ParaView issueshttps://gitlab.kitware.com/paraview/paraview/-/issues2021-03-23T13:09:53-04:00https://gitlab.kitware.com/paraview/paraview/-/issues/17295XDMF3 reader fails to read large file in parallel2021-03-23T13:09:53-04:00Jean M. FavreXDMF3 reader fails to read large file in parallelI have a 1.8Tb file in HDF5 format, with a single variable per file (uniform grid of size 7680*7680*7680). The XDMF reader version 2 reads it without problem, using 256 tasks (64 nodes of 64Gb each).
the XDMF reader version 3 crashes wi...I have a 1.8Tb file in HDF5 format, with a single variable per file (uniform grid of size 7680*7680*7680). The XDMF reader version 2 reads it without problem, using 256 tasks (64 nodes of 64Gb each).
the XDMF reader version 3 crashes with the error:
terminate called after throwing an instance of 'XdmfError'
what(): Number of values in hdf5 dataset (452984832000)
does not match allocated size in XdmfArray (2013265920).
Am not sure if it is a problem of syntax, or something worse. My XDMF file is:
>>>
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
<Domain>
<Grid GridType="Uniform">
<Topology TopologyType="3DCORECTMesh" Dimensions=" 7680 7680 7680"/>
<Geometry GeometryType="ORIGIN_DXDYDZ">
<DataItem Name="Origin" Dimensions="3" NumberType="Float" Precision="4" Format="XML">
0.0 0.0 0.0
</DataItem>
<DataItem Name="Spacing" Dimensions="3" NumberType="Float" Precision="4" Format="XML">
1.0E-00 1.0E-00 1.0E-00
</DataItem>
</Geometry>
<Attribute Name="phi0" Active="1" AttributeType="Scalar" Center="Node">
<DataItem Dimensions=" 7680 7680 7680" NumberType="Float" Precision="4" Format="HDF">lc_9600box_7680_lightcone_phi_0.h5:/data</DataItem>
</Attribute>
</Grid>
</Domain>
</Xdmf>
>>>https://gitlab.kitware.com/paraview/paraview/-/issues/17246Empty result on large rectilinear grid2021-03-23T13:15:44-04:00Paul MelisEmpty result on large rectilinear grid#17245 might be related to this.
On the same dataset (rectilinear grid of 1297x1536x1536 points read from an Xdmf file) filters applied to the loaded dataset have empty output (0 points, 0 cells). I tried Clip (plane and box) and Slice...#17245 might be related to this.
On the same dataset (rectilinear grid of 1297x1536x1536 points read from an Xdmf file) filters applied to the loaded dataset have empty output (0 points, 0 cells). I tried Clip (plane and box) and Slice, both give empty result. ExtractSubset does seem to work, though.https://gitlab.kitware.com/paraview/paraview/-/issues/17245Overflow in information panel2021-03-23T13:02:32-04:00Paul MelisOverflow in information panelOne of our users has a rectilinear grid of 1297x1536x1536 points, defined in an Xdmf file. When loaded in PV5.3.0RC2 (official binaries) the Information tab shows the number of Cells correctly as 3053667600, but the number of Points as -...One of our users has a rectilinear grid of 1297x1536x1536 points, defined in an Xdmf file. When loaded in PV5.3.0RC2 (official binaries) the Information tab shows the number of Cells correctly as 3053667600, but the number of Points as -1234960384.https://gitlab.kitware.com/paraview/paraview/-/issues/17207Memory allocation in Paraview2020-05-07T04:15:52-04:00Arthur P.Memory allocation in ParaviewHello,
I'm trying to make an animation (3D isocontour) using XDMF reader of HDF5 data (1Go per file). I have about a thousand files to process. When I'm creating the animation, Paraview always open and allocate the new timestep in memory...Hello,
I'm trying to make an animation (3D isocontour) using XDMF reader of HDF5 data (1Go per file). I have about a thousand files to process. When I'm creating the animation, Paraview always open and allocate the new timestep in memory meaning that after 10 time step the memory allocated by Paraview is already about 10Go, not enough for my system (8Go). Then, Paraview crashes...
I've tried a different approach by using python scripts to open each file independently but I got the same memory leaking problem. Even if I delete everything in my pipeline, Paraview always hold some data in memory. So when I move to the next time step, there is some memory (1Go) remaining from the last time step... The same issue happens, Paraview grows in memory and crashes...
Why is memory leaking in Paraview?
Why am I not able to free the memory of the application using python script? Delete(*) or del * does not seem to clear everything..
Any solution for me?
The only solution I see is to create a bash script to open and close the paraview application for each of my time step...
Thank you.https://gitlab.kitware.com/paraview/paraview/-/issues/16074Crash when loading XDMF file2023-06-19T10:33:41-04:00Kitware RobotCrash when loading XDMF file**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=16074). Further discussion may take place here.**
---
Opening the attached XDMF2 file crashes paraview version 5.01, when using ...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=16074). Further discussion may take place here.**
---
Opening the attached XDMF2 file crashes paraview version 5.01, when using the XDMF reader.
The same file can be read and displayed without problems in version 4.3.
This was tried with the version 5.0.1 from the webpage and from the Ubuntu repositories.https://gitlab.kitware.com/paraview/paraview/-/issues/15879Xdmf data not correctly displayed2020-05-05T23:24:33-04:00Kitware RobotXdmf data not correctly displayed**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15879). Further discussion may take place here.**
---
The attached XDMF file contains three cells:
* 2 triangles and
* 1 q...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15879). Further discussion may take place here.**
---
The attached XDMF file contains three cells:
* 2 triangles and
* 1 quad.
The triangles are read and displayed alright, the quad is not.https://gitlab.kitware.com/paraview/paraview/-/issues/15878Xdmf2Reader: Unknown Attribute Type None, number of components wrong2020-05-05T23:24:50-04:00Kitware RobotXdmf2Reader: Unknown Attribute Type None, number of components wrong**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15878). Further discussion may take place here.**
---
I've noticed some oddities with the vtkXdmfReader. The following script
`...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15878). Further discussion may take place here.**
---
I've noticed some oddities with the vtkXdmfReader. The following script
```
import vtk
reader = vtk.vtkXdmfReader()
reader.SetFileName('test.xmf')
reader.Update()
grid = reader.GetOutputDataObject(0)
point_data = grid.GetPointData()
for k in range(point_data.GetNumberOfArrays()):
array = point_data.GetArray(k)
print(array)
```
produces
```
XDMF Error in
/build/vtk6-01UJ_h/vtk6-7.1.0~20151212165543/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfAttribute.cxx
line 183 (Unknown Attribute Type None)
```
on `GetPointData()`. This is with a simple test file, attached.
The supposed "Error" doesn't stop the execution though. However, for the point data, one gets
```
NumberOfComponents: 1
```
while it is actually 2 (as can be seen by inspecting the file).https://gitlab.kitware.com/paraview/paraview/-/issues/15591ParaView crashes when trying to visualize Volume Data of a 3D microstructure2020-05-06T01:51:36-04:00Kitware RobotParaView crashes when trying to visualize Volume Data of a 3D microstructure**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15591). Further discussion may take place here.**
---
I am using Dream3D software to create a .XDMF file that is read into Parav...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15591). Further discussion may take place here.**
---
I am using Dream3D software to create a .XDMF file that is read into Paraview. It reads in OK, and for small files, I can visualize surfaces with no problem. Once I click on the Volume elements, it throws the following errors:
ERROR: In C:\bbd\b51c3c7f\source-paraview\VTK\Rendering\OpenGL\vtkOpenGLExtensionManager.cxx, line 757
vtkOpenGLExtensionManager (000000000CE5E830): Extension GL_VERSION_1_2 could not be loaded.
ERROR: In C:\bbd\b51c3c7f\source-paraview\VTK\Rendering\OpenGL\vtkOpenGLExtensionManager.cxx, line 757
vtkOpenGLExtensionManager (000000000CE5E830): Extension GL_VERSION_1_2 could not be loaded.
ERROR: In C:\bbd\b51c3c7f\source-paraview\VTK\Rendering\Volume\vtkGPUVolumeRayCastMapper.cxx, line 336
vtkOpenGLGPUVolumeRayCastMapper (000000001452D690): scalar of type VTK_CHAR is not supported because this type is platform dependent. Use VTK_SIGNED_CHAR or VTK_UNSIGNED_CHAR instead.
Usually, after this, the volume elements will be displayed OK. However, for larger files (256 voxels, cubed), when I try to switch to Volume elements, it immediately crashes Paraview. It opens the error message window, but crashes so quickly that it doesn't have time to show me the message. https://gitlab.kitware.com/paraview/paraview/-/issues/15164XDMF fails to save CELL data2023-06-15T11:25:19-04:00Kitware RobotXDMF fails to save CELL data**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15164). Further discussion may take place here.**
---
Load the following XDMF file.(This makes a simple 3x4 planar grid)
Save th...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=15164). Further discussion may take place here.**
---
Load the following XDMF file.(This makes a simple 3x4 planar grid)
Save the data to a new Xdmf file
The saved data contains an Attribute for Cell Centered Values, but the enclpsed DataItem is empty.
<Xdmf Version="2.2">
<Domain>
<Grid GridType="Uniform">
<Topology TopologyType="2DRectMesh" Dimensions="3 4"/>
<Geometry GeometryType="VXVYVZ">
<DataItem Dimensions="1" NumberType="Float" Precision="4" Format="XML">-1</DataItem>
<DataItem Dimensions="4" NumberType="Float" Precision="4" Format="XML">1 1.25 1.5 1.75 </DataItem>
<DataItem Dimensions="3" NumberType="Float" Precision="4" Format="XML">0 0.25 0.5 </DataItem>
</Geometry>
<Attribute Name="Cell Centered Values" Active="1" AttributeType="Scalar" Center="Cell">
<DataItem Dimensions="2 3" NumberType="Int" Precision="4" Format="XML">
1 2 3
4 5 6
</DataItem>
</Attribute>
<Attribute Name="Node Centered Values" Active="1" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="3 4" NumberType="Int" Precision="4" Format="XML">
0 1 1 0
1 2 2 1
2 3 3 2
</DataItem>
</Attribute>
</Grid>
</Domain>
</Xdmf>https://gitlab.kitware.com/paraview/paraview/-/issues/14932XDMF - 8 byte precision UInt is broken2020-05-07T09:44:10-04:00Kitware RobotXDMF - 8 byte precision UInt is broken**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=14932). Further discussion may take place here.**
---
This problem relates to opening XDMF files in Paraview 4.1.
Support for...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=14932). Further discussion may take place here.**
---
This problem relates to opening XDMF files in Paraview 4.1.
Support for XDMF DataItem elements of NumberType=UInt with Precision="8" is broken when using topology stored in an external data file with Format="Binary".
I suspect the driver is trying to interpret the binary value as a signed int rather than an unsigned int.
Using NumberType=Int works OK with Precision="8" and is a satisfatory work around for now.
This might be a trivial fix if it is just a case of correctly casting the data.
https://gitlab.kitware.com/paraview/paraview/-/issues/14353Problems reading 2nd order mixed meshes in xdmf format2023-06-15T11:00:33-04:00Kitware RobotProblems reading 2nd order mixed meshes in xdmf format**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=14353). Further discussion may take place here.**
---
<?xml version="1.0" ?>
<Xdmf>
<Domain Name="Unnamed">
<Grid Name="Mesh">
...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=14353). Further discussion may take place here.**
---
<?xml version="1.0" ?>
<Xdmf>
<Domain Name="Unnamed">
<Grid Name="Mesh">
<Geometry GeometryType="XYZ">
<DataItem Format="XML" Dimensions="10 3">
0.0 0.0 0.0
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
0.5 0.0 0.0
0.5 0.5 0.0
0.0 0.5 0.0
0.0 0.0 0.5
0.5 0.0 0.5
0.0 0.5 0.5
</DataItem>
</Geometry>
The following valid XDMF file causes an error when imported into ParaView 4.0.1:
<Topology TopologyType="Mixed" NumberOfElements="1" >
<DataItem Format="XML" DataType="Int" Dimensions="11">
26 0 1 2 3 4 5 6 7 8 9
</DataItem>
</Topology>
</Grid>
</Domain>
</Xdmf>https://gitlab.kitware.com/paraview/paraview/-/issues/14153xdmf reader crash using stride2023-08-31T04:55:06-04:00Kitware Robotxdmf reader crash using stride**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=14153). Further discussion may take place here.**
---
a simple ascii xdmf file make the reader crash when playing with the strid...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=14153). Further discussion may take place here.**
---
a simple ascii xdmf file make the reader crash when playing with the stride parameter.
to reproduce set Stride to 2 2 1
----- file Structured_Ascci_2D.xdmf ----
```
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0" xmlns:xi="http://www.w3.org/2001/XInclude" >
<Domain Name="tests/Structured_Ascii.pxdmf">
<Grid Name="PGD1" >
<Topology TopologyType="2DCORECTMESH" Dimensions="1 10 10" />
<Geometry GeometryType="ORIGIN_DXDYDZ">
<DataItem Name="Origin" Format="XML" NumberType="Float" Dimensions="3">
0 0 0
</DataItem>
<DataItem Name="Spacing" Format="XML" NumberType="Float" Dimensions="3">
1 1 1
</DataItem>
</Geometry>
<Attribute Name="dep_x_0" Center="Node" AttributeType="Scalar" >
<DataItem Format="XML" NumberType="Float" Precision="8" Dimensions="1 10 10">
10 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 8.0 8.1 8.1 8.3 8.4 8.5 8.6 8.6 8.8 8.9 9.0 9.1 9.1 9.3 9.4 9.5 9.6 9.6 9.8 9.9 0.0
</DataItem>
</Attribute>
</Grid>
</Domain>
</Xdmf>
```Mathieu Westphal (Kitware)Mathieu Westphal (Kitware)https://gitlab.kitware.com/paraview/paraview/-/issues/13978xdmf -binary files crashes with 7 time steps or more.2020-05-04T06:40:22-04:00Kitware Robotxdmf -binary files crashes with 7 time steps or more.**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=13978). Further discussion may take place here.**
---
When I wrap xdmf around numerous time variable binary files, ParaView ...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=13978). Further discussion may take place here.**
---
When I wrap xdmf around numerous time variable binary files, ParaView crashes when deleting this file.
Linux, local server, master (and 3.98.1). Test dataset is one I voodoo'd up. It basically has 8 4 byte floats that are 0 (i.e., 0x00000000). Dataset is attached, and is called stl-timestep-crash.
* Open crash-opening-seven.xmf.
* Delete crash-opening-seven.xmf.
It will crash.
https://gitlab.kitware.com/paraview/paraview/-/issues/12785XDMF Function SQRT results in segfault2023-06-15T08:18:56-04:00Kitware RobotXDMF Function SQRT results in segfault**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=12785). Further discussion may take place here.**
---
defining a node attribute
in an XDMF file (see uploaded file)
using the It...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=12785). Further discussion may take place here.**
---
defining a node attribute
in an XDMF file (see uploaded file)
using the ItemType "Function" as follows
results in a segfault
of a precompiled 64-bit ParaView 3.12.0
on CentOS 5.2
XDMF Function Definition:
Function="SQRT(($0 * $0) + ($1 * $1) + ($2 * $2))"https://gitlab.kitware.com/paraview/paraview/-/issues/11762Xdmf file with hyperslab itemtype crashes Paraview2023-06-15T08:38:35-04:00Kitware RobotXdmf file with hyperslab itemtype crashes Paraview**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=11762). Further discussion may take place here.**
---
The attached file, which is supposed to cut a 2x2x2 cube out of a larger 3...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=11762). Further discussion may take place here.**
---
The attached file, which is supposed to cut a 2x2x2 cube out of a larger 3x3x3 cube, causes Paraview to crash. ("*** glibc detected *** ... realloc(): invalid next size: 0x0000000008e1a800 ***")
To extract the subgrid [0,1]^3 from the larger [0,2]^3 grid, the start-stride-count in the first DataItem is set to
0 0 0
1 1 1
2 2 2
The same behavior occurs when trying to access the opposite corner [1,2]^3 (the one with values in the [8,15] range) using
1 1 1
1 1 1
2 2 2
instead. The crash can apparently be avoided using ranges whose count values are at least 3 (which should obviously be too large for the 2x2x2 target grid), and even grossly out-of-bound values such as
12 11 321
1 1 1
6 13 13
are accepted without complaints, and result in
1 2 0 3 4 0 0 0
i.e. a copy of the beginning of the source array.https://gitlab.kitware.com/paraview/paraview/-/issues/10129XDMF Reader doesn't create vtkIdType arrays out of GlobalID attributes2023-06-19T10:17:56-04:00Kitware RobotXDMF Reader doesn't create vtkIdType arrays out of GlobalID attributes**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=10129). Further discussion may take place here.**
---
The current Xdmf2 format supports AttributeType="GlobalID", but the reader...**This issue was created automatically from an original [Mantis Issue](http://paraview.org/Bug/view.php?id=10129). Further discussion may take place here.**
---
The current Xdmf2 format supports AttributeType="GlobalID", but the reader doesn't really create a vtkIdTypeArray for ParaView when reading in these attributes -- it creates an int type, so ParaView can't really use this as a Global ID.
(This is at least true when reading "heavy data" from an HDF5 file -- I'm not sure what happens when the data is just specified within the .xmf file as XML data...)
In case it helps, I'm detailing what I see as the major issue, plus an outline of my own hacky solution in the Additional Information.