Chenyue Xing wrote:
Hi David,
Thanks for your reply. I actually found the time difference (25 min
different) between my working machine and the other machine where files
are. I'll contact my sysadmin. But as I successfully installed
gromacs-3.1 under the same condition, does that mean this problem only
occurs on version3.3?
no, you probably don't what the time difference was before.
you can try to run first configure, then wait 30 minutes and then run make.
Thank you again!
Chenyue
On 8/13/06, *David van der Spoel* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Chenyue Xing wrote:
> Hi all,
>
> I'm trying to install gromacs-3.3.1. I first installed fftw-3.0.1
with
> --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw
include/ and
> lib/ directories. ./configure successfully passed all checking (seems
> so) but it stopped at ' config.status: executing depfiles
commands' and
> didn't print 'Gromacs is ready to compile. Binary and library
files are
> ...' such stuff. If I try to 'make', it'll go into some infinite
loop:
> keep printing sentences from
> ' /bin/sh ./config.status
> config.status: creating Makefile'
> ...to ...
> 'config.status: src/config.h is unchanged
> config.status: executing depfiles commands'
>
> No matter it's just 'make' or 'make install' or 'make distclean', it
> only prints the loop of the above 'config.status'.
>
could it be that the machine you are working on has a different
time/date than the machine where the files are?
(e.g. when using NFS)
> I'm posting the log of configure so that some experienced users
may help
> me find the error. I appreciate any response!
>
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... pax
> checking for cc... cc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether cc accepts -g... yes
> checking for cc option to accept ANSI C... none needed
> checking for style of include used by make... GNU
> checking dependency style of cc... gcc3
> checking how to run the C preprocessor... cc -E
> checking whether cc accepts -O3... yes
> checking whether cc accepts -malign-double... yes
> checking whether cc accepts -funroll-all-loops... yes
> checking whether cc accepts -O3 -fomit-frame-pointer
-finline-functions
> -Wall -
> Wno-unused -malign-double -funroll-all-loops... yes
> checking whether byte ordering is bigendian... no
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h.. . yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking for int... yes
> checking size of int... 4
> checking for long int... yes
> checking size of long int... 4
> checking for long long int... yes
> checking size of long long int... 8
> checking floating-point format... IEEE754 (little-endian byte and
word
> order)
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for a sed that does not truncate output... /bin/sed
> checking for ld used by cc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking how to recognise dependent libraries... pass_all
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3
> checking how to run the C++ preprocessor... g++ -E
> checking the maximum length of command line arguments... 32768
> checking command to parse /usr/bin/nm -B output from cc object... ok
> checking for objdir... .libs
> checking for ar... ar
> checking for ranlib... ranlib
> checking for strip... strip
> checking if cc supports -fno-rtti -fno-exceptions... yes
> checking for cc option to produce PIC... -fPIC
> checking if cc PIC flag -fPIC works... yes
> checking if cc static flag -static works... yes
> checking if cc supports -c -o file.o... yes
> checking whether the cc linker (/usr/bin/ld) supports shared
> libraries... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> configure: creating libtool
> appending configuration tag "CXX" to libtool
> checking for ld used by g++... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking whether the g++ linker (/usr/bin/ld) supports shared
> libraries... yes
> checking for g++ option to produce PIC... -fPIC
> checking if g++ PIC flag -fPIC works... yes
> checking if g++ static flag -static works... yes
> checking if g++ supports -c -o file.o... yes
> checking whether the g++ linker (/usr/bin/ld) supports shared
> libraries... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> appending configuration tag "F77" to libtool
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... 64
> checking for _LARGE_FILES value needed for large files... no
> checking for _LARGEFILE_SOURCE value needed for large files... 1
> checking for fseeko... yes
> checking for sqrt in -lm... yes
> checking for fftw3.h.. . yes
> checking for main in -lfftw3f... yes
> checking rpc/rpc.h usability... yes
> checking rpc/rpc.h presence... yes
> checking for rpc/rpc.h... yes
> checking for rpc/xdr.h... yes
> checking for xdr_float in -lnsl... yes
> checking for working memcmp... yes
> checking return type of signal handlers... void
> checking for vprintf... yes
> checking for _doprnt... no
> checking if malloc debugging is wanted... no
> checking for strcasecmp... yes
> checking for strdup... yes
> checking for bool... no
> checking for X... no
> checking for Motif... libraries (none), headers (none)
> checking for libXext and libXp... no
> checking for only libXext... no
> checking limits.h usability... yes
> checking limits.h presence... yes
> checking for limits.h... yes
> checking for strings.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for an ANSI C-conforming const... yes
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking for uid_t in sys/types.h... yes
> checking for inline... inline
> checking whether your compiler can handle assembly files (*.s)... yes
> checking whether as fully supports ia32 SSE... yes
> checking whether as fully supports ia32 3DNow! instructions... yes
> checking whether byte ordering is bigendian... (cached) no
> checking if the compiler supports gcc inline assembly... yes
> checking if the compiler supports MSVC inline assembly... no
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating src/Makefile
> config.status: creating src/gmxlib/Makefile
> config.status: creating src/gmxlib/gmx_blas/Makefile
> config.status : creating src/gmxlib/gmx_lapack/Makefile
> config.status: creating src/gmxlib/nonbonded/Makefile
> config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile
> config.status: creating
src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile
> config.status: creating include/Makefile
> config.status: creating include/types/Makefile
> config.status: creating src/mdlib/Makefile
> config.status: creating src/kernel/Makefile
> config.status: creating src/tools/Makefile
> config.status: creating src/ngmx/Makefile
> config.status: creating src/contrib/Makefile
> config.status : creating scripts/Makefile
> config.status: creating admin/Makefile
> config.status: creating share/Makefile
> config.status: creating share/tutor/Makefile
> config.status: creating share/tutor/gmxdemo/Makefile
> config.status: creating share/tutor/nmr1/Makefile
> config.status: creating share/tutor/nmr2/Makefile
> config.status: creating share/tutor/water/Makefile
> config.status: creating share/tutor/mixed/Makefile
> config.status: creating share/tutor/methanol/Makefile
> config.status: creating share/tutor/speptide/Makefile
> config.status: creating share/template/Makefile
> config.status: creating share/top/Makefile
> config.status: creating share/html/Makefile
> config.status: creating share/html/images/Makefile
> config.status: creating share/html/online/Makefile
> config.status: creating man/Makefile
> config.status: creating man/man1/Makefile
> config.status: creating src/config.h
> config.status: executing depfiles commands
>
> Thanks a lot!!!
>
>
>
>
>
>
>
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>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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