cd AmberTools/src && make install make[1]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src' Starting installation of AmberTools14 MPI at Sat Jan 14 10:05:39 EST 2017. (cd etc && make parallel) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/etc' mpif90 -DBINTRAJ -DEMIL -DMPI -o numprocs numprocs.F90 /bin/cp numprocs ../../test /bin/cp numprocs ../../../test make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/etc' (cd sff && make libsff_mpi ) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/sff' rm -f /ccs/home/adaa/AMBER/amber14/lib/libsff_mpi.a ar rv /ccs/home/adaa/AMBER/amber14/lib/libsff_mpi.a binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o atomic_number.o a - binpos.o a - conjgrad.o a - lmodC.o a - memutil.o a - nblist.o a - newton.o a - nmode.o a - prm.o a - rand2.o a - sasad.o a - sff.o a - time.o a - xminC.o a - AmberNetcdf.o a - atomic_number.o ranlib /ccs/home/adaa/AMBER/amber14/lib/libsff_mpi.a make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/sff' (cd pbsa && make libinstall ) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/pbsa' cd ../lib && make nxtsec.o random.o make[3]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/lib' make[3]: `nxtsec.o' is up to date. make[3]: `random.o' is up to date. make[3]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/lib' rm -f libpbsa.a ar rv libpbsa.a interface.o pbsaapi.LIBPBSA.o myopen.o pb_read.LIBPBSA.o pb_force.LIBPBSA.o pb_fddrv.o pb_iimdrv.o sa_driver.LIBPBSA.o pb_nlsolver.o pb_lsolver.o dsvdc.o timer.o pb_init.LIBPBSA.o pb_exmol.LIBPBSA.o np_force.LIBPBSA.o pb_direct.LIBPBSA.o pb_list.LIBPBSA.o pb_write.LIBPBSA.o pb_mpfrc.o decomp.o rgroup.o rfree.o coed20.o indexg.o irre32.o pbsa_lib.o phidev.o project.o qld.o coed6.o irre31.o miniop.o iimod.o prodis.o qint.o wint.o transf.o curv.o GrToPr.o jumps.o problem.LIBPBSA.o IIM.o regular.o pb_augdrv.o gmresX.o matvec3.o gmres.o bicg.o project.o transf.o dslubc.o dslugm.o curv.o irre31.o irre32.o interpX.o wint.o dchkw.o ds2y.o GrToPr.o dgmres.o dslui.o dsluti.o pb_fftsolv.LIBPBSA.o pb_fft.LIBPBSA.o dsmv.o dsmtv.o dsilus.o jumps.o dbcg.o qld.o phidev.o dpigmr.o dslui2.o dslui4.o isdbcg.o qs2i1d.o xermsg.o d1mach.o xercnt.o xerhlt.o drlcal.o j4save.o isdgmr.o fdump.o xerprn.o dorth.o dhels.o xersve.o dheqr.o i1mach.o xgetua.o dxlcal.o fftw3.LIBPBSA.o memory_module.o svdcmp.o svbksb.o pythag.o aug_iccg.o gen_dx_file.LIBPBSA.o membrane.LIBPBSA.o parms.LIBPBSA.o ../lib/random.o a - interface.o a - pbsaapi.LIBPBSA.o a - myopen.o a - pb_read.LIBPBSA.o a - pb_force.LIBPBSA.o a - pb_fddrv.o a - pb_iimdrv.o a - sa_driver.LIBPBSA.o a - pb_nlsolver.o a - pb_lsolver.o a - dsvdc.o a - timer.o a - pb_init.LIBPBSA.o a - pb_exmol.LIBPBSA.o a - np_force.LIBPBSA.o a - pb_direct.LIBPBSA.o a - pb_list.LIBPBSA.o a - pb_write.LIBPBSA.o a - pb_mpfrc.o a - decomp.o a - rgroup.o a - rfree.o a - coed20.o a - indexg.o a - irre32.o a - pbsa_lib.o a - phidev.o a - project.o a - qld.o a - coed6.o a - irre31.o a - miniop.o a - iimod.o a - prodis.o a - qint.o a - wint.o a - transf.o a - curv.o a - GrToPr.o a - jumps.o a - problem.LIBPBSA.o a - IIM.o a - regular.o a - pb_augdrv.o a - gmresX.o a - matvec3.o a - gmres.o a - bicg.o a - project.o a - transf.o a - dslubc.o a - dslugm.o a - curv.o a - irre31.o a - irre32.o a - interpX.o a - wint.o a - dchkw.o a - ds2y.o a - GrToPr.o a - dgmres.o a - dslui.o a - dsluti.o a - pb_fftsolv.LIBPBSA.o a - pb_fft.LIBPBSA.o a - dsmv.o a - dsmtv.o a - dsilus.o a - jumps.o a - dbcg.o a - qld.o a - phidev.o a - dpigmr.o a - dslui2.o a - dslui4.o a - isdbcg.o a - qs2i1d.o a - xermsg.o a - d1mach.o a - xercnt.o a - xerhlt.o a - drlcal.o a - j4save.o a - isdgmr.o a - fdump.o a - xerprn.o a - dorth.o a - dhels.o a - xersve.o a - dheqr.o a - i1mach.o a - xgetua.o a - dxlcal.o a - fftw3.LIBPBSA.o a - memory_module.o a - svdcmp.o a - svbksb.o a - pythag.o a - aug_iccg.o a - gen_dx_file.LIBPBSA.o a - membrane.LIBPBSA.o a - parms.LIBPBSA.o a - ../lib/random.o ranlib libpbsa.a /bin/mv libpbsa.a /ccs/home/adaa/AMBER/amber14/lib make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/pbsa' (cd cpptraj && make install_mpi ) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cpptraj' cd src && make -f Makefile_at install_mpi make[3]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cpptraj/src' mpicxx -o cpptraj ActionFrameCounter.o ActionList.o Action_Angle.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralScan.o Action_Dipole.o Action_DistRmsd.o Action_Distance.o Action_FilterByData.o Action_FixAtomOrder.o Action_Gist.o Action_Grid.o Action_GridFreeEnergy.o Action_Hbond.o Action_Image.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_Molsurf.o Action_MultiDihedral.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Rmsd.o Action_Rotate.o Action_Rotdif.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Translate.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Watershell.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_Divergence.o Analysis_FFT.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_RunningAvg.o Analysis_Spline.o Analysis_Statistics.o Analysis_Timecorr.o Analysis_VectorMath.o ArgList.o Array1D.o Atom.o AtomMap.o AtomMask.o AxisType.o Box.o BufferedFrame.o BufferedLine.o ByteRoutines.o CIFfile.o ClusterDist.o ClusterList.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_HierAgglo.o Command.o ComplexArray.o Corr.o Cpptraj.o CpptrajFile.o CpptrajState.o CpptrajStdio.o DataFile.o DataFileList.o DataIO.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Mdout.o DataIO_RemLog.o DataIO_Std.o DataIO_Xplor.o DataSet.o DataSetList.o DataSet_1D.o DataSet_2D.o DataSet_3D.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_TRJ.o DataSet_GridFlt.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_RemLog.o DataSet_Vector.o DataSet_double.o DataSet_float.o DataSet_integer.o DataSet_string.o DihedralSearch.o Dimension.o DistRoutines.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_Std.o FileName.o FileTypes.o Frame.o FrameList.o GridAction.o Hungarian.o ImageRoutines.o MapAtom.o MaskToken.o Matrix_3x3.o Mol2File.o NameType.o NetcdfFile.o PDBfile.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o ProgressBar.o PubFFT.o Random.o Range.o ReadLine.o ReferenceAction.o ReferenceFrame.o SDFfile.o StringRoutines.o SymmetricRmsdCalc.o Timer.o Topology.o TopologyList.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmDcd.o Traj_CIF.o Traj_Conflib.o Traj_GmxTrX.o Traj_Mol2File.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o TrajectoryFile.o Trajin.o TrajinList.o Trajin_Multi.o Trajin_Single.o Trajout.o TrajoutList.o Vec3.o main.o MpiRoutines.o molsurf.o pub_fft.o \ -L/ccs/home/adaa/AMBER/amber14/lib /ccs/home/adaa/AMBER/amber14/lib/libnetcdf.a -lz -lbz2 -larpack -llapack -lblas -lgfortran -w readline/libreadline.a mv cpptraj /ccs/home/adaa/AMBER/amber14/bin/cpptraj.MPI make[3]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cpptraj/src' make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cpptraj' (cd byacc && make install ) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/byacc' make[2]: Nothing to be done for `install'. make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/byacc' (cd ucpp-1.3 && make install ) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/ucpp-1.3' mpicc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o mv ucpp /ccs/home/adaa/AMBER/amber14/bin make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/ucpp-1.3' (cd cifparse && make install ) make[2]: Entering directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cifparse' /ccs/home/adaa/AMBER/amber14/bin/yacc -v -d cifparse.y make[2]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src/cifparse' make[1]: Leaving directory `/autofs/nccs-svm1_home2/adaa/AMBER/amber14/AmberTools/src'