Re: [AMBER] zlib issues during compilation.

From: Harris, Danni <>
Date: Tue, 10 Jun 2014 11:56:02 +0000

Thanks Dan. Your hunch was correct.

That was useful feedback re: zlib 1.2.8. You were right.
Indeed I had a libz.a in my search path that did not have the 64 bit
symbols------and I hadn't checked the symbols in the libz.a's!

Building 1.2.8 with the --64 specification and cleaning up the old links
resolved the serial build issue.
I appreciate your feedback. On to new CUDA and MPI builds…


On 6/9/14 11:17 PM, "Daniel Roe" <> wrote:

>I am able to compile cpptraj using zlib 1.2.8. I think there is
>probably a problem with your installed zlib 1.2.8 library. You can
>check the symbols in your library (assuming static library was
>compiled) like so:
>nm -o libz.a | grep gzseek64
>If there is no output from this, then 64-bit functions were not
>included in your library. There is an option (--64) that I believe is
>required during zlib configure for 64-bit functions to be present. You
>can try rebuilding your library after configuring with '--64' and see
>if that makes a difference.
>Hope this helps,
>On Mon, Jun 9, 2014 at 5:29 PM, Harris, Danni <> wrote:
>> Thanks for a second pair of eyes Dan---yah you are right ---not sure why
>> that happened ? Mis-paste?
>> I am doing a configure gnu ----and a make install of a fully patched
>> --and the added material below shows the -lz is being properly added in
>> the link step.
>> I have a suspicion this could be a ZLIB version compatibility issue:
>> I have a hunch, that downloading and compiling the latest ZLIB 1.2.8
>> (which was my decision). I am going to check that.
>> As per similar comments here (for a different package):
>> 64-when-building-samtools
>> Don't know why this later ZLIB version could be an issue as in the
>> comments there for another package---but I will roll back the 'new ZLIB'
>> install and check.
>> I appreciate the feedback ---I will dig in and look for the ZLIB source
>> the compilation issue.
>> Thanks for your input.
>> Danni
>> __________________
>> The -lz is specified in the config.h
>> And is being added in the link (pasted material below).
>> ____EXCERPT of config.h ______
>> NETCDF=$(INCDIR)/netcdf.mod
>> NETCDFLIB=$(LIBDIR)/libnetcdf.a
>> NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a
>> FFTWLIB=-lfftw3
>> EMILLIB=$(LIBDIR)/libemil.a -lstdc++
>> ZLIB=-lz
>> BZLIB=-lbz2
>> HASFC=yes
>> MTKPP=install_mtkpp
>> XBLAS=$(LIBDIR)/libxblas-amb.a
>> FFTW3=$(LIBDIR)/libfftw3.a
>> MDGX=yes
>> _______________
>> And redoing the install from tar files and:
>> configure gnu
>> make install
>> Of patched version (during configure gnu operation) still leads to the
>> same error.
>> The 'tail of my Make.log' piped output shows the same result (bottom of
>> this email)
>> g++ -o cpptraj ActionFrameCounter.o ActionList.o Action_Angle.o
>> Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o
>> Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o
>> Action_Center.o Action_CheckStructure.o Action_Closest.o
>> Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o
>> Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o
>> Action_Density.o Action_Diffusion.o Action_Dihedral.o
>> Action_DihedralScan.o Action_Dipole.o Action_DistRmsd.o
>> Action_FilterByData.o Action_FixAtomOrder.o Action_Gist.o Action_Grid.o
>> Action_GridFreeEnergy.o Action_Hbond.o Action_Image.o Action_Jcoupling.o
>> Action_LESsplit.o Action_LIE.o Action_MakeStructure.o Action_Mask.o
>> Action_Matrix.o Action_Molsurf.o Action_MultiDihedral.o
>> Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o
>> Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o
>> Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o
>> Action_RandomizeIons.o Action_Rmsd.o Action_Rotate.o Action_Rotdif.o
>> Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o
>> Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o
>> Action_SymmetricRmsd.o Action_Temperature.o Action_Translate.o
>> Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o
>> Action_Watershell.o AnalysisList.o Analysis_AmdBias.o
>> Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o
>> Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o
>> Analysis_Divergence.o Analysis_FFT.o Analysis_Hist.o
>> Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_Matrix.o
>> Analysis_MeltCurve.o Analysis_Modes.o Analysis_MultiHist.o
>> Analysis_Overlap.o Analysis_Regression.o Analysis_RemLog.o
>> Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_RunningAvg.o
>> Analysis_Spline.o Analysis_Statistics.o Analysis_Timecorr.o
>> Analysis_VectorMath.o ArgList.o Array1D.o Atom.o AtomMap.o AtomMask.o
>> AxisType.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CIFfile.o
>> ClusterDist.o ClusterList.o ClusterMatrix.o ClusterNode.o ClusterSieve.o
>> Cluster_DBSCAN.o Cluster_HierAgglo.o Command.o ComplexArray.o Corr.o
>> Cpptraj.o CpptrajFile.o CpptrajState.o CpptrajStdio.o DataFile.o
>> DataFileList.o DataIO.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o
>> DataIO_OpenDx.o DataIO_Mdout.o DataIO_RemLog.o DataIO_Std.o
>> DataSet.o DataSetList.o DataSet_1D.o DataSet_2D.o DataSet_3D.o
>> DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_TRJ.o
>> DataSet_GridFlt.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o
>> DataSet_Modes.o DataSet_RemLog.o DataSet_Vector.o DataSet_double.o
>> DataSet_float.o DataSet_integer.o DataSet_string.o DihedralSearch.o
>> Dimension.o DistRoutines.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o
>> FileIO_Std.o FileName.o FileTypes.o Frame.o FrameList.o GridAction.o
>> Hungarian.o ImageRoutines.o MapAtom.o MaskToken.o Matrix_3x3.o
>> NameType.o NetcdfFile.o PDBfile.o ParmFile.o Parm_Amber.o
>> Parm_CIF.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o ProgressBar.o PubFFT.o
>> Random.o Range.o ReadLine.o ReferenceAction.o ReferenceFrame.o SDFfile.o
>> StringRoutines.o SymmetricRmsdCalc.o Timer.o Topology.o TopologyList.o
>> TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o
>> Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmDcd.o Traj_CIF.o
>> Traj_Conflib.o Traj_GmxTrX.o Traj_Mol2File.o Traj_PDBfile.o Traj_SDF.o
>> Traj_SQM.o TrajectoryFile.o Trajin.o TrajinList.o Trajin_Multi.o
>> Trajin_Single.o Trajout.o TrajoutList.o Vec3.o main.o MpiRoutines.o
>> molsurf.o pub_fft.o \
>> -L/home/dannil/amber14/lib
>> /home/dannil/amber14/lib/libnetcdf.a -lz -lbz2 -larpack -llapack -lblas
>> -lgfortran -w readline/libreadline.a
>> FileIO_Gzip.o: In function `FileIO_Gzip::Seek(long)':
>> FileIO_Gzip.cpp:(.text+0x6b): undefined reference to `gzseek64'
>> FileIO_Gzip.o: In function `FileIO_Gzip::Open(char const*, char
>> FileIO_Gzip.cpp:(.text+0x1eb): undefined reference to `gzopen64'
>> FileIO_Gzip.o: In function `FileIO_Gzip::Tell()':
>> FileIO_Gzip.cpp:(.text+0x35): undefined reference to `gztell64'
>> collect2: ld returned 1 exit status
>> make[3]: *** [cpptraj] Error 1
>> make[3]: Leaving directory
>> `/home/dannil/amber14/AmberTools/src/cpptraj/src'
>> make[2]: *** [install] Error 2
>> make[2]: Leaving directory `/home/dannil/amber14/AmberTools/src/cpptraj'
>> make[1]: *** [serial] Error 2
>> make[1]: Leaving directory `/home/dannil/amber14/AmberTools/src'
>> make: *** [install] Error 2
>> On 6/9/14 5:44 PM, "Daniel Roe" <> wrote:
>>>Something seems strange about your configuration. The link command you
>>>posted doesn't appear to have an '-lz' (which essentially tells the
>>>linker to use the zlib library). What version of AmberTools are you
>>>using, and what flags did you provide to 'configure'? In your
>>>$AMBERHOME/config.h file, what does the value of the ZLIB variable
>>>On Mon, Jun 9, 2014 at 1:46 PM, Harris, Danni <>
>>>> I am puzzled by some errors I am getting during the initial stages of
>>>>compilation that I think are related to zlib / compression related
>>>> I am puzzled because I certainly have zlib related packages
>>>>installed---and even downloaded ‹compiled and installed the zlib-1.2.8
>>>> (I haven't run into any issues during past compilations/installations
>>>>of serial/MPI or CUDA based installs).
>>>> zlib-1.2.3-29.el6.x86_64
>>>> zlib-devel-1.2.3-29.el6.x86_64
>>>> jzlib-1.0.7-7.5.el6.x86_64
>>>> zlib-static-1.2.3-29.el6.x86_64
>>>> zlib-1.2.3-29.el6.i686
>>>> I see mention of gzseek64 etc in my zlib.h files etc ----but before I
>>>>did into this plebeian problem further ----
>>>> Let me ask the group if anyone has run into the error(s) below---below
>>>>the attempted compilation of cpptraj with the library links
>>>> I have tried this on Centos 6.5 and Centos 5.9 installations with
>>>>similar results.
>>>> Any input pushing me in the right direction for sleuthing would be
>>>>appreciated---as I am not seeing any path or 'package-missing' issues
>>>>first glanceŠ.
>>>> g++ -o cpptraj ActionFrameCounter.o ActionList.o Action_Angle.o
>>>>Action_AtomMapr.o Action_AtomicFluct.o Action_AutoImage.o
>>>>Action_Average.o Action_Bounds.o Actnter.o Action_CheckStructure.o
>>>>Action_Closest.o Action_ClusterDihedral.o Action_reateCrd.o
>>>>Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o
>>>>Action_ffusion.o Action_Dihedral.o Action_DihedralScan.o
>>>>Action_DistRms.o Action_FilterByData.o Action_FixAtomOrder.o
>>>>Action_Gist.o Action_Grid.o ActioAction_Hbond.o Action_Image.o
>>>>Action_Jcoupling.o Action_LESsplit.o Action_LIE.o e.o Action_Mask.o
>>>>Action_Matrix.o Action_Molsurf.o Action_MultiDihedral.o
>>>>ActionNativeContacts.o Action_NMRrst.o Action_OrderParameter.o
>>>>Action_Outtraj.o ActionPairwise.o Action_Principal.o
>>>>Action_Pucker.o Action_Radgyr.ction_RandomizeIons.o Action_Rmsd.o
>>>>Action_Rotate.o Action_Rotdif.o Action_Runni_Diffusion.o Action_Scale.o
>>>>Action_SetVelocity.o Action_Spam.o Action_Strip.o AcSymmetricRmsd.o
>>>>Action_Temperature.o Action_Translate.o Action_Unwrap.o
>>>>Action_VcityAutoCorr.o Action_Volmap.o Action_Watershell.o
>>>>AnalysisList.o Analysis_AmdBiorr.o Analysis_Average.o
>>>>Analysis_Clustering.o Analysis_Corr.o Analysis_CrankShauct.o
>>>>Analysis_CrossCorr.o Analysis_Divergence.o Analysis_FFT.o
>>>>Analysis_Hist.o o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o
>>>>Analysis_Matrix.o Analysis_s_Modes.o Analysis_MultiHist.o
>>>>Analysis_Overlap.o Analysis_Regression.o AnalysisRms2d.o
>>>>Analysis_RmsAvgCorr.o Analysis_RunningAvg.o Analysis_Spline.o
>>>>Analysis_Ss_Timecorr.o Analysis_VectorMath.o ArgList.o Array1D.o Atom.o
>>>>AtomMap.o AtomMask BufferedFrame.o BufferedLine.o ByteRoutines.o
>>>>CIFfile.o ClusterDist.o ClusterLio ClusterNode.o ClusterSieve.o
>>>>Cluster_DBSCAN.o Cluster_HierAgglo.o Command.o Co Cpptraj.o
>>>>CpptrajFile.o CpptrajState.o CpptrajStdio.o DataFile.o
>>>>DataFileList.oecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o
>>>>DataIO_Mdout.o DataIO_RemLataIO_Xplor.o DataSet.o DataSetList.o
>>>>DataSet_1D.o DataSet_2D.o DataSet_3D.o Datet_Coords_CRD.o
>>>>DataSet_Coords_TRJ.o DataSet_GridFlt.o DataSet_MatrixDbl.o
>>>>DataSSet_Mesh.o DataSet_Modes.o DataSet_RemLog.o DataSet_Vector.o
>>>>DataSet_double.o Daet_integer.o DataSet_string.o DihedralSearch.o
>>>>Dimension.o DistRoutines.o FileIOp.o FileIO_Mpi.o FileIO_Std.o
>>>>FileName.o FileTypes.o Frame.o FrameList.o GridActmageRoutines.o
>>>>MapAtom.o MaskToken.o Matrix_3x3.o Mol2File.o NameType.o NetcdfFiFile.o
>>>>Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Mol2.o Parm_PDB.o
>>>>Parm_SDF.FFT.o Random.o Range.o ReadLine.o ReferenceAction.o
>>>>ReferenceFrame.o SDFfile.o SmetricRmsdCalc.o Timer.o Topology.o
>>>>TopologyList.o TorsionRoutines.o Traj_AmberCtcdf.o Traj_AmberRestart.o
>>>>Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmDcd.o flib.o
>>>>Traj_GmxTrX.o Traj_Mol2File.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o
>>>>Trajec TrajinList.o Trajin_Multi.o Trajin_Single.o Trajout.o
>>>>TrajoutList.o Vec3.o mainlsurf.o pub_fft.o \o
>>>> -L/usr/local/lib/amber14/lib
>>>>/usr/local/lib/amber14/lib/libnetcdfck -llapack -lblas -lgfortran -w
>>>> FileIO_Gzip.o: In function `FileIO_Gzip::Seek(long)':
>>>> FileIO_Gzip.cpp:(.text+0x6b): undefined reference to `gzseek64'
>>>> FileIO_Gzip.o: In function `FileIO_Gzip::Open(char const*, char
>>>> FileIO_Gzip.cpp:(.text+0x1eb): undefined reference to `gzopen64'
>>>> FileIO_Gzip.o: In function `FileIO_Gzip::Tell()':
>>>> FileIO_Gzip.cpp:(.text+0x35): undefined reference to `gztell64'
>>>> collect2: ld returned 1 exit status
>>>> make[3]: *** [cpptraj] Error 1
>>>> Thanks for input.
>>>> Danni Harris
>>>> _______________________________________________
>>>> AMBER mailing list
>>>Daniel R. Roe, PhD
>>>Department of Medicinal Chemistry
>>>University of Utah
>>>30 South 2000 East, Room 201
>>>Salt Lake City, UT 84112-5820
>>>(801) 587-9652
>>>(801) 585-6208 (Fax)
>>>AMBER mailing list
>> _______________________________________________
>> AMBER mailing list
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 201
>Salt Lake City, UT 84112-5820
>(801) 587-9652
>(801) 585-6208 (Fax)
>AMBER mailing list

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Received on Tue Jun 10 2014 - 05:00:02 PDT
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