[gmx-users] Intel MKL taken in preference of the specified FFT library

[Mark Abraham]

Hi,

That's a problem at your end, please search the mail archives.

Mark

On Fri, 17 Jul 2015 12:50 Reuti <reuti at staff.uni-marburg.de> wrote:

> Hi Mark,
>
> thy for your reply and clarification about the library issue.
>
> > Am 16.07.2015 um 20:43 schrieb Mark Abraham <mark.j.abraham at gmail.com>:
> >
> > Hi,
> >
> > On Thu, Jul 16, 2015 at 5:47 PM Reuti <reuti at staff.uni-marburg.de>
> wrote:
> >
> >> Hi,
> >>
> >> I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU
> >> compilers and a self compiled FFTW*. I configured Gromacs with:
> >>
> >> $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1
> >> -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/home/reuti/local/fftw-3.3.4
> >>
> >> As there was now shared version of FFTW it complains about it, and
> hence I
> >> compiled FFTW again - this time with shared library flag and the
> configure
> >> step of Gromacs succeeded. But after `make` and `make install` I faced
> the
> >> result, that the binary `gmx` like the library in "lib64" were linked
> >> against Intel MKL. Well, there is an old version of the Intel MKL on the
> >> system and hence in the LD_LIBRARY_PATH. Once I cleared the
> LD_LIBRARY_PATH
> >> I got the result I expected.
> >>
> >
> > Older MKL had a "feature" of providing headers that look like FFTW but
> > execute MKL, and programs will find that if it precedes real FFTW in the
> > lookup path.
> >
> >
> >> Question: is this the intended behavior? IMO the GMX_FFT_LIBRARY=fftw3
> >> flag should be honored first and any set LD_LIBRARY_PATH ignored.
> >>
> >
> > Yes, but Intel decided to be "compatible" a.k.a. "deceptive." IIRC enough
> > people complained that it got fixed for subsequent MKL. Meanwhile, our
> > CMake code is quite complicated enough without double-checking for every
> > possible rare case ;-) Meanwhile, there are ways of forcing the find
> > mechanism to find the FFTW you really want.
> >
> >
> >>
> >> -- Reuti
> >>
> >> *) The automatic download (like outlined in the INSTALL:
> >> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON) of FFTW and the
> >> regression tests points to the Gromacs site, but AFAICS they were moved
> to
> >> box.com, hence the automatic download fails.
> >>
> >
> > No, the FFTW download goes to its site, and the tests download goes to
> > gerrit.gromacs.org. None of that has changed.
>
> For the FFTW you are right, I overlooked that it was complaining about the
> regression test only:
>
> *********************
> CMake Error at tests/CMakeLists.txt:57 (message):
>   error: downloading
>   'http://gerrit.gromacs.org/download/regressiontests-5.1-rc1.tar.gz'
> failed
>
>   status_code: 1
>
>   status_string: "Unsupported protocol"
>
>   log: Hostname was NOT found in DNS cache
>
>     Trying 130.237.25.133...
>
>   Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0)
>
>   GET /download/regressiontests-5.1-rc1.tar.gz HTTP/1.1
>
>   User-Agent: curl/7.38.0
>
>   Host: gerrit.gromacs.org
>
>   Accept: */*
>
>
>
>   HTTP/1.1 302 Found
>
>   Date: Fri, 17 Jul 2015 10:08:02 GMT
>
>   Server Apache/2.2.22 (Ubuntu) is not blacklisted
>
>   Server: Apache/2.2.22 (Ubuntu)
>
>   Location:
>   https://kth.box.com/shared/static/xq0o95adj3076allx3feugtw4qrjlk9f.gz
> *********************
>
> Without the protocol error it would have downloaded from the final
> destination without getting noticed. But " HTTP/1.1 302 Found" is an URL
> redirect.
>
> -- Reuti
>
>
> >
> > Mark
> >
> >
> >> --
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> >>
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