AMBER Archive (2009)

Subject: Re: [AMBER] pmemd

From: michael (
Date: Mon Aug 10 2009 - 14:51:59 CDT

On Fri, 2009-08-07 at 11:18 -0400, case wrote:
> On Fri, Aug 07, 2009, michael wrote:
> > Is this the right/best forum to raise a couple of points relating to
> > building pmemd ("bugs")? thanks, michael
> Yes...this is the correct place for that....dac

I've been trying to discover why pmemd (amber10 version) seems to fall
over with a certain MPI implementation on our system (Itanium-2, Linux)
so I've recompiled using ifort's strictest compile options. A couple of
issues have arisen and I'd welcome feedback:

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.

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

I hope that's useful,

Dr. Michael K Bane
Senior Development Officer
Univ. of Manchester M13 9PL

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