[gmx-users] gromacs-3.3.1 installation problem

Chenyue Xing cxing at ucdavis.edu
Mon Aug 14 09:34:16 CEST 2006


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?

Thank you again!
Chenyue


On 8/13/06, David van der Spoel <spoel at xray.bmc.uu.se> 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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> > http://www.gromacs.org/mailman/listinfo/gmx-users
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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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
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