Hello again,
The compilation using intel and checking Dave and David suggestions:
The config.h file created using ./configure intel:
--------------
# Amber configuration file.
# Created at Mon Oct 14 19:26:11 CEST 2019 via ./configure intel
###############################################################################
# (1) Location of the installation
BASEDIR=/home/dlaage/SEBOMD/amber18
AMBER_PREFIX=/home/dlaage/SEBOMD/amber18
BINDIR=/home/dlaage/SEBOMD/amber18/bin
LIBDIR=/home/dlaage/SEBOMD/amber18/lib
INCDIR=/home/dlaage/SEBOMD/amber18/include
DATDIR=/home/dlaage/SEBOMD/amber18/dat
LOGDIR=/home/dlaage/SEBOMD/amber18/logs
AMBER_SOURCE=/home/dlaage/SEBOMD/amber18
###############################################################################
# (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 -lpbsa -lrism -lfftw3 -larpack -llapack -lblas -lnetcdf
-lifport
-lifcore -lsvml
FLIBS_PTRAJ= -larpack -llapack -lblas -lifport -lifcore -lsvml
FLIBSF= -larpack -llapack -lblas -lxblas-amb -lsvml
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=serial
BUILDAMBER=
# 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=icc
CFLAGS=-fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -D__PLUMED_HAS_DLOPEN $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CNOOPTFLAGS=-std=gnu99
COPTFLAGS=-ip -O3 -std=gnu99 -xHost
AMBERCFLAGS= $(AMBERBUILDFLAGS)
WARNFLAGS=-Wall
CXX=icpc
CPLUSPLUS=icpc
CXXFLAGS=-fPIC $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
CXXNOOPTFLAGS=
CXXOPTFLAGS=-fPIC -O3
AMBERCXXFLAGS= $(AMBERBUILDFLAGS)
NABFLAGS= $(AMBERBUILDFLAGS)
PBSAFLAG=$(AMBERBUILDFLAGS)
FP_FLAGS=-fp-model precise -fp-model source
LDFLAGS= -shared-intel $(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=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
WINE=
# Information about Fortran compilation:
FC=ifort
FFLAGS= -fPIC $(LOCALFLAGS) $(CUSTOMBUILDFLAGS) -I$(INCDIR) $(NETCDFINC)
$(AMBERBUILDFLAGS)
FNOOPTFLAGS= -O0
FOPTFLAGS= -ip -O3 -xHost
AMBERFFLAGS=$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -FR
LM=-lm
FPP=cpp -traditional -P
FPPFLAGS= -DBINTRAJ -DEMIL $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS)
AMBERFPPFLAGS=$(AMBERBUILDFLAGS)
FCREAL8=
NOFORTRANMAIN=-lifport -lifcore -lsvml
FWARNFLAGS=
XHOME= /usr
XLIBS=
MAKE_XLEAP=install_xleap
NETCDF=$(INCDIR)/netcdf.mod
NETCDFLIB=$(LIBDIR)/libnetcdf.a
NETCDFLIBF=$(LIBDIR)/libnetcdff.a $(LIBDIR)/libnetcdf.a
NETCDFINC=-I$(INCDIR)
PNETCDFLIB=
PNETCDFINC=
PNETCDFDEF=
FFTWLIB=-lfftw3
SANDERAPI_LIB=-L$(LIBDIR) -lsander
SANDERAPI_DEF=-DUSE_SANDERLIB
SANDERAPI_DEP=$(LIBDIR)/libsander$(SHARED_SUFFIX)
BUILD_SANDERAPI=build_sanderapi
EMIL=EMIL
EMILLIB=$(LIBDIR)/libemil.a -lstdc++
FEP_MODE=gti
ZLIB=-lz
BZLIB=-lbz2
HASFC=yes
XBLAS=$(LIBDIR)/libxblas-amb.a
FFTW3=$(LIBDIR)/libfftw3.a
MDGX=yes
COMPILER=intel
MKL=
MKL_PROCESSOR=
READLINE=readline/libreadline.a
#CUDA Specific build flags
NVCC=
PMEMD_CU_INCLUDES=
PMEMD_CU_LIBS=
PMEMD_CU_DEFINES=
PMEMD_CU_EXTRA=
PBSA_CU_LIBS=
#PMEMD Specific build flags
PMEMD_F90=ifort -DBINTRAJ -DEMIL -DPUBFFT
PMEMD_FOPTFLAGS=-ipo -O3 -no-prec-div -xHost $(AMBERBUILDFLAGS)
PMEMD_CC=icc
PMEMD_COPTFLAGS=-ipo -O3 -no-prec-div -xHost -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ $(AMBERBUILDFLAGS)
PMEMD_FLIBSF=-larpack -llapack -lblas -lxblas-amb -lsvml $(LIBDIR)/libemil.a
-lstdc++
PMEMD_LD=ifort $(AMBERBUILDFLAGS)
LDOUT= -o
PMEMD_GNU_BUG303=
PMEMD_INTEL_BUG360=
# build pmemd.gem?
PMEMD_GEM=no
#for SFF:
SFF_INTEL_BUG361=
#for NAB:
MPI=
#1D-RISM
RISM=yes
#3D-RISM NAB
RISMSFF=-DRISMSFF
SFF_RISM_INTERFACE=../rism/amber_rism_interface.NAB.o
TESTRISMSFF=testrism
#3D-RISM SANDER
RISMSANDER=-DRISMSANDER
SANDER_RISM_INTERFACE=../rism/amber_rism_interface.SANDER.o
FLIBS_RISMSANDER=-lrism
#for EMIL:
EMIL_MPIFLAGS=
#PUPIL
PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
#Python interpreter we are using and install options
PYTHON=/home/dlaage/SEBOMD/amber18/bin/amber.python
PYTHON_INSTALL=--prefix=$(AMBER_PREFIX)
SKIP_PYTHON=no
PYTHONPATH=$(AMBER_PREFIX)/lib/python/site-packages
PYSANDER=skip
PYTRAJ=no_pytraj
LIBCPPTRAJ=no_libcpptraj
MAKE_SAXS=install
#For LIO QM GPU Library
LIOLIBS=
# OS-specific rules for making shared objects
SHARED_SUFFIX=.so
MAKE_SHARED=-shared
# PLUMED related variables:
PLUMED_INCLUDE_FILE=
PLUMED_LOAD=Plumed.o -ldl -Wl,-export-dynamic
PLUMED_DEPENDENCIES=Plumed.o
# MEMEMBED for packmol_memgen
MEMEMBED=
------------
However, when I looked for the libfftw3.a I found that it's date is not the
current date, albeit, getting this message during the configuration step:
Configuring fftw-3.3 (may be time-consuming)...
fftw-3.3 configure succeeded.
And, of course, using nm lib/libfftw3.a | grep fftw_execute_dft_r2c
returns "File format not recognized" for all the elements.
Being the current situation, a configure that does not compile the
libfftw3.a and does not signal it. What should I do?
Thanking you in advance for your help.
Best,
Margarita
Science is built with facts as a house is with stones, but a collection of
facts is no more a science than a heap of stones is a house. - Henri
Poincaré
°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
Margarita I. Bernal-Uruchurtu
Centro de Investigaciones Química, UAEM
+52.777.329.7000 ext 6003
mabel.uaem.mx
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Received on Mon Oct 14 2019 - 11:00:02 PDT
