[gmx-users] Identical energies generated in a rerun calculation ... but ...

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 27 16:16:38 CEST 2009

Hi Mark,

I tried applying your patch and found some odd installation behavior.  We have 
two systems that I am trying to patch.  The first uses gcc-3.3 and worked fine. 
  The other uses gcc-4.2.2, and the compilation failed with:

"md.c", line 933.18: 1506-046 (S) Syntax error.
"md.c", line 934.11: 1506-277 (S) Syntax error: possible missing ';' or ','?
make[3]: *** [md.o] Error 1
make[3]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/rdiv1001/gmx/gromacs-4.0.4/src'
make: *** [all-recursive] Error 1

The error seems to point to this line:

  } else { // DDMASTER(cr->dd) == TRUE

Is the statement at the end supposed to be a comment?  I'm only a novice at C, 
so I'm used to seeing something more like:

  } else { /* DDMASTER(cr->dd) == TRUE */

If I make that change, then the system using gcc-4.2.2 doesn't complain and the 
installation finishes successfully.  I don't want to go haphazardly commenting 
out lines of code, so I'd appreciate any feedback on what might be going on.



Mark Abraham wrote:
> Mark Abraham wrote:
>> Berk Hess wrote:
>>> Hi,
>>> I think you can replace all state-> by state_global-> within { } 
>>> after the if statement
>>> on line 929 of md.c.
>>> Then I think it should work for serial, PD and DD.
>>> Mark, could you test if this works and report back?
>> Thanks for the prompt response.
>> I had tried something equivalent to this earlier, and kept getting the 
>> same segfault. I now see why... state_global is only allocated on 
>> DDMASTER(cr) (or some such), so we need a slightly more cunning 
>> solution. I'll figure it out tomorrow.
> OK I have a complete fix. Under DD, non-DDMASTER processes should skip 
> this step copying data structures from rerun_fr to state_global. The 
> sizes of the various loop copies should be state_global->natoms, not 
> mdatoms->nr (which is smaller than state_global->natoms under DD, but 
> equal under other conditions). So attached is a patchfile to be applied 
> from src/kernel with
> patch md.c < dd_mdrun.patch
> I tested single-processor with and without mpi, four processors with DD 
> and no separate PME nodes, four processors with PD, and 16 processors 
> with DD and 5 PME nodes and got agreement between the leading 
> significant figures reported in the .log file for all cases compared 
> with single-processor plain 4.0.4.
> I had a quick look at CVS releases-4.0-patches and since this bit of 
> do_md() looks the same, this patch can probably be applied there and/or 
> to the head 4.1 branch painlessly.
> I will attach this patchfile to the bugzilla.
> Before a release of 4.0.5 or 4.1, normal users should do "mdrun -rerun 
> -pd", unless they're confident with applying this patch!
> Mark
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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