# Superbuild with Anaconda Python 3.7.1
**URL:** https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391
**Category:** ParaView Support
**Tags:** python
**Created:** [March 5, 2019, 4:41am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391 "2019-03-05T04:41:42Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 5, 2019, 4:41am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/1 "2019-03-05T04:41:42Z")
Hi, I’m attempting to build the Paraview 5.6 superbuild with Python 3 so that I can use PVPython with my existing code. I seem to be getting an issue with ‘undefined references’ similar to:
…/lib/libvtkWrappingPython37Core-pv5.6.so.1: undefined reference to `PyUnicode\_InternFromString’
…/lib/libvtkPVServerManagerCore-pv5.6.so.1: undefined reference to `PyLong\_FromLong’
and more of the same. I’ve tried building with Python 3.6 and 3.7 with similar results. To troubleshoot, I turned off all settings and only changed the following variables in my CMakeCache.txt:
CMAKE\_INSTALL\_PREFIX: /opt/paraview/ParaView-5.6.0
PYTHON\_EXECUTABLE: /home/tjim/anaconda3/envs/pv/bin/python
PYTHON\_INCLUDE\_DIR: /home/tjim/anaconda3/envs/pv/include/python3.7m
PYTHON\_LIBRARY: /home/tjim/anaconda3/envs/pv/lib/python3.7
PYTHON\_LIBRARY\_DEBUG: \*pdb.py
python\_FIND\_LIBRARIES: \*ON
superbuild\_python\_pip: /home/tjim/anaconda3/envs/pv/bin/pip
Can someone give me some pointers on how to build with Python 3?
Thanks and regards,
Tim
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 5, 2019, 9:28am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/2 "2019-03-05T09:28:26Z")
Looks like you are trying to build with your own Anaconda Python install instead of building Python within the superbuild, is that correct ?
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### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 5, 2019, 9:50am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/3 "2019-03-05T09:50:24Z")
Hi, yes that’s right!
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### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 5, 2019, 9:51am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/4 "2019-03-05T09:51:52Z")
Is the superbuild successful when building its own python ?
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### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 5, 2019, 10:01am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/5 "2019-03-05T10:01:44Z")
It appears to build successfully with it’s own python 2.7.
---
### Author:  [@ben.boeckel](https://discourse.paraview.org/u/ben.boeckel)
#### Post date: [March 5, 2019, 3:57pm UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/6 "2019-03-05T15:57:53Z")
I fear the superbuild might be a bit Python2-assumption heavy at the moment. Is there a specific reason you’re using the superbuild rather than trying to build a standalone ParaView source tree against Anaconda?
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 5, 2019, 4:22pm UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/7 "2019-03-05T16:22:54Z")
Only that I originally thought it might save me the trouble of locating and compiling all the other libraries required! Is there a minimal version that I could compile? I mainly would like to visualise flow blocks and perform simple slicing. Many thanks!
---
### Author:  [@ben.boeckel](https://discourse.paraview.org/u/ben.boeckel)
#### Post date: [March 5, 2019, 4:40pm UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/8 "2019-03-05T16:40:38Z")
ParaView ships most of its third party dependencies with its own source code. I think the only things that the superbuild provides on top are Python (which you have already), and these libraries (most of which are, I assume, easily obtainable from Anaconda if necessary):
- Mesa
- ADIOS (I/O file format)
- ParaViewWeb dependencies (should all be available via `pip`)
- libLAS (I/O file format)
- Boost (used in some libraries, but nothing “core”)
- FFmpeg (also not critical)
- Fontconfig/freetype
- Qt5
- an MPI
The other libraries in the superbuild are there so that ParaView can share with these dependencies (e.g., zlib).
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 6, 2019, 11:36am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/9 "2019-03-06T11:36:48Z")
Thanks for the email. I’ll give the standard build a go!
Are the items on the list all dependencies? I had a search for ParaViewWeb on pip but was only able to find wslink - is it sufficient to install that?
Thanks and regards.
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 6, 2019, 11:51am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/10 "2019-03-06T11:51:47Z")
Qt (if you need the GUI) and FontConfig are the only required dependencies.
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 6, 2019, 11:56am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/11 "2019-03-06T11:56:16Z")
Thank you! I am currently trying to generate using ccmake and I’m getting a lot of warnings along the lines of:
```
WARNING: Target "vtkPVPythonCatalystPythonD" requests linking to directory "/home/tjim/anaconda3/envs/pv/lib/python3.7". Targets may link
only to libraries. CMake is dropping the item.
WARNING: Target "vtkPVPythonCatalystPython" requests linking to directory "/home/tjim/anaconda3/envs/pv/lib/python3.7". Targets may link
only to libraries. CMake is dropping the item.
WARNING: Target "vtkPythonInterpreter" requests linking to directory "/home/tjim/anaconda3/envs/pv/lib/python3.7". Targets may link only
to libraries. CMake is dropping the item.
```
Are these safe to ignore?
Kind regards,
Tim
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 6, 2019, 11:58am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/12 "2019-03-06T11:58:02Z")
They are safe to ignore.
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 6, 2019, 3:38pm UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/13 "2019-03-06T15:38:53Z")
Thanks, Mathieu. I tried to make the build but it seems that I’m getting another issue with mpi4py. It seems to try to grab the version in my python directory and also in the Paraview directories. Can you give me some tips on how to fix this? Thank you. Here are are a few lines of the errors:
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protobuf-lite.dir/google/protobuf/message\_lite.cc.o
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py’…
Compiling ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/ **init**.py’…
Compiling ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/ **main**.py’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/include’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/include/mpi4py’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/lib-pmpi’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py’…
Compiling ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/ **init**.py’…
Compiling ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/ **main**.py’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/include’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/include/mpi4py’…
Listing ‘/opt/paraview/ParaView-5.6.0\_build/lib/python3.7/site-packages/mpi4py/lib-pmpi’…
[3%] Building CXX object VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/CMakeFiles/vtkm\_cont.dir/ArrayRangeCompute.cxx.o
[3%] Built target mpi4py
[3%] Building CXX object VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/CMakeFiles/vtkm\_cont.dir/CellSetExplicit.cxx.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protobuf-lite.dir/google/protobuf/repeated\_field.cc.o
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xmlsave.c.o
[3%] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/QtTesting.dir/pq3DViewEventPlayer.cxx.o
[3%] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/QtTesting.dir/pq3DViewEventTranslator.cxx.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protobuf-lite.dir/google/protobuf/wire\_format\_lite.cc.o
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xmlschemas.c.o
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xmlschemastypes.c.o
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xmlstring.c.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protobuf-lite.dir/google/protobuf/io/coded\_stream.cc.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protobuf-lite.dir/google/protobuf/io/zero\_copy\_stream.cc.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protobuf-lite.dir/google/protobuf/io/zero\_copy\_stream\_impl\_lite.cc.o
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xmlunicode.c.o
[3%] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/QtTesting.dir/pqAbstractActivateEventPlayer.cxx.o
[3%] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/QtTesting.dir/pqAbstractBooleanEventPlayer.cxx.o
Scanning dependencies of target mpi4py.MPI
[3%] Building CXX object VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/CMakeFiles/vtkm\_cont.dir/ColorTable.cxx.o
[3%] Linking CXX shared library …/…/…/…/lib/libprotobuf-lite.so
[3%] Building C object VTK/ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o
[3%] Built target protobuf-lite
[3%] Building CXX object VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/CMakeFiles/vtkm\_cont.dir/CoordinateSystem.cxx.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc\_compiler.dir/google/protobuf/generated\_message\_reflection.cc.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc\_compiler.dir/google/protobuf/message.cc.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc\_compiler.dir/google/protobuf/reflection\_ops.cc.o
In file included from /opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/MPI.c:4:0:
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c: In function ‘\_\_Pyx\_PyCFunction\_FastCall’:
[3%] Building CXX object VTK/ThirdParty/vtkm/vtk-m/vtkm/cont/CMakeFiles/vtkm\_cont.dir/serial/internal/ArrayManagerExecutionSerial.cxx.o
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:163017:5: error: too many arguments to function ‘(struct PyObject \* (\*)(struct PyObject _, struct PyObject \* const_, Py\_ssize\_t))meth’
return (\*((\_\_Pyx\_PyCFunctionFast)meth)) (self, args, nargs, NULL);
^
In file included from /opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/MPI.c:4:0:
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c: In function ‘\_\_Pyx\_\_ExceptionSave’:
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:163228:19: error: ‘PyThreadState’ has no member named ‘exc\_type’
\*type = tstate-\>exc\_type;
^
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xmlwriter.c.o
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:163229:20: error: ‘PyThreadState’ has no member named ‘exc\_value’
\*value = tstate-\>exc\_value;
^
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:163230:17: error: ‘PyThreadState’ has no member named ‘exc\_traceback’
\*tb = tstate-\>exc\_traceback;
^
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c: In function ‘\_\_Pyx\_\_ExceptionReset’:
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:163237:22: error: ‘PyThreadState’ has no member named ‘exc\_type’
tmp\_type = tstate-\>exc\_type;
^
…
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c: In function ‘\_\_Pyx\_PyDict\_Items’:
/opt/paraview/ParaView/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:164279:9: error: too many arguments to function ‘(struct PyObject \* (\*)(struct PyObject _, struct PyObject \* const_, Py\_ssize\_t))\_\_pyx\_umethod\_PyDict\_Type\_items.func’
return \_\_Pyx\_CallUnboundCMethod0(&\_\_pyx\_umethod\_PyDict\_Type\_items, d);
^
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xpath.c.o
[3%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xpointer.c.o
[3%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc\_compiler.dir/google/protobuf/service.cc.o
[3%] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/QtTesting.dir/pqAbstractDoubleEventPlayer.cxx.o
make[2]: \*\*\* [VTK/ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o] Error 1
make[1]: \*\*\* [VTK/ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/all] Error 2
make[1]: \*\*\* Waiting for unfinished jobs…
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 7, 2019, 8:12am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/14 "2019-03-07T08:12:45Z")
A quick solution would be to disable MPI.
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 7, 2019, 9:43am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/15 "2019-03-07T09:43:28Z")
I’ll try it without MPI. If I need to set it up with MPI, should it be picking up mpi4py in my install of python, or should it only pick up the ones that came in the VTK/ThirdParty directory? Thanks.
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 8, 2019, 6:45am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/16 "2019-03-08T06:45:08Z")
Hi, sorry. I tried to run make without MPI and I’m seeing some linking issues with QT5. Do I need to update my QT package?
Thanks and regards,
Tim
/home/tjim/anaconda3/lib/libQt5Widgets.so.5.9.7: undefined reference to `operator delete[](void\*, unsigned long)@CXXABI\_1.3.9’
/home/tjim/anaconda3/lib/libQt5Core.so.5.9.7: undefined reference to `\_\_cxa\_throw\_bad\_array\_new\_length@CXXABI\_1.3.8’
/home/tjim/anaconda3/lib/libQt5Widgets.so.5.9.7: undefined reference to `operator delete(void\*, unsigned long)@CXXABI\_1.3.9’
collect2: error: ld returned 1 exit status
make[2]: \*\*\* [bin/TestingDemo] Error 1
make[1]: \*\*\* [ThirdParty/QtTesting/vtkqttesting/Examples/CMakeFiles/TestingDemo.dir/all] Error 2
make: \*\*\* [all] Error 2
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 8, 2019, 9:17am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/17 "2019-03-08T09:17:57Z")
Are you bulding Qt within the superbuild or are you using an external Qt5 ?
---
### Author:  [@TimJim](https://discourse.paraview.org/u/TimJim)
#### Post date: [March 8, 2019, 10:25am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/18 "2019-03-08T10:25:02Z")
Based on your previous message, I’m not using the superbuild any more. Is there a QT package available inside? It seems that it’s picking up my anaconda installation QT: ~/anaconda3/lib/cmake/Qt5\*
Are these not fully featured? Should I install QT 5 separately?
Thanks and regards.
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [March 8, 2019, 10:49am UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/19 "2019-03-08T10:49:05Z")
Sorry, I mixed up answers.
You definitely need to install Qt, I would suggest using Qt 5.9.7 :
[https://download.qt.io/archive/qt/5.9/5.9.7/](https://download.qt.io/archive/qt/5.9/5.9.7/)
---
### Author:  [@eric](https://discourse.paraview.org/u/eric)
#### Post date: [March 8, 2019, 12:47pm UTC](https://discourse.paraview.org/t/superbuild-with-anaconda-python-3-7-1/1391/20 "2019-03-08T12:47:22Z")
Hi,
Maybe this could help. In order to compile paraview 5.6.0 with python 3.6.2 (own build),
I had to change in the source directory, paraview/5.6.0/VTK/CMake/vtkWrapSettings.cmake the following:
L5: replace set(VTK\_PYTHON\_VERSION 2 CACHE STRING with
set(VTK\_PYTHON\_VERSION 3 CACHE STRING)
I also used the following cmake flags (for python) for the build:
[…]
-DPYTHON\_LIBRARY=$PATH/python/3.6.2/lib/libpython3.6m.so.1.0 \
-DPYTHON\_EXECUTABLE=$PATH/python/3.6.2/bin/python3
-DPYTHON\_VERSION=3
[…]
(I also used Qt 5.9.3)
It seems to work fine for me.
Regards,
Eric
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