[gmx-users] gromacs 4.5.5 cygwin installation error message
Wholly Peach
whollypeach at yahoo.com
Mon Mar 12 02:57:38 CET 2012
Dear All,
The FFTW installation works. ABC/fftw exists after the make install.
But for Gromacs, the /home/ABC/GROMACS cannot be created with the make step even with the prefix in configuration. And if I create it manually, the Gromacs make still fail.
Please keep in mind that the Gromacs make fail from the following step:
----
-out-implib -Xlinker .libs/libmd.dll.a
Creating library file: .libs/libmd.dll.a
.libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to `_fftwf_plan_guru_dft'
.libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference to `_fftwf_plan_guru_dft_r2c'
----
In addition Mark, do you mean for "--enable-shared" for both means for both FFTW and GROMACS?
I am looking your reply.
Cheers,
Wholly
________________________________
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, 12 March 2012 10:21 AM
Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
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>
>>To: Wholly Peach <whollypeach at yahoo.com>; Discussion list for GROMACS users <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>
>>> To: Discussion list for GROMACS users <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
>>> >> -- gmx-users mailing list gmx-users at 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!
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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
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> www interface or send it to gmx-users-request at gromacs.org.
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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 | Birmingham AL 35294-4461
>>(205) 690-0808 |
>>==================================================================
>>
>>
>>
>>
>>
>>
>
>--
>gmx-users mailing list gmx-users at 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-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
--
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