAR's Yellowstone system info:
>
> uname -a
> Linux geyser05 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013
> x86_64 x86_64 x86_64 GNU/Linux
>
> Barbara, and Russ,
>
> Attached is a C code which I can reproduce this problem on NCAR's
> Yellowstone
> by read the NCL generated NetCDF file.
>
> Thank you all for check on this issue.
>
> Wei
>
>
>
> Wei
>
>
> ================================================
> 1850 Table Mesa Dr.
> Boulder, CO 80307
> Phone: 303-497-8924
>
> On Fri, Sep 26, 2014 at 11:06 AM, <address@hidden> wrote:
>
> > Hi Wei,
> >
> > I probably should have figured that out!
> > Joe Lee will look at this and we'll see what the next step is.
> > I'll bring it up in the HDF5 meeting on Monday, as well.
> >
> > -Barbara
> >
> >
> > On Fri, 26 Sep 2014, Wei Huang wrote:
> >
> >  Barbara,
> >>
> >> I am a NCL developer in the NCL team.
> >> As I mentioned in my last email, it seems that the problem
> >> shows up when we tried to read netCDF4classic file quite some
> >> million times. And the same script which worked with HDF5-1.8.12.
> >> This read end-up only read each point at time with the way
> >> the user coded in NCL. We know it is not an efficient way to read
> >> data, but our code should not fail, and so HDF5 should not fail either.
> >>
> >> If you need, I can FTP the data file to you, and you can try to read
> this
> >> data point by point with HDF5,
> >> which may reproduce the problem.
> >> If Russ wants to investigate more, I can FTP the data as well.
> >>
> >> Thanks for looking at this issue.
> >>
> >> Wei
> >>
> >> ================================================
> >> 1850 Table Mesa Dr.
> >> Boulder, CO 80307
> >> Phone: 303-497-8924
> >>
> >> On Fri, Sep 26, 2014 at 7:57 AM, <address@hidden> wrote:
> >>
> >>  Hi Wei,
> >>>
> >>> I'm not sure we'll be able to determine the issue with your NCL
> >>> scripts. However, I did find someone here who has used NCL before.
> >>> I will forward your scripts to him, in case he can help.
> >>>
> >>> He suggested you contact the ncl-talk mailing list, as they may be
> >>> familiar with this issue. It looks like you have to subscribe to
> >>> ncl-talk. See:
> >>>
> >>>    https://www.ncl.ucar.edu/Support/email_lists.shtml
> >>>
> >>> In the mean-time, we will see if we can determine anything from the
> >>> scripts.
> >>>
> >>> -Barbara
> >>> address@hidden
> >>>
> >>>
> >>>
> >>>  I have been able to reproduce this issue with a simple NCL scripts.
> >>>
> >>>> Attached are two NCL scripts, where wrt.ncl created a data file.
> >>>> Then read.ncl read a sub-set of the data in a loop.
> >>>>
> >>>> The read script can demonstrate that HDF5 error start to appear
> >>>> loop index 414. (where the first 414 read just normal).
> >>>>
> >>>> I understand that it seems not fair to send you NCL scripts,
> >>>> but that is how we got the problem, and little bit more frustrated
> >>>> is that it seems the same code worked fine on my Mac,
> >>>> but failed on NCAR's yellowstone.
> >>>>
> >>>> I hope I can give you more info, but that is what I got so far.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Wei
> >>>>
> >>>>
> >>>> ================================================
> >>>> 1850 Table Mesa Dr.
> >>>> Boulder, CO 80307
> >>>> Phone: 303-497-8924
> >>>>
> >>>> On Thu, Sep 25, 2014 at 8:16 AM, <address@hidden> wrote:
> >>>>
> >>>>
> >>>>  Hi Wei,
> >>>>>
> >>>>> Thanks for the update.
> >>>>> I'll wait to hear from you.
> >>>>>
> >>>>> -Barbara
> >>>>> address@hidden
> >>>>>
> >>>>>
> >>>>> On Wed, 24 Sep 2014, Wei Huang wrote:
> >>>>>
> >>>>>  Barbara,
> >>>>>
> >>>>>
> >>>>>> I am able to repeat this issue with a very short NCL script.
> >>>>>> We'll do more debug and will let you know if we still have problem.
> >>>>>>
> >>>>>> Thanks,
> >>>>>>
> >>>>>> Wei
> >>>>>>
> >>>>>> ================================================
> >>>>>> 1850 Table Mesa Dr.
> >>>>>> Boulder, CO 80307
> >>>>>> Phone: 303-497-8924
> >>>>>>
> >>>>>> On Wed, Sep 24, 2014 at 3:01 PM, Wei Huang <address@hidden>
> wrote:
> >>>>>>
> >>>>>>  Barbara,
> >>>>>>
> >>>>>>
> >>>>>>> The problem came from a user running NCL.
> >>>>>>> We got the data (two netcdf files, total of 35G), and could
> reproduce
> >>>>>>> the
> >>>>>>> issue when we compile NCL with HDF5-1.8.13, and NetCDF-4.3.2.
> >>>>>>> But there is no problem when we use HDF5-1.8.12, and NetCDF-4.3.2.
> >>>>>>> Then we try to reproduce the problem without read those two large
> >>>>>>> files,
> >>>>>>> but it seems NCL works with HDF5-1.8.13 and NetCDF-4.3.2 with
> >>>>>>> simple code.
> >>>>>>>
> >>>>>>> This kind of put us in a place of no where, which we do not know
> >>>>>>> where
> >>>>>>> and how to debug this problem. That is why I send the question to
> >>>>>>> netcdf-support.
> >>>>>>> I do not know if want to send you the data and NCL script to debug
> >>>>>>> this issue. If you feel the data is too much, and the problem is
> from
> >>>>>>> NCL,
> >>>>>>> could you please check with your developers to see if they have any
> >>>>>>> idea?
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>>
> >>>>>>> Wei
> >>>>>>>
> >>>>>>> ================================================
> >>>>>>> 1850 Table Mesa Dr.
> >>>>>>> Boulder, CO 80307
> >>>>>>> Phone: 303-497-8924
> >>>>>>>
> >>>>>>> On Wed, Sep 24, 2014 at 12:39 PM, <address@hidden> wrote:
> >>>>>>>
> >>>>>>>  Hi Wei,
> >>>>>>>
> >>>>>>>
> >>>>>>>> Yes, please do send us a way to reproduce the issue. (I don't know
> >>>>>>>> what
> >>>>>>>> the problem is off-hand.)
> >>>>>>>>
> >>>>>>>> Thanks!
> >>>>>>>> -Barbara
> >>>>>>>>
> >>>>>>>> ======================
> >>>>>>>> Barbara Jones
> >>>>>>>> The HDF Group Helpdesk
> >>>>>>>> address@hidden
> >>>>>>>> ======================
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>  Hi Wei,
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>  I will forward this question to address@hidden, because the
> >>>>>>>>> symptoms
> >>>>>>>>> are
> >>>>>>>>> something that doesn't work with HDF5-1.8.13 but did work with
> >>>>>>>>> HDF5-1.8.12.
> >>>>>>>>>
> >>>>>>>>> They may ask you for a way to duplicate the problem, unless they
> >>>>>>>>> can
> >>>>>>>>> tell what
> >>>>>>>>> the problem is from the HDF5 error messages you have supplied.
> >>>>>>>>>
> >>>>>>>>> --Russ
> >>>>>>>>>
> >>>>>>>>>  We try to create a netcdf file with write mode: netcdf4classic.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>  It works with a test program, but failed with a real case, with
> >>>>>>>>>> the
> >>>>>>>>>> error
> >>>>>>>>>> message below.
> >>>>>>>>>>
> >>>>>>>>>> We use HDF5-1.8.13 with netcdf4.3.2.
> >>>>>>>>>>
> >>>>>>>>>> If compiled with HDF5-1.8.12, and netcdf4.3.2, the real case
> >>>>>>>>>> worked.
> >>>>>>>>>>
> >>>>>>>>>> We have checked the real case code few times, but did not find
> >>>>>>>>>> anything
> >>>>>>>>>> wrong.
> >>>>>>>>>>
> >>>>>>>>>> Thanks for any help on this issue.
> >>>>>>>>>>
> >>>>>>>>>> Wei
> >>>>>>>>>>
> >>>>>>>>>> --------------------------------
> >>>>>>>>>>
> >>>>>>>>>> HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:
> >>>>>>>>>> #000: H5P.c line 303 in H5Pcreate(): unable to create property
> >>>>>>>>>> list
> >>>>>>>>>> major: Property lists
> >>>>>>>>>> minor: Unable to create file
> >>>>>>>>>> #001: H5Pint.c line 1747 in H5P_create_id(): unable to atomize
> >>>>>>>>>> property
> >>>>>>>>>> list
> >>>>>>>>>> major: Property lists
> >>>>>>>>>> minor: Unable to register new atom
> >>>>>>>>>> #002: H5I.c line 895 in H5I_register(): can't insert ID node
> into
> >>>>>>>>>> skip
> >>>>>>>>>> list
> >>>>>>>>>> major: Object atom
> >>>>>>>>>> minor: Unable to insert object
> >>>>>>>>>> #003: H5SL.c line 995 in H5SL_insert(): can't create new skip
> list
> >>>>>>>>>> node
> >>>>>>>>>> major: Skip Lists
> >>>>>>>>>> minor: Unable to insert object
> >>>>>>>>>> #004: H5SL.c line 687 in H5SL_insert_common(): can't insert
> >>>>>>>>>> duplicate
> >>>>>>>>>> key
> >>>>>>>>>> major: Skip Lists
> >>>>>>>>>> minor: Unable to insert object
> >>>>>>>>>>
> >>>>>>>>>> ================================================
> >>>>>>>>>> 1850 Table Mesa Dr.
> >>>>>>>>>> Boulder, CO 80307
> >>>>>>>>>> Phone: 303-497-8924
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>  Russ Rew                                         UCAR Unidata
> >>>>>>>>>> Program
> >>>>>>>>>>
> >>>>>>>>>>  address@hidden
> >>>>>>>>> http://www.unidata.ucar.edu
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Ticket Details
> >>>>>>>>> ===================
> >>>>>>>>> Ticket ID: MRA-585540
> >>>>>>>>> Department: Support netCDF
> >>>>>>>>> Priority: Normal
> >>>>>>>>> Status: Closed
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>  --
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>   --
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>  --
> >>>
> >>>
> >>
> > --
> >
>
>
>
> Ticket Details
> ===================
> Ticket ID: MRA-585540
> Department: Support netCDF
> Priority: Normal
> Status: Open
> Link:
> https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=24503
>



Ticket Details
===================
Ticket ID: MRA-585540
Department: Support netCDF
Priority: Normal
Status: Open