Re: [AMBER] Problems with amber14 intallation in parallel

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 1 Dec 2014 20:54:21 -0700

Hi,

Your problem is here:

On Mon, Dec 1, 2014 at 6:39 PM, Dailin Li <lidl.xmut.edu.cn> wrote:
> 8. Mpich2 has been installed in root account. We have made sure that mpirun and mpiexec packages come from the same place as mpif90 and mpicc. “mpif90 –show” and “mpicc -show” commands are shown as follows:
>
> [root.HPC ~]# mpif90 -show
> ifort -I/opt/mpich2.12/include -I/opt/mpich2.12/include -L/opt/mpich2.12/lib -L/opt/mpich2.12/lib -lmpichf90 -lmpichf90 -lmpich -lopa -lpthread -lrt
> [root.HPC ~]# mpicc -show
> gcc -I/opt/mpich2.12/include -L/opt/mpich2.12/lib -L/opt/mpich2.12/lib -lmpich -lopa -lpthread –lrt

You are configuring with 'gnu' but your MPI installation returns
'ifort' for mpif90 and 'gcc' for mpicc. You need to make sure that if
you are configuring 'gnu' that all of your MPI compilers are
gnu-based, which seems to not be the case.

-Dan

>
>
>
>
>
> 9. [lidl.HPC ~]$ cd $AMBERHOME
>
>
> [lidl.HPC amber14]$ ./configure -mpi gnu
>
>
> 10. [lidl.HPC amber14]$ vi config.h
>
>
> # Amber configuration file, created with: ./configure -mpi gnu
>
>
>
>
>
> ###############################################################################
>
>
>
>
>
> # (1) Location of the installation
>
>
>
>
>
> BASEDIR=/home/lidl/opt/amber14
>
>
> BINDIR=/home/lidl/opt/amber14/bin
>
>
> LIBDIR=/home/lidl/opt/amber14/lib
>
>
> INCDIR=/home/lidl/opt/amber14/include
>
>
> DATDIR=/home/lidl/opt/amber14/dat
>
>
> LOGDIR=/home/lidl/opt/amber14/logs
>
>
>
>
>
> ###############################################################################
>
>
>
>
>
>
>
>
> # (2) If you want NAB to search additional libraries by default, add them
>
>
> # to the FLIBS variable here. (External libraries can also be linked into
>
>
> # NAB programs simply by including them on the command line; libraries
>
>
> # included in FLIBS are always searched.)
>
>
>
>
>
> FLIBS= -lsff_mpi -lpbsa -lfftw3 -larpack -lnetcdf -Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -ldl -lgfortran -w
>
>
> FLIBS_PTRAJ= -larpack -Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -ldl -lgfortran -w
>
>
> FLIBSF= -larpack -Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -ldl
>
>
>
>
>
> FLIBS_FFTW3= -lfftw3
>
>
> ###############################################################################
>
>
>
>
>
> # (3) Modify any of the following if you need to change, e.g. to use gcc
>
>
> # rather than cc, etc.
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>
>
>
>
> SHELL=/bin/sh
>
>
> INSTALLTYPE=parallel
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>
> BUILDAMBER=amber
>
>
>
>
>
> # Set the C compiler, etc.
>
>
>
>
>
> # The configure script should be fine, but if you need to hand-edit,
>
>
> # here is some info:
>
>
>
>
>
> # Example: CC-->gcc; LEX-->flex; YACC-->yacc (built in byacc)
>
>
> # Note: If your lexer is "really" flex, you need to set
>
>
> # LEX=flex below. For example, on some distributions,
>
>
> # /usr/bin/lex is really just a pointer to /usr/bin/flex,
>
>
> # so LEX=flex is necessary. In general, gcc seems to need flex.
>
>
>
>
>
> # The compiler flags CFLAGS and CXXFLAGS should always be used.
>
>
> # By contrast, *OPTFLAGS and *NOOPTFLAGS will only be used with
>
>
> # certain files, and usually at compile-time but not link-time.
>
>
> # Where *OPTFLAGS and *NOOPTFLAGS are requested (in Makefiles,
>
>
> # makedepend and depend), they should come before CFLAGS or
>
>
> # CXXFLAGS; this allows the user to override *OPTFLAGS and
>
>
> # *NOOPTFLAGS using the BUILDFLAGS variable.
>
>
>
>
>
> # AMBERBUILDFLAGS provides a hook into all stages of the build process.
>
>
> # It can be used to build debug versions, invoke special features, etc.
>
>
> # Example: make AMBERBUILDFLAGS='-O0 -g' sander
>
>
> #
>
>
> CC=mpicc
>
>
> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI $(CUSTOMBUILDFLAGS) -I/opt/intel/mkl/include $(AMBERBUILDFLAGS)
>
>
> CNOOPTFLAGS=
>
>
> COPTFLAGS=-O3 -mtune=native
>
>
> AMBERCFLAGS= $(AMBERBUILDFLAGS)
>
>
>
>
>
> CXX=mpicxx
>
>
> CPLUSPLUS=mpicxx
>
>
> CXXFLAGS= -DMPI $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
>
>
> CXXNOOPTFLAGS=
>
>
> CXXOPTFLAGS=-O3
>
>
> AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
>
>
>
>
>
> NABFLAGS= $(AMBERBUILDFLAGS)
>
>
> PBSAFLAG= $(AMBERBUILDFLAGS)
>
>
>
>
>
> LDFLAGS= $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
>
>
> AMBERLDFLAGS=$(AMBERBUILDFLAGS)
>
>
>
>
>
> LEX= flex
>
>
> YACC= $(BINDIR)/yacc
>
>
> AR= ar rv
>
>
> M4= m4
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>
> RANLIB=ranlib
>
>
>
>
>
> # Set the C-preprocessor. Code for a small preprocessor is in
>
>
> # ucpp-1.3; it gets installed as $(BINDIR)/ucpp;
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>
>
>
>
> CPP=ucpp -l
>
>
>
>
>
> # These variables control whether we will use compiled versions of BLAS
>
>
> # and LAPACK (which are generally slower), or whether those libraries are
>
>
> # already available (presumably in an optimized form).
>
>
>
>
>
> LAPACK=skip
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>
> BLAS=skip
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>
> F2C=skip
>
>
>
>
>
> # These variables determine whether builtin versions of certain components
>
>
> # can be used, or whether we need to compile our own versions.
>
>
>
>
>
> UCPP=install
>
>
> C9XCOMPLEX=skip
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>
>
>
>
> # For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
>
>
> # Set OBJSFX to ".obj" instead of ".o" on Windows:
>
>
>
>
>
> SFX=
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>
> OSFX=.o
>
>
> MV=mv
>
>
> RM=rm
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>
> CP=cp
>
>
>
>
>
> # Information about Fortran compilation:
>
>
>
>
>
> FC=mpif90
>
>
> FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC) -I/opt/intel/mkl/include $(AMBERBUILDFLAGS)
>
>
> FNOOPTFLAGS= -O0
>
>
> FOPTFLAGS= -O3 -mtune=native
>
>
> AMBERFFLAGS=$(AMBERBUILDFLAGS)
>
>
> FREEFORMAT_FLAG= -ffree-form
>
>
> LM=-lm
>
>
> FPP=cpp -traditional -P
>
>
> FPPFLAGS= -DMKL -DBINTRAJ -DEMIL -DMPI $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
>
>
> AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
>
>
> FCREAL8=-fdefault-real-8
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>
> NOFORTRANMAIN=-lgfortran -w
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>
>
>
>
> XHOME= /usr
>
>
> XLIBS= -L/usr/lib64 -L/usr/lib
>
>
> MAKE_XLEAP=install_xleap
>
>
> NETCDF=$(INCDIR)/netcdf.mod
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>
> NETCDFLIB=$(LIBDIR)/libnetcdf.a
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>
> NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a
>
>
> NETCDFINC=-I$(INCDIR)
>
>
> FFTWLIB=-lfftw3
>
>
>
>
>
> EMIL=EMIL
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>
> EMILLIB=$(LIBDIR)/libemil.a -lstdc++
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>
>
>
>
> ZLIB=-lz
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> BZLIB=-lbz2
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>
>
>
>
> HASFC=yes
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>
> MTKPP=
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>
> XBLAS=
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>
> FFTW3=$(LIBDIR)/libfftw3.a
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>
> MDGX=parallel
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>
>
>
>
> COMPILER=gnu
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>
> MKL=/opt/intel/mkl
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>
> MKL_PROCESSOR=intel64
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>
>
>
>
> #CUDA Specific build flags
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>
> NVCC=
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>
> PMEMD_CU_INCLUDES=
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>
> PMEMD_CU_LIBS=
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>
> PMEMD_CU_DEFINES=
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>
>
>
>
> #PMEMD Specific build flags
>
>
> PMEMD_F90=mpif90 -DMPI -DMKL -DBINTRAJ -DEMIL -DPUBFFT
>
>
> PMEMD_FOPTFLAGS=-O3 -mtune=native $(AMBERBUILDFLAGS)
>
>
> PMEMD_CC=mpicc
>
>
> PMEMD_COPTFLAGS=-O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI $(AMBERBUILDFLAGS)
>
>
> PMEMD_FLIBSF=-Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -ldl $(LIBDIR)/libemil.a -lstdc++
>
>
> PMEMD_LD= mpif90 $(AMBERBUILDFLAGS)
>
>
> LDOUT= -o
>
>
>
>
>
> #for NAB:
>
>
> MPI=mpi
>
>
>
>
>
> #1D-RISM
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>
> RISM=no
>
>
>
>
>
> #3D-RISM NAB
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>
> RISMSFF=
>
>
> SFF_RISM_INTERFACE=
>
>
> TESTRISMSFF=
>
>
>
>
>
> #3D-RISM SANDER
>
>
> RISMSANDER=
>
>
> SANDER_RISM_INTERFACE=
>
>
> FLIBS_RISMSANDER=
>
>
> TESTRISMSANDER=
>
>
>
>
>
> #for EMIL:
>
>
> EMIL_MPIFLAGS=-DUSE_MPI
>
>
>
>
>
> #PUPIL
>
>
> PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
>
>
>
>
>
> #Python interpreter we are using
>
>
> PYTHON=/usr/bin/python2.4
>
>
>
>
>
> #Type of Amber_Phenix build and python include file
>
>
> AMBERPHENIX=no
>
>
> INCLUDE_PY=
>
>
> PYTHON_VER=
>
>
>
>
>
> #For LIO QM GPU Library
>
>
> LIOLIBS=
>
>
>
>
>
>
>
> 11. [lidl.HPC amber14]$ source amber.sh
>
> 12. [lidl.HPC amber14]$ make install #(Error occurred in this step. Part of output information was in the below)
>
>
>
>
> lude -I/home/lidl/opt/amber14/include -o Analysis_Modes.o Analysis_Modes.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_MultiHist.o Analysis_MultiHist.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_Overlap.o Analysis_Overlap.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_Regression.o Analysis_Regression.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_RemLog.o Analysis_RemLog.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_Rms2d.o Analysis_Rms2d.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_RmsAvgCorr.o Analysis_RmsAvgCorr.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_RunningAvg.o Analysis_RunningAvg.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_Spline.o Analysis_Spline.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_Statistics.o Analysis_Statistics.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_Timecorr.o Analysis_Timecorr.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Analysis_VectorMath.o Analysis_VectorMath.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ArgList.o ArgList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Array1D.o Array1D.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Atom.o Atom.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o AtomMap.o AtomMap.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o AtomMask.o AtomMask.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o AxisType.o AxisType.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Box.o Box.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o BufferedFrame.o BufferedFrame.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o BufferedLine.o BufferedLine.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ByteRoutines.o ByteRoutines.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o CIFfile.o CIFfile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ClusterDist.o ClusterDist.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ClusterList.o ClusterList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ClusterMatrix.o ClusterMatrix.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ClusterNode.o ClusterNode.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ClusterSieve.o ClusterSieve.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Cluster_DBSCAN.o Cluster_DBSCAN.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Cluster_HierAgglo.o Cluster_HierAgglo.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Command.o Command.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ComplexArray.o ComplexArray.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Corr.o Corr.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Cpptraj.o Cpptraj.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o CpptrajFile.o CpptrajFile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o CpptrajState.o CpptrajState.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o CpptrajStdio.o CpptrajStdio.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataFile.o DataFile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataFileList.o DataFileList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO.o DataIO.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_Evecs.o DataIO_Evecs.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_Gnuplot.o DataIO_Gnuplot.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_Grace.o DataIO_Grace.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_OpenDx.o DataIO_OpenDx.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_Mdout.o DataIO_Mdout.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_RemLog.o DataIO_RemLog.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_Std.o DataIO_Std.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataIO_Xplor.o DataIO_Xplor.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet.o DataSet.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSetList.o DataSetList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_1D.o DataSet_1D.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_2D.o DataSet_2D.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_3D.o DataSet_3D.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_Coords.o DataSet_Coords.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_Coords_CRD.o DataSet_Coords_CRD.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_Coords_TRJ.o DataSet_Coords_TRJ.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_GridFlt.o DataSet_GridFlt.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_MatrixDbl.o DataSet_MatrixDbl.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_MatrixFlt.o DataSet_MatrixFlt.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_Mesh.o DataSet_Mesh.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_Modes.o DataSet_Modes.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_RemLog.o DataSet_RemLog.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_Vector.o DataSet_Vector.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_double.o DataSet_double.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_float.o DataSet_float.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_integer.o DataSet_integer.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DataSet_string.o DataSet_string.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DihedralSearch.o DihedralSearch.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Dimension.o Dimension.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o DistRoutines.o DistRoutines.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FileIO_Bzip2.o FileIO_Bzip2.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FileIO_Gzip.o FileIO_Gzip.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FileIO_Mpi.o FileIO_Mpi.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FileIO_Std.o FileIO_Std.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FileName.o FileName.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FileTypes.o FileTypes.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Frame.o Frame.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o FrameList.o FrameList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o GridAction.o GridAction.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Hungarian.o Hungarian.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ImageRoutines.o ImageRoutines.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o MapAtom.o MapAtom.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o MaskToken.o MaskToken.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Matrix_3x3.o Matrix_3x3.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Mol2File.o Mol2File.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o NameType.o NameType.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o NetcdfFile.o NetcdfFile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o PDBfile.o PDBfile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ParmFile.o ParmFile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Parm_Amber.o Parm_Amber.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Parm_CharmmPsf.o Parm_CharmmPsf.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Parm_CIF.o Parm_CIF.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Parm_Mol2.o Parm_Mol2.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Parm_PDB.o Parm_PDB.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Parm_SDF.o Parm_SDF.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ProgressBar.o ProgressBar.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o PubFFT.o PubFFT.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Random.o Random.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Range.o Range.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -Ireadline -o ReadLine.o ReadLine.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ReferenceAction.o ReferenceAction.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o ReferenceFrame.o ReferenceFrame.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o SDFfile.o SDFfile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o StringRoutines.o StringRoutines.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o SymmetricRmsdCalc.o SymmetricRmsdCalc.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Timer.o Timer.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Topology.o Topology.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o TopologyList.o TopologyList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o TorsionRoutines.o TorsionRoutines.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_AmberCoord.o Traj_AmberCoord.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_AmberNetcdf.o Traj_AmberNetcdf.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_AmberRestart.o Traj_AmberRestart.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_AmberRestartNC.o Traj_AmberRestartNC.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_Binpos.o Traj_Binpos.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_CharmmDcd.o Traj_CharmmDcd.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_CIF.o Traj_CIF.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_Conflib.o Traj_Conflib.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_GmxTrX.o Traj_GmxTrX.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_Mol2File.o Traj_Mol2File.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_PDBfile.o Traj_PDBfile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_SDF.o Traj_SDF.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Traj_SQM.o Traj_SQM.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o TrajectoryFile.o TrajectoryFile.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Trajin.o Trajin.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o TrajinList.o TrajinList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Trajin_Multi.o Trajin_Multi.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Trajin_Single.o Trajin_Single.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Trajout.o Trajout.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o TrajoutList.o TrajoutList.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o Vec3.o Vec3.cpp
> mpicxx -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o main.o main.cpp
> mpicc -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o MpiRoutines.o MpiRoutines.c
> mpicc -c -I/home/lidl/opt/amber14/include -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -DMPI -I/opt/intel/mkl/include -I/home/lidl/opt/amber14/include -o molsurf.o molsurf.c
> mpif90 -DMKL -DBINTRAJ -DEMIL -DMPI -c -ffree-form -O3 -mtune=native -I/home/lidl/opt/amber14/include -I/home/lidl/opt/amber14/include -I/opt/intel/mkl/include -o pub_fft.o pub_fft.F90
> ifort: command line warning #10006: ignoring unknown option '-ffree-form'
> ifort: command line warning #10159: invalid argument for option '-m'
> cd ../../lapack && make skip
> make[4]: Entering directory `/home/lidl/opt/amber14/AmberTools/src/lapack'
> skipping compilation of LAPACK
> make[4]: Leaving directory `/home/lidl/opt/amber14/AmberTools/src/lapack'
> cd ../../blas && make skip
> make[4]: Entering directory `/home/lidl/opt/amber14/AmberTools/src/blas'
> skipping compilation of BLAS
> make[4]: Leaving directory `/home/lidl/opt/amber14/AmberTools/src/blas'
> 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/home/lidl/opt/amber14/lib /home/lidl/opt/amber14/lib/libnetcdf.a -lz -lbz2 -larpack -Wl,--start-group /opt/intel/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/mkl/lib/intel64/libmkl_sequential.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -ldl -lgfortran -w readline/libreadline.a
> pub_fft.o: In function `cffti_':
> pub_fft.F90:(.text+0x217): undefined reference to `__libm_sse2_sincos'
> pub_fft.o: In function `cffti1_':
> pub_fft.F90:(.text+0x597): undefined reference to `__libm_sse2_sincos'
> pub_fft.o: In function `cfftb_':
> pub_fft.F90:(.text+0x8ff): undefined reference to `_intel_fast_memcpy'
> pub_fft.o: In function `cfftb1_':
> pub_fft.F90:(.text+0x12c7): undefined reference to `_intel_fast_memcpy'
> pub_fft.o: In function `cfftb1_IP_passb_':
> pub_fft.F90:(.text+0x20b3): undefined reference to `_intel_fast_memcpy'
> pub_fft.F90:(.text+0x2dc1): undefined reference to `_intel_fast_memcpy'
> pub_fft.F90:(.text+0x3c2b): undefined reference to `_intel_fast_memcpy'
> pub_fft.o:pub_fft.F90:(.text+0x5a7f): more undefined references to `_intel_fast_memcpy' follow
> collect2: error: ld returned 1 exit status
> make[3]: *** [cpptraj] Error 1
> make[3]: Leaving directory `/home/lidl/opt/amber14/AmberTools/src/cpptraj/src'
> make[2]: *** [install_mpi] Error 2
> make[2]: Leaving directory `/home/lidl/opt/amber14/AmberTools/src/cpptraj'
> make[1]: *** [parallel] Error 2
> make[1]: Leaving directory `/home/lidl/opt/amber14/AmberTools/src'
> make: *** [install] Error 2
>
>
>
> I am looking forward to your kind reply. Thank you very much for your help and support.
> Regards,
> Dailin
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Dec 01 2014 - 20:00:02 PST