pyROOT: Fatal Python error: PyThreadState_Get

ROOT
1

Dear Experts,

I have problems using pyROOT on my mac Sierra 10.12.13.
When loading ROOT infact:
python -c "import ROOT"
I get:
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

I believe the reason is a mismatch between the python version I’m using and the one used by ROOT, but I have not been able to solve the problem.

My env are [1]. I installed root using the Binary distribution.
If I include in my .bashrc file the line
"export PYTHONPATH=$PYTHONPATH:/Applications/root_v6.06.08/lib/"
I get:
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
If I remove it, I get:
ImportError: No module named ROOT

The pyhton I’m using is:
/opt/local/bin/python -> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Also I defined LD_LIBRARY_PATH:
echo $LD_LIBRARY_PATH
/Applications/root_v6.06.08/lib

Do you have any idea what I should do?

Thanks a lot,
Luca

[1]
SHELL=/bin/bash
PATH=/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/ActivePerl-5.22/site/bin:/usr/local/ActivePerl-5.22/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin:/Applications/root_v6.06.08/bin:/Users/Luca2/Applications/apache-maven-3.3.1/bin:/usr/local/texlive/2009/bin/universal-darwin/:/opt/local/share/man/man8/:/Users/Luca2/Library/Android/sdk/platform-tools/:/Applications/root_v6.06.08/bin/
ROOTSYS=/Applications/root_v6.06.08
HOME=/Users/Luca2
PYTHONPATH=/usr/local/lib/python2.7/site-packages:/Users/Luca2/Library/Python/2.7/lib/python/site-packages:/Library/Python/2.7/site-packages:/Applications/root_v6.06.08/lib/
LOGNAME=Luca2

2

Do you have the possibility to build from source? I just ran into this problem this morning and had to rebuild root with the python version I wanted to use.

3

Hi ksmith,

I just tried, but I cannot finish the installation.
I added the python location into PATH, then I installed root for the source with:
% ./configure []
% make

But after a (long) while I get:
ld: library not found for -lCore
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [lib/libCore.dylib] Error 1

Full error in [1].
Do you have any suggestion?

Thanks a lot,
Luca

[1]
clang++ -dynamiclib -single_module -undefined suppress -install_name /lib/libCore.dylib -O2 -DNDEBUG -m64 -mmacosx-version-min=10.12 -stdlib=libc++ -Wl,-rpath,@loader_path/…/lib -bind_at_load -o lib/libCore.dylib core/base/src/G__Core.o core/base/src/InitGui.o core/base/src/Match.o core/base/src/String.o core/base/src/Stringio.o core/base/src/TApplication.o core/base/src/TApplicationImp.o core/base/src/TAtt3D.o core/base/src/TAttAxis.o core/base/src/TAttBBox.o core/base/src/TAttBBox2D.o core/base/src/TAttFill.o core/base/src/TAttLine.o core/base/src/TAttMarker.o core/base/src/TAttPad.o core/base/src/TAttText.o core/base/src/TBase64.o core/base/src/TBenchmark.o core/base/src/TBrowser.o core/base/src/TBrowserImp.o core/base/src/TBuffer.o core/base/src/TBuffer3D.o core/base/src/TCanvasImp.o core/base/src/TColor.o core/base/src/TColorGradient.o core/base/src/TContextMenu.o core/base/src/TContextMenuImp.o core/base/src/TControlBarImp.o core/base/src/TDatime.o core/base/src/TDirectory.o core/base/src/TEnv.o core/base/src/TError.o core/base/src/TException.o core/base/src/TExec.o core/base/src/TFileCollection.o core/base/src/TFileInfo.o core/base/src/TFolder.o core/base/src/TGuiFactory.o core/base/src/TInetAddress.o core/base/src/TInspectorImp.o core/base/src/TListOfTypes.o core/base/src/TMD5.o core/base/src/TMacro.o core/base/src/TMathBase.o core/base/src/TMemberInspector.o core/base/src/TMessageHandler.o core/base/src/TNamed.o core/base/src/TObjString.o core/base/src/TObject.o core/base/src/TObjectSpy.o core/base/src/TPRegexp.o core/base/src/TParameter.o core/base/src/TPluginManager.o core/base/src/TProcessID.o core/base/src/TProcessUUID.o core/base/src/TQCommand.o core/base/src/TQConnection.o core/base/src/TQObject.o core/base/src/TROOT.o core/base/src/TRef.o core/base/src/TRefCnt.o core/base/src/TRegexp.o core/base/src/TRemoteObject.o core/base/src/TStopwatch.o core/base/src/TStorage.o core/base/src/TString.o core/base/src/TStringLong.o core/base/src/TStyle.o core/base/src/TSysEvtHandler.o core/base/src/TSystem.o core/base/src/TSystemDirectory.o core/base/src/TSystemFile.o core/base/src/TTask.o core/base/src/TTime.o core/base/src/TTimeStamp.o core/base/src/TTimer.o core/base/src/TUUID.o core/base/src/TUri.o core/base/src/TUrl.o core/base/src/TVirtualFFT.o core/base/src/TVirtualGL.o core/base/src/TVirtualMonitoring.o core/base/src/TVirtualMutex.o core/base/src/TVirtualPS.o core/base/src/TVirtualPad.o core/base/src/TVirtualPadEditor.o core/base/src/TVirtualPadPainter.o core/base/src/TVirtualPerfStats.o core/base/src/TVirtualViewer3D.o core/base/src/TVirtualX.o core/cont/src/TArray.o core/cont/src/TArrayC.o core/cont/src/TArrayD.o core/cont/src/TArrayF.o core/cont/src/TArrayI.o core/cont/src/TArrayL.o core/cont/src/TArrayL64.o core/cont/src/TArrayS.o core/cont/src/TBits.o core/cont/src/TBtree.o core/cont/src/TClassTable.o core/cont/src/TClonesArray.o core/cont/src/TCollection.o core/cont/src/TExMap.o core/cont/src/THashList.o core/cont/src/THashTable.o core/cont/src/TIterator.o core/cont/src/TList.o core/cont/src/TMap.o core/cont/src/TObjArray.o core/cont/src/TObjectTable.o core/cont/src/TOrdCollection.o core/cont/src/TRefArray.o core/cont/src/TRefTable.o core/cont/src/TSeqCollection.o core/cont/src/TSortedList.o core/meta/src/TBaseClass.o core/meta/src/TClass.o core/meta/src/TClassGenerator.o core/meta/src/TClassMenuItem.o core/meta/src/TClassRef.o core/meta/src/TDataMember.o core/meta/src/TDataType.o core/meta/src/TDictAttributeMap.o core/meta/src/TDictionary.o core/meta/src/TEnum.o core/meta/src/TEnumConstant.o core/meta/src/TFunction.o core/meta/src/TFunctionTemplate.o core/meta/src/TGenericClassInfo.o core/meta/src/TGlobal.o core/meta/src/TInterpreter.o core/meta/src/TIsAProxy.o core/meta/src/TListOfDataMembers.o core/meta/src/TListOfEnums.o core/meta/src/TListOfEnumsWithLock.o core/meta/src/TListOfFunctionTemplates.o core/meta/src/TListOfFunctions.o core/meta/src/TMethod.o core/meta/src/TMethodArg.o core/meta/src/TMethodCall.o core/meta/src/TProtoClass.o core/meta/src/TRealData.o core/meta/src/TSchemaRule.o core/meta/src/TSchemaRuleSet.o core/meta/src/TStreamerElement.o core/meta/src/TToggle.o core/meta/src/TToggleGroup.o core/meta/src/TViewPubDataMembers.o core/meta/src/TViewPubFunctions.o core/meta/src/TVirtualStreamerInfo.o core/unix/src/TUnixSystem.o core/macosx/src/CocoaUtils.o core/macosx/src/TMacOSXSystem.o core/zip/src/ZDeflate.o core/zip/src/ZInflate.o core/zip/src/RZip.o core/zip/src/Compression.o core/lzma/src/ZipLZMA.o core/clib/src/Demangle.o core/clib/src/attach.o core/clib/src/detach.o core/clib/src/getpagesize.o core/clib/src/keys.o core/clib/src/mcalloc.o core/clib/src/mfree.o core/clib/src/mmalloc.o core/clib/src/mmapsup.o core/clib/src/mmcheck.o core/clib/src/mmemalign.o core/clib/src/mmstats.o core/clib/src/mmtrace.o core/clib/src/mrealloc.o core/clib/src/mvalloc.o core/clib/src/sbrksup.o core/clib/src/snprintf.o core/clib/src/strlcat.o core/clib/src/strlcpy.o core/metautils/src/RConversionRuleParser.o core/metautils/src/TClassEdit.o core/textinput/src/Getline.o core/textinput/src/Getline_color.o core/textinput/src/textinput/Editor.o core/textinput/src/textinput/History.o core/textinput/src/textinput/KeyBinding.o core/textinput/src/textinput/Range.o core/textinput/src/textinput/SignalHandler.o core/textinput/src/textinput/StreamReader.o core/textinput/src/textinput/StreamReaderUnix.o core/textinput/src/textinput/StreamReaderWin.o core/textinput/src/textinput/TerminalConfigUnix.o core/textinput/src/textinput/TerminalDisplay.o core/textinput/src/textinput/TerminalDisplayUnix.o core/textinput/src/textinput/TerminalDisplayWin.o core/textinput/src/textinput/TextInput.o core/textinput/src/textinput/TextInputContext.o -ldl -Llib -lCore -framework Cocoa -lz -L/opt/local/lib -llzma -L/opt/local/lib -lpcre
ld: library not found for -lCore
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [lib/libCore.dylib] Error 1

4

Try using cmake would be my first suggestion.

5

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