[gmx-users] gromacs-3.3.1 installation problem

[David van der Spoel]

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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-- 
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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