Hi Ben,
This is great. Would you consider posting this info on the Amber Wiki?
Gustavo.
On Tue, Sep 29, 2009 at 6:46 PM, Ben Roberts <roberts.qtp.ufl.edu> wrote:
> Hi all,
>
> Given the recent traffic on this topic, I apologise if I seem to be
> flagellating deceased equines here. But I've spent a good deal of time
> mucking around with this and thought I'd share my discoveries in case
> they're helpful.
>
> Detection of architecture
> -------------------------
>
> As has been pointed out by others, the "-m" compiler flag picks the machine
> type up. "-m64" is used, *if* the computer is booted with the "6" and "4"
> keys held down (I kid you not; this forces booting into the so-called 64-bit
> kernel).
>
> The Intel compilers
> -------------------
>
> I sent a message earlier today regarding an "internal error" which causes
> the compiler to choke for AmberTools. Amber itself, on the other hand,
> compiles with no significant problems (compiler warnings notwithstanding).
>
> The GNU compilers
> -----------------
>
> These can be used to build AmberTools OK. On the other hand, attempting to
> build sander generates a number of errors along these lines:
>
> gfortran -c -O3 -ffree-form -o pb_force.o _pb_force.f
> _pb_force.f: In function 'phintp.2255':
> _pb_force.f:1286:0: error: type mismatch in component reference
> real(kind=8)[0:D.2764] * restrict
>
> real(kind=8)[0:D.7772] *
>
> # VUSE <.MEM_173(D)>
> D.5358_39 = CHAIN.410_38(D)->phi;
>
> _pb_force.f:1286:0: error: type mismatch in component reference
> real(kind=8)[0:D.2764] * restrict
>
> and so on and so forth.
>
> Apparently this is not so much a sander bug, as a compiler bug related to
> gfortran 4.5.0 (although I'd be interested to know whether the sander code
> is doing something questionable to bring it about). Nevertheless, it can be
> avoided by reducing the Fortran optimisation level (FOPTFLAGS in config.h)
> from O3 to O2.
>
> I've cross-posted this at the main Amber list for the benefit of those users
> who may be stuck on this point in earlier versions of Amber.
>
> Tests
> -----
>
> Both Intel and GNU compilers produce a number of errors and failures of
> varying degrees of severity throughout the testing process. What I hope to
> do in the near future is come up with a list of what those are, so they can
> be marked for fixing (or not, as appropriate).
>
> Cheers,
> Ben
>
> --
> Benjamin P. Roberts
> Postdoctoral Research Associate
> Quantum Theory Project
> University of Florida
>
> 2301 New Physics Building #92
> PO Box 118435
> Gainesville FL 32611-8435
> USA
>
> Phone: +1 352 392 6712
> Cell: +1 352 222 3677
>
> Member of the Royal Australian Chemical Institute
> and of the American Chemical Society
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
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>
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Received on Wed Sep 30 2009 - 08:30:02 PDT
