AMBER Archive (2009)

Subject: Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64)

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Tue Jan 06 2009 - 13:23:29 CST

Hi,

On Fri, 19 Dec 2008, wl2290_at_columbia.edu wrote:

> I have been trying to install amber 10 on a linux with openSUSE 10.2 (x86-64).
> I downloaded both g95 and gfortran on the computer, ...
>
> /usr/include/c++/4.1.2/bits/locale_facets.h:699: error: ‘size_t’ does not name
> a type

On Tue, 23 Dec 2008, David A. Case wrote:

> For Amber11, we have rewritten elsize as a C program which is a lot more
> portable. [It's not the language per se, but it is true (in my
> experience) that C++ can be abused to give code that is both
> compiler-dependent and which gives compiler errors in other environments
> that are very hard to track down.]

On Tue, 30 Dec 2008, wl2290_at_columbia.edu wrote:

> ./configure_lam -> please see the attachment. Basically, the error is:
>
> configure: WARNING: *** Your C++ compiler does not seem to support the STL.
> configure: WARNING: *** STL support is necessary to compile LAM/MPI
> configure: error: cannot continue

> /opt/amber10/bin/mpif77 -c -O3 -fno-range-check -fno-second-underscore
> -ffree-form -o constants.o _constants.f
> f771: error: unrecognized option `-fno-range-check'

This latest fortran error is very likely due to faulty compiler
installations (as well as probably a faulty mpi installation)
as probably are all your problems.
Uninstall and reinstall them all or perhaps more easily -
fully reinstall your OS.

Here is my commentary on this thread.

The initial errors reported are highly suspicious of a faulty compiler
installation as was suggested despite a difficult to decrypt report.
Any C programmer should suspect the size_t complaint.
The lam configure errors are crystal clear and confirm the suspicion
although that was several days after the initial report.

For Amber10, we have a bug fix for elsize:
http://ambermd.org/bugfixes/10.0/bugfix.2
But this is probably a minor issue amongest all this user's problems.

Unfortunately, it is true in my experience that the language C++
is blamed for far more problems than the evidence indicates.
Here the direct cause of wl2290's problems may be operator
error during the gnu compilers installations (gfortran and/or g95)
or uses as well as maybe not applying bugfix 2
(but elsize.cc was correctly built at least once),
and the indirect cause may be OS's that do not
come with all the gnu compilers or tightwad OS installers.
Since disk space is about $100 per terabyte, my advice to
users is to fully install your OS.

Scott
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