Hi I'm running into the following issue when compiling with cuda/nvcc version 12
make exe -f makefile11 CUDAHOME=/usr/
------------------------------------------------
Util/CCufft2D.cpp has been compiled.
------------------------------------------------
Util/CFileName.cpp has been compiled.
------------------------------------------------
Util/CFlipImage.cpp has been compiled.
------------------------------------------------
Util/CFourierCrop2D.cpp has been compiled.
------------------------------------------------
Util/CGroupFrames.cpp has been compiled.
------------------------------------------------
Util/CNextItem.cpp has been compiled.
------------------------------------------------
Util/CPad2D.cpp has been compiled.
------------------------------------------------
Util/CParseArgs.cpp has been compiled.
------------------------------------------------
Util/CSplineFit1D.cpp has been compiled.
------------------------------------------------
Util/CRemoveSpikes1D.cpp has been compiled.
------------------------------------------------
Util/CSaveTempMrc.cpp has been compiled.
------------------------------------------------
Util/CSimpleFuncs.cpp has been compiled.
------------------------------------------------
Util/CMultiGpuBase.cpp has been compiled.
------------------------------------------------
DataUtil/CMrcStack.cpp has been compiled.
------------------------------------------------
DataUtil/CAlnSums.cpp has been compiled.
------------------------------------------------
DataUtil/CReadFmIntFile.cpp has been compiled.
------------------------------------------------
DataUtil/CFmIntegrateParam.cpp has been compiled.
------------------------------------------------
DataUtil/CFmGroupParam.cpp has been compiled.
------------------------------------------------
DataUtil/CDataPackage.cpp has been compiled.
------------------------------------------------
DataUtil/CStackFolder.cpp has been compiled.
------------------------------------------------
BadPixel/CCorrectMain.cpp has been compiled.
------------------------------------------------
BadPixel/CDetectMain.cpp has been compiled.
------------------------------------------------
BadPixel/CLocalCCMap.cpp has been compiled.
------------------------------------------------
BadPixel/CTemplate.cpp has been compiled.
------------------------------------------------
Align/CZbinStack.cpp has been compiled.
------------------------------------------------
Align/CAlignBase.cpp has been compiled.
------------------------------------------------
Align/CAlignedSum.cpp has been compiled.
------------------------------------------------
Align/CAlignMain.cpp has been compiled.
------------------------------------------------
Align/CAlignParam.cpp has been compiled.
------------------------------------------------
Align/CGenXcfStack.cpp has been compiled.
------------------------------------------------
Align/CFullAlign.cpp has been compiled.
------------------------------------------------
Align/CInterpolateShift.cpp has been compiled.
------------------------------------------------
Align/CAlignStack.cpp has been compiled.
------------------------------------------------
Align/CIterativeAlign.cpp has been compiled.
------------------------------------------------
Align/CExtractPatch.cpp has been compiled.
------------------------------------------------
Align/CMeasurePatches.cpp has been compiled.
------------------------------------------------
Align/CPatchAlign.cpp has been compiled.
------------------------------------------------
Align/CPatchShifts.cpp has been compiled.
------------------------------------------------
Align/CPeak2D.cpp has been compiled.
------------------------------------------------
Align/CSaveAlign.cpp has been compiled.
------------------------------------------------
Align/CLoadAlign.cpp has been compiled.
------------------------------------------------
Align/CSimpleSum.cpp has been compiled.
------------------------------------------------
Align/CStackShift.cpp has been compiled.
------------------------------------------------
Align/CTransformStack.cpp has been compiled.
------------------------------------------------
Align/CDetectFeatures.cpp has been compiled.
------------------------------------------------
Align/CPatchCenters.cpp has been compiled.
------------------------------------------------
Align/CEarlyMotion.cpp has been compiled.
------------------------------------------------
Correct/CCorrectFullShift.cpp has been compiled.
------------------------------------------------
Correct/CGenRealStack.cpp has been compiled.
------------------------------------------------
MotionDecon/CInFrameMotion.cpp has been compiled.
------------------------------------------------
MrcUtil/CAnalyzeMrc.cpp has been compiled.
------------------------------------------------
MrcUtil/CApplyRefs.cpp has been compiled.
------------------------------------------------
MrcUtil/CAsyncSingleSave.cpp has been compiled.
------------------------------------------------
MrcUtil/CLoadRefs.cpp has been compiled.
------------------------------------------------
MrcUtil/CLoadCryoEMStack.cpp has been compiled.
------------------------------------------------
MrcUtil/CLoadStack.cpp has been compiled.
------------------------------------------------
MrcUtil/CSaveSingleCryoEM.cpp has been compiled.
------------------------------------------------
MrcUtil/CSumFFTStack.cpp has been compiled.
------------------------------------------------
MrcUtil/CTiltAngles.cpp has been compiled.
------------------------------------------------
TiffUtil/CLoadTiffHeader.cpp has been compiled.
------------------------------------------------
TiffUtil/CLoadTiffImage.cpp has been compiled.
------------------------------------------------
TiffUtil/CLoadTiffStack.cpp has been compiled.
------------------------------------------------
EerUtil/CLoadEerHeader.cpp has been compiled.
------------------------------------------------
EerUtil/CLoadEerFrames.cpp has been compiled.
------------------------------------------------
EerUtil/CDecodeEerFrame.cpp has been compiled.
------------------------------------------------
EerUtil/CRenderMrcStack.cpp has been compiled.
------------------------------------------------
EerUtil/CLoadEerMain.cpp has been compiled.
------------------------------------------------
FindCtf/CCtfTheory.cpp has been compiled.
------------------------------------------------
FindCtf/CGenAvgSpectrum.cpp has been compiled.
------------------------------------------------
FindCtf/CFullSpectrum.cpp has been compiled.
------------------------------------------------
FindCtf/CFindCtfBase.cpp has been compiled.
------------------------------------------------
FindCtf/CFindCtf1D.cpp has been compiled.
------------------------------------------------
FindCtf/CFindCtf2D.cpp has been compiled.
------------------------------------------------
FindCtf/CFindDefocus1D.cpp has been compiled.
------------------------------------------------
FindCtf/CFindDefocus2D.cpp has been compiled.
------------------------------------------------
FindCtf/CFindCtfMain.cpp has been compiled.
------------------------------------------------
FindCtf/CFindCtfHelp.cpp has been compiled.
------------------------------------------------
CInput.cpp has been compiled.
------------------------------------------------
CGpuBuffer.cpp has been compiled.
------------------------------------------------
CStackBuffer.cpp has been compiled.
------------------------------------------------
CBufferPool.cpp has been compiled.
------------------------------------------------
CCheckFreeGpus.cpp has been compiled.
------------------------------------------------
CProcessThread.cpp has been compiled.
------------------------------------------------
CSaveSerialCryoEM.cpp has been compiled.
------------------------------------------------
CGenStarFile.cpp: In member function ‘void MotionCor2::CGenStarFile::SetHotPixels(unsigned char*, int*, bool)’:
CGenStarFile.cpp:152:56: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘int’ [-Wformat=]
152 | fprintf(m_pFile, "%13.6f %13.6f\n",
| ~~~~~^
| |
| double
| %13.6d
153 | x + 1.0f, iY);
| ~~
| |
| int
CGenStarFile.cpp has been compiled.
------------------------------------------------
CMain.cpp has been compiled.
------------------------------------------------
CMotionCor3.cpp has been compiled.
-----------------------------------------------
Util/GAddFrames.cu has been compiled.
------------------------------------------------
Util/GAddFrames.cpp has been compiled.
-----------------------------------------------
Util/GCalcMoment2D.cu has been compiled.
------------------------------------------------
Util/GCalcMoment2D.cpp has been compiled.
-----------------------------------------------
Util/GFindMinMax2D.cu has been compiled.
------------------------------------------------
Util/GFindMinMax2D.cpp has been compiled.
-----------------------------------------------
Util/GFFTUtil2D.cu has been compiled.
------------------------------------------------
Util/GFFTUtil2D.cpp has been compiled.
-----------------------------------------------
Util/GFourierResize2D.cu has been compiled.
------------------------------------------------
Util/GFourierResize2D.cpp has been compiled.
-----------------------------------------------
Util/GPartialCopy.cu has been compiled.
------------------------------------------------
Util/GPartialCopy.cpp has been compiled.
-----------------------------------------------
Util/GPositivity2D.cu has been compiled.
------------------------------------------------
Util/GPositivity2D.cpp has been compiled.
-----------------------------------------------
Util/GRoundEdge.cu has been compiled.
------------------------------------------------
Util/GRoundEdge.cpp has been compiled.
-----------------------------------------------
Util/GNormalize2D.cu has been compiled.
------------------------------------------------
Util/GNormalize2D.cpp has been compiled.
-----------------------------------------------
Util/GPad2D.cu has been compiled.
------------------------------------------------
Util/GPad2D.cpp has been compiled.
-----------------------------------------------
Util/GPhaseShift2D.cu has been compiled.
------------------------------------------------
Util/GPhaseShift2D.cpp has been compiled.
-----------------------------------------------
Util/GCorrLinearInterp.cu has been compiled.
------------------------------------------------
Util/GCorrLinearInterp.cpp has been compiled.
-----------------------------------------------
Util/GThreshold2D.cu has been compiled.
------------------------------------------------
Util/GThreshold2D.cpp has been compiled.
-----------------------------------------------
BadPixel/GCombineBadMap.cu has been compiled.
------------------------------------------------
BadPixel/GCombineBadMap.cpp has been compiled.
-----------------------------------------------
BadPixel/GCorrectBad.cu has been compiled.
------------------------------------------------
BadPixel/GCorrectBad.cpp has been compiled.
-----------------------------------------------
BadPixel/GDetectHot.cu has been compiled.
------------------------------------------------
BadPixel/GDetectHot.cpp has been compiled.
-----------------------------------------------
BadPixel/GDetectPatch.cu has been compiled.
------------------------------------------------
BadPixel/GDetectPatch.cpp has been compiled.
-----------------------------------------------
BadPixel/GLabelPatch.cu has been compiled.
------------------------------------------------
BadPixel/GLabelPatch.cpp has been compiled.
-----------------------------------------------
BadPixel/GLocalCC.cu has been compiled.
------------------------------------------------
BadPixel/GLocalCC.cpp has been compiled.
-----------------------------------------------
MrcUtil/G4BitImage.cu has been compiled.
------------------------------------------------
MrcUtil/G4BitImage.cpp has been compiled.
-----------------------------------------------
MrcUtil/G90Rotate2D.cu has been compiled.
------------------------------------------------
MrcUtil/G90Rotate2D.cpp has been compiled.
-----------------------------------------------
MrcUtil/GAugmentRef.cu has been compiled.
------------------------------------------------
MrcUtil/GAugmentRef.cpp has been compiled.
-----------------------------------------------
MrcUtil/GApplyRefsToFrame.cu has been compiled.
------------------------------------------------
MrcUtil/GApplyRefsToFrame.cpp has been compiled.
-----------------------------------------------
MrcUtil/GFlip2D.cu has been compiled.
------------------------------------------------
MrcUtil/GFlip2D.cpp has been compiled.
-----------------------------------------------
MrcUtil/GInverse2D.cu has been compiled.
------------------------------------------------
MrcUtil/GInverse2D.cpp has been compiled.
-----------------------------------------------
EerUtil/GAddRawFrame.cu has been compiled.
------------------------------------------------
EerUtil/GAddRawFrame.cpp has been compiled.
-----------------------------------------------
Align/GCorrelateSum2D.cu has been compiled.
------------------------------------------------
Align/GCorrelateSum2D.cpp has been compiled.
-----------------------------------------------
Align/GNormByStd2D.cu has been compiled.
------------------------------------------------
Align/GNormByStd2D.cpp has been compiled.
-----------------------------------------------
Align/GCC2D.cu has been compiled.
------------------------------------------------
Align/GCC2D.cpp has been compiled.
-----------------------------------------------
Correct/GCorrectPatchShift.cu has been compiled.
------------------------------------------------
Correct/GCorrectPatchShift.cpp has been compiled.
-----------------------------------------------
Correct/GStretch.cu has been compiled.
------------------------------------------------
Correct/GStretch.cpp has been compiled.
-----------------------------------------------
Correct/GWeightFrame.cu has been compiled.
------------------------------------------------
Correct/GWeightFrame.cpp has been compiled.
-----------------------------------------------
MotionDecon/GDeconFrame.cu has been compiled.
------------------------------------------------
MotionDecon/GDeconFrame.cpp has been compiled.
-----------------------------------------------
MotionDecon/GMotionWeight.cu has been compiled.
------------------------------------------------
MotionDecon/GMotionWeight.cpp has been compiled.
-----------------------------------------------
FindCtf/GCtfCC1D.cu has been compiled.
------------------------------------------------
FindCtf/GCtfCC1D.cpp has been compiled.
-----------------------------------------------
FindCtf/GCtfCC2D.cu has been compiled.
------------------------------------------------
FindCtf/GCtfCC2D.cpp has been compiled.
-----------------------------------------------
FindCtf/GCalcSpectrum.cu has been compiled.
------------------------------------------------
FindCtf/GCalcSpectrum.cpp has been compiled.
-----------------------------------------------
FindCtf/GRmBackground2D.cu has been compiled.
------------------------------------------------
FindCtf/GRmBackground2D.cpp has been compiled.
-----------------------------------------------
FindCtf/GCalcCTF1D.cu has been compiled.
------------------------------------------------
FindCtf/GCalcCTF1D.cpp has been compiled.
-----------------------------------------------
FindCtf/GCalcCTF2D.cu has been compiled.
------------------------------------------------
FindCtf/GCalcCTF2D.cpp has been compiled.
-----------------------------------------------
FindCtf/GRadialAvg.cu has been compiled.
------------------------------------------------
FindCtf/GRadialAvg.cpp has been compiled.
nvlink warning : Skipping incompatible '/usr/lib/x86_64-linux-gnu/libpthread.a' when searching for -lpthread
/usr/bin/ld: /home/.../software/MotionCor3/Lib/libmrcfile.a(CLoadExtHeader.o): relocation R_X86_64_32 against symbol `__gxx_personality_v0@@CXXABI_1.3' can not be used when making a PIE object; recompile with -fPIE
/usr/bin/ld: failed to set dynamic section sizes: bad value
collect2: error: ld returned 1 exit status
make: *** [makefile11:160: exe] Error 1
Hi I'm running into the following issue when compiling with cuda/nvcc version 12