Re: [AMBER] zlib issues during compilation.

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 9 Jun 2014 21:17:41 -0600

Hi,

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,

-Dan

On Mon, Jun 9, 2014 at 5:29 PM, Harris, Danni <danniharris.rti.org> 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
> AMBER14/AMBERTOOLS14.
>
> --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):
>
> http://unix.stackexchange.com/questions/77905/undefined-reference-to-gzopen
> 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 of
> the compilation issue.
>
> Thanks for your input.
>
> Danni
> __________________
>
>
>
> -DETAILED RESPONSE TO YOUR COMMENTS/QUESTIONS-
>
> 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 $(LIBDIR)/libnetcdf.a
> NETCDFINC=-I$(INCDIR)
> FFTWLIB=-lfftw3
>
> EMIL=EMIL
> 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
>
> COMPILER=gnu
> _______________
>
>
> 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 \
> -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 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
> `/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" <daniel.r.roe.gmail.com> wrote:
>
>>Hi,
>>
>>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
>>read?
>>
>>-Dan
>>
>>
>>On Mon, Jun 9, 2014 at 1:46 PM, Harris, Danni <danniharris.rti.org> 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 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
>>>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
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>--
>>-------------------------
>>Daniel R. Roe, PhD
>>Department of Medicinal Chemistry
>>University of Utah
>>30 South 2000 East, Room 201
>>Salt Lake City, UT 84112-5820
>>http://home.chpc.utah.edu/~cheatham/
>>(801) 587-9652
>>(801) 585-6208 (Fax)
>>
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 09 2014 - 20:30:03 PDT
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