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.
Thanks!
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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