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

From: Miguel Ortiz Lombardía <miguel.ortiz-lombardia.afmb.univ-mrs.fr>
Date: Fri, 26 Oct 2012 17:42:51 +0200

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

In the original installation the preprocessor was correctly found:

> checking how to run the C++ preprocessor... icpc -E

For MTK++ I don't even find a clue. The mtkpp_config.log file says:

> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... ./install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> checking whether the C++ compiler works... no
> configure: error: in `/a/progs/simu/amber/amber12/AmberTools/src/mtkpp':
> configure: error: C++ compiler cannot create executables
> See `config.log' for more details

I couldn't figure out anything from that config.log

I have updated the compilers to the latest 20120928 version to
no avail.

Thank you for any help or pointers.

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 - 09:00:03 PDT
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