Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

Mark Abraham Sun, 11 Mar 2012 17:22:12 -0700

On 12/03/2012 8:14 AM, Wholly Peach wrote:

Dear All,
For fftw, I use the following configure,
./configure --enable-threads --enable-float --enable-sse--prefix=/home/ABC/fftw

If /home/ABC exists, and you then did "make" and "make install" and theyboth succeeded then you will be able to see that /home/ABC/fftw existsand has stuff in it. You will have built non-shared libraries however.

For gromacs, I use the following configure,
./configure --with-fft=fftw3 --disable-threads--prefix=/home/ABC/GROMACS --enable-sharedLDFLAGS='-L/home/ABC/fftw/lib' CPPFLAGS='-I/home/ABC/fftw/include'

If the FFTW installation worked, then this should work. Possibly youwill need to choose --enable-shared for both, or --disable-shared forboth - I'm not sure.


Mark

But in the make step of gromacs, I still got a series of error message.
I am looking forward to getting some suggesrions to solve it.
Cheers,
Wholly
.......
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2489): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x249f): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24b5): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24cb): more undefinedreferences to `_fftwf_destroy_plan' follow.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2506): undefinedreference to `_fftwf_free'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2512): undefinedreference to `_fftwf_free'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x251e): undefinedreference to `_fftwf_free'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x25ce): undefinedreference to `_fftwf_execute_dft'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x268e): undefinedreference to `_fftwf_execute_dft'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2755): undefinedreference to `_fftwf_execute_dft_c2r'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2770): undefinedreference to `_fftwf_execute_dft_r2c'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2825): undefinedreference to `_fftwf_execute_dft_c2r'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2840): undefinedreference to `_fftwf_execute_dft_r2c'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x28ee): undefinedreference to `_fftwf_execute_dft'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29b5): undefinedreference to `_fftwf_execute_dft_c2r'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29d0): undefinedreference to `_fftwf_execute_dft_r2c'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2a7e): undefinedreference to `_fftwf_execute_dft'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b45): undefinedreference to `_fftwf_execute_dft_c2r'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b60): undefinedreference to `_fftwf_execute_dft_r2c'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b8a): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b9f): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefinedreference to `_fftwf_destroy_plan'
.......

----- Forwarded Message -----
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Sunday, 11 March 2012 6:26 PM
*Subject:* Re: Fw: [gmx-users] gromacs 4.5.5 cygwin installation errormessage
On 11/03/2012 7:03 PM, Wholly Peach wrote:
Dear All,
Fot the fftw3, I use the following configuration, and make installsuccess../configure --enable-threads --enable-float --enable-sse--prefix=/home/joe/fftw
Possibly not successful, because /home/joe probably doesn't exist onyour system. It's an *example* - you should install somewhere thatmakes sense on your system. So /home/YOURUSERNAMEHERE/fftw would makesome sense. However, on Cygwin you have write permission everywhere,so you may as well not get involved with --prefix.
For the gromacs 4.5.5, I use the following configuration:
./configure --with-fft=fftw3 --disable-threads -prefix=/home/joe/GROMACS
Above, you've installed FFTW to a non-standard location, and now youhaven't told GROMACS where to look for it. The normal installationinstructions tell you how to do this.
Also, "-prefix" is wrong. Use "--prefix".

Mark
But for the make step, I still got the following errors.
I am looking forward to getting a reply from you on how to solve it.
Cheers,
Wholly
....
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefinedreference to `_fftwf_destroy_plan'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefinedreferences to `_fftwf_destroy_plan' follow.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefinedreference to `_fftwf_free'.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefinedreference to `_fftwf_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`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib'
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

----- Forwarded Message -----
*From:* Peter C. Lai <p...@uab.edu> <mailto:p...@uab.edu>
*To:* Wholly Peach <whollype...@yahoo.com><mailto:whollype...@yahoo.com>; Discussion list for GROMACS users<gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org>
*Sent:* Sunday, 11 March 2012 11:54 AM
*Subject:* Re: [gmx-users] gromacs 4.5.5 cygwin installation errormessage
I don't think fftw3 has that option, since disable-threads pertains to
mdrun parallelization (forces MPI-only, basically).

On 2012-03-10 05:50:19PM -0800, Wholly Peach wrote:
> Hi Mark,
>
> If for Gromacs I use disable --disable-threads, for fftw3 show Ialso use --disable-threads?
>
> Wholley
>
>
> ________________________________
> From: Mark Abraham <mark.abra...@anu.edu.au<mailto:mark.abra...@anu.edu.au>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>>
> Sent: Sunday, 11 March 2012 11:43 AM
> Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation errormessage
>
> On 11/03/2012 12:20 PM, Peter C. Lai wrote:
> > Is fftw3 properly installed in /usr/local/lib?
>
> And of the right precision, like reading the installation guideswill warn you...
>
> Mark
>
> >
> > On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote:
> >>     Dear All,
> >>   For Gromacs installation, my configure command is:
> >> ./configure --enable-shared LDFLAGS='-L/usr/local/lib'--disable-threads.
> >> After make, the error message is as following.
> >> I am looking forward to getting a reply from you on how to avoidthe error message.
> >> Wholly
> >>     .....
> >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefinedreference to `_fftwf_destroy_plan'> >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefinedreference to `_fftwf_destroy_plan'> >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefinedreference to `_fftwf_destroy_plan'> >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): moreundefined references to `_fftwf_destroy_plan' follow> >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefinedreference to `_fftwf_free'> >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefinedreference to `_fftwf_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`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib'
> >> 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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Re: [gmx-users] gromacs 4.5.5 cygwin installation error message

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