[gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5
Rashek Kazi
rashek.kazi at gmail.com
Tue Jan 3 19:04:19 CET 2012
Hi Mark (and all)
Thanks for the response. I ran ./configure --disable-threads this time.
./configure went fine but again upon doing Make I have received a new error:
Creating library file: .libs/libmd.dll.a
.libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to
`_fftwf_plan_guru_d
ft'
.libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference to
`_fftwf_plan_guru_d
ft_r2c'
.libs/fft5d.o:fft5d.c:(.text+0x194b): undefined reference to
`_fftwf_plan_guru_d
ft_c2r'
.libs/fft5d.o:fft5d.c:(.text+0x1aef): undefined reference to
`_fftwf_execute'
.libs/fft5d.o:fft5d.c:(.text+0x2133): undefined reference to
`_fftwf_execute'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x4a): undefined reference to
`_fft
wf_malloc'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x67): undefined reference to
`_fft
wf_malloc'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x84): undefined reference to
`_fft
wf_malloc'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0xf4): undefined reference to
`_fft
wf_plan_many_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x14e): undefined reference to
`_ff
twf_plan_many_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1a5): undefined reference to
`_ff
twf_plan_many_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1fc): undefined reference to
`_ff
twf_plan_many_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x253): undefined reference to
`_ff
twf_plan_many_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2aa): more undefined
references t
o `_fftwf_plan_many_dft' follow
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3b1): undefined reference to
`_ff twf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3bd): undefined reference to
`_ff twf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3e7): undefined reference to
`_ff twf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3ef): undefined reference to
`_ff twf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x461): undefined reference to
`_ff
twf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x476): undefined reference to
`_ff
twf_destroy_plan'
this continues for a long time and then I get the error at the bottom:
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference
to `_f
ftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined
references
to `_fftwf_destroy_plan' follow
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference
to `_f
ftwf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference
to `_f
ftwf_free'
collect2: ld returned 1 exit status
Makefile:387: recipe for target `libmd.la' failed
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src/mdlib'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1
looks like a different set of errors here. Do you think it might have to do
with using FFTW-3.3?
On Fri, Dec 30, 2011 at 6:30 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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.htmlfor 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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>
--
Rashek Kazi
GS 2
MSTP Candidate
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