[gmx-users] problem with gromacs

[Mark Abraham]

On 11/01/2012 12:32 AM, Sylwia Chmielewska wrote:
> Hello,
> Thanks for the advice. For one moment everything was ok, but at some point appeared an error.

Use "make distclean" before configure if you have already configured and 
built and need to change stuff. Else things can get confused sometimes.

Mark

>
> $ 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.Abraham at anu.edu.au>
> Do: "Discussion list for GROMACS users"<gmx-users at 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
>