Dear Daniel and Amber team,
I'm trying to install the github version of Amber20, but I'm getting the
following error message during the compilation "make install" step for
which I can't find an easy solution online.
The full output from the configure and make steps are shown at the bottom.
Can you please suggest me on how to fix this error?
I want to use the AmberMDprep script along with the github version of the
cpptraj as recommended on the github repo.
Looking forward to your valuable suggestions and feedback.
thank you and best regards. Vaibhav
/usr/bin/ld: arpack/libarpack.a(dsaupd.o)(.text+0x135): unresolvable
R_X86_64_PC32 relocation against symbol `timing_'
*collect2: error: ld returned 1 exit status*
make[1]: *** [Makefile:23: cpptraj] Error 1
make[1]: Leaving directory '/home/niperg/Downloads/cpptraj-master/src'
make: *** [Makefile:10: install] Error 2
(base) niperg.niperg-dell:~/Downloads/cpptraj-master$ ./configure gnu
Testing C++ compiler: OK
Testing C compiler: OK
Testing Fortran compiler: OK
Testing basic C++11 support: OK
Testing system headers for C++11 support: OK
Checking BZLIB: OK
Checking ZLIB: OK
Checking NetCDF: Checking for bundled NetCDF: OK
Checking LAPACK/BLAS: Checking for bundled LAPACK/BLAS: OK
Checking FFTW3: OK
Checking for sanderlib: OK
Configuration summary:
Build type: Serial
Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile
sanderlib
Target platform: Linux, 64-bit.
gnu compilers in use.
C++11 support enabled.
PME support enabled.
Compiler optimizations are on.
Cleaning source directory.
--------------------------------------------------------------------------------
An environment resource file for CPPTRAJ has been created:
/home/niperg/Downloads/cpptraj-master/cpptraj.sh
You may 'source' this file to set up your environment for CPPTRAJ.
--------------------------------------------------------------------------------
CPPTRAJ configuration complete.
(base) niperg.niperg-dell:~/Downloads/cpptraj-master$ make install
cd src && make install
make[1]: Entering directory '/home/niperg/Downloads/cpptraj-master/src'
CXX SpaceGroup.cpp
CXX ActionFrameCounter.cpp
CXX ActionList.cpp
CXX ActionTopWriter.cpp
CXX Action_Align.cpp
CXX Action_Angle.cpp
CXX Action_AreaPerMol.cpp
CXX Action_AtomMap.cpp
CXX Action_AtomicCorr.cpp
CXX Action_AtomicFluct.cpp
CXX Action_AutoImage.cpp
CXX Action_Average.cpp
CXX Action_Bounds.cpp
CXX Action_Box.cpp
CXX Action_Center.cpp
CXX Action_Channel.cpp
CXX Action_CheckChirality.cpp
CXX Action_CheckStructure.cpp
CXX Action_Closest.cpp
CXX Action_ClusterDihedral.cpp
CXX Action_Contacts.cpp
CXX Action_CreateCrd.cpp
CXX Action_CreateReservoir.cpp
CXX Action_DNAionTracker.cpp
CXX Action_DSSP.cpp
CXX Action_Density.cpp
CXX Action_Diffusion.cpp
CXX Action_Dihedral.cpp
CXX Action_DihedralRMS.cpp
CXX Action_Dipole.cpp
CXX Action_Distance.cpp
CXX Action_DistRmsd.cpp
CXX Action_Energy.cpp
In file included from Ewald_ParticleMesh.h:5,
from Action_Energy.cpp:4:
helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2370 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2390 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3328 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3777 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3815 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3878 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3916 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4148 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4156: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4156 | #pragma omp for
|
helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4201 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4249 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4276 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4328 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4332 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4379 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4492 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4523 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4607 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4614: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4614 | #pragma omp for
|
helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4983 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
5015 | #pragma omp parallel for num_threads(nThreads_)
|
CXX Action_FilterByData.cpp
CXX Action_FixAtomOrder.cpp
CXX Action_FixImagedBonds.cpp
CXX Action_GIST.cpp
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from Action_GIST.h:11,
from Action_GIST.cpp:3:
helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2370 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2390 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3328 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3777 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3815 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3878 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3916 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4148 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4156: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4156 | #pragma omp for
|
helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4201 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4249 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4276 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4328 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4332 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4379 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4492 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4523 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4607 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4614: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4614 | #pragma omp for
|
helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4983 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
5015 | #pragma omp parallel for num_threads(nThreads_)
|
CXX Action_Grid.cpp
CXX Action_GridFreeEnergy.cpp
CXX Action_HydrogenBond.cpp
CXX Action_Image.cpp
CXX Action_InfraredSpectrum.cpp
CXX Action_Jcoupling.cpp
CXX Action_LESsplit.cpp
CXX Action_LIE.cpp
CXX Action_LipidOrder.cpp
CXX Action_MakeStructure.cpp
CXX Action_Mask.cpp
CXX Action_Matrix.cpp
CXX Action_MinImage.cpp
CXX Action_Molsurf.cpp
CXX Action_MultiDihedral.cpp
CXX Action_MultiPucker.cpp
CXX Action_MultiVector.cpp
CXX Action_NAstruct.cpp
CXX Action_NativeContacts.cpp
CXX Action_NMRrst.cpp
CXX Action_OrderParameter.cpp
CXX Action_Outtraj.cpp
CXX Action_PairDist.cpp
CXX Action_Pairwise.cpp
CXX Action_Principal.cpp
CXX Action_Projection.cpp
CXX Action_Pucker.cpp
CXX Action_Radgyr.cpp
CXX Action_Radial.cpp
CXX Action_RandomizeIons.cpp
CXX Action_Remap.cpp
CXX Action_ReplicateCell.cpp
CXX Action_Rmsd.cpp
CXX Action_Rotate.cpp
CXX Action_RunningAvg.cpp
CXX Action_STFC_Diffusion.cpp
CXX Action_Scale.cpp
CXX Action_SetVelocity.cpp
CXX Action_Spam.cpp
CXX Action_Strip.cpp
CXX Action_Surf.cpp
CXX Action_SymmetricRmsd.cpp
CXX Action_Temperature.cpp
CXX Action_Time.cpp
CXX Action_Translate.cpp
CXX Action_Unstrip.cpp
CXX Action_Unwrap.cpp
CXX Action_Vector.cpp
CXX Action_VelocityAutoCorr.cpp
CXX Action_Volmap.cpp
CXX Action_Volume.cpp
CXX Action_Watershell.cpp
CXX Action_XtalSymm.cpp
CXX AnalysisList.cpp
CXX Analysis_AmdBias.cpp
CXX Analysis_AutoCorr.cpp
CXX Analysis_Average.cpp
CXX Analysis_Clustering.cpp
CXX Analysis_Corr.cpp
CXX Analysis_ConstantPHStats.cpp
CXX Analysis_CrankShaft.cpp
CXX Analysis_CrdFluct.cpp
CXX Analysis_CrossCorr.cpp
CXX Analysis_CurveFit.cpp
CXX Analysis_Divergence.cpp
CXX Analysis_EvalPlateau.cpp
CXX Analysis_FFT.cpp
CXX Analysis_HausdorffDistance.cpp
CXX Analysis_Hist.cpp
CXX Analysis_Integrate.cpp
CXX Analysis_IRED.cpp
CXX Analysis_KDE.cpp
CXX Analysis_Lifetime.cpp
CXX Analysis_LowestCurve.cpp
CXX Analysis_Matrix.cpp
CXX Analysis_MeltCurve.cpp
CXX Analysis_Modes.cpp
CXX Analysis_Multicurve.cpp
CXX Analysis_MultiHist.cpp
CXX Analysis_Overlap.cpp
CXX Analysis_PhiPsi.cpp
CXX Analysis_Regression.cpp
CXX Analysis_RemLog.cpp
CXX Analysis_Rms2d.cpp
CXX Analysis_RmsAvgCorr.cpp
CXX Analysis_Rotdif.cpp
CXX Analysis_RunningAvg.cpp
CXX Analysis_Slope.cpp
CXX Analysis_Spline.cpp
CXX Analysis_State.cpp
CXX Analysis_Statistics.cpp
CXX Analysis_TI.cpp
CXX Analysis_Timecorr.cpp
CXX Analysis_VectorMath.cpp
CXX Analysis_Wavelet.cpp
CXX ArgList.cpp
CXX Array1D.cpp
CXX AssociatedData.cpp
CXX Atom.cpp
CXX AtomMap.cpp
CXX AtomMask.cpp
CXX AxisType.cpp
CXX BondSearch.cpp
CXX Box.cpp
CXX BoxArgs.cpp
CXX BufferedFrame.cpp
CXX BufferedLine.cpp
CXX ByteRoutines.cpp
CXX CharMask.cpp
CXX CharmmParamFile.cpp
CXX CIFfile.cpp
CXX ClusterMap.cpp
CXX Cmd.cpp
CXX CmdInput.cpp
CXX CmdList.cpp
CXX CompactFrameArray.cpp
CXX ComplexArray.cpp
CXX Constraints.cpp
CXX ControlBlock_For.cpp
CXX CoordinateInfo.cpp
CXX Corr.cpp
CXX Cph.cpp
CXX CpptrajFile.cpp
CXX CpptrajState.cpp
CXX CpptrajStdio.cpp
CXX CurveFit.cpp
CXX DataFile.cpp
CXX DataFileList.cpp
CXX DataFilter.cpp
CXX DataIO.cpp
CXX DataIO_CCP4.cpp
CXX DataIO_CharmmFastRep.cpp
CXX DataIO_CharmmOutput.cpp
CXX DataIO_CharmmRepLog.cpp
CXX DataIO_CharmmRtfPrm.cpp
CXX DataIO_Cmatrix_Binary.cpp
CXX DataIO_Cmatrix_NC.cpp
CXX DataIO_Cpout.cpp
CXX DataIO_Evecs.cpp
CXX DataIO_Gnuplot.cpp
CXX DataIO_Grace.cpp
CXX DataIO_OpenDx.cpp
CXX DataIO_Peaks.cpp
CXX DataIO_Mdout.cpp
CXX DataIO_RemLog.cpp
CXX DataIO_Std.cpp
CXX DataIO_VecTraj.cpp
CXX DataIO_Xplor.cpp
CXX DataIO_XVG.cpp
CXX DataSet.cpp
CXX DataSetList.cpp
CXX DataSet_1D.cpp
CXX DataSet_3D.cpp
CXX DataSet_Coords.cpp
CXX DataSet_Coords_CRD.cpp
CXX DataSet_Coords_REF.cpp
CXX DataSet_Coords_TRJ.cpp
CXX DataSet_GridDbl.cpp
CXX DataSet_GridFlt.cpp
CXX DataSet_Mat3x3.cpp
CXX DataSet_MatrixDbl.cpp
CXX DataSet_MatrixFlt.cpp
CXX DataSet_Mesh.cpp
CXX DataSet_Modes.cpp
CXX DataSet_PairwiseCache.cpp
CXX DataSet_PairwiseCache_MEM.cpp
CXX DataSet_PairwiseCache_NC.cpp
CXX DataSet_Parameters.cpp
CXX DataSet_pH.cpp
CXX DataSet_PHREMD_Explicit.cpp
CXX DataSet_PHREMD_Implicit.cpp
CXX DataSet_RemLog.cpp
CXX DataSet_Topology.cpp
CXX DataSet_Vector.cpp
CXX DataSet_Vector_Scalar.cpp
CXX DataSet_double.cpp
CXX DataSet_float.cpp
CXX DataSet_integer_disk.cpp
CXX DataSet_integer_mem.cpp
CXX DataSet_string.cpp
CXX DataSet_StringVar.cpp
CXX DataSet_Tensor.cpp
CXX DataSet_unsignedInt.cpp
CXX Deprecated.cpp
CXX DihedralSearch.cpp
CXX DistRoutines.cpp
CXX Energy.cpp
CXX EnergyArray.cpp
CXX EnsembleIn.cpp
CXX EnsembleIn_Multi.cpp
CXX EnsembleIn_Single.cpp
CXX EnsembleNavigator.cpp
CXX EnsembleOut.cpp
CXX EnsembleOut_Multi.cpp
CXX EnsembleOut_Single.cpp
CXX EnsembleOutList.cpp
CXX Ewald.cpp
CXX Ewald_ParticleMesh.cpp
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2370 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2390 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3328 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3777 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3815 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3878 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3916 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4148 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4156: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4156 | #pragma omp for
|
helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4201 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4249 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4276 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4328 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4332 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4379 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4492 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4523 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4607 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4614: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4614 | #pragma omp for
|
helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4983 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
5015 | #pragma omp parallel for num_threads(nThreads_)
|
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘std::pair<helpme::Matrix<Real>,
helpme::Matrix<Real> >
helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
[with Real = double]’:
helpme_standalone.h:4001:22: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
Ewald_ParticleMesh.cpp:234:68: required from here
helpme_standalone.h:1027:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
1027 | for (int val = 0; val < nRows_; ++val)
eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]});
| ~~~~^~~~~~~~
helpme_standalone.h:1030:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
1030 | for (int val = 0; val < nRows_; ++val) {
| ~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
<anonymous> >::sanityChecks(int, const RealMat&, const RealMat&, int) [with
Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’:
helpme_standalone.h:5194:9: required from ‘Real helpme::PMEInstance<Real,
<anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
= double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’
Ewald_ParticleMesh.cpp:235:63: required from here
helpme_standalone.h:3278:32: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3278 | if (parameters.nCols() != (nCartesian(parameterAngMom) -
cartesianOffset))
helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
<anonymous> >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with
Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’:
helpme_standalone.h:5195:9: required from ‘Real helpme::PMEInstance<Real,
<anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
= double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’
Ewald_ParticleMesh.cpp:235:63: required from here
helpme_standalone.h:3822:45: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3822 | for (size_t row = threadID; row < gridDimensionC_; row
+= nThreads_) {
| ~~~~^~~~~~~~~~~~~~~~~
helpme_standalone.h:3829:37: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
[-Wsign-compare]
3829 | for (int atom = 0; atom < nAtoms; ++atom) {
| ~~~~~^~~~~~~~
helpme_standalone.h:3837:61: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3837 | if (cGridIterator.size() && thisAtomsThread ==
threadID) {
|
~~~~~~~~~~~~~~~~^~~~~~~~~~~
helpme_standalone.h:3826:25: warning: unused variable ‘gridIteratorC’
[-Wunused-variable]
3826 | const auto &gridIteratorC =
threadedGridIteratorC_[threadID];
| ^~~~~~~~~~~~~
helpme_standalone.h:3870:55: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
[-Wsign-compare]
3870 | for (int atom = splineCache_.size(); atom < newSize;
++atom)
| ~~~~~^~~~~~~~~
helpme_standalone.h:3886:47: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3886 | for (size_t cRow = threadID; cRow < gridDimensionC_;
cRow += nThreads_) {
| ~~~~~^~~~~~~~~~~~~~~~~
helpme_standalone.h: In instantiation of ‘Real* helpme::PMEInstance<Real,
<anonymous> >::spreadParameters(int, const RealMat&) [with Real = double;
typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
<anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’:
helpme_standalone.h:5196:25: required from ‘Real
helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
const RealMat&) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’
Ewald_ParticleMesh.cpp:235:63: required from here
helpme_standalone.h:3784:45: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3784 | for (size_t row = threadID; row < myGridDimensionC_;
row += nThreads_) {
| ~~~~^~~~~~~~~~~~~~~~~~~
helpme_standalone.h: In instantiation of ‘helpme::PMEInstance<Real,
<anonymous> >::Complex* helpme::PMEInstance<Real, <anonymous>
>::forwardTransform(Real*) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0; helpme::PMEInstance<Real, <anonymous> >::Complex =
std::complex<double>]’:
helpme_standalone.h:5199:32: required from ‘Real
helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
const RealMat&) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’
Ewald_ParticleMesh.cpp:235:63: required from here
helpme_standalone.h:4108:28: warning: variable ‘realCBA’ set but not used
[-Wunused-but-set-variable]
4108 | Real *__restrict__ realCBA;
| ^~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘void
helpme::Matrix<Real>::assertSymmetric(const Real&) const [with Real =
double]’:
helpme_standalone.h:1017:9: required from
‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
[with Real = double]’
helpme_standalone.h:4001:22: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
Ewald_ParticleMesh.cpp:234:68: required from here
helpme_standalone.h:796:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
796 | for (int row = 0; row < nRows_; ++row) {
| ~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘void
helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with
Real = double]’:
helpme_standalone.h:1023:42: required from
‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
[with Real = double]’
helpme_standalone.h:4001:22: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
Ewald_ParticleMesh.cpp:234:68: required from here
helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used
[-Wunused-but-set-variable]
213 | Real sin_2phi, cos_2phi, cot_2phi;
| ^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
const [with Real = double]’:
helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::inverse() const [with Real = double]’
helpme_standalone.h:4013:26: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
Ewald_ParticleMesh.cpp:234:68: required from here
helpme_standalone.h:824:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
824 | for (int row = 0; row < nRows_; ++row) {
| ~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘void
helpme::BSpline<Real>::update(short int, Real, short int, short int) [with
Real = double]’:
helpme_standalone.h:3905:21: required from ‘void
helpme::PMEInstance<Real, <anonymous>
>::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double;
typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
<anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’
helpme_standalone.h:5195:9: required from ‘Real helpme::PMEInstance<Real,
<anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
= double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’
Ewald_ParticleMesh.cpp:235:63: required from here
helpme_standalone.h:2255:30: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
2255 | if (splines_.nRows() < derivativeLevel + 1 ||
splines_.nCols() != order)
helpme_standalone.h:2255:72: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘short int’
[-Wsign-compare]
2255 | if (splines_.nRows() < derivativeLevel + 1 ||
splines_.nCols() != order)
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
helpme::Matrix<Real>::multiply(const helpme::Matrix<Real>&) const [with
Real = double]’:
helpme_standalone.h:877:64: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::operator*(const helpme::Matrix<Real>&) const [with
Real = double]’
helpme_standalone.h:829:22: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
const [with Real = double]’
helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::inverse() const [with Real = double]’
helpme_standalone.h:4013:26: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
Ewald_ParticleMesh.cpp:234:68: required from here
helpme_standalone.h:860:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
860 | for (int row = 0; row < nRows_; ++row) {
| ~~~~^~~~~~~~
helpme_standalone.h:862:35: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
862 | for (int col = 0; col < other.nCols_; ++col) {
| ~~~~^~~~~~~~~~~~~~
helpme_standalone.h:863:41: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
863 | for (int link = 0; link < nCols_; ++link) {
| ~~~~~^~~~~~~~
helpme_standalone.h: In member function ‘void helpme::PMEInstance<Real,
<anonymous> >::setupCalculationMetadata(int, Real, int, int, int, int, int,
int, int, Real, int, void*, helpme::PMEInstance<Real, <anonymous>
>::NodeOrder, int, int, int) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’:
helpme_standalone.h:519:7: warning:
‘<anonymous>.helpme::Matrix<double>::data_’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
519 | class Matrix {
| ^~~~~~
helpme_standalone.h:519:7: warning:
‘<anonymous>.helpme::Matrix<double>::data_’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
519 | class Matrix {
| ^~~~~~
helpme_standalone.h:519:7: warning:
‘<anonymous>.helpme::Matrix<double>::data_’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
519 | class Matrix {
| ^~~~~~
In file included from Ewald_ParticleMesh.h:5,
from Ewald_ParticleMesh.cpp:4:
helpme_standalone.h: In member function ‘Real helpme::PMEInstance<Real,
<anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
= double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0]’:
helpme_standalone.h:5207:16: warning: ‘energy’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
5207 | return energy;
| ^~~~~~
CXX Ewald_Regular.cpp
CXX EwaldOptions.cpp
CXX ExclusionArray.cpp
CXX Exec_AddMissingRes.cpp
CXX Exec_Analyze.cpp
CXX Exec_Calc.cpp
CXX Exec_CatCrd.cpp
CXX Exec_Change.cpp
CXX Exec_ClusterMap.cpp
CXX Exec_CombineCoords.cpp
CXX Exec_Commands.cpp
CXX Exec_CompareTop.cpp
CXX Exec_CrdAction.cpp
CXX Exec_CrdOut.cpp
CXX Exec_CreateSet.cpp
CXX Exec_DataFile.cpp
CXX Exec_DataFilter.cpp
CXX Exec_DataSetCmd.cpp
CXX Exec_Emin.cpp
CXX Exec_Flatten.cpp
CXX Exec_GenerateAmberRst.cpp
CXX Exec_Graft.cpp
CXX Exec_Help.cpp
CXX Exec_LoadCrd.cpp
CXX Exec_LoadTraj.cpp
CXX Exec_ParallelAnalysis.cpp
CXX Exec_ParmBox.cpp
CXX Exec_ParmSolvent.cpp
CXX Exec_ParmStrip.cpp
CXX Exec_ParmWrite.cpp
CXX Exec_PermuteDihedrals.cpp
CXX Exec_Precision.cpp
CXX Exec_PrepareForLeap.cpp
CXX Exec_PrintData.cpp
CXX Exec_Random.cpp
CXX Exec_ReadData.cpp
CXX Exec_ReadEnsembleData.cpp
CXX Exec_ReadInput.cpp
CXX Exec_RotateDihedral.cpp
CXX Exec_RunAnalysis.cpp
CXX Exec_ScaleDihedralK.cpp
CXX Exec_Set.cpp
CXX Exec_SequenceAlign.cpp
CXX Exec_Show.cpp
CXX Exec_SortEnsembleData.cpp
CXX Exec_SplitCoords.cpp
CXX Exec_System.cpp
CXX Exec_Top.cpp
CXX Exec_Traj.cpp
CXX Exec_UpdateParameters.cpp
CXX Exec_ViewRst.cpp
CXX File_TempName.cpp
CXX FileIO_Bzip2.cpp
CXX FileIO_Gzip.cpp
CXX FileIO_Mpi.cpp
CXX FileIO_MpiShared.cpp
CXX FileIO_Std.cpp
CXX FileName.cpp
CXX FileType.cpp
CXX FileTypes.cpp
CXX ForLoop.cpp
CXX ForLoop_dataSetBlocks.cpp
CXX ForLoop_integer.cpp
CXX ForLoop_list.cpp
CXX ForLoop_mask.cpp
CXX ForLoop_overSets.cpp
CXX Frame.cpp
CXX GIST_PME.cpp
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2370 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2390 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3328 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3777 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3815 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3878 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3916 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4148 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4156: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4156 | #pragma omp for
|
helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4201 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4249 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4276 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4328 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4332 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4379 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4492 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4523 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4607 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4614: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4614 | #pragma omp for
|
helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4983 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
5015 | #pragma omp parallel for num_threads(nThreads_)
|
GIST_PME.cpp: In member function ‘int
GIST_PME::CalcNonbondEnergy_GIST(const Frame&, const std::vector<int>&,
const std::vector<bool>&, const std::vector<bool>&,
std::vector<std::vector<double> >&, std::vector<std::vector<double> >&,
std::vector<std::vector<double> >&, std::vector<std::vector<double> >&,
std::vector<std::vector<float> >&)’:
GIST_PME.cpp:123:10: warning: variable ‘e_vdw_lr_correction’ set but not
used [-Wunused-but-set-variable]
123 | double e_vdw_lr_correction;
| ^~~~~~~~~~~~~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘std::pair<helpme::Matrix<Real>,
helpme::Matrix<Real> >
helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
[with Real = double]’:
helpme_standalone.h:4001:22: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
GIST_PME.cpp:308:68: required from here
helpme_standalone.h:1027:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
1027 | for (int val = 0; val < nRows_; ++val)
eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]});
| ~~~~^~~~~~~~
helpme_standalone.h:1030:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
1030 | for (int val = 0; val < nRows_; ++val) {
| ~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
<anonymous> >::sanityChecks(int, const RealMat&, const RealMat&, int) [with
Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’:
helpme_standalone.h:5070:9: required from ‘void helpme::PMEInstance<Real,
<anonymous> >::computePRec(int, const RealMat&, const RealMat&, const
RealMat&, int, helpme::PMEInstance<Real, <anonymous> >::RealMat&) [with
Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’
GIST_PME.cpp:311:69: required from here
helpme_standalone.h:3278:32: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3278 | if (parameters.nCols() != (nCartesian(parameterAngMom) -
cartesianOffset))
helpme_standalone.h: In instantiation of ‘helpme::PMEInstance<Real,
<anonymous> >::Complex* helpme::PMEInstance<Real, <anonymous>
>::forwardTransform(Real*) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0; helpme::PMEInstance<Real, <anonymous> >::Complex =
std::complex<double>]’:
helpme_standalone.h:5125:32: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::computePRec(int, const RealMat&,
const RealMat&, const RealMat&, int, helpme::PMEInstance<Real, <anonymous>
>::RealMat&) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’
GIST_PME.cpp:311:69: required from here
helpme_standalone.h:4108:28: warning: variable ‘realCBA’ set but not used
[-Wunused-but-set-variable]
4108 | Real *__restrict__ realCBA;
| ^~~~~~~
helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance<Real,
<anonymous> >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with
Real = double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’:
helpme_standalone.h:5195:9: required from ‘Real helpme::PMEInstance<Real,
<anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
= double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’
GIST_PME.cpp:397:62: required from here
helpme_standalone.h:3822:45: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3822 | for (size_t row = threadID; row < gridDimensionC_; row
+= nThreads_) {
| ~~~~^~~~~~~~~~~~~~~~~
helpme_standalone.h:3829:37: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
[-Wsign-compare]
3829 | for (int atom = 0; atom < nAtoms; ++atom) {
| ~~~~~^~~~~~~~
helpme_standalone.h:3837:61: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3837 | if (cGridIterator.size() && thisAtomsThread ==
threadID) {
|
~~~~~~~~~~~~~~~~^~~~~~~~~~~
helpme_standalone.h:3826:25: warning: unused variable ‘gridIteratorC’
[-Wunused-variable]
3826 | const auto &gridIteratorC =
threadedGridIteratorC_[threadID];
| ^~~~~~~~~~~~~
helpme_standalone.h:3870:55: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’}
[-Wsign-compare]
3870 | for (int atom = splineCache_.size(); atom < newSize;
++atom)
| ~~~~~^~~~~~~~~
helpme_standalone.h:3886:47: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3886 | for (size_t cRow = threadID; cRow < gridDimensionC_;
cRow += nThreads_) {
| ~~~~~^~~~~~~~~~~~~~~~~
helpme_standalone.h: In instantiation of ‘Real* helpme::PMEInstance<Real,
<anonymous> >::spreadParameters(int, const RealMat&) [with Real = double;
typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
<anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’:
helpme_standalone.h:5196:25: required from ‘Real
helpme::PMEInstance<Real, <anonymous> >::computeERec(int, const RealMat&,
const RealMat&) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’
GIST_PME.cpp:397:62: required from here
helpme_standalone.h:3784:45: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
3784 | for (size_t row = threadID; row < myGridDimensionC_;
row += nThreads_) {
| ~~~~^~~~~~~~~~~~~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘void
helpme::Matrix<Real>::assertSymmetric(const Real&) const [with Real =
double]’:
helpme_standalone.h:1017:9: required from
‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
[with Real = double]’
helpme_standalone.h:4001:22: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
GIST_PME.cpp:308:68: required from here
helpme_standalone.h:796:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
796 | for (int row = 0; row < nRows_; ++row) {
| ~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘void
helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with
Real = double]’:
helpme_standalone.h:1023:42: required from
‘std::pair<helpme::Matrix<Real>, helpme::Matrix<Real> >
helpme::Matrix<Real>::diagonalize(helpme::Matrix<Real>::SortOrder) const
[with Real = double]’
helpme_standalone.h:4001:22: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
GIST_PME.cpp:308:68: required from here
helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used
[-Wunused-but-set-variable]
213 | Real sin_2phi, cos_2phi, cot_2phi;
| ^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
const [with Real = double]’:
helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::inverse() const [with Real = double]’
helpme_standalone.h:4013:26: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
GIST_PME.cpp:308:68: required from here
helpme_standalone.h:824:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
824 | for (int row = 0; row < nRows_; ++row) {
| ~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘void
helpme::BSpline<Real>::update(short int, Real, short int, short int) [with
Real = double]’:
helpme_standalone.h:3905:21: required from ‘void
helpme::PMEInstance<Real, <anonymous>
>::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double;
typename std::enable_if<std::is_floating_point<_Tp>::value, int>::type
<anonymous> = 0; helpme::PMEInstance<Real, <anonymous> >::RealMat =
helpme::Matrix<double>]’
helpme_standalone.h:5195:9: required from ‘Real helpme::PMEInstance<Real,
<anonymous> >::computeERec(int, const RealMat&, const RealMat&) [with Real
= double; typename std::enable_if<std::is_floating_point<_Tp>::value,
int>::type <anonymous> = 0; helpme::PMEInstance<Real, <anonymous>
>::RealMat = helpme::Matrix<double>]’
GIST_PME.cpp:397:62: required from here
helpme_standalone.h:2255:30: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’
[-Wsign-compare]
2255 | if (splines_.nRows() < derivativeLevel + 1 ||
splines_.nCols() != order)
helpme_standalone.h:2255:72: warning: comparison of integer expressions of
different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘short int’
[-Wsign-compare]
2255 | if (splines_.nRows() < derivativeLevel + 1 ||
splines_.nCols() != order)
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In instantiation of ‘helpme::Matrix<Real>
helpme::Matrix<Real>::multiply(const helpme::Matrix<Real>&) const [with
Real = double]’:
helpme_standalone.h:877:64: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::operator*(const helpme::Matrix<Real>&) const [with
Real = double]’
helpme_standalone.h:829:22: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::applyOperation(const std::function<void(Real&)>&)
const [with Real = double]’
helpme_standalone.h:785:26: required from ‘helpme::Matrix<Real>
helpme::Matrix<Real>::inverse() const [with Real = double]’
helpme_standalone.h:4013:26: required from ‘void
helpme::PMEInstance<Real, <anonymous> >::setLatticeVectors(Real, Real,
Real, Real, Real, Real, helpme::PMEInstance<Real, <anonymous>
>::LatticeType) [with Real = double; typename
std::enable_if<std::is_floating_point<_Tp>::value, int>::type <anonymous> =
0]’
GIST_PME.cpp:308:68: required from here
helpme_standalone.h:860:31: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
860 | for (int row = 0; row < nRows_; ++row) {
| ~~~~^~~~~~~~
helpme_standalone.h:862:35: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
862 | for (int col = 0; col < other.nCols_; ++col) {
| ~~~~^~~~~~~~~~~~~~
helpme_standalone.h:863:41: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned
int’} [-Wsign-compare]
863 | for (int link = 0; link < nCols_; ++link) {
| ~~~~~^~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In member function ‘double
GIST_PME::LJ_Recip_ParticleMesh_GIST(const Box&, GIST_PME::MatType&)’:
helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
5157 | Real gridVal = cbRow[aPoint.first];
| ~~~~~^
helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
5123 | Real *potentialGrid;
| ^~~~~~~~~~~~~
GIST_PME.cpp:400:10: warning: ‘energy’ may be used uninitialized in this
function [-Wmaybe-uninitialized]
400 | return evdwrecip;
| ^~~~~~~~~
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from GIST_PME.cpp:3:
helpme_standalone.h: In member function ‘double
GIST_PME::Recip_ParticleMesh_GIST(const Box&, const std::vector<int>&,
const std::vector<bool>&, Ewald::Darray&, Ewald::Darray&)’:
helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
5157 | Real gridVal = cbRow[aPoint.first];
| ~~~~~^
helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
5123 | Real *potentialGrid;
| ^~~~~~~~~~~~~
helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
5157 | Real gridVal = cbRow[aPoint.first];
| ~~~~~^
helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
5123 | Real *potentialGrid;
| ^~~~~~~~~~~~~
helpme_standalone.h:5157:45: warning: ‘potentialGrid’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
5157 | Real gridVal = cbRow[aPoint.first];
| ~~~~~^
helpme_standalone.h:5123:15: note: ‘potentialGrid’ was declared here
5123 | Real *potentialGrid;
| ^~~~~~~~~~~~~
CXX GridAction.cpp
CXX GridBin.cpp
CXX HistBin.cpp
CXX Hungarian.cpp
CXX ImageRoutines.cpp
CXX Image_List_Mask.cpp
CXX Image_List_Pair.cpp
CXX Image_List_Unit.cpp
CXX InputTrajCommon.cpp
CXX KDE.cpp
CXX MapAtom.cpp
CXX MaskArray.cpp
CXX MaskToken.cpp
CXX Matrix_3x3.cpp
CXX MdOpts.cpp
CXX MetaData.cpp
CXX Minimize_SteepestDescent.cpp
CXX Mol.cpp
CXX Mol2File.cpp
CXX NameType.cpp
CXX NC_Routines.cpp
CXX NetcdfFile.cpp
CXX OMM_helpers.cpp
CXX OutputTrajCommon.cpp
CXX ParameterSet.cpp
CXX PDBfile.cpp
CXX PairList.cpp
CXX Parallel.cpp
CXX ParallelNetcdf.cpp
CXX ParmFile.cpp
CXX Parm_Amber.cpp
CXX Parm_CharmmPsf.cpp
CXX Parm_CIF.cpp
CXX Parm_Gromacs.cpp
CXX Parm_Mol2.cpp
CXX Parm_PDB.cpp
CXX Parm_SDF.cpp
CXX Parm_Tinker.cpp
CXX PotentialFunction.cpp
CXX PotentialTerm.cpp
CXX PotentialTerm_Angle.cpp
CXX PotentialTerm_Bond.cpp
CXX PotentialTerm_Dihedral.cpp
CXX PotentialTerm_LJ_Coulomb.cpp
CXX PotentialTerm_OpenMM.cpp
CXX ProgressBar.cpp
CXX ProgressTimer.cpp
CXX PubFFT.cpp
CXX Pucker_PuckerMask.cpp
CXX Pucker_PuckerSearch.cpp
CXX Pucker_PuckerToken.cpp
CXX ExternalFxn.cpp
CXX Random.cpp
CXX Range.cpp
CXX RNG.cpp
CXX RNG_Marsaglia.cpp
CXX RNG_MersenneTwister.cpp
CXX RNG_PCG32.cpp
CXX RNG_Stdlib.cpp
CXX RNG_Xoshiro128pp.cpp
CXX RPNcalc.cpp
CXX ReferenceAction.cpp
CXX RemdReservoirNC.cpp
CXX Residue.cpp
CXX SDFfile.cpp
CXX SimplexMin.cpp
CXX Spline.cpp
CXX SplineFxnTable.cpp
CXX StringRoutines.cpp
CXX StructureCheck.cpp
CXX StructureMapper.cpp
CXX SymmetricRmsdCalc.cpp
CXX TextBlockBuffer.cpp
CXX TextFormat.cpp
CXX Timer.cpp
CXX TinkerFile.cpp
CXX TopInfo.cpp
CXX Topology.cpp
CXX TorsionRoutines.cpp
CXX Traj_AmberCoord.cpp
CXX Traj_AmberNetcdf.cpp
CXX Traj_AmberRestart.cpp
CXX Traj_AmberRestartNC.cpp
CXX Traj_Binpos.cpp
CXX Traj_CharmmCor.cpp
CXX Traj_CharmmDcd.cpp
CXX Traj_CharmmRestart.cpp
CXX Traj_CIF.cpp
CXX Traj_Conflib.cpp
CXX Traj_DTR.cpp
CXX Traj_GmxDump.cpp
CXX Traj_GmxTng.cpp
CXX Traj_GmxTrX.cpp
CXX Traj_GmxXtc.cpp
CXX Traj_Gro.cpp
CXX Traj_Mol2File.cpp
CXX Traj_NcEnsemble.cpp
CXX Traj_PDBfile.cpp
CXX Traj_SDF.cpp
CXX Traj_SQM.cpp
CXX Traj_Tinker.cpp
CXX Traj_XYZ.cpp
CXX TrajectoryFile.cpp
CXX TrajectoryIO.cpp
CXX TrajFrameCounter.cpp
CXX TrajinList.cpp
CXX Trajin_Multi.cpp
CXX Trajin_Single.cpp
CXX TrajIOarray.cpp
CXX Trajout_Single.cpp
CXX TrajoutList.cpp
CXX Vec3.cpp
CXX ViewRst.cpp
CXX vmdplugin/dtrplugin.cpp
In file included from vmdplugin/dtrplugin.cpp:65:
vmdplugin/vmddir.h:146:12: warning: ‘int vmd_file_is_executable(const
char*)’ defined but not used [-Wunused-function]
146 | static int vmd_file_is_executable(const char * filename) {
| ^~~~~~~~~~~~~~~~~~~~~~
vmdplugin/dtrplugin.cpp: In function ‘void DDmkdir(const string&, mode_t,
int, int)’:
vmdplugin/dtrplugin.cpp:716:16: warning: ‘%03x’ directive writing between 3
and 8 bytes into a region of size 6 [-Wformat-overflow=]
716 | sprintf(sub, "%03x/", i);
| ^~~~
vmdplugin/dtrplugin.cpp:716:15: note: directive argument in the range [0,
2147483646]
716 | sprintf(sub, "%03x/", i);
| ^~~~~~~
In file included from /usr/include/stdio.h:867,
from vmdplugin/dtrplugin.hxx:56,
from vmdplugin/dtrplugin.cpp:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination
of size 6
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vmdplugin/dtrplugin.cpp:724:23: warning: ‘%03x’ directive writing between 3
and 8 bytes into a region of size 6 [-Wformat-overflow=]
724 | sprintf(subsub, "%03x", j);
| ^~~~
vmdplugin/dtrplugin.cpp:724:22: note: directive argument in the range [0,
2147483646]
724 | sprintf(subsub, "%03x", j);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from vmdplugin/dtrplugin.hxx:56,
from vmdplugin/dtrplugin.cpp:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination
of size 6
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vmdplugin/dtrplugin.cpp: In function ‘std::string framefile(const string&,
size_t, size_t, int, int)’:
vmdplugin/dtrplugin.cpp:677:28: warning: ‘__builtin___sprintf_chk’ may
write a terminating nul past the end of the destination [-Wformat-overflow=]
677 | sprintf(answer, "%03x/", d1);
| ^
In file included from /usr/include/stdio.h:867,
from vmdplugin/dtrplugin.hxx:56,
from vmdplugin/dtrplugin.cpp:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination
of size 9
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
vmdplugin/dtrplugin.cpp:675:28: warning: ‘%03x’ directive writing between 3
and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=]
675 | sprintf(answer, "%03x/%03x/", d1, d2);
| ^~~~
vmdplugin/dtrplugin.cpp:675:22: note: directive argument in the range [0,
2147483646]
675 | sprintf(answer, "%03x/%03x/", d1, d2);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from vmdplugin/dtrplugin.hxx:56,
from vmdplugin/dtrplugin.cpp:42:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note:
‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination
of size 9
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CXX xoshiro128plusplus.cpp
xoshiro128plusplus.cpp: In function ‘void jump()’:
xoshiro128plusplus.cpp:60:19: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
xoshiro128plusplus.cpp: In function ‘void long_jump()’:
xoshiro128plusplus.cpp:90:19: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CXX Action_Esander.cpp
CXX Command.cpp
In file included from Ewald_ParticleMesh.h:5,
from GIST_PME.h:5,
from Action_GIST.h:11,
from Command.cpp:123:
helpme_standalone.h:2370: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2370 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:2390: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
2390 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3062: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3062 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3169: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3169 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz,
Vyz, Vzz) num_threads(nThreads)
|
helpme_standalone.h:3328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3328 | #pragma omp parallel for num_threads(nThreads)
|
helpme_standalone.h:3777: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3777 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3815: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3815 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3878: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3878 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:3916: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
3916 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4148: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4148 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4156: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4156 | #pragma omp for
|
helpme_standalone.h:4201: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4201 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4249: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4249 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4276: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4276 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4328: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4328 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4332: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4332 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4379: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4379 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:4492: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4492 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4523: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4523 | #pragma omp parallel for reduction(+ : energy)
num_threads(nThreads_)
|
helpme_standalone.h:4607: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4607 | #pragma omp parallel num_threads(nThreads_)
|
helpme_standalone.h:4614: warning: ignoring #pragma omp for
[-Wunknown-pragmas]
4614 | #pragma omp for
|
helpme_standalone.h:4983: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
4983 | #pragma omp parallel for num_threads(nThreads_)
|
helpme_standalone.h:5015: warning: ignoring #pragma omp parallel
[-Wunknown-pragmas]
5015 | #pragma omp parallel for num_threads(nThreads_)
|
CXX Cpptraj.cpp
CXX Energy_Sander.cpp
CXX ReadLine.cpp
CXX main.cpp
CC molsurf.c
cd readline && make all
make[2]: Entering directory
'/home/niperg/Downloads/cpptraj-master/src/readline'
CC bind.c
bind.c: In function ‘rl_translate_keyseq’:
bind.c:445:19: warning: suggest parentheses around assignment used as truth
value [-Wparentheses]
445 | for (i = l = 0; c = seq[i]; i++)
| ^
bind.c: In function ‘rl_parse_and_bind’:
bind.c:1188:19: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
1188 | for (i = 1; c = string[i]; i++)
| ^
bind.c:1279:23: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
1279 | for (passc = 0; c = string[i]; i++)
| ^
bind.c: In function ‘rl_function_dumper’:
bind.c:2051:15: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
2051 | for (i = 0; name = names[i]; i++)
| ^~~~
CC callback.c
CC compat.c
CC complete.c
complete.c: In function ‘fnwidth’:
complete.c:604:12: warning: implicit declaration of function ‘wcwidth’; did
you mean ‘fnwidth’? [-Wimplicit-function-declaration]
604 | w = wcwidth (wc);
| ^~~~~~~
| fnwidth
complete.c: In function ‘_rl_find_completion_word’:
complete.c:886:14: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
886 | while (rl_point = MB_PREVCHAR (rl_line_buffer, rl_point,
MB_FIND_ANY))
| ^~~~~~~~
complete.c: In function ‘rl_completion_matches’:
complete.c:1805:10: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
1805 | while (string = (*entry_function) (text, matches))
| ^~~~~~
complete.c: In function ‘rl_username_completion_function’:
complete.c:1856:10: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
1856 | while (entry = getpwent ())
| ^~~~~
CC display.c
display.c: In function ‘rl_redisplay’:
display.c:714:15: warning: implicit declaration of function ‘wcwidth’
[-Wimplicit-function-declaration]
714 | temp = wcwidth (wc);
| ^~~~~~~
In file included from /usr/include/string.h:495,
from rldefs.h:59,
from display.c:45:
In function ‘strncpy’,
inlined from ‘rl_redisplay’ at display.c:558:7:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
‘__builtin_strncpy’ output truncated before terminating nul copying as many
bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
(__dest));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
display.c: In function ‘rl_redisplay’:
display.c:550:40: note: length computed here
550 | prompt_physical_chars = pmtlen = strlen (prompt_this_line);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
display.c:829:8: warning: ‘wc_width’ may be used uninitialized in this
function [-Wmaybe-uninitialized]
829 | for (i = 0; i < wc_width; i++)
| ^~~
display.c:462:38: warning: ‘n0’ may be used uninitialized in this function
[-Wmaybe-uninitialized]
462 | int newlines, lpos, temp, modmark, n0, num;
| ^~
CC funmap.c
CC histexpand.c
histexpand.c: In function ‘get_history_event’:
histexpand.c:206:25: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
206 | for (local_index = i; c = string[i]; i++)
| ^
histexpand.c: In function ‘history_expand_internal’:
histexpand.c:696:41: warning: variable ‘ws’ set but not used
[-Wunused-but-set-variable]
696 | int delimiter, failed, si, l_temp, ws, we;
| ^~
CC histfile.c
histfile.c: In function ‘history_truncate_file’:
histfile.c:401:7: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
401 | write (file, bp, chars_read - (bp - buffer));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CC history.c
CC histsearch.c
CC input.c
input.c: In function ‘rl_read_key’:
input.c:423:11: warning: suggest parentheses around assignment used as
truth value [-Wparentheses]
423 | if (c = _rl_next_macro_key ())
| ^
CC isearch.c
isearch.c: In function ‘rl_search_history’:
isearch.c:620:7: warning: variable ‘c’ set but not used
[-Wunused-but-set-variable]
620 | int c, r;
| ^
isearch.c: In function ‘_rl_isearch_callback’:
isearch.c:658:7: warning: variable ‘c’ set but not used
[-Wunused-but-set-variable]
658 | int c, r;
| ^
CC keymaps.c
CC kill.c
CC macro.c
CC mbutil.c
mbutil.c: In function ‘_rl_find_next_mbchar_internal’:
mbutil.c:118:12: warning: implicit declaration of function ‘wcwidth’
[-Wimplicit-function-declaration]
118 | if (wcwidth (wc) == 0)
| ^~~~~~~
CC misc.c
CC nls.c
CC parens.c
parens.c: In function ‘rl_insert_close’:
parens.c:118:36: warning: variable ‘ready’ set but not used
[-Wunused-but-set-variable]
118 | int orig_point, match_point, ready;
| ^~~~~
CC readline.c
readline.c: In function ‘readline_internal_char’:
readline.c:450:21: warning: variable ‘eof_found’ set but not used
[-Wunused-but-set-variable]
450 | static int lastc, eof_found;
| ^~~~~~~~~
At top level:
readline.c:1078:1: warning: ‘reset_default_bindings’ defined but not used
[-Wunused-function]
1078 | reset_default_bindings ()
| ^~~~~~~~~~~~~~~~~~~~~~
CC rltty.c
CC savestring.c
CC search.c
CC shell.c
CC signals.c
CC termcap.c
termcap.c: In function ‘memory_out’:
termcap.c:95:3: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
95 | write (2, "virtual memory exhausted\n", 25);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CC terminal.c
CC text.c
text.c: In function ‘_rl_overwrite_char’:
text.c:814:7: warning: variable ‘k’ set but not used
[-Wunused-but-set-variable]
814 | int k;
| ^
In file included from /usr/include/string.h:495,
from rldefs.h:59,
from text.c:45:
In function ‘strncpy’,
inlined from ‘rl_insert_text’ at text.c:94:3:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
‘__builtin_strncpy’ output truncated before terminating nul copying as many
bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
(__dest));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
text.c: In function ‘rl_insert_text’:
text.c:85:29: note: length computed here
85 | l = (string && *string) ? strlen (string) : 0;
| ^~~~~~~~~~~~~~~
CC tilde.c
tilde.c: In function ‘tilde_expand’:
tilde.c:199:7: warning: suggest parentheses around assignment used as truth
value [-Wparentheses]
199 | if (result = strchr (string, '~'))
| ^~~~~~
CC tparam.c
tparam.c: In function ‘memory_out’:
tparam.c:55:3: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
55 | write (2, "virtual memory exhausted\n", 25);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CC undo.c
undo.c: In function ‘_rl_copy_undo_list’:
undo.c:157:16: warning: ‘roving’ may be used uninitialized in this function
[-Wmaybe-uninitialized]
157 | roving->next = 0;
| ~~~~~~~~~~~~~^~~
CC util.c
CC version.c
version.c:2:14: warning: ‘version_string’ defined but not used
[-Wunused-variable]
2 | static char *version_string = "\n$Version: GNU termcap 1.3.1 $\n";
| ^~~~~~~~~~~~~~
CC vi_mode.c
CC xmalloc.c
/bin/rm -f libreadline.a
ar cqs libreadline.a bind.o callback.o compat.o complete.o display.o
funmap.o histexpand.o histfile.o history.o histsearch.o input.o isearch.o
keymaps.o kill.o macro.o mbutil.o misc.o nls.o parens.o readline.o rltty.o
savestring.o search.o shell.o signals.o termcap.o terminal.o text.o tilde.o
tparam.o undo.o util.o version.o vi_mode.o xmalloc.o
make[2]: Leaving directory
'/home/niperg/Downloads/cpptraj-master/src/readline'
cd Cluster && make all
make[2]: Entering directory
'/home/niperg/Downloads/cpptraj-master/src/Cluster'
CXX Algorithm.cpp
CXX Algorithm_DBscan.cpp
CXX Algorithm_DPeaks.cpp
CXX Algorithm_HierAgglo.cpp
CXX Algorithm_Kmeans.cpp
CXX BestReps.cpp
CXX Centroid_Coord.cpp
CXX CentroidArray.cpp
CXX Cframes.cpp
CXX Cmatrix_Binary.cpp
CXX Cmatrix_NC.cpp
CXX Control.cpp
CXX DrawGraph.cpp
CXX DynamicMatrix.cpp
CXX List.cpp
CXX MetricArray.cpp
CXX Metric_DME.cpp
CXX Metric_RMS.cpp
CXX Metric_Scalar.cpp
CXX Metric_SRMSD.cpp
CXX Metric_Torsion.cpp
CXX Node.cpp
CXX Output.cpp
CXX Results_Coords.cpp
CXX Sieve.cpp
/bin/rm -f libcpptraj_cluster.a
ar cqs libcpptraj_cluster.a Algorithm.o Algorithm_DBscan.o
Algorithm_DPeaks.o Algorithm_HierAgglo.o Algorithm_Kmeans.o BestReps.o
Centroid_Coord.o CentroidArray.o Cframes.o Cmatrix_Binary.o Cmatrix_NC.o
Control.o DrawGraph.o DynamicMatrix.o List.o MetricArray.o Metric_DME.o
Metric_RMS.o Metric_Scalar.o Metric_SRMSD.o Metric_Torsion.o Node.o
Output.o Results_Coords.o Sieve.o
make[2]: Leaving directory
'/home/niperg/Downloads/cpptraj-master/src/Cluster'
cd xdrfile && make all
make[2]: Entering directory
'/home/niperg/Downloads/cpptraj-master/src/xdrfile'
CC xdrfile.c
CC xdr_seek.c
CC xdrfile_trr.c
CC xdrfile_xtc.c
/bin/rm -f libxdrfile.a
ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o
make[2]: Leaving directory
'/home/niperg/Downloads/cpptraj-master/src/xdrfile'
cd arpack && make install
make[2]: Entering directory
'/home/niperg/Downloads/cpptraj-master/src/arpack'
FC ivout.f
FC dvout.f
FC dgetv0.f
dgetv0.f:120:26:
120 | & ( ido, bmat, itry, initv, n, j, v, ldv, resid, rnorm,
| 1
Warning: Unused dummy argument ‘itry’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dlaqrb.f
dlaqrb.f:497:0:
497 | & cs, sn )
|
Warning: ‘i2’ may be used uninitialized in this function
[-Wmaybe-uninitialized]
FC dnaitr.f
dnaitr.f:210:33:
210 | & (ido, bmat, n, k, np, nb, resid, rnorm, v, ldv, h, ldh,
| 1
Warning: Unused dummy argument ‘nb’ at (1) [-Wunused-dummy-argument]
FC dnapps.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dnaup2.f
dnaup2.f:316:5:
316 | 10 continue
| 1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
dnaup2.f:175:63:
175 | & ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
| 1
Warning: Unused dummy argument ‘iupd’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dnaupd.f
dnaupd.f:541:24:
541 | if (nb .le. 0) nb = 1
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
dnaupd.f:542:28:
542 | if (tol .le. zero) tol = dlamch('EpsMach')
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
dnaupd.f:447:32:
447 | & ldh, ldq, levec, mode, msglvl, mxiter, nb,
| 1
Warning: Unused variable ‘levec’ declared at (1) [-Wunused-variable]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dnconv.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dneigh.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dmout.f
FC dneupd.f
dneupd.f:587:17:
587 | jj = workl(bounds + ncv - j)
| 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4)
at (1) [-Wconversion]
stat.h:8:19:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dngets.f
dngets.f:96:40:
96 | & shiftr, shifti )
| 1
Warning: Unused dummy argument ‘shifti’ at (1) [-Wunused-dummy-argument]
dngets.f:96:32:
96 | & shiftr, shifti )
| 1
Warning: Unused dummy argument ‘shiftr’ at (1) [-Wunused-dummy-argument]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsaitr.f
FC dsapps.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsaup2.f
dsaup2.f:809:5:
809 | 130 continue
| 1
Warning: Label 130 at (1) defined but not used [-Wunused-label]
dsaup2.f:324:5:
324 | 10 continue
| 1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
dsaup2.f:180:63:
180 | & ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
| 1
Warning: Unused dummy argument ‘iupd’ at (1) [-Wunused-dummy-argument]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsaupd.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsconv.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dseigt.f
dseigt.f:124:18:
124 | integer i, k, msglvl
| 1
Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsesrt.f
FC dseupd.f
dseupd.f:499:17:
499 | jj = workl(bounds + ncv - j)
| 1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4)
at (1) [-Wconversion]
stat.h:8:19:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsgets.f
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dsortc.f
FC dsortr.f
FC dstatn.f
stat.h:8:19:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dstats.f
stat.h:8:19:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t0’ declared at (1) [-Wunused-variable]
stat.h:8:23:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t1’ declared at (1) [-Wunused-variable]
stat.h:8:27:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
stat.h:8:31:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t3’ declared at (1) [-Wunused-variable]
stat.h:8:35:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t4’ declared at (1) [-Wunused-variable]
stat.h:8:39:
8 | real t0, t1, t2, t3, t4, t5
| 1
Warning: Unused variable ‘t5’ declared at (1) [-Wunused-variable]
FC dstqrb.f
FC arsecond.f
arsecond.f:27:30:
27 | REAL ETIME
| 1
Warning: Unused variable ‘etime’ declared at (1) [-Wunused-variable]
/bin/rm -f libarpack.a
ar rv libarpack.a ivout.o dvout.o dgetv0.o dlaqrb.o dnaitr.o dnapps.o
dnaup2.o dnaupd.o dnconv.o dneigh.o dmout.o dneupd.o dngets.o dsaitr.o
dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o
dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o arsecond.o
ar: creating libarpack.a
a - ivout.o
a - dvout.o
a - dgetv0.o
a - dlaqrb.o
a - dnaitr.o
a - dnapps.o
a - dnaup2.o
a - dnaupd.o
a - dnconv.o
a - dneigh.o
a - dmout.o
a - dneupd.o
a - dngets.o
a - dsaitr.o
a - dsapps.o
a - dsaup2.o
a - dsaupd.o
a - dsconv.o
a - dseigt.o
a - dsesrt.o
a - dseupd.o
a - dsgets.o
a - dsortc.o
a - dsortr.o
a - dstatn.o
a - dstats.o
a - dstqrb.o
a - arsecond.o
ranlib libarpack.a
make[2]: Leaving directory
'/home/niperg/Downloads/cpptraj-master/src/arpack'
cd tng && make all
make[2]: Entering directory '/home/niperg/Downloads/cpptraj-master/src/tng'
CC md5.c
CC tng_io.c
In file included from /usr/include/string.h:495,
from tng/tng_io.h:310,
from tng_io.c:20:
In function ‘strncpy’,
inlined from ‘tng_gen_data_block_add’ at tng_io.c:12600:9,
inlined from ‘tng_data_block_add.constprop’ at tng_io.c:12788:12:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
‘__builtin_strncpy’ specified bound depends on the length of the source
argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
(__dest));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tng_io.c: In function ‘tng_data_block_add.constprop’:
tng_io.c:12600:47: note: length computed here
12600 | strncpy(data->block_name, block_name, strlen(block_name) +
1);
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from tng/tng_io.h:310,
from tng_io.c:20:
In function ‘strncpy’,
inlined from ‘tng_gen_data_block_add’ at tng_io.c:12600:9,
inlined from ‘tng_data_block_add’ at tng_io.c:12788:12:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
‘__builtin_strncpy’ specified bound depends on the length of the source
argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
(__dest));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tng_io.c: In function ‘tng_data_block_add’:
tng_io.c:12600:47: note: length computed here
12600 | strncpy(data->block_name, block_name, strlen(block_name) +
1);
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from tng/tng_io.h:310,
from tng_io.c:20:
In function ‘strncpy’,
inlined from ‘tng_gen_data_block_add’ at tng_io.c:12600:9,
inlined from ‘tng_particle_data_block_add’ at tng_io.c:12813:12:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning:
‘__builtin_strncpy’ specified bound depends on the length of the source
argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos
(__dest));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tng_io.c: In function ‘tng_particle_data_block_add’:
tng_io.c:12600:47: note: length computed here
12600 | strncpy(data->block_name, block_name, strlen(block_name) +
1);
| ^~~~~~~~~~~~~~~~~~
CC tng_compress.c
CC coder.c
CC warnmalloc.c
CC fixpoint.c
CC xtc3.c
CC bwlzh.c
CC xtc2.c
xtc2.c: In function ‘Ptngc_pack_array_xtc2’:
xtc2.c:680:47: warning: array subscript [54, 2147483646] is outside array
bounds of ‘int[54]’ [-Warray-bounds]
680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
| ~~~~~~~~~~~~~~^~~~~~~~~~~
xtc2.c:717:7: note: while referencing ‘has_large_ints’
717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
| ^~~~~~~~~~~~~~
xtc2.c:680:47: warning: array subscript [55, 2147483647] is outside array
bounds of ‘int[54]’ [-Warray-bounds]
680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
| ~~~~~~~~~~~~~~^~~~~~~~~~~
xtc2.c:717:7: note: while referencing ‘has_large_ints’
717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
| ^~~~~~~~~~~~~~
xtc2.c:680:47: warning: array subscript [56, 2147483647] is outside array
bounds of ‘int[54]’ [-Warray-bounds]
680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
| ~~~~~~~~~~~~~~^~~~~~~~~~~
xtc2.c:717:7: note: while referencing ‘has_large_ints’
717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
| ^~~~~~~~~~~~~~
xtc2.c:680:47: warning: array subscript [54, 2147483646] is outside array
bounds of ‘int[54]’ [-Warray-bounds]
680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
| ~~~~~~~~~~~~~~^~~~~~~~~~~
xtc2.c:717:7: note: while referencing ‘has_large_ints’
717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
| ^~~~~~~~~~~~~~
xtc2.c:680:47: warning: array subscript [55, 2147483647] is outside array
bounds of ‘int[54]’ [-Warray-bounds]
680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
| ~~~~~~~~~~~~~~^~~~~~~~~~~
xtc2.c:717:7: note: while referencing ‘has_large_ints’
717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
| ^~~~~~~~~~~~~~
xtc2.c:680:47: warning: array subscript [56, 2147483647] is outside array
bounds of ‘int[54]’ [-Warray-bounds]
680 | has_large_ints[i*3+j]=has_large_ints[(i+n)*3+j];
| ~~~~~~~~~~~~~~^~~~~~~~~~~
xtc2.c:717:7: note: while referencing ‘has_large_ints’
717 | int has_large_ints[54]; /* Large cache. Up to 18 large atoms. */
| ^~~~~~~~~~~~~~
CC widemuldiv.c
CC huffmem.c
CC vals16.c
CC bwt.c
CC mtf.c
CC rle.c
CC lz77.c
CC dict.c
CC huffman.c
CC merge_sort.c
/bin/rm -f libtng_io.a
ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o
fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o
mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o
make[2]: Leaving directory '/home/niperg/Downloads/cpptraj-master/src/tng'
g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o
ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o
Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o
Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o
Action_Center.o Action_Channel.o Action_CheckChirality.o
Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o
Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o
Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o
Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o
Action_DistRmsd.o Action_Energy.o Action_FilterByData.o
Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o
Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o
Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o
Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o
Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o
Action_MultiPucker.o Action_MultiVector.o Action_NAstruct.o
Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o
Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o
Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o
Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o
Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o
Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o
Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o
Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o
Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o
Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o
Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o
Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o
Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o
Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o
Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o
Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o
Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o
Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o
Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o
Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o
Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o
Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o
ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o
BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o
CharMask.o CharmmParamFile.o CIFfile.o ClusterMap.o Cmd.o CmdInput.o
CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o
ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o
CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o
DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o
DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o
DataIO_Cmatrix_Binary.o DataIO_Cmatrix_NC.o DataIO_Cpout.o DataIO_Evecs.o
DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o
DataIO_Mdout.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o
DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o
DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o
DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o
DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o
DataSet_PairwiseCache.o DataSet_PairwiseCache_MEM.o
DataSet_PairwiseCache_NC.o DataSet_Parameters.o DataSet_pH.o
DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o
DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o
DataSet_double.o DataSet_float.o DataSet_integer_disk.o
DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o
DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o
EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o
EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o
EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o
EwaldOptions.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o
Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o
Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o
Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o
Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o
Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o
Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o
Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o
Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o
Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o
Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o
Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o
Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o
File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o
FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o
ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o
ForLoop_overSets.o Frame.o GIST_PME.o GridAction.o GridBin.o HistBin.o
Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o
Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o
Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o
Mol2File.o NameType.o NC_Routines.o NetcdfFile.o OMM_helpers.o
OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o
ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o
Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o
PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o
PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o
PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o
Pucker_PuckerMask.o Pucker_PuckerSearch.o Pucker_PuckerToken.o
ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o
RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o
RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o
SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o
SymmetricRmsdCalc.o TextBlockBuffer.o TextFormat.o Timer.o TinkerFile.o
TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o
Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o
Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o
Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o
Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o
Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o
TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o
TrajoutList.o Vec3.o ViewRst.o vmdplugin/dtrplugin.o xoshiro128plusplus.o
Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o
molsurf.o Cluster/libcpptraj_cluster.a readline/libreadline.a
arpack/libarpack.a /home/niperg/Downloads/cpptraj-master/lib/liblapack.a
/home/niperg/Downloads/cpptraj-master/lib/libblas.a -lfftw3
/home/niperg/Downloads/amber20/lib/libsander.so -lgfortran
/home/niperg/Downloads/cpptraj-master/lib/libnetcdf.a -lbz2 tng/libtng_io.a
-lz xdrfile/libxdrfile.a
/usr/bin/ld: arpack/libarpack.a(dsaupd.o)(.text+0x135): unresolvable
R_X86_64_PC32 relocation against symbol `timing_'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:23: cpptraj] Error 1
make[1]: Leaving directory '/home/niperg/Downloads/cpptraj-master/src'
make: *** [Makefile:10: install] Error 2
(base) niperg.niperg-dell:~/Downloads/cpptraj-master$ uname -a
Linux niperg-dell 5.11.0-38-generic #42~20.04.1-Ubuntu SMP Tue Sep 28
20:41:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
(base) niperg.niperg-dell:~/Downloads/cpptraj-master$
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhavadixit.gmail.com
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
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Received on Mon Nov 08 2021 - 02:00:02 PST
