[root@KWFPrimary cpptraj]# ./configure gnu
  The version of gcc is 8.5.0

  Testing C++ compiler: OK
  Testing C compiler: OK
  Testing Fortran compiler: OK
  Testing basic C++11 support: OK
  Testing system headers for C++11 support: OK
  Checking BZLIB: OK
  Checking ZLIB: OK
  Checking NetCDF4/HDF5:   Checking HDF5:   Checking for bundled HDF5: Should CPPTRAJ attempt to build its own hdf5? {y|n}: y
    Downloading hdf5...
--2025-01-04 18:36:41--  https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-1_10_9.tar.gz
Resolving github.com (github.com)... 140.82.113.3
Connecting to github.com (github.com)|140.82.113.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/HDFGroup/hdf5/tar.gz/refs/tags/hdf5-1_10_9 [following]
--2025-01-04 18:36:41--  https://codeload.github.com/HDFGroup/hdf5/tar.gz/refs/tags/hdf5-1_10_9
Resolving codeload.github.com (codeload.github.com)... 140.82.112.9
Connecting to codeload.github.com (codeload.github.com)|140.82.112.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘hdf5-1_10_9.tar.gz’

hdf5-1_10_9.tar.gz                   [            <=>                                         ]  13.53M  5.67MB/s    in 2.4s

2025-01-04 18:36:44 (5.67 MB/s) - ‘hdf5-1_10_9.tar.gz’ saved [14185565]

    Unpacking hdf5...
    Configuring hdf5... Success.
    MAKE_COMMAND is not set; set to 'make -j128'
    Compiling hdf5 (may be time-consuming)... Success.
  Checking built HDF5: OK
  Checking NetCDF:   Checking for bundled NetCDF: Setting MAKE_COMMAND to 'make -j1' to avoid NetCDF4/HDF5 race conditions.
Should CPPTRAJ attempt to build its own netcdf? {y|n}: y
    Downloading netcdf...
--2025-01-04 18:40:37--  https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/Unidata/netcdf-c/tar.gz/refs/tags/v4.9.2 [following]
--2025-01-04 18:40:38--  https://codeload.github.com/Unidata/netcdf-c/tar.gz/refs/tags/v4.9.2
Resolving codeload.github.com (codeload.github.com)... 140.82.114.9
Connecting to codeload.github.com (codeload.github.com)|140.82.114.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘v4.9.2.tar.gz’

v4.9.2.tar.gz                        [                    <=>                                 ]  18.62M  3.86MB/s    in 4.0s

2025-01-04 18:40:42 (4.61 MB/s) - ‘v4.9.2.tar.gz’ saved [19527342]

    Unpacking netcdf...
    Configuring netcdf... Success.
    Compiling netcdf (may be time-consuming)... Success.
  Checking built NetCDF: OK
  Checking LAPACK/BLAS: OK
  Checking FFTW3: OK
  Checking gnu RPATH type for libsander: OK

Configuration summary:
  Build type: Serial
  Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile hdf5 sanderlib
  Target platform: Linux, 64-bit.
  gnu compilers in use.
  C++11 support enabled.
  PME support enabled.
  Compiler optimizations are on.

Cleaning source directory.

--------------------------------------------------------------------------------
An environment resource file for CPPTRAJ has been created:
  /work/cpptraj/cpptraj.sh
You may 'source' this file to set up your environment for CPPTRAJ.
--------------------------------------------------------------------------------

CPPTRAJ configuration complete.

[root@KWFPrimary cpptraj]# make install
cd src && make install
make[1]: Entering directory '/work/cpptraj/src'
CXX SpaceGroup.cpp
CXX ActionFrameCounter.cpp
CXX ActionList.cpp
CXX ActionTopWriter.cpp
CXX Action_AddAtom.cpp
CXX Action_Align.cpp
CXX Action_Angle.cpp
CXX Action_AreaPerMol.cpp
CXX Action_AtomMap.cpp
CXX Action_AtomicCorr.cpp
CXX Action_AtomicFluct.cpp
CXX Action_AutoImage.cpp
CXX Action_Average.cpp
CXX Action_AvgBox.cpp
CXX Action_Bounds.cpp
CXX Action_Box.cpp
CXX Action_Center.cpp
CXX Action_Channel.cpp
CXX Action_CheckChirality.cpp
CXX Action_CheckStructure.cpp
CXX Action_Closest.cpp
CXX Action_ClusterDihedral.cpp
CXX Action_Contacts.cpp
CXX Action_ConvertToFrac.cpp
CXX Action_CreateCrd.cpp
CXX Action_CreateReservoir.cpp
CXX Action_DNAionTracker.cpp
CXX Action_DSSP.cpp
CXX Action_Density.cpp
CXX Action_Diffusion.cpp
CXX Action_Dihedral.cpp
CXX Action_DihedralRMS.cpp
CXX Action_Dipole.cpp
CXX Action_Distance.cpp
CXX Action_DistRmsd.cpp
CXX Action_EneDecomp.cpp
CXX Action_Energy.cpp
CXX Action_FilterByData.cpp
CXX Action_FixAtomOrder.cpp
CXX Action_FixImagedBonds.cpp
CXX Action_GIST.cpp
CXX Action_Grid.cpp
CXX Action_GridFreeEnergy.cpp
CXX Action_HydrogenBond.cpp
CXX Action_Image.cpp
CXX Action_InfraredSpectrum.cpp
CXX Action_Jcoupling.cpp
CXX Action_Keep.cpp
CXX Action_LESsplit.cpp
CXX Action_LIE.cpp
CXX Action_LipidOrder.cpp
CXX Action_MakeStructure.cpp
CXX Action_Mask.cpp
CXX Action_Matrix.cpp
CXX Action_MinMaxDist.cpp
CXX Action_MinImage.cpp
CXX Action_Molsurf.cpp
CXX Action_MultiDihedral.cpp
CXX Action_MultiPucker.cpp
CXX Action_MultiVector.cpp
CXX Action_NAstruct.cpp
CXX Action_NativeContacts.cpp
CXX Action_NMRrst.cpp
CXX Action_OrderParameter.cpp
CXX Action_Outtraj.cpp
CXX Action_PairDist.cpp
CXX Action_Pairwise.cpp
CXX Action_Principal.cpp
CXX Action_Projection.cpp
CXX Action_Pucker.cpp
CXX Action_Radgyr.cpp
CXX Action_Radial.cpp
CXX Action_RandomizeIons.cpp
CXX Action_Remap.cpp
CXX Action_ReplicateCell.cpp
CXX Action_Rmsd.cpp
CXX Action_Rotate.cpp
CXX Action_RunningAvg.cpp
CXX Action_STFC_Diffusion.cpp
CXX Action_Scale.cpp
CXX Action_SetVelocity.cpp
CXX Action_Spam.cpp
CXX Action_Strip.cpp
CXX Action_Surf.cpp
CXX Action_SymmetricRmsd.cpp
CXX Action_Temperature.cpp
CXX Action_Test.cpp
CXX Action_Time.cpp
CXX Action_ToroidalDiffusion.cpp
CXX Action_Translate.cpp
CXX Action_Unstrip.cpp
CXX Action_Unwrap.cpp
CXX Action_Vector.cpp
CXX Action_VelocityAutoCorr.cpp
CXX Action_Volmap.cpp
CXX Action_Volume.cpp
CXX Action_Watershell.cpp
CXX Action_XtalSymm.cpp
CXX AnalysisList.cpp
CXX Analysis_AmdBias.cpp
CXX Analysis_AutoCorr.cpp
CXX Analysis_Average.cpp
CXX Analysis_CalcDiffusion.cpp
CXX Analysis_Clustering.cpp
CXX Analysis_Corr.cpp
CXX Analysis_ConstantPHStats.cpp
CXX Analysis_CrankShaft.cpp
CXX Analysis_CrdFluct.cpp
CXX Analysis_CrossCorr.cpp
CXX Analysis_CurveFit.cpp
CXX Analysis_Divergence.cpp
CXX Analysis_EvalPlateau.cpp
CXX Analysis_FFT.cpp
CXX Analysis_HausdorffDistance.cpp
CXX Analysis_Hist.cpp
CXX Analysis_Integrate.cpp
CXX Analysis_IRED.cpp
CXX Analysis_KDE.cpp
CXX Analysis_Lifetime.cpp
CXX Analysis_LowestCurve.cpp
CXX Analysis_Matrix.cpp
CXX Analysis_MeltCurve.cpp
CXX Analysis_Modes.cpp
CXX Analysis_Multicurve.cpp
CXX Analysis_MultiHist.cpp
CXX Analysis_Overlap.cpp
CXX Analysis_PhiPsi.cpp
CXX Analysis_Project.cpp
CXX Analysis_Regression.cpp
CXX Analysis_RemLog.cpp
CXX Analysis_Rms2d.cpp
CXX Analysis_RmsAvgCorr.cpp
CXX Analysis_Rotdif.cpp
CXX Analysis_RunningAvg.cpp
CXX Analysis_Slope.cpp
CXX Analysis_Spline.cpp
CXX Analysis_State.cpp
CXX Analysis_Statistics.cpp
CXX Analysis_TI.cpp
CXX Analysis_TICA.cpp
CXX Analysis_Timecorr.cpp
CXX Analysis_VectorMath.cpp
CXX Analysis_Wavelet.cpp
CXX ArgList.cpp
CXX Array1D.cpp
CXX AssociatedData_Connect.cpp
CXX AssociatedData_NOE.cpp
CXX Atom.cpp
CXX AtomMap.cpp
CXX AtomMask.cpp
CXX AxisType.cpp
CXX BondSearch.cpp
CXX Box.cpp
CXX BoxArgs.cpp
CXX BufferedFrame.cpp
CXX BufferedLine.cpp
CXX ByteRoutines.cpp
CXX CharMask.cpp
CXX CharmmParamFile.cpp
CXX CIFfile.cpp
CXX ClusterMap.cpp
CXX Cmd.cpp
CXX CmdInput.cpp
CXX CmdList.cpp
CXX CompactFrameArray.cpp
CXX ComplexArray.cpp
CXX Constraints.cpp
CXX ControlBlock_For.cpp
CXX CoordCovarMatrix.cpp
CXX CoordCovarMatrix_Full.cpp
CXX CoordCovarMatrix_Half.cpp
CXX CoordinateInfo.cpp
CXX Corr.cpp
CXX Cph.cpp
CXX CpptrajFile.cpp
CXX CpptrajState.cpp
CXX CpptrajStdio.cpp
CXX CurveFit.cpp
CXX DataFile.cpp
CXX DataFileList.cpp
CXX DataFilter.cpp
CXX DataIO.cpp
CXX DataIO_AmberEne.cpp
CXX DataIO_AmberLib.cpp
CXX DataIO_AmberPrep.cpp
CXX DataIO_CCP4.cpp
CXX DataIO_CharmmFastRep.cpp
CXX DataIO_CharmmOutput.cpp
CXX DataIO_CharmmRepLog.cpp
CXX DataIO_CharmmRtfPrm.cpp
CXX DataIO_Cmatrix_Binary.cpp
CXX DataIO_Cmatrix_NC.cpp
CXX DataIO_Cpout.cpp
CXX DataIO_Evecs.cpp
CXX DataIO_Gnuplot.cpp
CXX DataIO_Grace.cpp
CXX DataIO_OpenDx.cpp
CXX DataIO_Peaks.cpp
CXX DataIO_Mdout.cpp
CXX DataIO_NetCDF.cpp
CXX DataIO_Numpy.cpp
CXX DataIO_RemLog.cpp
CXX DataIO_Std.cpp
CXX DataIO_VecTraj.cpp
CXX DataIO_Xplor.cpp
CXX DataIO_XVG.cpp
CXX DataSet.cpp
CXX DataSetList.cpp
CXX DataSet_1D.cpp
CXX DataSet_2D.cpp
CXX DataSet_3D.cpp
CXX DataSet_Coords.cpp
CXX DataSet_Coords_CRD.cpp
CXX DataSet_Coords_FRM.cpp
CXX DataSet_Coords_REF.cpp
CXX DataSet_Coords_TRJ.cpp
CXX DataSet_GridDbl.cpp
CXX DataSet_GridFlt.cpp
CXX DataSet_Mat3x3.cpp
CXX DataSet_MatrixDbl.cpp
CXX DataSet_MatrixFlt.cpp
CXX DataSet_Mesh.cpp
CXX DataSet_Modes.cpp
CXX DataSet_PairwiseCache.cpp
CXX DataSet_PairwiseCache_MEM.cpp
CXX DataSet_PairwiseCache_NC.cpp
CXX DataSet_Parameters.cpp
CXX DataSet_pH.cpp
CXX DataSet_PHREMD_Explicit.cpp
CXX DataSet_PHREMD_Implicit.cpp
CXX DataSet_RemLog.cpp
CXX DataSet_Topology.cpp
CXX DataSet_Vector.cpp
CXX DataSet_Vector_Scalar.cpp
CXX DataSet_double.cpp
CXX DataSet_float.cpp
CXX DataSet_integer_disk.cpp
CXX DataSet_integer_mem.cpp
CXX DataSet_string.cpp
CXX DataSet_StringVar.cpp
CXX DataSet_Tensor.cpp
CXX DataSet_unsignedInt.cpp
CXX DataSet_Zmatrix.cpp
CXX Deprecated.cpp
CXX DihedralSearch.cpp
CXX DiffusionResults.cpp
CXX DistRoutines.cpp
CXX Dist_Imaged.cpp
CXX Energy.cpp
CXX EnergyArray.cpp
CXX EnsembleIn.cpp
CXX EnsembleIn_Multi.cpp
CXX EnsembleIn_Single.cpp
CXX EnsembleNavigator.cpp
CXX EnsembleOut.cpp
CXX EnsembleOut_Multi.cpp
CXX EnsembleOut_Single.cpp
CXX EnsembleOutList.cpp
CXX EwaldOptions.cpp
CXX ExclusionArray.cpp
CXX Exec_AddMissingRes.cpp
CXX Exec_Analyze.cpp
CXX Exec_Calc.cpp
CXX Exec_CatCrd.cpp
CXX Exec_Change.cpp
CXX Exec_ClusterMap.cpp
CXX Exec_CombineCoords.cpp
CXX Exec_Commands.cpp
CXX Exec_CompareClusters.cpp
CXX Exec_CompareEnergy.cpp
CXX Exec_CompareTop.cpp
CXX Exec_CrdAction.cpp
CXX Exec_CrdOut.cpp
CXX Exec_CrdTransform.cpp
CXX Exec_CreateSet.cpp
CXX Exec_DataFile.cpp
CXX Exec_DataFilter.cpp
CXX Exec_DataSetCmd.cpp
CXX Exec_Emin.cpp
CXX Exec_ExtendedComparison.cpp
CXX Exec_Flatten.cpp
CXX Exec_GenerateAmberRst.cpp
CXX Exec_Graft.cpp
CXX Exec_Help.cpp
CXX Exec_HmassRepartition.cpp
CXX Exec_LoadCrd.cpp
CXX Exec_LoadTraj.cpp
CXX Exec_ParallelAnalysis.cpp
CXX Exec_ParmBox.cpp
CXX Exec_ParmSolvent.cpp
CXX Exec_ParmStrip.cpp
CXX Exec_ParmWrite.cpp
CXX Exec_ParseTiming.cpp
CXX Exec_PermuteDihedrals.cpp
CXX Exec_Precision.cpp
CXX Exec_PrepareForLeap.cpp
CXX Exec_PrintData.cpp
CXX Exec_Random.cpp
CXX Exec_ReadData.cpp
CXX Exec_ReadEnsembleData.cpp
CXX Exec_ReadInput.cpp
CXX Exec_RotateDihedral.cpp
CXX Exec_RunAnalysis.cpp
CXX Exec_ScaleDihedralK.cpp
CXX Exec_Set.cpp
CXX Exec_Sequence.cpp
CXX Exec_SequenceAlign.cpp
CXX Exec_Show.cpp
CXX Exec_SortEnsembleData.cpp
CXX Exec_SplitCoords.cpp
CXX Exec_System.cpp
CXX Exec_Top.cpp
CXX Exec_Traj.cpp
CXX Exec_UpdateParameters.cpp
CXX Exec_ViewRst.cpp
CXX Exec_Zmatrix.cpp
CXX ExtendedSimilarity.cpp
CXX File_TempName.cpp
CXX FileIO_Bzip2.cpp
CXX FileIO_Gzip.cpp
CXX FileIO_Mpi.cpp
CXX FileIO_MpiShared.cpp
CXX FileIO_Std.cpp
CXX FileName.cpp
CXX FileType.cpp
CXX FileTypes.cpp
CXX ForLoop.cpp
CXX ForLoop_dataSetBlocks.cpp
CXX ForLoop_inData.cpp
CXX ForLoop_integer.cpp
CXX ForLoop_list.cpp
CXX ForLoop_mask.cpp
CXX ForLoop_overSets.cpp
CXX Frame.cpp
CXX GistEntropyUtils.cpp
CXX GIST_PME.cpp
CXX Gpu.cpp
CXX GridAction.cpp
CXX GridMover.cpp
CXX GridBin.cpp
CXX HistBin.cpp
CXX Hungarian.cpp
CXX ImageRoutines.cpp
CXX Image_List_Mask.cpp
CXX Image_List_Pair.cpp
CXX Image_List_Unit.cpp
CXX InteractionData.cpp
CXX InputTrajCommon.cpp
CXX KDE.cpp
CXX LeapInterface.cpp
CXX MapAtom.cpp
CXX MaskArray.cpp
CXX MaskToken.cpp
CXX Matrix_3x3.cpp
CXX MdOpts.cpp
CXX MetaData.cpp
CXX Minimize_SteepestDescent.cpp
CXX Mol.cpp
CXX Mol2File.cpp
CXX NameType.cpp
CXX NC_Routines.cpp
CXX NDiff.cpp
CXX NetcdfFile.cpp
CXX OMM_helpers.cpp
CXX OutputTrajCommon.cpp
CXX ParameterSet.cpp
CXX PDBfile.cpp
CXX PairList.cpp
CXX Parallel.cpp
CXX ParallelNetcdf.cpp
CXX ParallelSetFrameNum.cpp
CXX ParmFile.cpp
CXX Parm_Amber.cpp
CXX Parm_CharmmPsf.cpp
CXX Parm_CIF.cpp
CXX Parm_Gromacs.cpp
CXX Parm_Mol2.cpp
CXX Parm_PDB.cpp
CXX Parm_SDF.cpp
CXX Parm_Tinker.cpp
CXX PotentialFunction.cpp
CXX PotentialTerm.cpp
CXX PotentialTerm_Angle.cpp
CXX PotentialTerm_Bond.cpp
CXX PotentialTerm_Dihedral.cpp
CXX PotentialTerm_LJ_Coulomb.cpp
CXX PotentialTerm_OpenMM.cpp
CXX ProgressBar.cpp
CXX ProgressTimer.cpp
CXX PubFFT.cpp
CXX qcprot.cpp
CXX QuaternionRMSD.cpp
CXX Pucker_PuckerMask.cpp
CXX Pucker_PuckerSearch.cpp
CXX Pucker_PuckerToken.cpp
CXX ExternalFxn.cpp
CXX Random.cpp
CXX Range.cpp
CXX RNG.cpp
CXX RNG_Marsaglia.cpp
CXX RNG_MersenneTwister.cpp
CXX RNG_PCG32.cpp
CXX RNG_Stdlib.cpp
CXX RNG_Xoshiro128pp.cpp
CXX RPNcalc.cpp
CXX ReferenceAction.cpp
CXX RemdReservoirNC.cpp
CXX Residue.cpp
CXX SDFfile.cpp
CXX SimplexMin.cpp
CXX Spline.cpp
CXX SplineFxnTable.cpp
CXX Stats_Reduce.cpp
CXX StringRoutines.cpp
CXX StructureCheck.cpp
CXX StructureMapper.cpp
CXX SymmetricRmsdCalc.cpp
CXX TextBlockBuffer.cpp
CXX TextFormat.cpp
CXX Timer.cpp
CXX TinkerFile.cpp
CXX TopInfo.cpp
CXX Topology.cpp
CXX TorsionRoutines.cpp
CXX Traj_AmberCoord.cpp
CXX Traj_AmberNetcdf.cpp
CXX Traj_AmberRestart.cpp
CXX Traj_AmberRestartNC.cpp
CXX Traj_Binpos.cpp
CXX Traj_CharmmCor.cpp
CXX Traj_CharmmDcd.cpp
CXX Traj_CharmmRestart.cpp
CXX Traj_CIF.cpp
CXX Traj_Conflib.cpp
CXX Traj_DTR.cpp
CXX Traj_GmxDump.cpp
CXX Traj_GmxTng.cpp
CXX Traj_GmxTrX.cpp
CXX Traj_GmxXtc.cpp
CXX Traj_Gro.cpp
CXX Traj_H5.cpp
CXX Traj_H5MD.cpp
CXX Traj_Mol2File.cpp
CXX Traj_NcEnsemble.cpp
CXX Traj_PDBfile.cpp
CXX Traj_SDF.cpp
CXX Traj_SQM.cpp
CXX Traj_Tinker.cpp
CXX Traj_XYZ.cpp
CXX TrajectoryFile.cpp
CXX TrajectoryIO.cpp
CXX TrajFrameCounter.cpp
CXX TrajinList.cpp
CXX Trajin_Multi.cpp
CXX Trajin_Single.cpp
CXX TrajIOarray.cpp
CXX Trajout_Single.cpp
CXX TrajoutList.cpp
CXX Units.cpp
CXX Vec3.cpp
CXX ViewRst.cpp
CXX vmdplugin/dtrplugin.cpp
In file included from vmdplugin/dtrplugin.cpp:65:
vmdplugin/vmddir.h:146:12: warning: ‘int vmd_file_is_executable(const char*)’ defined but not used [-Wunused-function]
 static int vmd_file_is_executable(const char * filename) {
            ^~~~~~~~~~~~~~~~~~~~~~
CXX xoshiro128plusplus.cpp
xoshiro128plusplus.cpp: In function ‘void jump()’:
xoshiro128plusplus.cpp:60:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++)
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
xoshiro128plusplus.cpp: In function ‘void long_jump()’:
xoshiro128plusplus.cpp:90:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++)
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CXX Action_Esander.cpp
CXX Command.cpp
CXX Cpptraj.cpp
CXX Energy_Sander.cpp
CXX ReadLine.cpp
CXX main.cpp
CC molsurf.c
CXX Cluster/Algorithm.cpp
CXX Cluster/Algorithm_DBscan.cpp
CXX Cluster/Algorithm_DPeaks.cpp
CXX Cluster/Algorithm_HierAgglo.cpp
CXX Cluster/Algorithm_Kmeans.cpp
CXX Cluster/BestReps.cpp
CXX Cluster/CentroidArray.cpp
CXX Cluster/Centroid_Coord.cpp
CXX Cluster/Cframes.cpp
CXX Cluster/Cmatrix_Binary.cpp
CXX Cluster/Cmatrix_NC.cpp
CXX Cluster/Control.cpp
CXX Cluster/DBI.cpp
CXX Cluster/DrawGraph.cpp
CXX Cluster/DynamicMatrix.cpp
CXX Cluster/List.cpp
CXX Cluster/MetricArray.cpp
CXX Cluster/Metric_DME.cpp
CXX Cluster/Metric_Matrix2D.cpp
CXX Cluster/Metric_QuatRMSD.cpp
CXX Cluster/Metric_RMS.cpp
CXX Cluster/Metric_SRMSD.cpp
CXX Cluster/Metric_Scalar.cpp
CXX Cluster/Metric_Torsion.cpp
CXX Cluster/Node.cpp
CXX Cluster/Output.cpp
CXX Cluster/PseudoF.cpp
CXX Cluster/Results_Coords.cpp
CXX Cluster/Sieve.cpp
CXX Cluster/Silhouette.cpp
CXX Structure/Builder.cpp
CXX Structure/Chirality.cpp
CXX Structure/Disulfide.cpp
CXX Structure/FunctionalGroup.cpp
CXX Structure/FxnGroupBuilder.cpp
CXX Structure/HisProt.cpp
CXX Structure/InternalCoords.cpp
CXX Structure/Model.cpp
CXX Structure/StructureEnum.cpp
CXX Structure/StructureRoutines.cpp
CXX Structure/SugarBuilder.cpp
CXX Structure/Sugar.cpp
CXX Structure/SugarLinkAtoms.cpp
CXX Structure/SugarToken.cpp
CXX Structure/Zmatrix.cpp
CXX Energy/Ecalc_Nonbond.cpp
CXX Energy/EnergyDecomposer.cpp
CXX Energy/ErfcFxn.cpp
CXX Energy/EwaldCalc_Decomp_LJPME.cpp
CXX Energy/EwaldCalc_Decomp_PME.cpp
CXX Energy/EwaldCalc_LJPME.cpp
CXX Energy/EwaldCalc_PME.cpp
CXX Energy/EwaldCalc_Regular.cpp
CXX Energy/EwaldParams.cpp
CXX Energy/EwaldParams_LJPME.cpp
CXX Energy/Ewald_Recip.cpp
CXX Energy/PME_Recip.cpp
CXX Energy/PME_RecipParams.cpp
CXX Energy/VDW_LongRange_Correction.cpp
cd readline && make all
make[2]: Entering directory '/work/cpptraj/src/readline'
[READLINE] CC bind.c
bind.c: In function ‘rl_translate_keyseq’:
bind.c:445:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   for (i = l = 0; c = seq[i]; i++)
                   ^
bind.c: In function ‘rl_parse_and_bind’:
bind.c:1197:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       for (i = 1; c = string[i]; i++)
                   ^
bind.c:1288:23: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       for (passc = 0; c = string[i]; i++)
                       ^
bind.c: In function ‘rl_function_dumper’:
bind.c:2060:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   for (i = 0; name = names[i]; i++)
               ^~~~
[READLINE] CC callback.c
[READLINE] CC compat.c
[READLINE] CC complete.c
complete.c: In function ‘fnwidth’:
complete.c:604:12: warning: implicit declaration of function ‘wcwidth’; did you mean ‘fnwidth’? [-Wimplicit-function-declaration]
        w = wcwidth (wc);
            ^~~~~~~
            fnwidth
complete.c: In function ‘_rl_find_completion_word’:
complete.c:886:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point, MB_FIND_ANY))
              ^~~~~~~~
complete.c: In function ‘rl_completion_matches’:
complete.c:1805:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   while (string = (*entry_function) (text, matches))
          ^~~~~~
complete.c: In function ‘rl_username_completion_function’:
complete.c:1856:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   while (entry = getpwent ())
          ^~~~~
[READLINE] CC display.c
display.c: In function ‘rl_redisplay’:
display.c:714:15: warning: implicit declaration of function ‘wcwidth’ [-Wimplicit-function-declaration]
        temp = wcwidth (wc);
               ^~~~~~~
display.c:558:7: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
       strncpy (line + out,  prompt_this_line, pmtlen);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
display.c:550:40: note: length computed here
       prompt_physical_chars = pmtlen = strlen (prompt_this_line);
                                        ^~~~~~~~~~~~~~~~~~~~~~~~~
display.c:829:8: warning: ‘wc_width’ may be used uninitialized in this function [-Wmaybe-uninitialized]
        for (i = 0; i < wc_width; i++)
        ^~~
display.c:462:38: warning: ‘n0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int newlines, lpos, temp, modmark, n0, num;
                                      ^~
[READLINE] CC funmap.c
[READLINE] CC histexpand.c
histexpand.c: In function ‘get_history_event’:
histexpand.c:206:25: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   for (local_index = i; c = string[i]; i++)
                         ^
histexpand.c: In function ‘history_expand_internal’:
histexpand.c:696:41: warning: variable ‘ws’ set but not used [-Wunused-but-set-variable]
      int delimiter, failed, si, l_temp, ws, we;
                                         ^~
[READLINE] CC histfile.c
[READLINE] CC history.c
[READLINE] CC histsearch.c
[READLINE] CC input.c
input.c: In function ‘rl_read_key’:
input.c:423:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       if (c = _rl_next_macro_key ())
           ^
[READLINE] CC isearch.c
isearch.c: In function ‘rl_search_history’:
isearch.c:620:7: warning: variable ‘c’ set but not used [-Wunused-but-set-variable]
   int c, r;
       ^
isearch.c: In function ‘_rl_isearch_callback’:
isearch.c:658:7: warning: variable ‘c’ set but not used [-Wunused-but-set-variable]
   int c, r;
       ^
[READLINE] CC keymaps.c
[READLINE] CC kill.c
[READLINE] CC macro.c
[READLINE] CC mbutil.c
mbutil.c: In function ‘_rl_find_next_mbchar_internal’:
mbutil.c:118:12: warning: implicit declaration of function ‘wcwidth’ [-Wimplicit-function-declaration]
        if (wcwidth (wc) == 0)
            ^~~~~~~
[READLINE] CC misc.c
[READLINE] CC nls.c
[READLINE] CC parens.c
parens.c: In function ‘rl_insert_close’:
parens.c:118:36: warning: variable ‘ready’ set but not used [-Wunused-but-set-variable]
       int orig_point, match_point, ready;
                                    ^~~~~
[READLINE] CC readline.c
readline.c: In function ‘readline_internal_char’:
readline.c:450:21: warning: variable ‘eof_found’ set but not used [-Wunused-but-set-variable]
   static int lastc, eof_found;
                     ^~~~~~~~~
At top level:
readline.c:1078:1: warning: ‘reset_default_bindings’ defined but not used [-Wunused-function]
 reset_default_bindings ()
 ^~~~~~~~~~~~~~~~~~~~~~
[READLINE] CC rltty.c
[READLINE] CC savestring.c
[READLINE] CC search.c
[READLINE] CC shell.c
[READLINE] CC signals.c
[READLINE] CC termcap.c
[READLINE] CC terminal.c
[READLINE] CC text.c
text.c: In function ‘_rl_overwrite_char’:
text.c:814:7: warning: variable ‘k’ set but not used [-Wunused-but-set-variable]
   int k;
       ^
text.c: In function ‘rl_insert_text’:
text.c:94:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
   strncpy (rl_line_buffer + rl_point, string, l);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
text.c:85:29: note: length computed here
   l = (string && *string) ? strlen (string) : 0;
                             ^~~~~~~~~~~~~~~
[READLINE] CC tilde.c
tilde.c: In function ‘tilde_expand’:
tilde.c:199:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   if (result = strchr (string, '~'))
       ^~~~~~
[READLINE] CC tparam.c
[READLINE] CC undo.c
undo.c: In function ‘_rl_copy_undo_list’:
undo.c:157:16: warning: ‘roving’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   roving->next = 0;
   ~~~~~~~~~~~~~^~~
[READLINE] CC util.c
[READLINE] CC version.c
version.c:2:14: warning: ‘version_string’ defined but not used [-Wunused-variable]
 static char *version_string = "\n$Version: GNU termcap 1.3.1 $\n";
              ^~~~~~~~~~~~~~
[READLINE] CC vi_mode.c
[READLINE] CC xmalloc.c
/bin/rm -f libreadline.a
ar cqs libreadline.a bind.o callback.o compat.o complete.o display.o funmap.o histexpand.o histfile.o history.o histsearch.o input.o isearch.o keymaps.o kill.o macro.o mbutil.o misc.o nls.o parens.o readline.o rltty.o savestring.o search.o shell.o signals.o termcap.o terminal.o text.o tilde.o tparam.o undo.o util.o version.o vi_mode.o xmalloc.o
make[2]: Leaving directory '/work/cpptraj/src/readline'
cd xdrfile && make all
make[2]: Entering directory '/work/cpptraj/src/xdrfile'
[XDRFILE] CC xdrfile.c
[XDRFILE] CC xdr_seek.c
[XDRFILE] CC xdrfile_trr.c
[XDRFILE] CC xdrfile_xtc.c
/bin/rm -f libxdrfile.a
ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o
make[2]: Leaving directory '/work/cpptraj/src/xdrfile'
cd arpack && make install
make[2]: Entering directory '/work/cpptraj/src/arpack'
[ARPACK] FC ivout.f
[ARPACK] FC dvout.f
[ARPACK] FC dgetv0.f
dgetv0.f:120:26:

      &   ( ido, bmat, itry, initv, n, j, v, ldv, resid, rnorm,
                          1
Warning: Unused dummy argument ‘itry’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dlaqrb.f
dlaqrb.f:495:0:

             if( i2.gt.i )

Warning: ‘i2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
[ARPACK] FC dnaitr.f
dnaitr.f:210:33:

      &   (ido, bmat, n, k, np, nb, resid, rnorm, v, ldv, h, ldh,
                                 1
Warning: Unused dummy argument ‘nb’ at (1) [-Wunused-dummy-argument]
[ARPACK] FC dnapps.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dnaup2.f
dnaup2.f:316:5:

    10 continue
     1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
dnaup2.f:175:63:

      &   ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
                                                               1
Warning: Unused dummy argument ‘iupd’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dnaupd.f
dnaupd.f:541:24:

          if (nb .le. 0)    nb = 1
                        1
Warning: Nonconforming tab character at (1) [-Wtabs]
dnaupd.f:542:28:

          if (tol .le. zero)   tol = dlamch('EpsMach')
                            1
Warning: Nonconforming tab character at (1) [-Wtabs]
dnaupd.f:447:32:

      &           ldh, ldq, levec, mode, msglvl, mxiter, nb,
                                1
Warning: Unused variable ‘levec’ declared at (1) [-Wunused-variable]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dnconv.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dneigh.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dmout.f
[ARPACK] FC dneupd.f
dneupd.f:587:17:

             jj = workl(bounds + ncv - j)
                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
stat.h:8:19:

       real       t0, t1, t2, t3, t4, t5
                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

       real       t0, t1, t2, t3, t4, t5
                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dngets.f
dngets.f:96:40:

      &                    shiftr, shifti )
                                        1
Warning: Unused dummy argument ‘shifti’ at (1) [-Wunused-dummy-argument]
dngets.f:96:32:

      &                    shiftr, shifti )
                                1
Warning: Unused dummy argument ‘shiftr’ at (1) [-Wunused-dummy-argument]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsaitr.f
[ARPACK] FC dsapps.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsaup2.f
dsaup2.f:809:5:

   130    continue
     1
Warning: Label 130 at (1) defined but not used [-Wunused-label]
dsaup2.f:324:5:

    10 continue
     1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
dsaup2.f:180:63:

      &   ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
                                                               1
Warning: Unused dummy argument ‘iupd’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsaupd.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsconv.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dseigt.f
dseigt.f:124:18:

       integer    i, k, msglvl
                  1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsesrt.f
[ARPACK] FC dseupd.f
dseupd.f:499:17:

             jj = workl(bounds + ncv - j)
                 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
stat.h:8:19:

       real       t0, t1, t2, t3, t4, t5
                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

       real       t0, t1, t2, t3, t4, t5
                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsgets.f
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dsortc.f
[ARPACK] FC dsortr.f
[ARPACK] FC dstatn.f
stat.h:8:19:

       real       t0, t1, t2, t3, t4, t5
                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

       real       t0, t1, t2, t3, t4, t5
                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dstats.f
stat.h:8:19:

       real       t0, t1, t2, t3, t4, t5
                   1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:

       real       t0, t1, t2, t3, t4, t5
                       1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:

       real       t0, t1, t2, t3, t4, t5
                           1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:

       real       t0, t1, t2, t3, t4, t5
                               1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:

       real       t0, t1, t2, t3, t4, t5
                                   1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:

       real       t0, t1, t2, t3, t4, t5
                                       1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
[ARPACK] FC dstqrb.f
[ARPACK] FC arsecond.f
arsecond.f:27:30:

       REAL               ETIME
                              1
Warning: Unused variable ‘etime’ declared at (1) [-Wunused-variable]
/bin/rm -f libarpack.a
ar rv  libarpack.a ivout.o dvout.o dgetv0.o dlaqrb.o dnaitr.o dnapps.o dnaup2.o dnaupd.o dnconv.o dneigh.o dmout.o dneupd.o dngets.o dsaitr.o dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o arsecond.o
ar: creating libarpack.a
a - ivout.o
a - dvout.o
a - dgetv0.o
a - dlaqrb.o
a - dnaitr.o
a - dnapps.o
a - dnaup2.o
a - dnaupd.o
a - dnconv.o
a - dneigh.o
a - dmout.o
a - dneupd.o
a - dngets.o
a - dsaitr.o
a - dsapps.o
a - dsaup2.o
a - dsaupd.o
a - dsconv.o
a - dseigt.o
a - dsesrt.o
a - dseupd.o
a - dsgets.o
a - dsortc.o
a - dsortr.o
a - dstatn.o
a - dstats.o
a - dstqrb.o
a - arsecond.o
ranlib libarpack.a
make[2]: Leaving directory '/work/cpptraj/src/arpack'
cd tng && make all
make[2]: Entering directory '/work/cpptraj/src/tng'
[TNG] CC md5.c
[TNG] CC tng_io.c
tng_io.c:16: warning: "_LARGEFILE_SOURCE" redefined
 #define _LARGEFILE_SOURCE

<command-line>: note: this is the location of the previous definition
In function ‘tng_gen_data_block_add.constprop’,
    inlined from ‘tng_data_block_add.constprop’ at tng_io.c:12788:12:
tng_io.c:12600:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
         strncpy(data->block_name, block_name, strlen(block_name) + 1);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tng_io.c: In function ‘tng_data_block_add.constprop’:
tng_io.c:12600:47: note: length computed here
         strncpy(data->block_name, block_name, strlen(block_name) + 1);
                                               ^~~~~~~~~~~~~~~~~~
In function ‘tng_gen_data_block_add.constprop’,
    inlined from ‘tng_data_block_add’ at tng_io.c:12788:12:
tng_io.c:12600:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
         strncpy(data->block_name, block_name, strlen(block_name) + 1);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tng_io.c: In function ‘tng_data_block_add’:
tng_io.c:12600:47: note: length computed here
         strncpy(data->block_name, block_name, strlen(block_name) + 1);
                                               ^~~~~~~~~~~~~~~~~~
In function ‘tng_gen_data_block_add’,
    inlined from ‘tng_particle_data_block_add’ at tng_io.c:12813:12:
tng_io.c:12600:9: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
         strncpy(data->block_name, block_name, strlen(block_name) + 1);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tng_io.c: In function ‘tng_particle_data_block_add’:
tng_io.c:12600:47: note: length computed here
         strncpy(data->block_name, block_name, strlen(block_name) + 1);
                                               ^~~~~~~~~~~~~~~~~~
[TNG] CC tng_compress.c
[TNG] CC coder.c
[TNG] CC warnmalloc.c
[TNG] CC fixpoint.c
[TNG] CC xtc3.c
[TNG] CC bwlzh.c
[TNG] CC xtc2.c
[TNG] CC widemuldiv.c
[TNG] CC huffmem.c
[TNG] CC vals16.c
[TNG] CC bwt.c
[TNG] CC mtf.c
[TNG] CC rle.c
[TNG] CC lz77.c
[TNG] CC dict.c
[TNG] CC huffman.c
[TNG] CC merge_sort.c
/bin/rm -f libtng_io.a
ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o
make[2]: Leaving directory '/work/cpptraj/src/tng'
Link cpptraj
/usr/bin/ld: arpack/libarpack.a(dsaupd.o)(.text+0x124): unresolvable R_X86_64_PC32 relocation against symbol `timing_'
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:50: cpptraj] Error 1
make[1]: Leaving directory '/work/cpptraj/src'
make: *** [Makefile:10: install] Error 2
[root@KWFPrimary cpptraj]#