Hi,
I coded the PIMD part in Amber but the TI module was implemented later
by Jiri (cc'd here) so I am not quite sure about how it works and how
it was coupled to both PIMD and EVB. I will take a look at it to see
if I can fix the problem.
All the best,
Francesco
On Mar 30, 2010, at 7:51 AM, Daniel Roe wrote:
> Using a sander.LES.MPI compiled on 2010-03-02 I get errors for the two
> segfaulting tests, but no errors for the others:
>
> cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_2D-PMF && ./Run.evb
> [aborts]
> cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF && ./Run.evb [aborts]
>
> I was able to track down the segfault to the pimd_part_spring_force()
> subroutine; there is a do loop that begins around line 162 in
> pimd_force.f
> that makes use of the array dmdlm(:), which is part of the pimd_vars
> module. According to the description, "dmdlm = d mass / d lambda /
> mass
> (for TI w.r.t. mass)". Further searching shows that this array is
> allocated
> and initialized in the rdparm2() subroutine (rdparm.f) around line
> 557.
> However, it is only allocated and set up if itimass is greater than
> 0, and
> according to the nxtsec() call this requires a TI_MASS section in
> the prmtop
> file (which doesn't appear to be present, at least in the 2D-PMF
> test case).
> Setting itimass equal to 1 just causes sander.LES.MPI to complain
> about the
> missing TI_MASS section. There is this comment:
> ! JVAN: dmdlm must be allocated here, not in pimd_init.
> which seems to indicate at some point initialization used to be inside
> pimd_init, but I have no idea how it used to be done and whether it
> required
> the itimass variable to be set before.
>
> Does anyone more familiar with EVB stuff have any idea what might be
> the
> right way to fix this?
>
> For the time being I will try and track down the other EVB errors I
> have
> been seeing in the release candidate that don't seem present in the
> 2010-03-02 version.
>
> -Dan
>
>
> On Tue, Mar 30, 2010 at 8:52 AM, case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Mon, Mar 29, 2010, Daniel Roe wrote:
>>
>>> So on two separate platforms I get similar errors, all for EVB
>>> tests with
>>> sander.LES.MPI:
>>
>> There is a good chance that this is related to the "state.f" stuff
>> Mark put
>> in. Someone who has some experience with this (or not) could look
>> at the
>> evb code for places where the old ener() arrays are being used.
>>
>> Another step would be to go back in CVS to before March 19, and see
>> if the
>> EVB
>> was working at that point. That would help to pin the blame on (or
>> absolve)
>> the state.f code.
>>
>> ...thx...dac
>>
>>
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>> AMBER-Developers.ambermd.org
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>>
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
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Received on Tue Mar 30 2010 - 08:30:03 PDT
