[ncl-install] HDF5 and NC4 messages in NCL

[Christina Karamperidou]

thank you Will and apologies for my inefficient search of previous posts.

Indeed, nc-config gives me version 4.6.2. Interestingly, when I run cdo in the same ncl_stable environment, it indicates that it runs version 4.6.3…  

In any case, for now I will not fight with 6.6.2, since 6.5.0 meets my needs. I restored the whole miniconda3 file from my backups and I’m back to 6.5.0 with netcdf 4.6.1 and no warnings. 
 
Christina 


> On Apr 11, 2019, at 4:30 PM, Will Hobbs <will.hobbs at utas.edu.au> wrote:
> 
> Christina
>  
> There have been a number of posts about this issue, it seems to be that conda installs an older version of netcdf (4.62.) with this bug, instead of the latest version (4.6.3). You could fix it by somehow installing the latest version of netcdf4 into your conda environment, or installing NCL from binary like back in the good old days.
>  
> An alternative hack – which I in no way advocate or endorse, nor would I ever admit to using myself – is to invoke NCL in the following fashion:
>  
> ncl 2>dev/null …
>  
> You’ll still get NCL error/warning messages
>  
> Will
>  
> From: ncl-install <ncl-install-bounces at ucar.edu> on behalf of Christina Karamperidou via ncl-install <ncl-install at ucar.edu>
> Reply-To: Christina Karamperidou <ckaramp at hawaii.edu>
> Date: Friday, 12 April 2019 at 12:16 PM
> To: "ncl-install at ucar.edu" <ncl-install at ucar.edu>
> Subject: [ncl-install] HDF5 and NC4 messages in NCL
>  
> Hello NCL-install  
>  
> I believe this may be an installation issue but I cannot trace it back to its source to make it stop. 
> NCL (version 6.6.2) prints a list of messages when I read datasets. 
> Examples: 
>  
> f5      = addfile ("test.nc <http://test.nc/>", "r")
> NC4_open: path test.nc <http://test.nc/> mode 4096 params 0
> HDF5 error messages turned on.
> nc4_open_file: path test.nc <http://test.nc/> mode 4096
> nc4_grp_list_add: name / 
> nc4_rec_read_metadata: grp->hdr.name <http://hdr.name/> /
> found dataset lon
> found dataset lat
> found dataset lev
>  
> When I exit NCL (after having read the dataset), I get the following (with many similar lines following): 
> 
> 
> ncl 1> exit
> NC4_close: ncid 0x10000
> nc4_close_hdf5_file: h5->path /test.nc <http://test.nc/> abort 0
> nc4_rec_grp_HDF5_del: grp->name /
> closing HDF5 dataset 360287970189639751
> closing HDF5 dataset 360287970189639752
> closing HDF5 dataset 360287970189639753
> closing HDF5 dataset 360287970189639754
> closing HDF5 dataset 360287970189639756
> 
> 
> 
> 
> Is there a way to mute these warnings/notifications? 
> I tried uninstalling and reinstalling HDF5 and NCL via conda, but it didn’t help. 
> I do not get these messages outside the ncl_stable environment, where I run NCL version 6.2.1.   
> 
> 
> thank you,
> Christina 
>  
> 
> 
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