That was acutally cluster compilation, but I have used standarad:
/cofigure gnu
not sure if I have to use mpi, because it is supposed to be a single processor usage, not parallel:
Here is config.h:
# Amber configuration file, created with: ./configure gnu
###############################################################################
# (1) Location of the installation
BINDIR=/home/voronkov/amber11/bin
LIBDIR=/home/voronkov/amber11/lib
INCDIR=/home/voronkov/amber11/include
DATDIR=/home/voronkov/amber11/dat
###############################################################################
# (2) If you want 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= -L$(LIBDIR) -lsff -lpbsa -lrism -ldrfftw -ldfftw $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a $(LIBDIR)/libnetcdf.a -lgfortran
FLIBS_PTRAJ= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a -lgfortran
FLIBSF= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a
FLIBS_FFTW2=-L$(LIBDIR) -ldrfftw -ldfftw
###############################################################################
# (3) Modify any of the following if you need to change, e.g. to use gcc
# rather than cc, etc.
SHELL=/bin/sh
INSTALLTYPE=serial
# Set the C compiler, etc.
# For GNU: CC-->gcc; LEX-->flex; YACC-->bison -y -t;
# Note: If your lexer is "really" flex, you need to set
# LEX=flex below. For example, on many linux 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.
CC=gcc
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ $(CUSTOMBUILDFLAGS)
CNOOPTFLAGS=
COPTFLAGS=-O3 -DBINTRAJ -DHASGZ
AMBERCFLAGS= $(AMBERBUILDFLAGS)
CXX=g++
CPLUSPLUS=g++
CXXFLAGS= $(CUSTOMBUILDFLAGS)
CXXNOOPTFLAGS=
CXXOPTFLAGS=-O3
AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
NABFLAGS=
LDFLAGS= $(CUSTOMBUILDFLAGS)
AMBERLDFLAGS=$(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;
# this can generally be used (maybe not on 64-bit machines like altix).
CPP= $(BINDIR)/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=install
BLAS=install
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=gfortran
FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS)
FNOOPTFLAGS= -O0
FOPTFLAGS= -O3
AMBERFFLAGS=$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LM=-lm
FPP=cpp -traditional
FPPFLAGS=-P -DBINTRAJ $(CUSTOMBUILDFLAGS)
AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
BUILD_SLEAP=install_sleap
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
MAKE_XLEAP=install_xleap
NETCDF=netcdf.mod
NETCDFLIB=$(LIBDIR)/libnetcdf.a
PNETCDF=no
PNETCDFLIB=
ZLIB=-lz
BZLIB=
HASFC=yes
MDGX=yes
CPPTRAJ=yes
MTKPP=install_mtkpp
COMPILER=gnu
MKL=
MKL_PROCESSOR=
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
#PMEMD Specific build flags
PMEMD_FPP=cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
PMEMD_F90=gfortran
PMEMD_FOPTFLAGS=-O3
PMEMD_CC=gcc
PMEMD_COPTFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
PMEMD_FLIBSF=
PMEMD_LD= gfortran
LDOUT= -o
#3D-RISM MPI
RISMSFF=-DRISMSFF
SANDER_RISM_MPI=
TESTRISM=rism
#PUPIL
PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
#Python
PYINSTALL=
Sincerely yours,
Andrey
28.05.2011, 05:38, "David A. Case" <case.biomaps.rutgers.edu>:
> On Thu, May 26, 2011, Andrew Voronkov wrote:
>
>> šYes, there is error with make nabonly after make clean. Maybe I can
>> šinstall it without nab? I actually need mmpbsa.py only.
>>
>> š[voronkov.t60-2 src]$ x86_64-alt-linux-gcc: cgen.o: No such file or directory
>> š-bash: x86_64-alt-linux-gcc:: command not found
>
> At first I thought that the problem was the cgen.o was not found, but now I
> suspect the second line, "x86_64-alt-linux-gcc:: command not found" is the
> real error. šWhat commands did you give to configure? šWhat does the CC
> variable point to in config.h?
>
> ....dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun May 29 2011 - 08:30:02 PDT
