[gmx-users] failure message in GROMACS installation

[Mark Abraham]

On 11/01/2012 6:15 PM, Dialing Pretty wrote:
> Dear All,
> I am trying to install GROMACS 455. I got a series of error message in 
> the "MAKE" step. Will you please take a look at the following MAKE 
> screen file to see on how to make the installation successful?

You should provide the command lines you used when seeking help. As it 
is, I can only presume you haven't correctly followed point 4 of 
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO 
about disabling threads.

Mark

> Cheers,
> Dialing
> 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 pthreads.lo -MD -MP -MF 
> .deps/pthreads.Tpo -c pthreads.c -DPIC -o .libs/pthreads.o
> 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 pthreads.lo -MD -MP -MF 
> .deps/pthreads.Tpo -c pthreads.c -o pthreads.o >/dev/null 2>&1
> mv -f .deps/pthreads.Tpo .deps/pthreads.Plo
> /bin/sh ../../../libtool --tag=CC --mode=compile 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 -o numa_malloc.lo 
> numa_malloc.c
> 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[4]: *** [numa_malloc.lo] Error 1
> make[4]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/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 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib'
> Makefile:302: recipe for target `all-recursive' failed
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> Makefile:238: recipe for target `all' failed
> make[1]: *** [all] Error 2
> make[1]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> Makefile:347: recipe for target `all-recursive' failed
> make: *** [all-recursive] Error 1
>
>
>
>

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