Hello,
Add "-free" to FOPTFLAGS. :)
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=
> _______________________________________________
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Received on Thu Sep 22 2011 - 17:30:02 PDT
