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 - 11:00:02 PDT
