[gmx-users] problem in compiling GMX with MPI
Jinan Niu
njn0516 at 163.com
Wed Sep 21 11:59:35 CEST 2011
Hi, everyone:
when I compiled GMX4.5.5, I encountered a problem and failed many times， SOS!
Below is my config.log:
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/grace/bin
PATH: /usr/lib64/openmpi/bin
PATH: /home/njn/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:3028: checking build system type
configure:3042: result: x86_64-unknown-linux-gnu
configure:3062: checking host system type
configure:3075: result: x86_64-unknown-linux-gnu
configure:3112: checking for a BSD-compatible install
configure:3180: result: /usr/bin/install -c
configure:3191: checking whether build environment is sane
configure:3241: result: yes
configure:3382: checking for a thread-safe mkdir -p
configure:3421: result: /bin/mkdir -p
configure:3434: checking for gawk
configure:3450: found /usr/bin/gawk
configure:3461: result: gawk
configure:3472: checking whether make sets $(MAKE)
configure:3494: result: yes
configure:3569: checking how to create a ustar tar archive
configure:3582: tar --version
tar (GNU tar) 1.23
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by John Gilmore and Jay Fenlason.
configure:3585: $? = 0
configure:3625: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar
configure:3628: $? = 0
configure:3632: tar -xf - <conftest.tar
configure:3635: $? = 0
configure:3648: result: gnutar
configure:4308: checking for cc
configure:4324: found /usr/bin/cc
configure:4335: result: cc
configure:4366: checking for C compiler version
configure:4375: cc --version >&5
cc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:4386: $? = 0
configure:4375: cc -v >&5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC)
configure:4386: $? = 0
configure:4375: cc -V >&5
cc: '-V' option must have argument
configure:4386: $? = 1
configure:4375: cc -qversion >&5
cc: unrecognized option '-qversion'
cc: no input files
configure:4386: $? = 1
configure:4408: checking for C compiler default output file name
configure:4430: cc conftest.c >&5
configure:4434: $? = 0
configure:4471: result: a.out
configure:4487: checking whether the C compiler works
configure:4496: ./a.out
configure:4500: $? = 0
configure:4515: result: yes
configure:4522: checking whether we are cross compiling
configure:4524: result: no
configure:4527: checking for suffix of executables
configure:4534: cc -o conftest conftest.c >&5
configure:4538: $? = 0
configure:4560: result:
configure:4566: checking for suffix of object files
configure:4588: cc -c conftest.c >&5
configure:4592: $? = 0
configure:4613: result: o
configure:4617: checking whether we are using the GNU C compiler
configure:4636: cc -c conftest.c >&5
configure:4636: $? = 0
configure:4645: result: yes
configure:4654: checking whether cc accepts -g
configure:4674: cc -c -g conftest.c >&5
configure:4674: $? = 0
configure:4715: result: yes
configure:4732: checking for cc option to accept ISO C89
configure:4796: cc -c -g -O2 conftest.c >&5
configure:4796: $? = 0
configure:4809: result: none needed
configure:4840: checking for style of include used by make
configure:4868: result: GNU
configure:4893: checking dependency style of cc
configure:5003: result: gcc3
configure:5262: checking dependency style of cc
configure:5370: result: gcc3
configure:6229: checking how to run the C preprocessor
configure:6260: cc -E conftest.c
configure:6260: $? = 0
configure:6274: cc -E conftest.c
conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
configure:6274: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.5"
| #define PACKAGE_STRING "gromacs 4.5.5"
| #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.5"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Wed Sep 21 12:48:07 CST 2011"
| #define BUILD_USER "njn at njn-SL"
| #define BUILD_MACHINE "Linux 2.6.32-131.0.15.el6.x86_64 x86_64"
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include <ac_nonexistent.h>"'
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run tar'
AR='ar'
AS='cc '
ASFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99'
AUTOCONF='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run autoconf'
AUTOHEADER='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run autoheader'
AUTOMAKE='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run automake-1.11'
AWK='gawk'
CC='cc '
CCAS='cc '
CCASDEPMODE='depmode=gcc3'
CCASFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include'
CCDEPMODE='depmode=gcc3'
CC_FOR_BUILD='cc'
CFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include'
CPP='cc -E'
CPPFLAGS=''
CXX='g++'
CXXCPP='g++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS=' -pthread -I./include'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
DLLTOOL='dlltool'
DLOPEN_LIBS='-ldl'
ECHO='echo'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEEXT=''
F77=''
F77LINK='$(LINK)'
FFLAGS=''
FFT_LIBS='-lfftw3f'
FLIBS=''
GMX_BLUEGENE_FALSE=''
GMX_BLUEGENE_TRUE='#'
GMX_DOUBLE_FALSE=''
GMX_DOUBLE_TRUE='#'
GMX_EXTERNAL_BLAS_FALSE=''
GMX_EXTERNAL_BLAS_TRUE='#'
GMX_EXTERNAL_LAPACK_FALSE=''
GMX_EXTERNAL_LAPACK_TRUE='#'
GMX_FAHCORE_FALSE=''
GMX_FAHCORE_TRUE='#'
GMX_FORTRAN_FALSE=''
GMX_FORTRAN_TRUE='#'
GMX_IA32_SSE2_FALSE=''
GMX_IA32_SSE2_TRUE='#'
GMX_IA32_SSE_FALSE=''
GMX_IA32_SSE_TRUE='#'
GMX_IA64_ASM_FALSE=''
GMX_IA64_ASM_TRUE='#'
GMX_POWER6_FALSE=''
GMX_POWER6_TRUE='#'
GMX_PPC_ALTIVEC_FALSE=''
GMX_PPC_ALTIVEC_TRUE='#'
GMX_SOFTWARE_INVSQRT_FALSE='#'
GMX_SOFTWARE_INVSQRT_TRUE=''
GMX_X86_64_SSE2_FALSE=''
GMX_X86_64_SSE2_TRUE='#'
GMX_X86_64_SSE_FALSE='#'
GMX_X86_64_SSE_TRUE=''
GREP='/bin/grep'
GSL_LIBS=''
INCLUDES=' -I/usr/include/libxml2'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS=' '
LIBOBJS=''
LIBS='-lnsl -lm '
LIBSUFFIX=''
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LMKL=''
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run makeinfo'
MKDIR_P='/bin/mkdir -p'
MPICC=''
NO_LA_FILES_FALSE=''
NO_LA_FILES_TRUE='#'
OBJDUMP='objdump'
OBJEXT='o'
PACKAGE='gromacs'
PACKAGE_BUGREPORT='gmx-users at gromacs.org'
PACKAGE_NAME='gromacs'
PACKAGE_STRING='gromacs 4.5.5'
PACKAGE_TARNAME='gromacs'
PACKAGE_URL=''
PACKAGE_VERSION='4.5.5'
PATH_SEPARATOR=':'
PKG_CFLAGS=' -DGMX_SOFTWARE_INVSQRT -DGMX_THREADS'
PKG_FFT='fftw3f'
PKG_FFT_LIBS=''
PKG_GSL=''
PKG_XML='libxml-2.0'
PTHREAD_CC='cc'
PTHREAD_CFLAGS='-pthread'
PTHREAD_LIBS=''
RANLIB='ranlib'
RPM='rpm'
SET_MAKE=''
SHARED_VERSION_INFO='6:0:0'
SHELL='/bin/sh'
STRIP='strip'
THREAD_PARALLEL_FALSE='#'
THREAD_PARALLEL_TRUE=''
USE_VERSION_H_FALSE=''
USE_VERSION_H_TRUE='#'
USE_X11_FALSE='#'
USE_X11_TRUE=''
VERSION='4.5.5'
XMKMF=''
XML_LIBS='-lxml2'
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=' -lSM -lICE'
ac_ct_CC='cc'
ac_ct_CXX='g++'
ac_ct_F77=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCCAS_FALSE='#'
am__fastdepCCAS_TRUE=''
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__quote=''
am__tar='tar --format=ustar -chf - "$$tardir"'
am__untar='tar -xf -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
have_git=''
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/home/njn/zms/1gmx4.5.5'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "gromacs"
#define PACKAGE_TARNAME "gromacs"
#define PACKAGE_VERSION "4.5.5"
#define PACKAGE_STRING "gromacs 4.5.5"
#define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
#define PACKAGE_URL ""
#define PACKAGE "gromacs"
#define VERSION "4.5.5"
#define GMX_SOFTWARE_INVSQRT /**/
#define GMX_QMMM_GAUSSIAN /**/
#define GMX_QMMM_ORCA /**/
#define BUILD_TIME "Wed Sep 21 12:48:07 CST 2011"
#define BUILD_USER "njn at njn-SL"
#define BUILD_MACHINE "Linux 2.6.32-131.0.15.el6.x86_64 x86_64"
#define F77_OR_C_FUNC(name,NAME) name
#define F77_OR_C_FUNC_(name,NAME) name
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_UNISTD_H 1
#define HAVE_SYS_TIME_H 1
#define HAVE_SCHED_H 1
#define HAVE_SYSCONF 1
#define HAVE_PTHREAD 1
#define THREAD_PTHREADS /**/
#define HAVE_PTHREAD_SETAFFINITY 1
#define GMX_THREADS /**/
#define GMX_MPI /**/
#define HAVE_SIGUSR1 /**/
#define HAVE_PIPES /**/
#define FLOAT_FORMAT_IEEE754 /**/
#define HAVE_DLFCN_H 1
#define HAVE_FSEEKO 1
#define HAVE_LIBM 1
#define HAVE_LIBFFTW3F 1
#define GMX_FFT_FFTW3 /**/
#define HAVE_RPC_RPC_H 1
#define HAVE_RPC_XDR_H 1
#define HAVE_LIBNSL 1
#define HAVE_LIMITS_H 1
#define HAVE_UNISTD_H 1
#define HAVE_UNISTD_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_TIME_H 1
#define HAVE_DIRENT_H 1
#define HAVE_REGEX_H 1
#define RETSIGTYPE void
#define HAVE_VPRINTF 1
#define HAVE_STRCASECMP 1
#define HAVE_STRDUP 1
#define HAVE_GETTIMEOFDAY 1
#define HAVE_CBRT 1
#define HAVE_ISNAN 1
#define HAVE_FSYNC 1
#define HAVE_FILENO 1
#define HAVE_POSIX_MEMALIGN 1
#define HAVE_MEMALIGN 1
#define SIZEOF_INT 4
#define SIZEOF_LONG_INT 8
#define SIZEOF_LONG_LONG_INT 8
#define SIZEOF_OFF_T 8
#define SIZEOF_VOIDP 8
#define HAVE_LIBXML_PARSER_H 1
#define HAVE_LIBXML2 1
#define restrict __restrict
#define HAVE_UID_T 1
#define HAVE_GID_T 1
#define HAVE_SIG_ATOMIC_T 1
#define GMX_X86_64_SSE /**/
#define GMX_DLOPEN /**/
configure: exit 0
I'm a rookie, and can't solve it, please help me!!! SOS!
--
Sincerely yours
Dr Ji-Nan Niu
School of Materials Science and Engineering.
China University of Mining and Technology.
Jiangsu Province, XuZhou 221116
P. R. China
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