On Thu, Sep 22, 2011 at 8:28 PM, K T <tussey1.illinois.gmail.com> wrote:
> Hello,
>
> Add "-free" to FOPTFLAGS. :)
>
Amber's configure does this by default (almost every fortran source file is
free-format). I'm pretty sure that the error the OP is getting is because
they didn't run AT15_Amber11.py prior to building Amber 11, like Ross
suggested. The configure script and config.h files changed from Amber11 ->
AmberTools 1.5, so we had to write a utility to convert the AmberTools 1.5
config.h file into one that Amber11 understood (which is one of the jobs of
that script).
All the best,
Jason
> Ken
>
>
>
> On 09/22/2011 12:56 PM, matheus froeyen wrote:
> > Hi
> >
> > I try to install a parallel version of amber on a Redhat linux system,
> > using the latest intel compilers, openmpi 1.5.2 and mpich-2.1.4
> > but get errors all the time when trying a parallel compilation of
> Amber11.
> > mpif90 is taken from /usr/local/bin which i compiled first using the
> intel
> > compilers.
> >
> > I run out of ideas.
> > thanks for any help!
> >
> > mathy
> >
> >
> > # serial compilation works fine
> >
> >
> > uname -a
> > Linux kwak 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 12 17:58:20 EDT 2007 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> >
> > setenv AMBERHOME /usr/local/chem/amber/amber11
> > source /opt/intel/bin/compilervars.csh intel64
> > cd $AMBERHOME
> > patch -p0 -N< bugfix.at.all
> > ./apply_bugfix.x /usr/local/chem/amber/amber11/bugfix.1to17.tar.bz2
> >
> > # use local python
> > ./configure -nopython intel
> > make serial
> >
> > cd ../..
> > cd ../..
> > ./AT15_Amber11.py
> > cd src
> > make clean
> > make serial
> > # works fine
> >
> >
> > # parallel ???
> >
> > cd ../ambertools/src
> >
> > gunzip -c openmpi-1.5.2.tar.gz | tar xvf -
> > ./configure_openmpi intel
> > # no problems here
> >
> > gunzip -c mpich2-1.4.1p1.tar.gz | tar xvf -
> > cd mpich2-1.4.1p1
> > ./configure
> > make
> > su
> > -> make install
> > #installed in usr/local
> > # no visible errors
> >
> > rehash
> >
> > cd $AMBERHOME/ambertools/src
> > ./configure -nopython -mpi intel
> >
> > cd $AMBERHOME/src
> > make parallel
> >
> > ...
> > make[5]: Entering directory
> > `/usr/local/chem/amber/amber11/AmberTools/src/netcdf/src'
> > make[5]: Leaving directory
> > `/usr/local/chem/amber/amber11/AmberTools/src/netcdf/src'
> > make[4]: Leaving directory
> > `/usr/local/chem/amber/amber11/AmberTools/src/netcdf/src'
> > make[3]: Leaving directory
> > `/usr/local/chem/amber/amber11/AmberTools/src/netcdf/src'
> > make[2]: Leaving directory
> > `/usr/local/chem/amber/amber11/AmberTools/src/netcdf/src'
> > cp ../../include/*.mod .
> > cpp -traditional constants.f> _constants.f
> > mpif90 -c -ip -O3 -axSTPW -o constants.o _constants.f
> > ifort: command line remark #10279: option '-axS' is deprecated and will
> be
> > removed in a future release. See '-help deprecated'
> > ifort: command line remark #10279: option '-axT' is deprecated and will
> be
> > removed in a future release. See '-help deprecated'
> > ifort: command line remark #10279: option '-axP' is deprecated and will
> be
> > removed in a future release. See '-help deprecated'
> > ifort: command line remark #10279: option '-axW' is deprecated and will
> be
> > removed in a future release. See '-help deprecated'
> > constants.f(24): error #5149: Illegal character in statement label field
> > [m]
> > module constants
> > ^
> > constants.f(24): error #5149: Illegal character in statement label field
> > [o]
> > module constants
> > -^
> > constants.f(24): error #5149: Illegal character in statement label field
> > [d]
> > module constants
> > --^
> > constants.f(24): error #5149: Illegal character in statement label field
> > [u]
> > module constants
> > ---^
> > constants.f(24): error #5149: Illegal character in statement label field
> > [l]
> > module constants
> > ----^
> > constants.f(24): error #5118: First statement in file must not be
> continued
> > module constants
> > -----^
> > constants.f(158): error #5149: Illegal character in statement label field
> > [i]
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > ^
> > constants.f(158): error #5149: Illegal character in statement label field
> > [n]
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > -^
> > constants.f(158): error #5149: Illegal character in statement label field
> > [t]
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > --^
> > constants.f(158): error #5149: Illegal character in statement label field
> > [e]
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > ---^
> > constants.f(158): error #5149: Illegal character in statement label field
> > [g]
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > ----^
> > constants.f(159): error #5149: Illegal character in statement label field
> > [i]
> > integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
> > ^
> > constants.f(159): error #5149: Illegal character in statement label field
> > [n]
> > integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
> > -^
> > constants.f(159): error #5149: Illegal character in statement label field
> > [t]
> > integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
> > --^
> > constants.f(159): error #5149: Illegal character in statement label field
> > [e]
> > integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
> > ---^
> > constants.f(159): error #5149: Illegal character in statement label field
> > [g]
> > integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
> > ----^
> > constants.f(161): error #5149: Illegal character in statement label field
> > [e]
> > end module constants
> > ^
> > constants.f(161): error #5149: Illegal character in statement label field
> > [n]
> > end module constants
> > -^
> > constants.f(161): error #5149: Illegal character in statement label field
> > [d]
> > end module constants
> > --^
> > constants.f(161): error #5149: Illegal character in statement label field
> > [m]
> > end module constants
> > ----^
> > constants.f(158): error #5082: Syntax error, found ',' when expecting one
> > of: ( % [ : . = =>
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > -------^
> > constants.f(158): error #5082: Syntax error, found '=' when expecting one
> > of: ( * ) :: ,<END-OF-STATEMENT> ; . % (/ + - [ : ] /) . ** / // ...
> > integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
> > palindromic prime
> > -------------------------------------------^
> > constants.f(162): error #5082: Syntax error, found END-OF-FILE when
> > expecting one of:<LABEL> <END-OF-STATEMENT> ; BLOCK BLOCKDATA PROGRAM
> > MODULE TYPE BYTE CHARACTER ...
> >
> > ^
> > compilation aborted for _constants.f (code 1)
> > make[1]: *** [constants.o] Error 1
> > make[1]: Leaving directory `/usr/local/chem/amber/amber11/src/sander'
> > make: *** [parallel] Error 2
> >
> >
> >
> > config.h:
> >
> > # Amber configuration file, created with: ./configure -nopython -mpi
> intel
> >
> >
> ###############################################################################
> >
> > # (1) Location of the installation
> >
> > BINDIR=/usr/local/chem/amber/amber11/bin
> > LIBDIR=/usr/local/chem/amber/amber11/lib
> > INCDIR=/usr/local/chem/amber/amber11/include
> > DATDIR=/usr/local/chem/amber/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_mpi -lpbsa $(LIBDIR)/arpack.a
> $(LIBDIR)/lapack.a
> > $(LIBDIR)/b
> > las.a $(LIBDIR)/libnetcdf.a
> > -L/opt/intel/composer_xe_2011_sp1.6.233/lib/intel64/ -lifp
> > ort -lifcore -lsvml
> > FLIBS_PTRAJ= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a
> > -L/opt/intel/compo
> > ser_xe_2011_sp1.6.233/lib/intel64/ -lifport -lifcore -lsvml
> > FLIBSF= $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a -lsvml
> > FLIBS_FFTW2=-L$(LIBDIR)
> >
> ###############################################################################
> >
> > # (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
> >
> > # 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=mpicc
> > CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
> > $(CUSTOMBUILDFLAGS)
> > CNOOPTFLAGS=
> > COPTFLAGS=-ip -O3 -axSTPW -DBINTRAJ -DHASGZ -DHASBZ2
> > AMBERCFLAGS= $(AMBERBUILDFLAGS)
> >
> > CXX=icpc
> > CPLUSPLUS=icpc
> > CXXFLAGS= -DMPI $(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=mpif90
> > FFLAGS= $(LOCALFLAGS) $(CUSTOMBUILDFLAGS)
> > FNOOPTFLAGS= -O0
> > FOPTFLAGS= -ip -O3 -axSTPW
> > AMBERFFLAGS=$(AMBERBUILDFLAGS)
> > FREEFORMAT_FLAG= -FR
> > LM=-lm
> > FPP=cpp -traditional
> > FPPFLAGS=-P -DBINTRAJ -DMPI $(CUSTOMBUILDFLAGS)
> > AMBERFPPFLAGS=$(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=$(LIBDIR)/libnetcdf.a
> > PNETCDF=yes
> > PNETCDFLIB=$(LIBDIR)/libpnetcdf.a
> >
> > ZLIB=-lz
> > BZLIB=-lbz2
> >
> > HASFC=yes
> > MDGX=yes
> > CPPTRAJ=yes
> > MTKPP=
> >
> > COMPILER=intel
> > 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 -DMPI -P -DBINTRAJ -DDIRFRC_EFS
> > -DDIRFRC_COMTRANS -DDIRFRC_
> > NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
> > PMEMD_F90=mpif90
> > PMEMD_FOPTFLAGS=-ipo -O3 -no-prec-div -xP
> > PMEMD_CC=mpicc
> > PMEMD_COPTFLAGS=-ipo -O3 -no-prec-div -xP -D_FILE_OFFSET_BITS=64
> > -D_LARGEFILE_SOURCE -DB
> > INTRAJ -DMPI
> > PMEMD_FLIBSF=
> > PMEMD_LD= mpif90
> > LDOUT= -o
> >
> > #3D-RISM MPI
> > RISMSFF=
> > SANDER_RISM_MPI=sander.RISM.MPI$(SFX)
> > TESTRISM=
> >
> > #PUPIL
> > PUPILLIBS=-lrt -lm -lc -L${PUPIL_PATH}/lib -lPUPIL -lPUPILBlind
> >
> > #Python
> > PYINSTALL=
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 22 2011 - 18:00:02 PDT
