Re: [AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27

From: Miguel Ortiz Lombardia <>
Date: Fri, 26 Oct 2012 23:39:17 +0200

El 26/10/12 18:19, Jason Swails escribió:
> On Fri, Oct 26, 2012 at 11:42 AM, Miguel Ortiz Lombardía <
>> 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 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

Hi Jason,

Thank you for your email.

It turned out to be a problem with the installation of the intel
compilers. At some point I had to install other software that would not
compile with the gnu compilers shipped by Apple (4.2.1), so I manually
installed the 4.6.2 version of the gnu compilers. I had links pointing
gcc and g++ to this newer version. A closer examination of the
config.log files produced during the configuration of netcdf and mtk++
showed that the intel compilers had "gcc version 4.6.2 compatibility"
instead of "gcc version 4.2.1 compatibility", which resulted in all
kinds of trouble, like libstdc++ libraries not being found among others.

Reinstalling the intel compilers after having removed the 'gcc' and
'g++' links, so they would point to the original 4.2.1 versions, solved
the configuration problems. The programs have all compiled in serial and
parallel and all tests passed, also in serial and parallel.

Best regards,

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
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Received on Fri Oct 26 2012 - 15:00:03 PDT
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