Re: [AMBER] zlib issues during compilation.

From: Daniel Roe <>
Date: Mon, 9 Jun 2014 15:44:56 -0600


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 <> wrote:
> I am puzzled by some errors I am getting during the initial stages of compilation that I think are related to zlib / compression related routines.
> I am puzzled because I certainly have zlib related packages installed---and even downloaded —compiled and installed the zlib-1.2.8 release.
> (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 at first glance….
> 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_Dipole.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_Projection.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 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 const*)':
> 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)
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Received on Mon Jun 09 2014 - 15:00:02 PDT
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