[gmx-users] problem with gromacs

[Mark Abraham]

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 
<http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO#section_2> 
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

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