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IDProjectCategoryView StatusDate SubmittedLast Update
0012970ParaView(No Category)public2012-02-29 14:162012-07-25 20:09
ReporterOrion Poplawski 
Assigned ToDave DeMarle 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusclosedResolutionfixed 
PlatformOSOS Version
Product Version 
Target Version3.14.1Fixed in Version3.14.1 
Summary0012970: No way to use netcdf4 with system netcdf
DescriptionThere appears to be no way to set USE_NETCDF4=ON when using the system netcdf libraries. I also see the following:

ENABLE_NETCDF4 not allowed because netcdf4 functionality requires HDF5_BUILD_HL_LIB.

Though I'm not explicitly setting ENABLE_NETCDF4. I'm using system versions of hdf5 and netcdf4.
TagsNo tags attached.
ProjectTBD
Topic Name0012790-netcdf4-with-system-hdf5
Typefeature
Attached Files

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  Notes
(0028330)
Dave DeMarle (administrator)
2012-02-29 14:25

 The message:
ENABLE_NETCDF4 not allowed because netcdf4 functionality requires HDF5_BUILD_HL_LIB.
is expected.

It just means that until your system HDF5 has this flag set, you won't be able to use the new (to us) parts of netcdf that use hdf5. Instead you get the old (netcdf3) behavior we've had for years.

Try turning HDF5_BUILD_HL_LIB on in your system hdf5, and report on the bug if it still doesn't work.
(0028331)
Orion Poplawski (reporter)
2012-02-29 15:19

 HDF5_BUILD_HL_LIB is a VTKism, hdf5 does not define this. Our system hdf5 does have the _hl library.
(0028380)
Dave DeMarle (administrator)
2012-03-21 10:49

 fixed vtknetcdf's cmakelists to recognize external hdf5's hl lib
fixed paraview superbuild to turn on hl lib and use it

tested paraview with vtkhdf5, system hdf5 from macports, and the superbuild built hdf5
all could open the exodus on hdf5 file I have access to

for system hdf5, I started my cmakecache with
VTK_USE_SYSTEM_HDF5:BOOL=ON
HDF5_INCLUDE_DIR:PATH:/opt/local/include.
I suspect on other platforms it will be similar.
(0028381)
Orion Poplawski (reporter)
2012-03-21 14:47

 Is this in git master? Can't any changes to vtknetcdf/CMakeLists.txt.
(0028382)
Dave DeMarle (administrator)
2012-03-21 14:52

 It's only in the next branch until Friday when the next gatekeeper review happens.

It is in VTK master and release branches if you want to try the VTK level out.
(0028383)
Orion Poplawski (reporter)
2012-03-21 15:07

 Hmm, getting:

[orion@orca ParaView (next *)]$ git submodule update
fatal: reference is not a tree: d673341b51ab8e4fdbabf3accd1c494f70a10513
Unable to checkout 'd673341b51ab8e4fdbabf3accd1c494f70a10513' in submodule path 'VTK'
[orion@orca ParaView (next *)]$ git diff
diff --git a/VTK b/VTK
index d673341..b327915 160000
--- a/VTK
+++ b/VTK
@@ -1 +1 @@
-Subproject commit d673341b51ab8e4fdbabf3accd1c494f70a10513
+Subproject commit b327915a5ae65f3747e2d84619ad4cf522511b8b
(0028384)
Dave DeMarle (administrator)
2012-03-22 11:41

 I think your checkout of ParaView only has the VTK remote and needs the PVVTK remote.

The VTK one is sufficient for the master branch since pvvtk changes get merged there when they are
fully cooked.

For the next branch, you need the PVVTK remote, which is where ParaView's vtk changes live until they get promoted to VTK proper.

cd VTK
git remote add pvvtk git://paraview.org/PVVTK.git [^]
git fetch pvvtk
cd ..
git submodule update
(0028388)
Orion Poplawski (reporter)
2012-03-23 11:44

 Okay, that looks pretty good, though I suspect from the following you end up overlinking:

-- Found HDF5: debug;/usr/lib64/libhdf5_hl.so;debug;/usr/lib64/libhdf5.so;debug;/usr/lib64/libz.so;debug;/usr/lib64/librt.so;debug;/usr/lib64/libm.so;optimized;/usr/lib64/libhdf5_hl.so;optimized;/usr/lib64/libhdf5.so;optimized;/usr/lib64/libz.so;optimized;/usr/lib64/librt.so;optimized;/usr/lib64/libm.so

Thanks!
(0028939)
Alan Scott (manager)
2012-07-25 20:09

 User stated it is fixed. Closed.

 Issue History
Date Modified Username Field Change
2012-02-29 14:16 Orion Poplawski New Issue
2012-02-29 14:25 Dave DeMarle Note Added: 0028330
2012-02-29 15:19 Orion Poplawski Note Added: 0028331
2012-02-29 15:22 Dave DeMarle Assigned To => Dave DeMarle
2012-02-29 15:22 Dave DeMarle Status backlog => tabled
2012-03-05 13:17 Utkarsh Ayachit Project VTK => ParaView
2012-03-05 13:18 Utkarsh Ayachit Status tabled => todo
2012-03-05 13:18 Utkarsh Ayachit Product Version 5.8.0 =>
2012-03-05 13:18 Utkarsh Ayachit Target Version => 3.14.1
2012-03-21 10:43 Dave DeMarle Status todo => active development
2012-03-21 10:49 Dave DeMarle Topic Name => 001279-netcdf4-with-system-hdf5
2012-03-21 10:49 Dave DeMarle Note Added: 0028380
2012-03-21 10:49 Dave DeMarle Status active development => gatekeeper review
2012-03-21 10:49 Dave DeMarle Fixed in Version => git-next
2012-03-21 10:49 Dave DeMarle Resolution open => fixed
2012-03-21 14:47 Orion Poplawski Note Added: 0028381
2012-03-21 14:52 Dave DeMarle Note Added: 0028382
2012-03-21 15:07 Orion Poplawski Note Added: 0028383
2012-03-22 11:41 Dave DeMarle Note Added: 0028384
2012-03-23 11:44 Orion Poplawski Note Added: 0028388
2012-03-26 10:28 Utkarsh Ayachit Fixed in Version git-next => git-master
2012-03-26 10:28 Utkarsh Ayachit Status gatekeeper review => customer review
2012-03-26 10:43 Utkarsh Ayachit Topic Name 001279-netcdf4-with-system-hdf5 => 0012790-netcdf4-with-system-hdf5
2012-04-05 17:03 Utkarsh Ayachit Fixed in Version git-master => 3.14.1
2012-07-25 20:09 Alan Scott Note Added: 0028939
2012-07-25 20:09 Alan Scott Status customer review => closed

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