AMBER Archive (2009)

Subject: Re: [AMBER] pmemd

From: michael (michael.bane_at_manchester.ac.uk)
Date: Sat Aug 15 2009 - 06:30:28 CDT

On 11 Aug 2009, at 01:00, Ross Walker wrote:

> Hi Michael,
>
> > a) does pmemd presume some variables initialised to zero? On our
> > system
> > with `ifort -O0 -g` this appears not to be the case and caused
> > immediate
> > abort. Initialising inerr to zero in file mdin_ewald_dat.fpp fixes
> > this.
>
> See bugfix.24: http://ambermd.org/bugfixes/10.0/bugfix.24

:)
thanks!

>
>
> > b) using `ifort -O0 -g -check all` throws error at line 144 of
> > pmeall_tasks_setup.f90 where it calls a sub with arg EP_FRAMES but
> > EP_FRAMES is dynamic and hasn't been declared. Tracing back shows
> > gbl_frame_cnt is zero in bcast_extra_pnts_nb14_dat() in file
> > extra_pnts_nb14.fpp/f90 meaning alloc_nb14_mem_only() is called
> > rather
> > than alloc_extra_pnts_nb14_mem (which is the one that allocates
> > EP_FRAMES)
>
> I will let Bob comment on this some more. It seems to me this comes
> about
> because it is only required when extra points are in use. In other
> words
> when frame_cnt > 0. Thus although frames is passed in as unallocated
> it is
> never referenced in the file.

Noted

> Thus I believe it is legal code and just the
> -check all being too overzealous.

Possibly but I can see that if EP_FRAMES is not allocated that a
'random' mem loc will be used in the sub call (but also that said mem
loc isn't being read from)

> Do you see problems because this array is
> not allocated?

I'm no chemistry nor pmemd expert but if I remove the array bounds check
then it does seem to run

> Does the fortran style require all arguments to a subroutine
> to have been allocated even if they are not used? I am not sure on
> this last
> point and it would be interesting to know. Perhaps it isn't allowed,
> or it
> should be initialized as null for example.

I'm not 100% of the spec but it was Intel's run-time check that was
pulling it as an error.

Thanks, Michael

> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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