Dear Sir,
We have bought Amber14 recently and met problems with installation in parallel on CentOS 5.4 with gcc-4.9.1. According to Amber14 reference manual, we have implemented the following steps and error occurred in step 12:
1. [lidl.HPC ~]$ cd /home/lidl/opt
2. [lidl.HPC opt]$ tar xvfj AmberTools14.tar.bz2
[lidl.HPC opt]$ tar xvfj Amber14.tar.bz2
3. [lidl.HPC opt]$ export AMBERHOME=/home/lidl/opt/amber14 # (bash was used.)
4. [lidl.HPC opt]$ cd $AMBERHOME
[lidl.HPC amber14]$ ./configure gnu
5. [lidl.HPC amber14]$ source /home/lidl/opt/amber14/amber.sh
6. [lidl.HPC amber14]$ make install
7. [lidl.HPC amber14]$ make test #(2014-12-01_11-07-58.diff and 2014-12-01_11-07-58.log saved in test_amber_serial directory and 2014-12-01_09-39-20.log and at_summary saved in test_at_serial directory were uploaded seperately as email attachments.)
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 ¨Cshow¡± 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 ¨Clrt
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.
SHELL=/bin/sh
INSTALLTYPE=parallel
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
RANLIB=ranlib
# Set the C-preprocessor. Code for a small preprocessor is in
# ucpp-1.3; it gets installed as $(BINDIR)/ucpp;
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
BLAS=skip
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
# For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
# Set OBJSFX to ".obj" instead of ".o" on Windows:
SFX=
OSFX=.o
MV=mv
RM=rm
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
NOFORTRANMAIN=-lgfortran -w
XHOME= /usr
XLIBS= -L/usr/lib64 -L/usr/lib
MAKE_XLEAP=install_xleap
NETCDF=$(INCDIR)/netcdf.mod
NETCDFLIB=$(LIBDIR)/libnetcdf.a
NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a
NETCDFINC=-I$(INCDIR)
FFTWLIB=-lfftw3
EMIL=EMIL
EMILLIB=$(LIBDIR)/libemil.a -lstdc++
ZLIB=-lz
BZLIB=-lbz2
HASFC=yes
MTKPP=
XBLAS=
FFTW3=$(LIBDIR)/libfftw3.a
MDGX=parallel
COMPILER=gnu
MKL=/opt/intel/mkl
MKL_PROCESSOR=intel64
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
#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 $(AMBERBUILDFLAGS)
LDOUT= -o
#for NAB:
MPI=mpi
#1D-RISM
RISM=no
#3D-RISM NAB
RISMSFF=
SFF_RISM_INTERFACE=
TESTRISMSFF=
#3D-RISM SANDER
RISMSANDER=
SANDER_RISM_INTERFACE=
FLIBS_RISMSANDER=
TESTRISMSANDER=
#for EMIL:
EMIL_MPIFLAGS=-DUSE_MPI
#PUPIL
PUPILLIBS=-lrt -lm -lc -L${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
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Received on Mon Dec 01 2014 - 18:00:02 PST
