Thanks Dan,
I'm running this on Lonestar (16 12 processor nodes w/24GB mem each). The
system is a small solvated box of about 6000 atoms (~3 MB for QM
calculation, I don't know where to look for other memory usage).
What would be the workaround here? Do I need to dump the restraints that
need reference coordinates for something else or can I just be more
judicious in how I request memory?
Brian
On Mon, Feb 11, 2013 at 1:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Without knowing more about your system, your input, and where you're
> trying to run I can only speculate, but it seems like memory is being
> blown during mask parsing. The eval() function allocates a stack for
> use when converting the mask string into tokens which are then parsed
> to get the final mask selection. This stack is 256*natom*4 bytes
> (assuming integer size of 4 bytes), so depending on how many atoms are
> in your system, that's how much memory each thread needs at that
> point. For even a moderately large system (say 100k atoms) that's not
> too much memory per thread (~100MB), but if threads are sharing memory
> this can add up (i.e. if all 192 groups have to share memory you'll
> need 19.2 GB free in addition to all other allocated memory).
>
> -Dan
>
> On Mon, Feb 11, 2013 at 8:42 AM, Brian Radak <radak004.umn.edu> wrote:
> > I've been running a large number of (independent) QM/MM umbrella sampling
> > simulations using multisander. I haven't done exhaustive tests, but
> running
> > a small (12) or modestly large (108) number of jobs works just fine.
> > However, using a larger number of jobs (192) results in a few errors:
> >
> > === STDERR ===
> > out of dynamic memory in opal_show_help_yylex()
> >
> > <MPI_ABORT message omitted for brevity>
> >
> > [c314-113.ls4.tacc.utexas.edu:11115] 4 more processes have sent help
> > message help-mpi-api.txt / mpi-abort
> > [c314-113.ls4.tacc.utexas.edu:11115] Set MCA parameter
> > "orte_base_help_aggregate" to 0 to see all help / error messages
> > ======
> >
> > === STDOUT ===
> > Error in group input::atommask.f::eval
> > stack allocation error
> > ======
> >
> > A typical groupfile entry looks like:
> >
> > -O -i r0/HEEP_QMMM_US_3.inp -o r0/HEEP_QMMM_US_3.out -p
> ../input/HEEP.parm7
> > -c r0/HEEP_QMMM_US_2.rst7 -r r0/HEEP_QMMM_US_3.rst7 -x
> r0/HEEP_QMMM_US_3.nc
> > -ref ../equilibration/minimize0.rst7
> >
> > The only thing here that seems not so smart is that ALL of the
> trajectories
> > use the same file for the reference coordinates. Does that sound like it
> > could be a problem? Does that make any sense in giving rise to the errors
> > here? Other ideas?
> >
> > Thanks,
> > Brian
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Feb 11 2013 - 11:00:03 PST
