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.abra...@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 > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Rashek Kazi GS 2 MSTP Candidate
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