Dear Dan,
I used both the options you suggested and I think it has worked as seen
from the make check command output.
Thank you for your quick response.
Thank you and best regards.
Vaibhav
********************************************************************************
TEST: /home/niperg/Downloads/cpptraj-master/test/Test_LJC
CPPTRAJ: Test reading/writing topology with LJ C coefficients
All 1 comparisons passed.
make[2]: Leaving directory '/home/niperg/Downloads/cpptraj-master/test'
-rwxrwxr-x 1 niperg niperg 8377592 Nov 8 20:19 ../bin/cpptraj
===================== TEST SUMMARY ======================
923 out of 928 comparisons OK (0 failed, 0 warnings, 5 skipped).
512 out of 512 program executions completed.
178 out of 180 tests completed with no issues.
2 tests skipped.
=========================================================
make[1]: Leaving directory '/home/niperg/Downloads/cpptraj-master/test'
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 7:06 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> > 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_'
>
> Usually this kind of message appears when you mix libraries with
> position-independent code with those without. I'm guessing maybe the
> libraries you are pulling from the "niperg" directory have PIC. There
> are 2 things you can try:
>
> 1) ./configure with the '-shared' flag to turn on PIC for your build.
> 2) Unset CPPTRAJHOME and ./configure with the '--buildlibs' flag to
> build your own versions of these libraries.
>
> Hopefully one or both of these will do the trick.
>
> -Dan
>
> On Mon, Nov 8, 2021 at 4:31 AM 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 08 2021 - 07:00:02 PST
