Hi,
Yes i fixed the rism_interp issue, and this patch doesnt break
any tests. Also I delayed this message until i committed a new
test case for missing box info.
scott
On Sun, Aug 16, 2009 at 06:10:27PM -0700, Ross Walker wrote:
> I have applied a similar patch to the AMBER 11 PMEMD tree.
>
> > -----Original Message-----
> > From: amber-developers-bounces.ambermd.org [mailto:amber-developers-
> > bounces.ambermd.org] On Behalf Of Scott Brozell
> > Sent: Sunday, August 16, 2009 2:52 PM
> > To: AMBER Developers Mailing List
> > Subject: Re: [AMBER-Developers] Patch for sander hang with missing box
> >
> > Thanks for reporting this, Tom.
> > I committed similar patches in amber11:
> > For check_prime_factors the input is now validated with an assert.
> > Regarding peek_ewald_inpcrd, it seems best for this to fail,
> > rather than to return, if box information is not found; this makes
> > peek_ewald_inpcrd consistent with AM_RUNMD_get_ucell_info.
> >
> > Note that this commit is untested since I cannot build sander
> > with ifort or pgf90. I might get back to this later today;
> > see below for the errors.
> >
> > Note that this issue might exist for pmemd, but I did not check.
> >
> > Scott
> >
> > On Fri, Aug 14, 2009 at 04:56:29PM -0500, Tom Joseph wrote:
> > > AMBER 10 sander hangs when box information is expected but not
> > present
> > > in the inpcrd file. I've attached sample input that reproduces this
> > > problem. Admittedly it's not necessarily the most common mistake but
> > I
> > > think an error message would be nice.
> > >
> > > peek_ewald_inpcrd() in ew_setup.f returns zeros for a, b, c if they
> > > are not found. This leads to check_prime_factors() being called with
> > > n=0, which causes it to loop infinitely. Below are a couple of
> > patches
> > > that fix this. The first gives an error message before the infinite
> > > loop, and the second fixes the infinite loop itself.
> > >
> > > Thanks,
> > > --Tom
> > >
> > > --- orig/src/sander/ew_setup.f 2008-04-16 21:34:52.000000000 -0400
> > > +++ new/src/sander/ew_setup.f 2009-08-14 17:39:41.000000000 -0400
> > > .. -974,6 +974,11 ..
> > > call peek_ewald_inpcrd(inpcrd,ax,bx,cx,alphax,betax,gammax)
> > > end if
> > >
> > > + if ( a == 0.0d0 .and. b == 0.0d0 .and. c == 0.0d0) then
> > > + call sander_bomb('load_ewald_info', &
> > > + 'Box information expected but not found', '')
> > > + end if
> > > +
> > > end if
> > > call read_ewald(ax,bx,cx,alphax,betax,gammax)
> > >
> > > --- orig/src/sander/ew_setup.f 2008-04-16 21:34:52.000000000 -0400
> > > +++ new/src/sander/ew_setup.f 2009-08-14 17:45:39.000000000 -0400
> > > .. -268,6 +268,8 ..
> > > ! this routine checks n to see if its a product of powers of
> > 2,3,5
> > > ! essential for FFTs
> > > ! result is 1 of it is such a product, 0 if not
> > > +
> > > + if (n == 0) return 0
> > >
> > > ! don't hurt n
> > > nl = n
> >
> >
> > cpp -traditional -P -DNO_SANDER_DIVCON -DBINTRAJ rism_interp.f >
> > _rism_interp.f
> > ifort -c -w95 -vec_report0 -ip -O3 -axP -FR -o rism_interp.o
> > _rism_interp.f
> > fortcom: Error: _rism_interp.f, line 68: The statement following a
> > CONTAINS is not a function-stmt or a subroutine-stmt.
> > end module rism_interp
> > ^
> > compilation aborted for _rism_interp.f (code 1)
> >
> >
> > cpp -traditional -P -DNO_SANDER_DIVCON -DBINTRAJ xray_utils.f >
> > _xray_utils.f
> > pgf90 -c -O1 -Mfree -o xray_utils.o _xray_utils.f
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 80)
> > 0 inform, 0 warnings, 1 severes, 0 fatal for
> > coordinate_transform_inverse
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 115)
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 116)
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 117)
> > 0 inform, 0 warnings, 3 severes, 0 fatal for matrix3_inverse_pure
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 131)
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 132)
> > PGF90-S-0153-Array objects are not conformable (_xray_utils.f: 133)
> > 0 inform, 0 warnings, 3 severes, 0 fatal for matrix3_inverse_det
> >
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Received on Wed Aug 19 2009 - 23:22:37 PDT
