Re: [AMBER] zlib issues during compilation.

From: Harris, Danni <>
Date: Mon, 9 Jun 2014 23:29:24 +0000

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.E.
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):

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 of
the compilation issue.

Thanks for your input.



The -lz is specified in the config.h

And is being added in the link (pasted material below).

____EXCERPT of config.h ______

NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a

EMILLIB=$(LIBDIR)/libemil.a -lstdc++




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_Distance.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_NAstruct.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_Volmap.o
Action_Watershell.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.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_Integrate.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 DataIO_Xplor.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 Mol2File.o
NameType.o NetcdfFile.o PDBfile.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.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_AmberRestart.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 \
/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 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
make[3]: Leaving directory
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 <> 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
>> 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 at
>>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_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
>> 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

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Received on Mon Jun 09 2014 - 17:00:02 PDT
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