Hello, Thanks for the advice. For one moment everything was ok, but at some point appeared an error.
$ cd gromacs-4.5.5 ./configure --disable-threads make .libs/xlate.o:xlate.c:(.text+0x774): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0x7a0): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0x7da): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0x801): more undefined references to `_save_free' follow .libs/xlate.o:xlate.c:(.text+0x9d5): undefined reference to `_gmx_residuetype_is_rna' .libs/xlate.o:xlate.c:(.text+0xa9b): undefined reference to `_put_symtab' .libs/xlate.o:xlate.c:(.text+0xb3a): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xba6): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xc0d): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xc6d): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xc99): undefined reference to `_save_free' collect2: ld returned 1 exit status Makefile:459: recipe for target `libgmxpreprocess.la' failed make[3]: *** [libgmxpreprocess.la] Error 1 make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/kernel' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 What have I done now? Sylwia Chmielewska ----- Oryginalna wiadomość ----- Od: "Mark Abraham" <mark.abra...@anu.edu.au> Do: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Wysłane: niedziela, 8 styczeń 2012 23:37:42 Temat: Re: [gmx-users] problem with gromacs On 9/01/2012 3:44 AM, Sylwia Chmielewska wrote: Hello Folder with the program GROMACS save in a folder cygwin / home / Sylwia. then: $ cd gromacs-4.5.5 ./configure --enable-sse --enable-float no errors occurred only at the end: configure: WARNING: unrecognized options: - enable-sse You'll note that http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO does not recommend --enable-sse for this part of the procedure. make no errors occurred only at the end: numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’ numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’ numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘smalloc_GetNumaProcessorNodeEx’ numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘smalloc_GetCurrentProcessorNumberEx’ numa_malloc.c: In function ‘InitNumaHeapSupport’: numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ undeclared (first use in this function) numa_malloc.c:151:5: note: each undeclared identifier is reported only once for each function it appears in numa_malloc.c:151:44: error: ‘func_GetCurrentProcessorNumberEx_t’ undeclared (first use in this function) numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’ numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared (first use in this function) numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared (first use in this function) numa_malloc.c:152:69: error: expected ‘;’ before ‘GetProcAddress’ numa_malloc.c: In function ‘ReturnHeapHandle’: numa_malloc.c:246:5: error: ‘PROCESSOR_NUMBER’ undeclared (first use in this function) numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’ numa_malloc.c:285:5: warning: implicit declaration of function ‘smalloc_GetCurrentProcessorNumberEx’ numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use in this function) numa_malloc.c:287:5: warning: implicit declaration of function ‘smalloc_GetNumaProcessorNodeEx’ numa_malloc.c:324:9: warning: implicit declaration of function ‘HeapSetInformation’ Makefile:332: recipe for target `numa_malloc.lo' failed make[4]: *** [numa_malloc.lo] Error 1 make[4]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib/thread_mpi' Makefile:599: recipe for target `all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 make install Once something goes wrong, trying to press forward is normally fruitless. There's a bug with threading that shows up with version 4.5.5 on Cygwin. Use "configure --disable-threads" (and whatever else you need to use). Mark the same thing: cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -I./include -MT numa_malloc.lo -MD -MP -MF .deps/numa_malloc.Tpo -c numa_malloc.c -DPIC -o .libs/numa_malloc.o numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’ numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’ numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘smalloc_GetNumaProcessorNodeEx’ numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘smalloc_GetCurrentProcessorNumberEx’ numa_malloc.c: In function ‘InitNumaHeapSupport’: numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ undeclared (first use in this function) numa_malloc.c:151:5: note: each undeclared identifier is reported only once for each function it appears in numa_malloc.c:151:44: error: ‘func_GetCurrentProcessorNumberEx_t’ undeclared (first use in this function) numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’ numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared (first use in this function) numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared (first use in this function) numa_malloc.c:152:69: error: expected ‘;’ before ‘GetProcAddress’ numa_malloc.c: In function ‘ReturnHeapHandle’: numa_malloc.c:246:5: error: ‘PROCESSOR_NUMBER’ undeclared (first use in this function) numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’ numa_malloc.c:285:5: warning: implicit declaration of function ‘smalloc_GetCurrentProcessorNumberEx’ numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use in this function) numa_malloc.c:287:5: warning: implicit declaration of function ‘smalloc_GetNumaProcessorNodeEx’ numa_malloc.c:324:9: warning: implicit declaration of function ‘HeapSetInformation’ Makefile:332: recipe for target `numa_malloc.lo' failed make[3]: *** [numa_malloc.lo] Error 1 make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib/thread_mpi' Makefile:599: recipe for target `install-recursive' failed make[2]: *** [install-recursive] Error 1 make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib' Makefile:302: recipe for target `install-recursive' failed make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:347: recipe for target `install-recursive' failed make: *** [install-recursive] Error 1 $ source /usr/local/gromacs/bin/GMXRC -bash: /usr/local/gromacs/bin/GMXRC: No such file or directory Thanks for any help. Sylwia Chmielewska -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
