On Fri, Oct 26, 2012 at 11:42 AM, Miguel Ortiz Lombardía <
miguel.ortiz-lombardia.afmb.univ-mrs.fr> wrote:
> Hello everyone,
>
> I have an Amber11/AmberTools12 combo installed as per Jason's detailed
> instructions. It had been updated up to bugfix 14 and was working
> perfectly well, but then I decided to apply the latest bugfixes.
>
> I ran the convenient patch_amber.py script three times until it reported
>
> AmberTools12 is up to date. Nothing to download
>
> Then, I ran configure for a serial install, as I had done when
> installing Amber11 and AmberTools12, that is:
>
> ./configure -macAccelerate intel
>
> By the way, the system is:
>
> OS 10.6.8 (Snow Leopard Server)
> intel compilers (12.1.4 20120423)
>
> The configuration script goes essentially fine but chokes on NetCDF and
> MTK++. This is what I get:
>
> > (...)
> > Configuring NetCDF (may be time-consuming)...
> >
> > Error: NetCDF configure returned 1
> > NetCDF configure failed! Check the netcdf_config.log file
> > in the /a/progs/simu/amber/amber12/AmberTools/src directory.
> > Continuing anyway, but NetCDF will be skipped.
> >
> > Checking for zlib: OK
> >
> > Checking for libbz2: OK
> >
> > Configuring fftw-3.3 (may be time-consuming)...
> >
> > fftw-3.3 configure succeeded.
> >
> > Configuring XBLAS (may be time-consuming)...
> >
> > XBLAS configure succeeded.
> >
> > Configuring MTK++ (may be time-consuming)...
> >
> > Warning: MTK++ configure returned 77
> > MTK++ configure failed! Check the mtkpp_config.log file
> > in the /a/progs/simu/amber/amber12/AmberTools/src directory.
> > MTK++ will not be built alongside AmberTools.
> >
> > The configuration file, config.h, was successfully created.
>
> The last lines of netcdf_config.log say:
>
> > (...)
> > checking dlfcn.h usability... yes
> > checking dlfcn.h presence... yes
> > checking for dlfcn.h... yes
> > checking how to run the C++ preprocessor... /lib/cpp
> > configure: error: C++ preprocessor "/lib/cpp" fails sanity check
> > See `config.log' for more details.
>
> Well, cpp is certainly not in /lib/cpp
>
Where is it? I don't have my Mac handy to check (and I don't have OS X
10.6.8, anyway). The key here is to correctly pass cpp in to the NetCDF
configure via your top-level configure script, so if you know what you're
doing here, see if you can modify $AMBERHOME/AmberTools/src/configure2 to
try and do that.
May I also suggest using the GNU compilers as installed from MacPorts
instead? Unless you're running production-level simulations using pmemd,
you will probably not gain much by using the Intel compilers.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 26 2012 - 09:30:05 PDT
