Hi,
It seems like you should have enough memory. The only thing I can
think of to try increasing your stack size before you execute
sander.MPI, something like e.g.
ulimit -s 20480
sander.MPI -0 ...
-Dan
On Mon, Feb 11, 2013 at 11:48 AM, Brian Radak <radak004.umn.edu> wrote:
> 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
>> AMBER.ambermd.org
>> 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.
> _______________________________________________
> 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)
_______________________________________________
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Received on Mon Feb 11 2013 - 12:00:03 PST
