[gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5

Mark Abraham Mark.Abraham at anu.edu.au
Sat Dec 31 00:30:18 CET 2011


On 31/12/2011 3:13 AM, Rashek Kazi wrote:
> I am currently attempting to install gromacs-4.5.5. on a winXP 32bit 
> system through Cygwin. I had previously installed gromacs-4.5.4 
> without any issue but now I get an error during Make that reads like 
> the following...

Yep. See 
http://lists.gromacs.org/pipermail/gmx-users/2011-November/065886.html 
for explanation and work-around for 4.5.5.

Mark

>
> 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 
> -I/usr/local/include  -O3                                             
>                                                                       
>                                                                       
>        -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
> -msse2 -funroll-all-lo                                                 
>                                                                       
>                                                                       
>   ops -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                                                     
>                                                                       
>                                                                     
>  -I/usr/local/include -O3 -fomit-frame-pointer -finline-functions 
> -Wall -Wno-unu                                                         
>                                                                       
>                                                                 sed 
> -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 .li                                                         
>                                                                       
>                                                                 
> bs/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__' be                                                     
>                                                                       
>                                                                     
> fore 'smalloc_GetNumaProcessorNodeEx'
> numa_malloc.c:122:45: error: expected '=', ',', ';', 'asm' or 
> '__attribute__' be                                                     
>                                                                       
>                                                                     
> fore 'smalloc_GetCurrentProcessorNumberEx'
> numa_malloc.c: In function 'InitNumaHeapSupport':
> numa_malloc.c:151:5: error: 'smalloc_GetCurrentProcessorNumberEx' 
> undeclared (fi                                                         
>                                                                       
>                                                                 rst 
> 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 (fi                                                         
>                                                                       
>                                                                 rst 
> use in this function)
> numa_malloc.c:151:79: error: expected ';' before 'GetProcAddress'
> numa_malloc.c:152:5: error: 'smalloc_GetNumaProcessorNodeEx' 
> undeclared (first u                                                   
>                                                                       
>                                                                       
> se in this function)
> numa_malloc.c:152:39: error: 'func_GetNumaProcessorNodeEx_t' 
> undeclared (first u                                                   
>                                                                       
>                                                                       
> se 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 fun                                                           
>                                                                       
>                                                               ction)
> numa_malloc.c:246:22: error: expected ';' before 'CurrentProcessorNumber'
> numa_malloc.c:285:5: warning: implicit declaration of function 
> 'smalloc_GetCurre                                                     
>                                                                       
>                                                                     
> ntProcessorNumberEx'
> numa_malloc.c:285:42: error: 'CurrentProcessorNumber' undeclared 
> (first use in t                                                       
>                                                                       
>                                                                   his 
> function)
> numa_malloc.c:287:5: warning: implicit declaration of function 
> 'smalloc_GetNumaP                                                     
>                                                                       
>                                                                     
> rocessorNodeEx'
> numa_malloc.c:324:9: warning: implicit declaration of function 
> 'HeapSetInformati                                                     
>                                                                       
>                                                                     on'
> Makefile:332: recipe for target `numa_malloc.lo' failed
> make[4]: *** [numa_malloc.lo] Error 1
> make[4]: Leaving directory 
> `/home/Administrator/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/Administrator/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/Administrator/gromacs-4.5.5/src'
> Makefile:238: recipe for target `all' failed
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/Administrator/gromacs-4.5.5/src'
> Makefile:347: recipe for target `all-recursive' failed
> make: *** [all-recursive] Error 1
>
>
> I have no idea why this is and how to fix it, below are all of the 
> steps I followed exactly as I did for 4.5.4.
>
> I first uninstalled fftw and manually installed fftw-3.3 for single 
> precision with the following...
>
> ./configure --with-our-malloc16 --with-windows-f77-mangling 
> --enable-shared --disable-static --enable-
> threads --with-combined-threads --enable-portable-binary 
> --enable-float --enable-sse
> make
> make install
>
> I didn't see any glitches in there.
>
> I cd-ed into the gromacs-4.5.5 folder and did the following:
>
> export CPPFLAGS="-I/usr/local/include"
> export LDFLAGS="-L/usr/local/lib"
>
> ./configure --enable-cpu-optimization --enable-largefile
>
> make
>
> and that's where I'm stuck. I tried re-installing 4.5.4 and was unable 
> to so I'm wondering if the updated fftw build is causing this. Any 
> help would be appreciated. I'm not a linux user so please spell out 
> explanations for me, sorry for the inconvenience. Thanks!
>
> -- 
> Rashek Kazi
> GS 2
> MSTP Candidate
>
>

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