<div>Hi David,</div>
<div> </div>
<div>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? </div>
<div> </div>
<div>Thank you again!</div>
<div>Chenyue<br><br> </div>
<div><span class="gmail_quote">On 8/13/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Chenyue Xing wrote:<br>> Hi all,<br>><br>> I'm trying to install gromacs-3.3.1. I first installed
fftw-3.0.1 with<br>> --enable-float and setenv CPPFLAGS and LDFLAGS to my fftw include/ and<br>> lib/ directories. ./configure successfully passed all checking (seems<br>> so) but it stopped at ' config.status: executing depfiles commands' and
<br>> didn't print 'Gromacs is ready to compile. Binary and library files are<br>> ...' such stuff. If I try to 'make', it'll go into some infinite loop:<br>> keep printing sentences from<br>> ' /bin/sh ./config.status
<br>> config.status: creating Makefile'<br>> ...to ...<br>> 'config.status: src/config.h is unchanged<br>> config.status: executing depfiles commands'<br>><br>> No matter it's just 'make' or 'make install' or 'make distclean', it
<br>> only prints the loop of the above 'config.status'.<br>><br><br>could it be that the machine you are working on has a different<br>time/date than the machine where the files are?<br>(e.g. when using NFS)<br><br>
<br>> I'm posting the log of configure so that some experienced users may help<br>> me find the error. I appreciate any response!<br>><br>> checking build system type... i686-pc-linux-gnu<br>> checking host system type... i686-pc-linux-gnu
<br>> checking for a BSD-compatible install... /usr/bin/install -c<br>> checking whether build environment is sane... yes<br>> checking for gawk... gawk<br>> checking whether make sets $(MAKE)... yes<br>> checking how to create a ustar tar archive... pax
<br>> checking for cc... cc<br>> checking for C compiler default output file name... a.out<br>> checking whether the C compiler works... yes<br>> checking whether we are cross compiling... no<br>> checking for suffix of executables...
<br>> checking for suffix of object files... o<br>> checking whether we are using the GNU C compiler... yes<br>> checking whether cc accepts -g... yes<br>> checking for cc option to accept ANSI C... none needed
<br>> checking for style of include used by make... GNU<br>> checking dependency style of cc... gcc3<br>> checking how to run the C preprocessor... cc -E<br>> checking whether cc accepts -O3... yes<br>> checking whether cc accepts -malign-double... yes
<br>> checking whether cc accepts -funroll-all-loops... yes<br>> checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions<br>> -Wall -<br>> Wno-unused -malign-double -funroll-all-loops... yes<br>
> checking whether byte ordering is bigendian... no<br>> checking for egrep... grep -E<br>> checking for ANSI C header files... yes<br>> checking for sys/types.h... yes<br>> checking for sys/stat.h... yes<br>
> checking for stdlib.h.. . yes<br>> checking for string.h... yes<br>> checking for memory.h... yes<br>> checking for strings.h... yes<br>> checking for inttypes.h... yes<br>> checking for stdint.h... yes
<br>> checking for unistd.h... yes<br>> checking for int... yes<br>> checking size of int... 4<br>> checking for long int... yes<br>> checking size of long int... 4<br>> checking for long long int... yes
<br>> checking size of long long int... 8<br>> checking floating-point format... IEEE754 (little-endian byte and word<br>> order)<br>> checking for a BSD-compatible install... /usr/bin/install -c<br>> checking whether ln -s works... yes
<br>> checking whether make sets $(MAKE)... (cached) yes<br>> checking for a sed that does not truncate output... /bin/sed<br>> checking for ld used by cc... /usr/bin/ld<br>> checking if the linker (/usr/bin/ld) is GNU ld... yes
<br>> checking for /usr/bin/ld option to reload object files... -r<br>> checking for BSD-compatible nm... /usr/bin/nm -B<br>> checking how to recognise dependent libraries... pass_all<br>> checking dlfcn.h usability... yes
<br>> checking dlfcn.h presence... yes<br>> checking for dlfcn.h... yes<br>> checking for g++... g++<br>> checking whether we are using the GNU C++ compiler... yes<br>> checking whether g++ accepts -g... yes
<br>> checking dependency style of g++... gcc3<br>> checking how to run the C++ preprocessor... g++ -E<br>> checking the maximum length of command line arguments... 32768<br>> checking command to parse /usr/bin/nm -B output from cc object... ok
<br>> checking for objdir... .libs<br>> checking for ar... ar<br>> checking for ranlib... ranlib<br>> checking for strip... strip<br>> checking if cc supports -fno-rtti -fno-exceptions... yes<br>> checking for cc option to produce PIC... -fPIC
<br>> checking if cc PIC flag -fPIC works... yes<br>> checking if cc static flag -static works... yes<br>> checking if cc supports -c -o file.o... yes<br>> checking whether the cc linker (/usr/bin/ld) supports shared
<br>> libraries... yes<br>> checking dynamic linker characteristics... GNU/Linux ld.so<br>> checking how to hardcode library paths into programs... immediate<br>> checking whether stripping libraries is possible... yes
<br>> checking if libtool supports shared libraries... yes<br>> checking whether to build shared libraries... no<br>> checking whether to build static libraries... yes<br>> configure: creating libtool<br>> appending configuration tag "CXX" to libtool
<br>> checking for ld used by g++... /usr/bin/ld<br>> checking if the linker (/usr/bin/ld) is GNU ld... yes<br>> checking whether the g++ linker (/usr/bin/ld) supports shared<br>> libraries... yes<br>> checking for g++ option to produce PIC... -fPIC
<br>> checking if g++ PIC flag -fPIC works... yes<br>> checking if g++ static flag -static works... yes<br>> checking if g++ supports -c -o file.o... yes<br>> checking whether the g++ linker (/usr/bin/ld) supports shared
<br>> libraries... yes<br>> checking dynamic linker characteristics... GNU/Linux ld.so<br>> checking how to hardcode library paths into programs... immediate<br>> appending configuration tag "F77" to libtool
<br>> checking for special C compiler options needed for large files... no<br>> checking for _FILE_OFFSET_BITS value needed for large files... 64<br>> checking for _LARGE_FILES value needed for large files... no<br>
> checking for _LARGEFILE_SOURCE value needed for large files... 1<br>> checking for fseeko... yes<br>> checking for sqrt in -lm... yes<br>> checking for fftw3.h.. . yes<br>> checking for main in -lfftw3f... yes
<br>> checking rpc/rpc.h usability... yes<br>> checking rpc/rpc.h presence... yes<br>> checking for rpc/rpc.h... yes<br>> checking for rpc/xdr.h... yes<br>> checking for xdr_float in -lnsl... yes<br>> checking for working memcmp... yes
<br>> checking return type of signal handlers... void<br>> checking for vprintf... yes<br>> checking for _doprnt... no<br>> checking if malloc debugging is wanted... no<br>> checking for strcasecmp... yes<br>
> checking for strdup... yes<br>> checking for bool... no<br>> checking for X... no<br>> checking for Motif... libraries (none), headers (none)<br>> checking for libXext and libXp... no<br>> checking for only libXext... no
<br>> checking limits.h usability... yes<br>> checking limits.h presence... yes<br>> checking for limits.h... yes<br>> checking for strings.h... (cached) yes<br>> checking for unistd.h... (cached) yes<br>> checking for
unistd.h... (cached) yes<br>> checking for an ANSI C-conforming const... yes<br>> checking for size_t... yes<br>> checking whether struct tm is in sys/time.h or time.h... time.h<br>> checking for uid_t in sys/types.h... yes
<br>> checking for inline... inline<br>> checking whether your compiler can handle assembly files (*.s)... yes<br>> checking whether as fully supports ia32 SSE... yes<br>> checking whether as fully supports ia32 3DNow! instructions... yes
<br>> checking whether byte ordering is bigendian... (cached) no<br>> checking if the compiler supports gcc inline assembly... yes<br>> checking if the compiler supports MSVC inline assembly... no<br>> configure: creating ./config.status
<br>> config.status: creating Makefile<br>> config.status: creating src/Makefile<br>> config.status: creating src/gmxlib/Makefile<br>> config.status: creating src/gmxlib/gmx_blas/Makefile<br>> config.status
: creating src/gmxlib/gmx_lapack/Makefile<br>> config.status: creating src/gmxlib/nonbonded/Makefile<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile
<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile
<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile
<br>> config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile<br>> config.status: creating include/Makefile<br>> config.status: creating include/types/Makefile<br>> config.status: creating src/mdlib/Makefile
<br>> config.status: creating src/kernel/Makefile<br>> config.status: creating src/tools/Makefile<br>> config.status: creating src/ngmx/Makefile<br>> config.status: creating src/contrib/Makefile<br>> config.status
: creating scripts/Makefile<br>> config.status: creating admin/Makefile<br>> config.status: creating share/Makefile<br>> config.status: creating share/tutor/Makefile<br>> config.status: creating share/tutor/gmxdemo/Makefile
<br>> config.status: creating share/tutor/nmr1/Makefile<br>> config.status: creating share/tutor/nmr2/Makefile<br>> config.status: creating share/tutor/water/Makefile<br>> config.status: creating share/tutor/mixed/Makefile
<br>> config.status: creating share/tutor/methanol/Makefile<br>> config.status: creating share/tutor/speptide/Makefile<br>> config.status: creating share/template/Makefile<br>> config.status: creating share/top/Makefile
<br>> config.status: creating share/html/Makefile<br>> config.status: creating share/html/images/Makefile<br>> config.status: creating share/html/online/Makefile<br>> config.status: creating man/Makefile<br>>
config.status: creating man/man1/Makefile<br>> config.status: creating src/config.h<br>> config.status: executing depfiles commands<br>><br>> Thanks a lot!!!<br>><br>><br>><br>><br>><br>><br>
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<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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