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

Mark Abraham Sun, 11 Mar 2012 20:21:45 -0700

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

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