[gmx-users] gromacs 4.5.5 cygwin installation error message

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 12 04:21:00 CET 2012 

On 12/03/2012 1:18 PM, Peter C. Lai wrote:
> Oops I just saw this. Yeah it could be --enable-shared is broken on this
> for cygwin, since the build is breaking during linking.

Yes, that is possible.

> In an unrelated note, is running gromacs in cygwin supposed to be faster
> than running it in a unix/linux virtual machine with paravirt I/O?

I'm not aware that anyone's compared them.

Mark

>
> On 2012-03-12 11:21:26AM +1100, Mark Abraham wrote:
>> 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 they
>> both succeeded then you will be able to see that /home/ABC/fftw exists
>> and 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-shared
>>> LDFLAGS='-L/home/ABC/fftw/lib' CPPFLAGS='-I/home/ABC/fftw/include'
>> If the FFTW installation worked, then this should work. Possibly you
>> will need to choose --enable-shared for both, or --disable-shared for
>> both - 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): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x249f): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24b5): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24cb): more undefined
>>> references to `_fftwf_destroy_plan' follow
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2506): undefined
>>> reference to `_fftwf_free'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2512): undefined
>>> reference to `_fftwf_free'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x251e): undefined
>>> reference to `_fftwf_free'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x25ce): undefined
>>> reference to `_fftwf_execute_dft'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x268e): undefined
>>> reference to `_fftwf_execute_dft'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2755): undefined
>>> reference to `_fftwf_execute_dft_c2r'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2770): undefined
>>> reference to `_fftwf_execute_dft_r2c'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2825): undefined
>>> reference to `_fftwf_execute_dft_c2r'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2840): undefined
>>> reference to `_fftwf_execute_dft_r2c'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x28ee): undefined
>>> reference to `_fftwf_execute_dft'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29b5): undefined
>>> reference to `_fftwf_execute_dft_c2r'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29d0): undefined
>>> reference to `_fftwf_execute_dft_r2c'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2a7e): undefined
>>> reference to `_fftwf_execute_dft'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b45): undefined
>>> reference to `_fftwf_execute_dft_c2r'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b60): undefined
>>> reference to `_fftwf_execute_dft_r2c'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b8a): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b9f): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined
>>> reference to `_fftwf_destroy_plan'
>>> .......
>>>
>>> ----- Forwarded Message -----
>>> *From:* Mark Abraham<Mark.Abraham at anu.edu.au>
>>> *To:* Discussion list for GROMACS users<gmx-users at gromacs.org>
>>> *Sent:* Sunday, 11 March 2012 6:26 PM
>>> *Subject:* Re: Fw: [gmx-users] gromacs 4.5.5 cygwin installation error
>>> message
>>>
>>> On 11/03/2012 7:03 PM, Wholly Peach wrote:
>>>> Dear All,
>>>> Fot the fftw3, I use the following configuration, and make install
>>>> success.
>>>> ./configure --enable-threads --enable-float --enable-sse
>>>> --prefix=/home/joe/fftw
>>> Possibly not successful, because /home/joe probably doesn't exist on
>>> your system. It's an *example* - you should install somewhere that
>>> makes sense on your system. So /home/YOURUSERNAMEHERE/fftw would make
>>> some 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 you
>>> haven't told GROMACS where to look for it. The normal installation
>>> instructions 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): undefined
>>>> reference to `_fftwf_destroy_plan'
>>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined
>>>> reference to `_fftwf_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 `_fftwf_free'
>>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined
>>>> reference 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<pcl at uab.edu>  <mailto:pcl at uab.edu>
>>>> *To:* Wholly Peach<whollypeach at yahoo.com>
>>>> <mailto:whollypeach at yahoo.com>; Discussion list for GROMACS users
>>>> <gmx-users at gromacs.org>  <mailto:gmx-users at gromacs.org>
>>>> *Sent:* Sunday, 11 March 2012 11:54 AM
>>>> *Subject:* Re: [gmx-users] gromacs 4.5.5 cygwin installation error
>>>> message
>>>>
>>>> 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 I
>>>> also use --disable-threads?
>>>>> Wholley
>>>>>
>>>>>
>>>>> ________________________________
>>>>>   From: Mark Abraham<Mark.Abraham at anu.edu.au
>>>> <mailto:Mark.Abraham at anu.edu.au>>
>>>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org
>>>> <mailto:gmx-users at gromacs.org>>
>>>>> Sent: Sunday, 11 March 2012 11:43 AM
>>>>> Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error
>>>> message
>>>>> 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 guides
>>>> will 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 avoid
>>>> the error message.
>>>>>>> Wholly
>>>>>>>      .....
>>>>>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined
>>>> reference to `_fftwf_destroy_plan'
>>>>>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined
>>>> reference to `_fftwf_destroy_plan'
>>>>>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined
>>>> reference to `_fftwf_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 `_fftwf_free'
>>>>>>> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined
>>>> reference 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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>>>>> -- gmx-users mailing list gmx-users at gromacs.org
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>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> <mailto:gmx-users at gromacs.org>
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>
>>>> -- 
>>>> ==================================================================
>>>> Peter C. Lai            | University of Alabama-Birmingham
>>>> Programmer/Analyst        | KAUL 752A
>>>> Genetics, Div. of Research    | 705 South 20th Street
>>>> pcl at uab.edu<mailto:pcl at uab.edu>             | Birmingham AL 35294-4461
>>>> (205) 690-0808            |
>>>> ==================================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> -- 
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>>>
>> -- 
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>

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