subject:"\[Paraview\] segmentation fault with netCDF when loading state file"

Re: [Paraview] segmentation fault with netCDF when loading state file

2015-10-30 Thread David Lonie

On Wed, Oct 28, 2015 at 9:47 PM, Ryan Abernathey 
wrote:

> Yes, I can confirm that this state loads without crashing in 4.4.
> The fields are not actually accessible at the current timestep (appear
> with a "?"), but can be rewound to the beginning and restarted without
> crashing.
>

By fields, I assume you are referring to the data arrays in the information
panel? These seem to load correctly for me here, but then the sample data I
have appears to only be a single timestep. Do you have a small dataset that
reproduces this issue?

Thanks,
Dave
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Re: [Paraview] segmentation fault with netCDF when loading state file

2015-10-28 Thread Ryan Abernathey

Yes, I can confirm that this state loads without crashing in 4.4.
The fields are not actually accessible at the current timestep (appear with
a "?"), but can be rewound to the beginning and restarted without crashing.

On Tue, Oct 27, 2015 at 1:16 PM, Ryan Abernathey 
wrote:

> David,
> Thanks for your investigation. I will be able to try this tomorrow. The
> original issue was with Paraview 4.3.1. We recently built the latest
> master, so I will be able to confirm whether it was fixed in between.
> Best,
> Ryan
>
>
>
> On Tue, Oct 27, 2015 at 10:23 AM, David Lonie 
> wrote:
>
>> Hi Ryan,
>>
>> I'm looking into this issue.
>>
>> I download the sample data you provided, and the state file loads and
>> renders fine for me with the current (as of this morning) master branch of
>> ParaView. What version of ParaView are you using? Can you test the latest
>> master branch? It appears that whatever the bug was, it has been fixed.
>>
>> Dave
>>
>> On Wed, Oct 21, 2015 at 9:50 AM, Aashish Chaudhary <
>> aashish.chaudh...@kitware.com> wrote:
>>
>>> Ryan,
>>>
>>> would it be possible for you to share a sample dataset? The NetCDF
>>> reader has fails to read data in certain corner cases but without having
>>> the data to reproduce the issue it is kind of little tricky to get to the
>>> problem.
>>>
>>> - Aashish
>>>
>>> On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey <
>>> ryan.abernat...@gmail.com> wrote:
>>>
 Does anyone have any feedback on this issue?

 I have no idea how to debug or continue. I will have to abandon
 paraview for my project unless I can get some help somehow.

 Thanks,

 Ryan Abernathey
 Assistant Professor
 Columbia University, Department of Earth & Environmental Sciences
 Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
 205 C Oceanography
 61 Route 9W - PO Box 1000
 Palisades, NY 10964-8000
 http://rabernat.github.io
 r...@ldeo.columbia.edu


 On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <
 ryan.abernat...@gmail.com> wrote:

> Hello,
>
> I am extremely frustrated and stuck on this problem. Any advice would
> be appreciated.
>
> I am working with a dataset of 2400 sequentially numbered netCDF files
> (generic & CF conventions).
>
> In a fresh pipeline, Paraview is able to recognizes these files as a
> single source and load them correctly. I then create a standard pipeline
> involving various filters (contour, etc., nothing funny) and save a state
> file.
>
> When I attempt to load the state file, I get the following
> segmentation fault. Further down you can see a ncdump of the offending 
> file.
>
> Would appreciate any advice on how to debug / overcome this issue. Is
> it a bug? It sure feels like one...
>
> Best,
> Ryan Abernathey
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
> line 822
> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
> dimension bound
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: 
> vtkInformation
> (0x8141700)
>   Debug: Off
>   Modified Time: 05
>   Reference Count: 1
>   Registered Events: (none)
>   Request: REQUEST_DATA
>   FORWARD_DIRECTION: 0
>   FROM_OUTPUT_PORT: 0
>   ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkCompositeDataPipeline (0x744fde0): Algorithm
> vtkPVGeometryFilter(0x7436500) returned failure for request: 
> vtkInformation
> (0x5737250)
>   Debug: Off
>   Modified Time: 43
>   Reference Count: 1
>   Registered Events: (none)
>   Request: REQUEST_DATA_OBJECT
>   FORWARD_DIRECTION: 0
>   FROM_OUTPUT_PORT: 0
>   ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> Segmentation fault (core dumped)
>
>
>
>
>
> 
> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
> dimensions:
> x = 512 ;
> y = 512 ;
> z = 64 ;
> time = UNLIMITED ; // (1 currently)
> variables:
> float x(x) ;
> x:units = "m" ;
> float y(y) ;
> y:units = "m" ;
> float z(z) ;
> z:units = "m" ;
>

Re: [Paraview] segmentation fault with netCDF when loading state file

2015-10-27 Thread Ryan Abernathey

David,
Thanks for your investigation. I will be able to try this tomorrow. The
original issue was with Paraview 4.3.1. We recently built the latest
master, so I will be able to confirm whether it was fixed in between.
Best,
Ryan



On Tue, Oct 27, 2015 at 10:23 AM, David Lonie 
wrote:

> Hi Ryan,
>
> I'm looking into this issue.
>
> I download the sample data you provided, and the state file loads and
> renders fine for me with the current (as of this morning) master branch of
> ParaView. What version of ParaView are you using? Can you test the latest
> master branch? It appears that whatever the bug was, it has been fixed.
>
> Dave
>
> On Wed, Oct 21, 2015 at 9:50 AM, Aashish Chaudhary <
> aashish.chaudh...@kitware.com> wrote:
>
>> Ryan,
>>
>> would it be possible for you to share a sample dataset? The NetCDF reader
>> has fails to read data in certain corner cases but without having the data
>> to reproduce the issue it is kind of little tricky to get to the problem.
>>
>> - Aashish
>>
>> On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey <
>> ryan.abernat...@gmail.com> wrote:
>>
>>> Does anyone have any feedback on this issue?
>>>
>>> I have no idea how to debug or continue. I will have to abandon paraview
>>> for my project unless I can get some help somehow.
>>>
>>> Thanks,
>>>
>>> Ryan Abernathey
>>> Assistant Professor
>>> Columbia University, Department of Earth & Environmental Sciences
>>> Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
>>> 205 C Oceanography
>>> 61 Route 9W - PO Box 1000
>>> Palisades, NY 10964-8000
>>> http://rabernat.github.io
>>> r...@ldeo.columbia.edu
>>>
>>>
>>> On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <
>>> ryan.abernat...@gmail.com> wrote:
>>>
 Hello,

 I am extremely frustrated and stuck on this problem. Any advice would
 be appreciated.

 I am working with a dataset of 2400 sequentially numbered netCDF files
 (generic & CF conventions).

 In a fresh pipeline, Paraview is able to recognizes these files as a
 single source and load them correctly. I then create a standard pipeline
 involving various filters (contour, etc., nothing funny) and save a state
 file.

 When I attempt to load the state file, I get the following segmentation
 fault. Further down you can see a ncdump of the offending file.

 Would appreciate any advice on how to debug / overcome this issue. Is
 it a bug? It sure feels like one...

 Best,
 Ryan Abernathey


 ERROR: In
 /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
 line 822
 vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
 dimension bound


 ERROR: In
 /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
 line 784
 vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
 vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
 (0x8141700)
   Debug: Off
   Modified Time: 05
   Reference Count: 1
   Registered Events: (none)
   Request: REQUEST_DATA
   FORWARD_DIRECTION: 0
   FROM_OUTPUT_PORT: 0
   ALGORITHM_AFTER_FORWARD: 1




 ERROR: In
 /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
 line 784
 vtkCompositeDataPipeline (0x744fde0): Algorithm
 vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
 (0x5737250)
   Debug: Off
   Modified Time: 43
   Reference Count: 1
   Registered Events: (none)
   Request: REQUEST_DATA_OBJECT
   FORWARD_DIRECTION: 0
   FROM_OUTPUT_PORT: 0
   ALGORITHM_AFTER_FORWARD: 1




 Segmentation fault (core dumped)





 
 $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
 netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
 dimensions:
 x = 512 ;
 y = 512 ;
 z = 64 ;
 time = UNLIMITED ; // (1 currently)
 variables:
 float x(x) ;
 x:units = "m" ;
 float y(y) ;
 y:units = "m" ;
 float z(z) ;
 z:units = "m" ;
 z:long_name = "height" ;
 float time(time) ;
 time:units = "d" ;
 time:long_name = "time" ;
 float p(z) ;
 p:units = "mb" ;
 p:long_name = "pressure" ;
 float zi(z) ;
 zi:units = "m" ;
 zi:long_name = "intfc_ht" ;
 float U(time, z, y, x) ;
 U:long_name = "X Wind
 Component" 
 ;
 U:units =

Re: [Paraview] segmentation fault with netCDF when loading state file

2015-10-27 Thread David Lonie

Hi Ryan,

I'm looking into this issue.

I download the sample data you provided, and the state file loads and
renders fine for me with the current (as of this morning) master branch of
ParaView. What version of ParaView are you using? Can you test the latest
master branch? It appears that whatever the bug was, it has been fixed.

Dave

On Wed, Oct 21, 2015 at 9:50 AM, Aashish Chaudhary <
aashish.chaudh...@kitware.com> wrote:

> Ryan,
>
> would it be possible for you to share a sample dataset? The NetCDF reader
> has fails to read data in certain corner cases but without having the data
> to reproduce the issue it is kind of little tricky to get to the problem.
>
> - Aashish
>
> On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey <
> ryan.abernat...@gmail.com> wrote:
>
>> Does anyone have any feedback on this issue?
>>
>> I have no idea how to debug or continue. I will have to abandon paraview
>> for my project unless I can get some help somehow.
>>
>> Thanks,
>>
>> Ryan Abernathey
>> Assistant Professor
>> Columbia University, Department of Earth & Environmental Sciences
>> Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
>> 205 C Oceanography
>> 61 Route 9W - PO Box 1000
>> Palisades, NY 10964-8000
>> http://rabernat.github.io
>> r...@ldeo.columbia.edu
>>
>>
>> On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <
>> ryan.abernat...@gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I am extremely frustrated and stuck on this problem. Any advice would be
>>> appreciated.
>>>
>>> I am working with a dataset of 2400 sequentially numbered netCDF files
>>> (generic & CF conventions).
>>>
>>> In a fresh pipeline, Paraview is able to recognizes these files as a
>>> single source and load them correctly. I then create a standard pipeline
>>> involving various filters (contour, etc., nothing funny) and save a state
>>> file.
>>>
>>> When I attempt to load the state file, I get the following segmentation
>>> fault. Further down you can see a ncdump of the offending file.
>>>
>>> Would appreciate any advice on how to debug / overcome this issue. Is it
>>> a bug? It sure feels like one...
>>>
>>> Best,
>>> Ryan Abernathey
>>>
>>>
>>> ERROR: In
>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
>>> line 822
>>> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
>>> dimension bound
>>>
>>>
>>> ERROR: In
>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
>>> line 784
>>> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
>>> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
>>> (0x8141700)
>>>   Debug: Off
>>>   Modified Time: 05
>>>   Reference Count: 1
>>>   Registered Events: (none)
>>>   Request: REQUEST_DATA
>>>   FORWARD_DIRECTION: 0
>>>   FROM_OUTPUT_PORT: 0
>>>   ALGORITHM_AFTER_FORWARD: 1
>>>
>>>
>>>
>>>
>>> ERROR: In
>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
>>> line 784
>>> vtkCompositeDataPipeline (0x744fde0): Algorithm
>>> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
>>> (0x5737250)
>>>   Debug: Off
>>>   Modified Time: 43
>>>   Reference Count: 1
>>>   Registered Events: (none)
>>>   Request: REQUEST_DATA_OBJECT
>>>   FORWARD_DIRECTION: 0
>>>   FROM_OUTPUT_PORT: 0
>>>   ALGORITHM_AFTER_FORWARD: 1
>>>
>>>
>>>
>>>
>>> Segmentation fault (core dumped)
>>>
>>>
>>>
>>>
>>>
>>> 
>>> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
>>> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
>>> dimensions:
>>> x = 512 ;
>>> y = 512 ;
>>> z = 64 ;
>>> time = UNLIMITED ; // (1 currently)
>>> variables:
>>> float x(x) ;
>>> x:units = "m" ;
>>> float y(y) ;
>>> y:units = "m" ;
>>> float z(z) ;
>>> z:units = "m" ;
>>> z:long_name = "height" ;
>>> float time(time) ;
>>> time:units = "d" ;
>>> time:long_name = "time" ;
>>> float p(z) ;
>>> p:units = "mb" ;
>>> p:long_name = "pressure" ;
>>> float zi(z) ;
>>> zi:units = "m" ;
>>> zi:long_name = "intfc_ht" ;
>>> float U(time, z, y, x) ;
>>> U:long_name = "X Wind
>>> Component" ;
>>> U:units = "m/s   " ;
>>> float V(time, z, y, x) ;
>>> V:long_name = "Y Wind
>>> Component" ;
>>> V:units = "m/s   " ;
>>> float W(time, z, y, x) ;
>>> W:long_name = "Z Wind
>>> Component" ;
>>> W:units = "m/s   " ;
>>> float PP(time, z, y, x) ;
>>> PP:long_name = "Pressure
>>> Perturbation

Re: [Paraview] segmentation fault with netCDF when loading state file

2015-10-21 Thread Ryan Abernathey

Does anyone have any feedback on this issue?

I have no idea how to debug or continue. I will have to abandon paraview
for my project unless I can get some help somehow.

Thanks,

Ryan Abernathey
Assistant Professor
Columbia University, Department of Earth & Environmental Sciences
Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
205 C Oceanography
61 Route 9W - PO Box 1000
Palisades, NY 10964-8000
http://rabernat.github.io
r...@ldeo.columbia.edu


On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey 
wrote:

> Hello,
>
> I am extremely frustrated and stuck on this problem. Any advice would be
> appreciated.
>
> I am working with a dataset of 2400 sequentially numbered netCDF files
> (generic & CF conventions).
>
> In a fresh pipeline, Paraview is able to recognizes these files as a
> single source and load them correctly. I then create a standard pipeline
> involving various filters (contour, etc., nothing funny) and save a state
> file.
>
> When I attempt to load the state file, I get the following segmentation
> fault. Further down you can see a ncdump of the offending file.
>
> Would appreciate any advice on how to debug / overcome this issue. Is it a
> bug? It sure feels like one...
>
> Best,
> Ryan Abernathey
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
> line 822
> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
> dimension bound
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
> (0x8141700)
>   Debug: Off
>   Modified Time: 05
>   Reference Count: 1
>   Registered Events: (none)
>   Request: REQUEST_DATA
>   FORWARD_DIRECTION: 0
>   FROM_OUTPUT_PORT: 0
>   ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkCompositeDataPipeline (0x744fde0): Algorithm
> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
> (0x5737250)
>   Debug: Off
>   Modified Time: 43
>   Reference Count: 1
>   Registered Events: (none)
>   Request: REQUEST_DATA_OBJECT
>   FORWARD_DIRECTION: 0
>   FROM_OUTPUT_PORT: 0
>   ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> Segmentation fault (core dumped)
>
>
>
>
>
> 
> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
> dimensions:
> x = 512 ;
> y = 512 ;
> z = 64 ;
> time = UNLIMITED ; // (1 currently)
> variables:
> float x(x) ;
> x:units = "m" ;
> float y(y) ;
> y:units = "m" ;
> float z(z) ;
> z:units = "m" ;
> z:long_name = "height" ;
> float time(time) ;
> time:units = "d" ;
> time:long_name = "time" ;
> float p(z) ;
> p:units = "mb" ;
> p:long_name = "pressure" ;
> float zi(z) ;
> zi:units = "m" ;
> zi:long_name = "intfc_ht" ;
> float U(time, z, y, x) ;
> U:long_name = "X Wind
> Component" ;
> U:units = "m/s   " ;
> float V(time, z, y, x) ;
> V:long_name = "Y Wind
> Component" ;
> V:units = "m/s   " ;
> float W(time, z, y, x) ;
> W:long_name = "Z Wind
> Component" ;
> W:units = "m/s   " ;
> float PP(time, z, y, x) ;
> PP:long_name = "Pressure
> Perturbation   " ;
> PP:units = "Pa" ;
> float QRAD(time, z, y, x) ;
> QRAD:long_name = "Radiative heating
> rate  " ;
> QRAD:units = "K/day " ;
> float TABS(time, z, y, x) ;
> TABS:long_name = "Absolute
> Temperature" ;
> TABS:units = "K " ;
> float QV(time, z, y, x) ;
> QV:long_name = "Water
> Vapor "
> ;
> QV:units = "g/kg  " ;
> float QN(time, z, y, x) ;
> QN:long_name = "Non-precipitating Condensate
> (Water+Ice)" ;
> QN:units = "g/kg  " ;
> float QP(time, z, y, x) ;
> QP:long_name = "Precipitating Water
> (Rain+Snow) " ;
> QP:units = "g/kg  " ;
> float LQRAD(time, z, y, x) ;
>

Re: [Paraview] segmentation fault with netCDF when loading state file

2015-10-21 Thread Aashish Chaudhary

Ryan,

would it be possible for you to share a sample dataset? The NetCDF reader
has fails to read data in certain corner cases but without having the data
to reproduce the issue it is kind of little tricky to get to the problem.

- Aashish

On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey 
wrote:

> Does anyone have any feedback on this issue?
>
> I have no idea how to debug or continue. I will have to abandon paraview
> for my project unless I can get some help somehow.
>
> Thanks,
>
> Ryan Abernathey
> Assistant Professor
> Columbia University, Department of Earth & Environmental Sciences
> Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
> 205 C Oceanography
> 61 Route 9W - PO Box 1000
> Palisades, NY 10964-8000
> http://rabernat.github.io
> r...@ldeo.columbia.edu
>
>
> On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <
> ryan.abernat...@gmail.com> wrote:
>
>> Hello,
>>
>> I am extremely frustrated and stuck on this problem. Any advice would be
>> appreciated.
>>
>> I am working with a dataset of 2400 sequentially numbered netCDF files
>> (generic & CF conventions).
>>
>> In a fresh pipeline, Paraview is able to recognizes these files as a
>> single source and load them correctly. I then create a standard pipeline
>> involving various filters (contour, etc., nothing funny) and save a state
>> file.
>>
>> When I attempt to load the state file, I get the following segmentation
>> fault. Further down you can see a ncdump of the offending file.
>>
>> Would appreciate any advice on how to debug / overcome this issue. Is it
>> a bug? It sure feels like one...
>>
>> Best,
>> Ryan Abernathey
>>
>>
>> ERROR: In
>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
>> line 822
>> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
>> dimension bound
>>
>>
>> ERROR: In
>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
>> line 784
>> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
>> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
>> (0x8141700)
>>   Debug: Off
>>   Modified Time: 05
>>   Reference Count: 1
>>   Registered Events: (none)
>>   Request: REQUEST_DATA
>>   FORWARD_DIRECTION: 0
>>   FROM_OUTPUT_PORT: 0
>>   ALGORITHM_AFTER_FORWARD: 1
>>
>>
>>
>>
>> ERROR: In
>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
>> line 784
>> vtkCompositeDataPipeline (0x744fde0): Algorithm
>> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
>> (0x5737250)
>>   Debug: Off
>>   Modified Time: 43
>>   Reference Count: 1
>>   Registered Events: (none)
>>   Request: REQUEST_DATA_OBJECT
>>   FORWARD_DIRECTION: 0
>>   FROM_OUTPUT_PORT: 0
>>   ALGORITHM_AFTER_FORWARD: 1
>>
>>
>>
>>
>> Segmentation fault (core dumped)
>>
>>
>>
>>
>>
>> 
>> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
>> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
>> dimensions:
>> x = 512 ;
>> y = 512 ;
>> z = 64 ;
>> time = UNLIMITED ; // (1 currently)
>> variables:
>> float x(x) ;
>> x:units = "m" ;
>> float y(y) ;
>> y:units = "m" ;
>> float z(z) ;
>> z:units = "m" ;
>> z:long_name = "height" ;
>> float time(time) ;
>> time:units = "d" ;
>> time:long_name = "time" ;
>> float p(z) ;
>> p:units = "mb" ;
>> p:long_name = "pressure" ;
>> float zi(z) ;
>> zi:units = "m" ;
>> zi:long_name = "intfc_ht" ;
>> float U(time, z, y, x) ;
>> U:long_name = "X Wind
>> Component" ;
>> U:units = "m/s   " ;
>> float V(time, z, y, x) ;
>> V:long_name = "Y Wind
>> Component" ;
>> V:units = "m/s   " ;
>> float W(time, z, y, x) ;
>> W:long_name = "Z Wind
>> Component" ;
>> W:units = "m/s   " ;
>> float PP(time, z, y, x) ;
>> PP:long_name = "Pressure
>> Perturbation   " ;
>> PP:units = "Pa" ;
>> float QRAD(time, z, y, x) ;
>> QRAD:long_name = "Radiative heating
>> rate  " ;
>> QRAD:units = "K/day " ;
>> float TABS(time, z, y, x) ;
>> TABS:long_name = "Absolute
>> Temperature" ;
>> TABS:units = "K " ;
>> float QV(time, z, y, x) ;
>> QV:long_name = "Water
>> Vapor

[Paraview] segmentation fault with netCDF when loading state file

2015-10-19 Thread Ryan Abernathey

Hello,

I am extremely frustrated and stuck on this problem. Any advice would be
appreciated.

I am working with a dataset of 2400 sequentially numbered netCDF files
(generic & CF conventions).

In a fresh pipeline, Paraview is able to recognizes these files as a single
source and load them correctly. I then create a standard pipeline involving
various filters (contour, etc., nothing funny) and save a state file.

When I attempt to load the state file, I get the following segmentation
fault. Further down you can see a ncdump of the offending file.

Would appreciate any advice on how to debug / overcome this issue. Is it a
bug? It sure feels like one...

Best,
Ryan Abernathey


ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
line 822
vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
dimension bound


ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
line 784
vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
(0x8141700)
  Debug: Off
  Modified Time: 05
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA
  FORWARD_DIRECTION: 0
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1




ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
line 784
vtkCompositeDataPipeline (0x744fde0): Algorithm
vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
(0x5737250)
  Debug: Off
  Modified Time: 43
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FORWARD_DIRECTION: 0
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1




Segmentation fault (core dumped)






$ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
dimensions:
x = 512 ;
y = 512 ;
z = 64 ;
time = UNLIMITED ; // (1 currently)
variables:
float x(x) ;
x:units = "m" ;
float y(y) ;
y:units = "m" ;
float z(z) ;
z:units = "m" ;
z:long_name = "height" ;
float time(time) ;
time:units = "d" ;
time:long_name = "time" ;
float p(z) ;
p:units = "mb" ;
p:long_name = "pressure" ;
float zi(z) ;
zi:units = "m" ;
zi:long_name = "intfc_ht" ;
float U(time, z, y, x) ;
U:long_name = "X Wind
Component" ;
U:units = "m/s   " ;
float V(time, z, y, x) ;
V:long_name = "Y Wind
Component" ;
V:units = "m/s   " ;
float W(time, z, y, x) ;
W:long_name = "Z Wind
Component" ;
W:units = "m/s   " ;
float PP(time, z, y, x) ;
PP:long_name = "Pressure
Perturbation   " ;
PP:units = "Pa" ;
float QRAD(time, z, y, x) ;
QRAD:long_name = "Radiative heating
rate  " ;
QRAD:units = "K/day " ;
float TABS(time, z, y, x) ;
TABS:long_name = "Absolute
Temperature" ;
TABS:units = "K " ;
float QV(time, z, y, x) ;
QV:long_name = "Water
Vapor "
;
QV:units = "g/kg  " ;
float QN(time, z, y, x) ;
QN:long_name = "Non-precipitating Condensate
(Water+Ice)" ;
QN:units = "g/kg  " ;
float QP(time, z, y, x) ;
QP:long_name = "Precipitating Water
(Rain+Snow) " ;
QP:units = "g/kg  " ;
float LQRAD(time, z, y, x) ;
LQRAD:long_name = "LW Radiative heating
rate   " ;
LQRAD:units = "K/day " ;
float SQRAD(time, z, y, x) ;
SQRAD:long_name = "SW Radiative heating
rate   " ;
SQRAD:units = "K/day " ;
}
___
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Re: [Paraview] segmentation fault with netCDF when loading state file

Re: [Paraview] segmentation fault with netCDF when loading state file

Re: [Paraview] segmentation fault with netCDF when loading state file

Re: [Paraview] segmentation fault with netCDF when loading state file

Re: [Paraview] segmentation fault with netCDF when loading state file

Re: [Paraview] segmentation fault with netCDF when loading state file

[Paraview] segmentation fault with netCDF when loading state file

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