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
>
> Hi,
>
> 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 - 23:14:02 PDT
