sorry, I'm trying to install github version of cpptraj (not Amber20)
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhavadixit.gmail.com
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
On Mon, Nov 8, 2021 at 3:01 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear Daniel and Amber team,
> I'm trying to install the github version of Amber20, but I'm getting the
> following error message during the compilation "make install" step for
> which I can't find an easy solution online.
> The full output from the configure and make steps are shown at the bottom.
> Can you please suggest me on how to fix this error?
> I want to use the AmberMDprep script along with the github version of the
> cpptraj as recommended on the github repo.
> Looking forward to your valuable suggestions and feedback.
> thank you and best regards. Vaibhav
>
> /usr/bin/ld: arpack/libarpack.a(dsaupd.o)(.text+0x135): unresolvable
> R_X86_64_PC32 relocation against symbol `timing_'
> *collect2: error: ld returned 1 exit status*
> make[1]: *** [Makefile:23: cpptraj] Error 1
> make[1]: Leaving directory '/home/niperg/Downloads/cpptraj-master/src'
> make: *** [Makefile:10: install] Error 2
>
> (base) niperg.niperg-dell:~/Downloads/cpptraj-master$ ./configure gnu
>
> 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 NetCDF: Checking for bundled NetCDF: OK
> Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: OK
> Checking FFTW3: OK
> Checking for sanderlib: OK
>
> Configuration summary:
> Build type: Serial
> Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile
> 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:
> /home/niperg/Downloads/cpptraj-master/cpptraj.sh
> You may 'source' this file to set up your environment for CPPTRAJ.
>
> --------------------------------------------------------------------------------
>
> CPPTRAJ configuration complete.
>
> (base) niperg.niperg-dell:~/Downloads/cpptraj-master$ make install
> cd src && make install
> make[1]: Entering directory '/home/niperg/Downloads/cpptraj-master/src'
> CXX SpaceGroup.cpp
> CXX ActionFrameCounter.cpp
> CXX ActionList.cpp
> CXX ActionTopWriter.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_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_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_Energy.cpp
> In file included from Ewald_ParticleMesh.h:5,
> from Action_Energy.cpp:4:
> helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2370 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2390 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3328 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3777 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3815 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3878 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3916 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4148 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4156: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4156 | #pragma omp for
> |
> helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4201 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4249 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4276 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4328 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4332 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4379 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4492 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4523 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4607 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4614: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4614 | #pragma omp for
> |
> helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4983 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 5015 | #pragma omp parallel for num_threads(nThreads_)
> |
> CXX Action_FilterByData.cpp
> CXX Action_FixAtomOrder.cpp
> CXX Action_FixImagedBonds.cpp
> CXX Action_GIST.cpp
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from Action_GIST.h:11,
> from Action_GIST.cpp:3:
> helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2370 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2390 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3328 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3777 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3815 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3878 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3916 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4148 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4156: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4156 | #pragma omp for
> |
> helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4201 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4249 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4276 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4328 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4332 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4379 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4492 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4523 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4607 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4614: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4614 | #pragma omp for
> |
> helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4983 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 5015 | #pragma omp parallel for num_threads(nThreads_)
> |
> 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_LESsplit.cpp
> CXX Action_LIE.cpp
> CXX Action_LipidOrder.cpp
> CXX Action_MakeStructure.cpp
> CXX Action_Mask.cpp
> CXX Action_Matrix.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_Time.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_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_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_Timecorr.cpp
> CXX Analysis_VectorMath.cpp
> CXX Analysis_Wavelet.cpp
> CXX ArgList.cpp
> CXX Array1D.cpp
> CXX AssociatedData.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 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_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_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_3D.cpp
> CXX DataSet_Coords.cpp
> CXX DataSet_Coords_CRD.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 Deprecated.cpp
> CXX DihedralSearch.cpp
> CXX DistRoutines.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 Ewald.cpp
> CXX Ewald_ParticleMesh.cpp
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2370 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2390 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3328 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3777 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3815 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3878 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3916 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4148 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4156: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4156 | #pragma omp for
> |
> helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4201 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4249 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4276 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4328 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4332 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4379 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4492 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4523 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4607 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4614: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4614 | #pragma omp for
> |
> helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4983 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 5015 | #pragma omp parallel for num_threads(nThreads_)
> |
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘std::pair<helpme::Matrix<Real>,
> helpme::Matrix<Real> >
> helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
> [with Real = double]’:
> helpme_standalone.h:4001:22: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> Ewald_ParticleMesh.cpp:234:68: required from here
> helpme_standalone.h:1027:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 1027 | for (int val = 0; val < nRows_; ++val)
> eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]});
> | ~~~~^~~~~~~~
> helpme_standalone.h:1030:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 1030 | for (int val = 0; val < nRows_; ++val) {
> | ~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
> <anonymous> >::sanityChecks(int, const RealMat&, const RealMat&, int) [with
> Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
> int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
> >::RealMat = helpme::Matrix<double>]’:
> helpme_standalone.h:5194:9: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> Ewald_ParticleMesh.cpp:235:63: required from here
> helpme_standalone.h:3278:32: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3278 | if (parameters.nCols() != (nCartesian(parameterAngMom) -
> cartesianOffset))
> helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
> <anonymous> >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with
> Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
> int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
> >::RealMat = helpme::Matrix<double>]’:
> helpme_standalone.h:5195:9: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> Ewald_ParticleMesh.cpp:235:63: required from here
> helpme_standalone.h:3822:45: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3822 | for (size_t row = threadID; row < gridDimensionC_; row
> += nThreads_) {
> | ~~~~^~~~~~~~~~~~~~~~~
> helpme_standalone.h:3829:37: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
> [-Wsign-compare]
> 3829 | for (int atom = 0; atom < nAtoms; ++atom) {
> | ~~~~~^~~~~~~~
> helpme_standalone.h:3837:61: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3837 | if (cGridIterator.size() && thisAtomsThread ==
> threadID) {
> |
> ~~~~~~~~~~~~~~~~^~~~~~~~~~~
> helpme_standalone.h:3826:25: warning: unused variable ‘gridIteratorC’
> [-Wunused-variable]
> 3826 | const auto &gridIteratorC =
> threadedGridIteratorC_[threadID];
> | ^~~~~~~~~~~~~
> helpme_standalone.h:3870:55: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
> [-Wsign-compare]
> 3870 | for (int atom = splineCache_.size(); atom < newSize;
> ++atom)
> | ~~~~~^~~~~~~~~
> helpme_standalone.h:3886:47: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3886 | for (size_t cRow = threadID; cRow < gridDimensionC_;
> cRow += nThreads_) {
> | ~~~~~^~~~~~~~~~~~~~~~~
> helpme_standalone.h: In instantiation of ‘Real* helpme::PMEInstance<Real,
> <anonymous> >::spreadParameters(int, const RealMat&) [with Real = double;
> typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
> <anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’:
> helpme_standalone.h:5196:25: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> Ewald_ParticleMesh.cpp:235:63: required from here
> helpme_standalone.h:3784:45: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3784 | for (size_t row = threadID; row < myGridDimensionC_;
> row += nThreads_) {
> | ~~~~^~~~~~~~~~~~~~~~~~~
> helpme_standalone.h: In instantiation of ‘helpme::PMEInstance<Real,
> <anonymous> >::Complex* helpme::PMEInstance<Real, <anonymous>
> >::forwardTransform(Real*) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::Complex =
> std::complex<double>]’:
> helpme_standalone.h:5199:32: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> Ewald_ParticleMesh.cpp:235:63: required from here
> helpme_standalone.h:4108:28: warning: variable ‘realCBA’ set but not used
> [-Wunused-but-set-variable]
> 4108 | Real *__restrict__ realCBA;
> | ^~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘void
> helpme::Matrix<Real>::assertSymmetric(const Real&) const [with Real =
> double]’:
> helpme_standalone.h:1017:9: required from
> ‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
> helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
> [with Real = double]’
> helpme_standalone.h:4001:22: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> Ewald_ParticleMesh.cpp:234:68: required from here
> helpme_standalone.h:796:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 796 | for (int row = 0; row < nRows_; ++row) {
> | ~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘void
> helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with
> Real = double]’:
> helpme_standalone.h:1023:42: required from
> ‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
> helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
> [with Real = double]’
> helpme_standalone.h:4001:22: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> Ewald_ParticleMesh.cpp:234:68: required from here
> helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used
> [-Wunused-but-set-variable]
> 213 | Real sin_2phi, cos_2phi, cot_2phi;
> | ^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
> const [with Real = double]’:
> helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::inverse() const [with Real = double]’
> helpme_standalone.h:4013:26: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> Ewald_ParticleMesh.cpp:234:68: required from here
> helpme_standalone.h:824:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 824 | for (int row = 0; row < nRows_; ++row) {
> | ~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘void
> helpme::BSpline<Real>::update(short int, Real, short int, short int) [with
> Real = double]’:
> helpme_standalone.h:3905:21: required from ‘void
> helpme::PMEInstance<Real, <anonymous>
> >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double;
> typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
> <anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> helpme_standalone.h:5195:9: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> Ewald_ParticleMesh.cpp:235:63: required from here
> helpme_standalone.h:2255:30: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 2255 | if (splines_.nRows() < derivativeLevel + 1 ||
> splines_.nCols() != order)
> helpme_standalone.h:2255:72: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘short int’
> [-Wsign-compare]
> 2255 | if (splines_.nRows() < derivativeLevel + 1 ||
> splines_.nCols() != order)
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::multiply(const helpme::Matrix<Real>&) const [with
> Real = double]’:
> helpme_standalone.h:877:64: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::operator*(const helpme::Matrix<Real>&) const [with
> Real = double]’
> helpme_standalone.h:829:22: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
> const [with Real = double]’
> helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::inverse() const [with Real = double]’
> helpme_standalone.h:4013:26: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> Ewald_ParticleMesh.cpp:234:68: required from here
> helpme_standalone.h:860:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 860 | for (int row = 0; row < nRows_; ++row) {
> | ~~~~^~~~~~~~
> helpme_standalone.h:862:35: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 862 | for (int col = 0; col < other.nCols_; ++col) {
> | ~~~~^~~~~~~~~~~~~~
> helpme_standalone.h:863:41: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 863 | for (int link = 0; link < nCols_; ++link) {
> | ~~~~~^~~~~~~~
> helpme_standalone.h: In member function ‘void helpme::PMEInstance<Real,
> <anonymous> >::setupCalculationMetadata(int, Real, int, int, int, int, int,
> int, int, Real, int, void*, helpme::PMEInstance<Real, <anonymous>
> >::NodeOrder, int, int, int) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’:
> helpme_standalone.h:519:7: warning:
> ‘<anonymous>.helpme::Matrix<double>::data_’ may be used uninitialized in
> this function [-Wmaybe-uninitialized]
> 519 | class Matrix {
> | ^~~~~~
> helpme_standalone.h:519:7: warning:
> ‘<anonymous>.helpme::Matrix<double>::data_’ may be used uninitialized in
> this function [-Wmaybe-uninitialized]
> 519 | class Matrix {
> | ^~~~~~
> helpme_standalone.h:519:7: warning:
> ‘<anonymous>.helpme::Matrix<double>::data_’ may be used uninitialized in
> this function [-Wmaybe-uninitialized]
> 519 | class Matrix {
> | ^~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from Ewald_ParticleMesh.cpp:4:
> helpme_standalone.h: In member function ‘Real helpme::PMEInstance<Real,
> <anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
> = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
> int>::type <anonymous> = 0]’:
> helpme_standalone.h:5207:16: warning: ‘energy’ may be used uninitialized
> in this function [-Wmaybe-uninitialized]
> 5207 | return energy;
> | ^~~~~~
> CXX Ewald_Regular.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_CompareTop.cpp
> CXX Exec_CrdAction.cpp
> CXX Exec_CrdOut.cpp
> CXX Exec_CreateSet.cpp
> CXX Exec_DataFile.cpp
> CXX Exec_DataFilter.cpp
> CXX Exec_DataSetCmd.cpp
> CXX Exec_Emin.cpp
> CXX Exec_Flatten.cpp
> CXX Exec_GenerateAmberRst.cpp
> CXX Exec_Graft.cpp
> CXX Exec_Help.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_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_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 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_integer.cpp
> CXX ForLoop_list.cpp
> CXX ForLoop_mask.cpp
> CXX ForLoop_overSets.cpp
> CXX Frame.cpp
> CXX GIST_PME.cpp
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2370 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2390 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3328 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3777 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3815 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3878 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3916 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4148 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4156: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4156 | #pragma omp for
> |
> helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4201 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4249 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4276 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4328 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4332 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4379 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4492 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4523 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4607 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4614: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4614 | #pragma omp for
> |
> helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4983 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 5015 | #pragma omp parallel for num_threads(nThreads_)
> |
> GIST_PME.cpp: In member function ‘int
> GIST_PME::CalcNonbondEnergy_GIST(const Frame&, const std::vector<int>&,
> const std::vector<bool>&, const std::vector<bool>&,
> std::vector<std::vector<double> >&, std::vector<std::vector<double> >&,
> std::vector<std::vector<double> >&, std::vector<std::vector<double> >&,
> std::vector<std::vector<float> >&)’:
> GIST_PME.cpp:123:10: warning: variable ‘e_vdw_lr_correction’ set but not
> used [-Wunused-but-set-variable]
> 123 | double e_vdw_lr_correction;
> | ^~~~~~~~~~~~~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘std::pair<helpme::Matrix<Real>,
> helpme::Matrix<Real> >
> helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
> [with Real = double]’:
> helpme_standalone.h:4001:22: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> GIST_PME.cpp:308:68: required from here
> helpme_standalone.h:1027:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 1027 | for (int val = 0; val < nRows_; ++val)
> eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]});
> | ~~~~^~~~~~~~
> helpme_standalone.h:1030:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 1030 | for (int val = 0; val < nRows_; ++val) {
> | ~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
> <anonymous> >::sanityChecks(int, const RealMat&, const RealMat&, int) [with
> Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
> int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
> >::RealMat = helpme::Matrix<double>]’:
> helpme_standalone.h:5070:9: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::computePRec(int, const RealMat&,
> const RealMat&, const RealMat&, int, helpme::PMEInstance<Real, <anonymous>
> >::RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> GIST_PME.cpp:311:69: required from here
> helpme_standalone.h:3278:32: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3278 | if (parameters.nCols() != (nCartesian(parameterAngMom) -
> cartesianOffset))
> helpme_standalone.h: In instantiation of ‘helpme::PMEInstance<Real,
> <anonymous> >::Complex* helpme::PMEInstance<Real, <anonymous>
> >::forwardTransform(Real*) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::Complex =
> std::complex<double>]’:
> helpme_standalone.h:5125:32: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::computePRec(int, const RealMat&,
> const RealMat&, const RealMat&, int, helpme::PMEInstance<Real, <anonymous>
> >::RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> GIST_PME.cpp:311:69: required from here
> helpme_standalone.h:4108:28: warning: variable ‘realCBA’ set but not used
> [-Wunused-but-set-variable]
> 4108 | Real *__restrict__ realCBA;
> | ^~~~~~~
> helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
> <anonymous> >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with
> Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
> int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
> >::RealMat = helpme::Matrix<double>]’:
> helpme_standalone.h:5195:9: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> GIST_PME.cpp:397:62: required from here
> helpme_standalone.h:3822:45: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3822 | for (size_t row = threadID; row < gridDimensionC_; row
> += nThreads_) {
> | ~~~~^~~~~~~~~~~~~~~~~
> helpme_standalone.h:3829:37: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
> [-Wsign-compare]
> 3829 | for (int atom = 0; atom < nAtoms; ++atom) {
> | ~~~~~^~~~~~~~
> helpme_standalone.h:3837:61: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3837 | if (cGridIterator.size() && thisAtomsThread ==
> threadID) {
> |
> ~~~~~~~~~~~~~~~~^~~~~~~~~~~
> helpme_standalone.h:3826:25: warning: unused variable ‘gridIteratorC’
> [-Wunused-variable]
> 3826 | const auto &gridIteratorC =
> threadedGridIteratorC_[threadID];
> | ^~~~~~~~~~~~~
> helpme_standalone.h:3870:55: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
> [-Wsign-compare]
> 3870 | for (int atom = splineCache_.size(); atom < newSize;
> ++atom)
> | ~~~~~^~~~~~~~~
> helpme_standalone.h:3886:47: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3886 | for (size_t cRow = threadID; cRow < gridDimensionC_;
> cRow += nThreads_) {
> | ~~~~~^~~~~~~~~~~~~~~~~
> helpme_standalone.h: In instantiation of ‘Real* helpme::PMEInstance<Real,
> <anonymous> >::spreadParameters(int, const RealMat&) [with Real = double;
> typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
> <anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’:
> helpme_standalone.h:5196:25: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> GIST_PME.cpp:397:62: required from here
> helpme_standalone.h:3784:45: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 3784 | for (size_t row = threadID; row < myGridDimensionC_;
> row += nThreads_) {
> | ~~~~^~~~~~~~~~~~~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘void
> helpme::Matrix<Real>::assertSymmetric(const Real&) const [with Real =
> double]’:
> helpme_standalone.h:1017:9: required from
> ‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
> helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
> [with Real = double]’
> helpme_standalone.h:4001:22: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> GIST_PME.cpp:308:68: required from here
> helpme_standalone.h:796:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 796 | for (int row = 0; row < nRows_; ++row) {
> | ~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘void
> helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with
> Real = double]’:
> helpme_standalone.h:1023:42: required from
> ‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
> helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
> [with Real = double]’
> helpme_standalone.h:4001:22: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> GIST_PME.cpp:308:68: required from here
> helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used
> [-Wunused-but-set-variable]
> 213 | Real sin_2phi, cos_2phi, cot_2phi;
> | ^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
> const [with Real = double]’:
> helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::inverse() const [with Real = double]’
> helpme_standalone.h:4013:26: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> GIST_PME.cpp:308:68: required from here
> helpme_standalone.h:824:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 824 | for (int row = 0; row < nRows_; ++row) {
> | ~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘void
> helpme::BSpline<Real>::update(short int, Real, short int, short int) [with
> Real = double]’:
> helpme_standalone.h:3905:21: required from ‘void
> helpme::PMEInstance<Real, <anonymous>
> >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double;
> typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
> <anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> helpme_standalone.h:5195:9: required from ‘Real
> helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
> const RealMat&) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
> helpme::Matrix<double>]’
> GIST_PME.cpp:397:62: required from here
> helpme_standalone.h:2255:30: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
> [-Wsign-compare]
> 2255 | if (splines_.nRows() < derivativeLevel + 1 ||
> splines_.nCols() != order)
> helpme_standalone.h:2255:72: warning: comparison of integer expressions of
> different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘short int’
> [-Wsign-compare]
> 2255 | if (splines_.nRows() < derivativeLevel + 1 ||
> splines_.nCols() != order)
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::multiply(const helpme::Matrix<Real>&) const [with
> Real = double]’:
> helpme_standalone.h:877:64: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::operator*(const helpme::Matrix<Real>&) const [with
> Real = double]’
> helpme_standalone.h:829:22: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
> const [with Real = double]’
> helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
> helpme::Matrix<Real>::inverse() const [with Real = double]’
> helpme_standalone.h:4013:26: required from ‘void
> helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
> Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
> >::LatticeType) [with Real = double; typename
> std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
> 0]’
> GIST_PME.cpp:308:68: required from here
> helpme_standalone.h:860:31: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 860 | for (int row = 0; row < nRows_; ++row) {
> | ~~~~^~~~~~~~
> helpme_standalone.h:862:35: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 862 | for (int col = 0; col < other.nCols_; ++col) {
> | ~~~~^~~~~~~~~~~~~~
> helpme_standalone.h:863:41: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
> int’} [-Wsign-compare]
> 863 | for (int link = 0; link < nCols_; ++link) {
> | ~~~~~^~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In member function ‘double
> GIST_PME::LJ_Recip_ParticleMesh_GIST(const Box&, GIST_PME::MatType&)’:
> helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> 5157 | Real gridVal = cbRow[aPoint.first];
> | ~~~~~^
> helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
> 5123 | Real *potentialGrid;
> | ^~~~~~~~~~~~~
> GIST_PME.cpp:400:10: warning: ‘energy’ may be used uninitialized in this
> function [-Wmaybe-uninitialized]
> 400 | return evdwrecip;
> | ^~~~~~~~~
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from GIST_PME.cpp:3:
> helpme_standalone.h: In member function ‘double
> GIST_PME::Recip_ParticleMesh_GIST(const Box&, const std::vector<int>&,
> const std::vector<bool>&, Ewald::Darray&, Ewald::Darray&)’:
> helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> 5157 | Real gridVal = cbRow[aPoint.first];
> | ~~~~~^
> helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
> 5123 | Real *potentialGrid;
> | ^~~~~~~~~~~~~
> helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> 5157 | Real gridVal = cbRow[aPoint.first];
> | ~~~~~^
> helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
> 5123 | Real *potentialGrid;
> | ^~~~~~~~~~~~~
> helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> 5157 | Real gridVal = cbRow[aPoint.first];
> | ~~~~~^
> helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
> 5123 | Real *potentialGrid;
> | ^~~~~~~~~~~~~
> CXX GridAction.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 InputTrajCommon.cpp
> CXX KDE.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 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 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 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 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_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 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]
> 146 | static int vmd_file_is_executable(const char * filename) {
> | ^~~~~~~~~~~~~~~~~~~~~~
> vmdplugin/dtrplugin.cpp: In function ‘void DDmkdir(const string&, mode_t,
> int, int)’:
> vmdplugin/dtrplugin.cpp:716:16: warning: ‘%03x’ directive writing between
> 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
> 716 | sprintf(sub, "%03x/", i);
> | ^~~~
> vmdplugin/dtrplugin.cpp:716:15: note: directive argument in the range [0,
> 2147483646]
> 716 | sprintf(sub, "%03x/", i);
> | ^~~~~~~
> In file included from /usr/include/stdio.h:867,
> from vmdplugin/dtrplugin.hxx:56,
> from vmdplugin/dtrplugin.cpp:42:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
> ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination
> of size 6
> 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 37 | __bos (__s), __fmt, __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> vmdplugin/dtrplugin.cpp:724:23: warning: ‘%03x’ directive writing between
> 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
> 724 | sprintf(subsub, "%03x", j);
> | ^~~~
> vmdplugin/dtrplugin.cpp:724:22: note: directive argument in the range [0,
> 2147483646]
> 724 | sprintf(subsub, "%03x", j);
> | ^~~~~~
> In file included from /usr/include/stdio.h:867,
> from vmdplugin/dtrplugin.hxx:56,
> from vmdplugin/dtrplugin.cpp:42:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
> ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination
> of size 6
> 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 37 | __bos (__s), __fmt, __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> vmdplugin/dtrplugin.cpp: In function ‘std::string framefile(const string&,
> size_t, size_t, int, int)’:
> vmdplugin/dtrplugin.cpp:677:28: warning: ‘__builtin___sprintf_chk’ may
> write a terminating nul past the end of the destination [-Wformat-overflow=]
> 677 | sprintf(answer, "%03x/", d1);
> | ^
> In file included from /usr/include/stdio.h:867,
> from vmdplugin/dtrplugin.hxx:56,
> from vmdplugin/dtrplugin.cpp:42:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
> ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination
> of size 9
> 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 37 | __bos (__s), __fmt, __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> vmdplugin/dtrplugin.cpp:675:28: warning: ‘%03x’ directive writing between
> 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=]
> 675 | sprintf(answer, "%03x/%03x/", d1, d2);
> | ^~~~
> vmdplugin/dtrplugin.cpp:675:22: note: directive argument in the range [0,
> 2147483646]
> 675 | sprintf(answer, "%03x/%03x/", d1, d2);
> | ^~~~~~~~~~~~
> In file included from /usr/include/stdio.h:867,
> from vmdplugin/dtrplugin.hxx:56,
> from vmdplugin/dtrplugin.cpp:42:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
> ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination
> of size 9
> 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 37 | __bos (__s), __fmt, __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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]
> 60 | 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]
> 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++)
> | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> CXX Action_Esander.cpp
> CXX Command.cpp
> In file included from Ewald_ParticleMesh.h:5,
> from GIST_PME.h:5,
> from Action_GIST.h:11,
> from Command.cpp:123:
> helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2370 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 2390 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
> Vyz, Vzz) num_threads(nThreads)
> |
> helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3328 | #pragma omp parallel for num_threads(nThreads)
> |
> helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3777 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3815 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3878 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 3916 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4148 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4156: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4156 | #pragma omp for
> |
> helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4201 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4249 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4276 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4328 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4332 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4379 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4492 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4523 | #pragma omp parallel for reduction(+ : energy)
> num_threads(nThreads_)
> |
> helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4607 | #pragma omp parallel num_threads(nThreads_)
> |
> helpme_standalone.h:4614: warning: ignoring #pragma omp for
> [-Wunknown-pragmas]
> 4614 | #pragma omp for
> |
> helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 4983 | #pragma omp parallel for num_threads(nThreads_)
> |
> helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
> [-Wunknown-pragmas]
> 5015 | #pragma omp parallel for num_threads(nThreads_)
> |
> CXX Cpptraj.cpp
> CXX Energy_Sander.cpp
> CXX ReadLine.cpp
> CXX main.cpp
> CC molsurf.c
> cd readline && make all
> make[2]: Entering directory
> '/home/niperg/Downloads/cpptraj-master/src/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]
> 445 | for (i = l = 0; c = seq[i]; i++)
> | ^
> bind.c: In function ‘rl_parse_and_bind’:
> bind.c:1188:19: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> 1188 | for (i = 1; c = string[i]; i++)
> | ^
> bind.c:1279:23: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> 1279 | for (passc = 0; c = string[i]; i++)
> | ^
> bind.c: In function ‘rl_function_dumper’:
> bind.c:2051:15: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> 2051 | for (i = 0; name = names[i]; i++)
> | ^~~~
> CC callback.c
> CC compat.c
> 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]
> 604 | 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]
> 886 | 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]
> 1805 | 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]
> 1856 | while (entry = getpwent ())
> | ^~~~~
> CC display.c
> display.c: In function ‘rl_redisplay’:
> display.c:714:15: warning: implicit declaration of function ‘wcwidth’
> [-Wimplicit-function-declaration]
> 714 | temp = wcwidth (wc);
> | ^~~~~~~
> In file included from /usr/include/string.h:495,
> from rldefs.h:59,
> from display.c:45:
> In function ‘strncpy’,
> inlined from ‘rl_redisplay’ at display.c:558:7:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
> ‘__builtin_strncpy’ output truncated before terminating nul copying as many
> bytes from a string as its length [-Wstringop-truncation]
> 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
> (__dest));
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> display.c: In function ‘rl_redisplay’:
> display.c:550:40: note: length computed here
> 550 | prompt_physical_chars = pmtlen = strlen (prompt_this_line);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~
> display.c:829:8: warning: ‘wc_width’ may be used uninitialized in this
> function [-Wmaybe-uninitialized]
> 829 | for (i = 0; i < wc_width; i++)
> | ^~~
> display.c:462:38: warning: ‘n0’ may be used uninitialized in this function
> [-Wmaybe-uninitialized]
> 462 | int newlines, lpos, temp, modmark, n0, num;
> | ^~
> CC funmap.c
> CC histexpand.c
> histexpand.c: In function ‘get_history_event’:
> histexpand.c:206:25: warning: suggest parentheses around assignment used
> as truth value [-Wparentheses]
> 206 | 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]
> 696 | int delimiter, failed, si, l_temp, ws, we;
> | ^~
> CC histfile.c
> histfile.c: In function ‘history_truncate_file’:
> histfile.c:401:7: warning: ignoring return value of ‘write’, declared with
> attribute warn_unused_result [-Wunused-result]
> 401 | write (file, bp, chars_read - (bp - buffer));
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> CC history.c
> CC histsearch.c
> CC input.c
> input.c: In function ‘rl_read_key’:
> input.c:423:11: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> 423 | if (c = _rl_next_macro_key ())
> | ^
> 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]
> 620 | 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]
> 658 | int c, r;
> | ^
> CC keymaps.c
> CC kill.c
> CC macro.c
> 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]
> 118 | if (wcwidth (wc) == 0)
> | ^~~~~~~
> CC misc.c
> CC nls.c
> 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]
> 118 | int orig_point, match_point, ready;
> | ^~~~~
> 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]
> 450 | static int lastc, eof_found;
> | ^~~~~~~~~
> At top level:
> readline.c:1078:1: warning: ‘reset_default_bindings’ defined but not used
> [-Wunused-function]
> 1078 | reset_default_bindings ()
> | ^~~~~~~~~~~~~~~~~~~~~~
> CC rltty.c
> CC savestring.c
> CC search.c
> CC shell.c
> CC signals.c
> CC termcap.c
> termcap.c: In function ‘memory_out’:
> termcap.c:95:3: warning: ignoring return value of ‘write’, declared with
> attribute warn_unused_result [-Wunused-result]
> 95 | write (2, "virtual memory exhausted\n", 25);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> CC terminal.c
> 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]
> 814 | int k;
> | ^
> In file included from /usr/include/string.h:495,
> from rldefs.h:59,
> from text.c:45:
> In function ‘strncpy’,
> inlined from ‘rl_insert_text’ at text.c:94:3:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
> ‘__builtin_strncpy’ output truncated before terminating nul copying as many
> bytes from a string as its length [-Wstringop-truncation]
> 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
> (__dest));
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> text.c: In function ‘rl_insert_text’:
> text.c:85:29: note: length computed here
> 85 | l = (string && *string) ? strlen (string) : 0;
> | ^~~~~~~~~~~~~~~
> CC tilde.c
> tilde.c: In function ‘tilde_expand’:
> tilde.c:199:7: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> 199 | if (result = strchr (string, '~'))
> | ^~~~~~
> CC tparam.c
> tparam.c: In function ‘memory_out’:
> tparam.c:55:3: warning: ignoring return value of ‘write’, declared with
> attribute warn_unused_result [-Wunused-result]
> 55 | write (2, "virtual memory exhausted\n", 25);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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]
> 157 | roving->next = 0;
> | ~~~~~~~~~~~~~^~~
> CC util.c
> CC version.c
> version.c:2:14: warning: ‘version_string’ defined but not used
> [-Wunused-variable]
> 2 | static char *version_string = "\n$Version: GNU termcap 1.3.1 $\n";
> | ^~~~~~~~~~~~~~
> CC vi_mode.c
> 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
> '/home/niperg/Downloads/cpptraj-master/src/readline'
> cd Cluster && make all
> make[2]: Entering directory
> '/home/niperg/Downloads/cpptraj-master/src/Cluster'
> CXX Algorithm.cpp
> CXX Algorithm_DBscan.cpp
> CXX Algorithm_DPeaks.cpp
> CXX Algorithm_HierAgglo.cpp
> CXX Algorithm_Kmeans.cpp
> CXX BestReps.cpp
> CXX Centroid_Coord.cpp
> CXX CentroidArray.cpp
> CXX Cframes.cpp
> CXX Cmatrix_Binary.cpp
> CXX Cmatrix_NC.cpp
> CXX Control.cpp
> CXX DrawGraph.cpp
> CXX DynamicMatrix.cpp
> CXX List.cpp
> CXX MetricArray.cpp
> CXX Metric_DME.cpp
> CXX Metric_RMS.cpp
> CXX Metric_Scalar.cpp
> CXX Metric_SRMSD.cpp
> CXX Metric_Torsion.cpp
> CXX Node.cpp
> CXX Output.cpp
> CXX Results_Coords.cpp
> CXX Sieve.cpp
> /bin/rm -f libcpptraj_cluster.a
> ar cqs libcpptraj_cluster.a Algorithm.o Algorithm_DBscan.o
> Algorithm_DPeaks.o Algorithm_HierAgglo.o Algorithm_Kmeans.o BestReps.o
> Centroid_Coord.o CentroidArray.o Cframes.o Cmatrix_Binary.o Cmatrix_NC.o
> Control.o DrawGraph.o DynamicMatrix.o List.o MetricArray.o Metric_DME.o
> Metric_RMS.o Metric_Scalar.o Metric_SRMSD.o Metric_Torsion.o Node.o
> Output.o Results_Coords.o Sieve.o
> make[2]: Leaving directory
> '/home/niperg/Downloads/cpptraj-master/src/Cluster'
> cd xdrfile && make all
> make[2]: Entering directory
> '/home/niperg/Downloads/cpptraj-master/src/xdrfile'
> CC xdrfile.c
> CC xdr_seek.c
> CC xdrfile_trr.c
> 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
> '/home/niperg/Downloads/cpptraj-master/src/xdrfile'
> cd arpack && make install
> make[2]: Entering directory
> '/home/niperg/Downloads/cpptraj-master/src/arpack'
> FC ivout.f
> FC dvout.f
> FC dgetv0.f
> dgetv0.f:120:26:
>
> 120 | & ( 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:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dlaqrb.f
> dlaqrb.f:497:0:
>
> 497 | & cs, sn )
> |
> Warning: ‘i2’ may be used uninitialized in this function
> [-Wmaybe-uninitialized]
> FC dnaitr.f
> dnaitr.f:210:33:
>
> 210 | & (ido, bmat, n, k, np, nb, resid, rnorm, v, ldv, h, ldh,
> | 1
> Warning: Unused dummy argument ‘nb’ at (1) [-Wunused-dummy-argument]
> FC dnapps.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dnaup2.f
> dnaup2.f:316:5:
>
> 316 | 10 continue
> | 1
> Warning: Label 10 at (1) defined but not used [-Wunused-label]
> dnaup2.f:175:63:
>
> 175 | & ( 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:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dnaupd.f
> dnaupd.f:541:24:
>
> 541 | if (nb .le. 0) nb = 1
> | 1
> Warning: Nonconforming tab character at (1) [-Wtabs]
> dnaupd.f:542:28:
>
> 542 | if (tol .le. zero) tol = dlamch('EpsMach')
> | 1
> Warning: Nonconforming tab character at (1) [-Wtabs]
> dnaupd.f:447:32:
>
> 447 | & ldh, ldq, levec, mode, msglvl, mxiter, nb,
> | 1
> Warning: Unused variable ‘levec’ declared at (1) [-Wunused-variable]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dnconv.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dneigh.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dmout.f
> FC dneupd.f
> dneupd.f:587:17:
>
> 587 | 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:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
> stat.h:8:23:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dngets.f
> dngets.f:96:40:
>
> 96 | & shiftr, shifti )
> | 1
> Warning: Unused dummy argument ‘shifti’ at (1) [-Wunused-dummy-argument]
> dngets.f:96:32:
>
> 96 | & shiftr, shifti )
> | 1
> Warning: Unused dummy argument ‘shiftr’ at (1) [-Wunused-dummy-argument]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsaitr.f
> FC dsapps.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsaup2.f
> dsaup2.f:809:5:
>
> 809 | 130 continue
> | 1
> Warning: Label 130 at (1) defined but not used [-Wunused-label]
> dsaup2.f:324:5:
>
> 324 | 10 continue
> | 1
> Warning: Label 10 at (1) defined but not used [-Wunused-label]
> dsaup2.f:180:63:
>
> 180 | & ( 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:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsaupd.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsconv.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dseigt.f
> dseigt.f:124:18:
>
> 124 | integer i, k, msglvl
> | 1
> Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsesrt.f
> FC dseupd.f
> dseupd.f:499:17:
>
> 499 | 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:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
> stat.h:8:23:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsgets.f
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dsortc.f
> FC dsortr.f
> FC dstatn.f
> stat.h:8:19:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
> stat.h:8:23:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dstats.f
> stat.h:8:19:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
> stat.h:8:23:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
> stat.h:8:27:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
> stat.h:8:31:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
> stat.h:8:35:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
> stat.h:8:39:
>
> 8 | real t0, t1, t2, t3, t4, t5
> | 1
> Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
> FC dstqrb.f
> FC arsecond.f
> arsecond.f:27:30:
>
> 27 | 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
> '/home/niperg/Downloads/cpptraj-master/src/arpack'
> cd tng && make all
> make[2]: Entering directory '/home/niperg/Downloads/cpptraj-master/src/tng'
> CC md5.c
> CC tng_io.c
> In file included from /usr/include/string.h:495,
> from tng/tng_io.h:310,
> from tng_io.c:20:
> In function ‘strncpy’,
> inlined from ‘tng_gen_data_block_add’ at tng_io.c:12600:9,
> inlined from ‘tng_data_block_add.constprop’ at tng_io.c:12788:12:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
> ‘__builtin_strncpy’ specified bound depends on the length of the source
> argument [-Wstringop-overflow=]
> 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
> (__dest));
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> tng_io.c: In function ‘tng_data_block_add.constprop’:
> tng_io.c:12600:47: note: length computed here
> 12600 | strncpy(data->block_name, block_name, strlen(block_name) +
> 1);
> | ^~~~~~~~~~~~~~~~~~
> In file included from /usr/include/string.h:495,
> from tng/tng_io.h:310,
> from tng_io.c:20:
> In function ‘strncpy’,
> inlined from ‘tng_gen_data_block_add’ at tng_io.c:12600:9,
> inlined from ‘tng_data_block_add’ at tng_io.c:12788:12:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
> ‘__builtin_strncpy’ specified bound depends on the length of the source
> argument [-Wstringop-overflow=]
> 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
> (__dest));
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> tng_io.c: In function ‘tng_data_block_add’:
> tng_io.c:12600:47: note: length computed here
> 12600 | strncpy(data->block_name, block_name, strlen(block_name) +
> 1);
> | ^~~~~~~~~~~~~~~~~~
> In file included from /usr/include/string.h:495,
> from tng/tng_io.h:310,
> from tng_io.c:20:
> In function ‘strncpy’,
> inlined from ‘tng_gen_data_block_add’ at tng_io.c:12600:9,
> inlined from ‘tng_particle_data_block_add’ at tng_io.c:12813:12:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
> ‘__builtin_strncpy’ specified bound depends on the length of the source
> argument [-Wstringop-overflow=]
> 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
> (__dest));
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> tng_io.c: In function ‘tng_particle_data_block_add’:
> tng_io.c:12600:47: note: length computed here
> 12600 | strncpy(data->block_name, block_name, strlen(block_name) +
> 1);
> | ^~~~~~~~~~~~~~~~~~
> CC tng_compress.c
> CC coder.c
> CC warnmalloc.c
> CC fixpoint.c
> CC xtc3.c
> CC bwlzh.c
> CC xtc2.c
> xtc2.c: In function ‘Ptngc_pack_array_xtc2’:
> xtc2.c:680:47: warning: array subscript [54, 2147483646] is outside array
> bounds of ‘int[54]’ [-Warray-bounds]
> 680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
> | ~~~~~~~~~~~~~~^~~~~~~~~~~
> xtc2.c:717:7: note: while referencing ‘has_large_ints’
> 717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
> | ^~~~~~~~~~~~~~
> xtc2.c:680:47: warning: array subscript [55, 2147483647] is outside array
> bounds of ‘int[54]’ [-Warray-bounds]
> 680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
> | ~~~~~~~~~~~~~~^~~~~~~~~~~
> xtc2.c:717:7: note: while referencing ‘has_large_ints’
> 717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
> | ^~~~~~~~~~~~~~
> xtc2.c:680:47: warning: array subscript [56, 2147483647] is outside array
> bounds of ‘int[54]’ [-Warray-bounds]
> 680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
> | ~~~~~~~~~~~~~~^~~~~~~~~~~
> xtc2.c:717:7: note: while referencing ‘has_large_ints’
> 717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
> | ^~~~~~~~~~~~~~
> xtc2.c:680:47: warning: array subscript [54, 2147483646] is outside array
> bounds of ‘int[54]’ [-Warray-bounds]
> 680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
> | ~~~~~~~~~~~~~~^~~~~~~~~~~
> xtc2.c:717:7: note: while referencing ‘has_large_ints’
> 717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
> | ^~~~~~~~~~~~~~
> xtc2.c:680:47: warning: array subscript [55, 2147483647] is outside array
> bounds of ‘int[54]’ [-Warray-bounds]
> 680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
> | ~~~~~~~~~~~~~~^~~~~~~~~~~
> xtc2.c:717:7: note: while referencing ‘has_large_ints’
> 717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
> | ^~~~~~~~~~~~~~
> xtc2.c:680:47: warning: array subscript [56, 2147483647] is outside array
> bounds of ‘int[54]’ [-Warray-bounds]
> 680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
> | ~~~~~~~~~~~~~~^~~~~~~~~~~
> xtc2.c:717:7: note: while referencing ‘has_large_ints’
> 717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
> | ^~~~~~~~~~~~~~
> CC widemuldiv.c
> CC huffmem.c
> CC vals16.c
> CC bwt.c
> CC mtf.c
> CC rle.c
> CC lz77.c
> CC dict.c
> CC huffman.c
> 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 '/home/niperg/Downloads/cpptraj-master/src/tng'
> g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o
> ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.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_Channel.o Action_CheckChirality.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_DihedralRMS.o Action_Dipole.o Action_Distance.o
> Action_DistRmsd.o Action_Energy.o Action_FilterByData.o
> Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o
> Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o
> Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o
> Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o
> Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o
> Action_MultiPucker.o Action_MultiVector.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_Remap.o Action_ReplicateCell.o Action_Rmsd.o
> Action_Rotate.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_Time.o
> Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o
> Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o
> Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o
> Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o
> Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o
> Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o
> Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o
> Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o
> Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o
> Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o
> Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o
> Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o
> Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o
> Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o
> Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o
> ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o
> BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o
> CharMask.o CharmmParamFile.o CIFfile.o ClusterMap.o Cmd.o CmdInput.o
> CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o
> ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o
> CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o
> DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o
> DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o
> DataIO_Cmatrix_Binary.o DataIO_Cmatrix_NC.o DataIO_Cpout.o DataIO_Evecs.o
> DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o
> DataIO_Mdout.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o
> DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o
> DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o
> DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o
> DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o
> DataSet_PairwiseCache.o DataSet_PairwiseCache_MEM.o
> DataSet_PairwiseCache_NC.o DataSet_Parameters.o DataSet_pH.o
> DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o
> DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o
> DataSet_double.o DataSet_float.o DataSet_integer_disk.o
> DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o
> DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o
> EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o
> EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o
> EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o
> EwaldOptions.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o
> Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o
> Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o
> Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o
> Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o
> Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o
> Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o
> Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o
> Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o
> Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o
> Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o
> Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o
> Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o
> File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o
> FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o
> ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o
> ForLoop_overSets.o Frame.o GIST_PME.o GridAction.o GridBin.o HistBin.o
> Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o
> Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o
> Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o
> Mol2File.o NameType.o NC_Routines.o NetcdfFile.o OMM_helpers.o
> OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o
> ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o
> Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o
> PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o
> PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o
> PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o
> Pucker_PuckerMask.o Pucker_PuckerSearch.o Pucker_PuckerToken.o
> ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o
> RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o
> RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o
> SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o
> SymmetricRmsdCalc.o TextBlockBuffer.o TextFormat.o Timer.o TinkerFile.o
> TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o
> Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o
> Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o
> Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o
> Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o
> Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o
> TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o
> TrajoutList.o Vec3.o ViewRst.o vmdplugin/dtrplugin.o xoshiro128plusplus.o
> Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o
> molsurf.o Cluster/libcpptraj_cluster.a readline/libreadline.a
> arpack/libarpack.a /home/niperg/Downloads/cpptraj-master/lib/liblapack.a
> /home/niperg/Downloads/cpptraj-master/lib/libblas.a -lfftw3
> /home/niperg/Downloads/amber20/lib/libsander.so -lgfortran
> /home/niperg/Downloads/cpptraj-master/lib/libnetcdf.a -lbz2 tng/libtng_io.a
> -lz xdrfile/libxdrfile.a
> /usr/bin/ld: arpack/libarpack.a(dsaupd.o)(.text+0x135): unresolvable
> R_X86_64_PC32 relocation against symbol `timing_'
> collect2: error: ld returned 1 exit status
> make[1]: *** [Makefile:23: cpptraj] Error 1
> make[1]: Leaving directory '/home/niperg/Downloads/cpptraj-master/src'
> make: *** [Makefile:10: install] Error 2
> (base) niperg.niperg-dell:~/Downloads/cpptraj-master$ uname -a
> Linux niperg-dell 5.11.0-38-generic #42~20.04.1-Ubuntu SMP Tue Sep 28
> 20:41:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
> (base) niperg.niperg-dell:~/Downloads/cpptraj-master$
>
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Asst. Prof., Department of Medicinal Chemistry,
>
> National Institute of Pharmaceutical Education and Research, Guwahati
> (NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
> 781101, Assam, India
>
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhavadixit.gmail.com
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> NCBI bibliography:
> https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> Please consider the environment before printing this e-mail
>
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Received on Mon Nov 08 2021 - 02:00:02 PST
