[MOAB-dev] Redundant -L/usr/lib causing problems

[Jed Brown]

On Mon, 01 Mar 2010 15:58:44 -0600, Jason Kraftcheck <kraftche at cae.wisc.edu> wrote:
> I haven't seen this error before.  My first guess is that something on your
> system changed with respect to the C++ compiler and you need to re-build MOAB.

I did "make clean" and rebuilt.

> > Perhaps this is due to the use of -nostdlib?
> > 
> 
> We don't use that.  I grepped every file in the MOAB source and build
> results.  The only files that contain 'nostdlib' are generated by autotools
> (aclocal.m4 and therefore configure).

Well, it's creeping in there somehow, the logs say

libtool: link: mpicxx -shared -nostdlib /usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0/../../../crti.o /usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0/crtbeginS.o  .libs/AEntityFactory.o .libs/BitTagServer.o .libs/DualTool.o .libs/EntitySequence.o .libs/ExoIIUtil.o .libs/FileOptions.o .libs/FileTokenizer.o .libs/GeomTopoTool.o .libs/GmshUtil.o .libs/HigherOrderFactory.o .libs/HomXform.o .libs/MBAdaptiveKDTree.o .libs/MBAffineXform.o .libs/MBAlloc.o .libs/MBAxisBox.o .libs/MBBSPTree.o .libs/MBCN.o .libs/MBCartVect.o .libs/MBMatrix3.o .libs/MBCore.o .libs/MBFactory.o .libs/MBGeomUtil.o .libs/MBMeshSet.o .libs/MBOrientedBox.o .libs/MBOrientedBoxTreeTool.o .libs/BSPTreePoly.o .libs/MBRange.o .libs/MBRangeSeqIntersectIter.o .libs/MBReadUtil.o .libs/MBReaderWriterSet.o .libs/MBSkinner.o .libs/MBSysUtil.o .libs/MBUtil.o .libs/MBWriteUtil.o .libs/MeshSetSequence.o .libs/MeshTopoUtil.o .libs/PolyElementSeq.o .libs/ReadGmsh.o .libs/ReadSms.o .libs/ReadSTL.o .libs/ReadVtk.o .libs/ReadSmf.o .libs/SMF_State.o .libs/ReadIDEAS.o .libs/ReadMCNP5.o .libs/ReadNASTRAN.o .libs/ReadABAQUS.o .libs/ReadTetGen.o .libs/ScdElementData.o .libs/ScdVertexData.o .libs/SequenceData.o .libs/SequenceManager.o .libs/SparseTagSuperCollection.o .libs/SparseTagCollection.o .libs/StructuredElementSeq.o .libs/SweptElementData.o .libs/SweptElementSeq.o .libs/SweptVertexData.o .libs/TagInfo.o .libs/TagServer.o .libs/Tqdcfr.o .libs/TypeSequenceManager.o .libs/UnstructuredElemSeq.o .libs/VertexSequence.o .libs/VtkUtil.o .libs/WriteAns.o .libs/WriteGMV.o .libs/WriteGmsh.o .libs/WriteSTL.o .libs/WriteTemplate.o .libs/WriteVtk.o .libs/WriteSmf.o .libs/ReadNCDF.o .libs/WriteNCDF.o .libs/WriteSLAC.o .libs/ReadHDF5.o .libs/WriteHDF5.o  -Wl,--whole-archive ./mhdf/.libs/libmhdf.a ./parallel/.libs/libMOABpar.a -Wl,--no-whole-archive  -lnetcdf_c++ -lnetcdf -lhdf5 -L/usr/lib/openmpi -L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0 -L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0/../../.. /usr/lib/openmpi/libmpi_cxx.so /usr/lib/openmpi/libmpi.so /usr/lib/openmpi/libopen-rte.so /usr/lib/openmpi/libopen-pal.so -lnsl -lutil -ldl -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0/crtendS.o /usr/lib/gcc/x86_64-unknown-linux-gnu/4.5.0/../../../crtn.o    -pthread -Wl,-soname -Wl,libMOAB.so.0 -o .libs/libMOAB.so.0.0.0

Jed