Hi,
>From this message it seems that you don't have enough memory to store
all of the non-bonded pairs. How many atoms are in your system, and
how much memory does each node have available? Are you running in
explicit solvent?
-Dan
On Wed, Mar 13, 2013 at 5:30 PM, David Winogradoff <dwino218.gmail.com> wrote:
> Hey Dan,
>
> Everything passed for the 2 processor case, but their were a few
> failed tests for the 8 processor case. One of the error messages read,
>
> cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0
>
> * NB pairs 145 185645 exceeds capacity ( 185750) 3
> SIZE OF NONBOND LIST = 185750
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 3 with PID 3048 on
> node login-2.deepthought.umd.edu exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
>
>
> This is similar to the error message I receive when running my simulation.
>
> -David
>
> On Wed, Mar 13, 2013 at 2:57 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> Hi,
>>
>> Have you been able to successfully run the test cases in parallel?
>>
>> -Dan
>>
>> On Wednesday, March 13, 2013, David Winogradoff wrote:
>>
>>> Hey Jason,
>>>
>>> I followed the directions on your wiki for installing amber 12,
>>> running ./patch_amber.py --update-tree until it returns that Amber12
>>> and AmberTools12 are up to date.
>>>
>>> The error messages from the supercomputer I'm using are,
>>>
>>>
>>> "[compute-f17-1.deepthought.umd.edu:21064] [[44012,1],39]
>>> ORTE_ERROR_LOG: Data unpack would read past end of buffer in file
>>> runtime/orte_init.c at line 132
>>> --------------------------------------------------------------------------
>>> It looks like MPI_INIT failed for some reason; your parallel process is
>>> likely to abort. There are many reasons that a parallel process can
>>> fail during MPI_INIT; some of which are due to configuration or environment
>>> problems. This failure appears to be an internal failure; here's some
>>> additional information (which may only be relevant to an Open MPI
>>> developer):
>>>
>>> ompi_mpi_init: orte_init failed
>>> --> Returned "Data unpack would read past end of buffer" (-26)
>>> instead of "Success" (0)
>>> --------------------------------------------------------------------------
>>> *** The MPI_Init() function was called before MPI_INIT was invoked.
>>> *** This is disallowed by the MPI standard.
>>> *** Your MPI job will now abort.
>>> [compute-f17-1.deepthought.umd.edu:21061] Abort before MPI_INIT
>>> completed successfully; not able to guarantee that all other processes
>>> were killed!"
>>>
>>>
>>> which I thought were generic openmpi error messages. For your
>>> reference, the version of openmpi I am using is openmpi16-gnu.
>>>
>>> I have also attempted to use the openmpi143-gnu version of openmpi,
>>> obtaining the error message,
>>>
>>>
>>> "[compute-f16-26.deepthought.umd.edu:30072] mca: base: component_find:
>>> unable to open
>>> /cell_root/software/openmpi/1.4.3/gnu46/sys/lib/openmpi/mca_btl_openib:
>>> perhaps a missing symbol, or compiled for a different version of Open
>>> MPI? (ignored)
>>> --------------------------------------------------------------------------
>>> MPI_ABORT was invoked on rank 14 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them."
>>>
>>>
>>> My REMD simulation is 50 replicas at different temperatures in NVT
>>> ensembles attempting exchanges every 5 ps. The template for my mdin
>>> files is
>>>
>>> replica exchange
>>> &cntrl
>>> imin=0, irest=1, ntx=5,
>>> ntt=3, temp0=XXXXX, gamma_ln=2.0, ig=-1,
>>> nstlim=2500, dt=0.002,
>>> ntb=1, ntc=2, ntf=2,
>>> ntr=0, ntp=0,
>>> ntwr=100000, ntwx=2500, ntpr=2500,
>>> cut=12,
>>> numexchg=1000,
>>> /
>>> &wt type='END'
>>> /
>>>
>>>
>>>
>>> Hopefully this answers your questions, thanks,
>>> David
>>>
>>> On Mon, Mar 11, 2013 at 6:56 PM, Jason Swails <jason.swails.gmail.com<javascript:;>>
>>> wrote:
>>> > On Mon, Mar 11, 2013 at 6:34 PM, David Winogradoff <dwino218.gmail.com<javascript:;>
>>> >wrote:
>>> >
>>> >> I am currently working on a project using amber in parallel to conduct
>>> >> a long REMD run. A few weeks ago, using the same input file that
>>> >> worked before (modified to start from where the previous simulation
>>> >> ended), my parallel run failed with a generic openmpi error message.
>>> >> After some initial hesitation, I decided to delete my installation of
>>> >> amber 12 and recompile and rebuild. I have run 'make test'
>>> >> successfully with my new serial and parallel versions of amber 12, but
>>> >> my REMD simulation still won't run. After many unsuccessful attempts
>>> >> to run, I decided to look at some of my previous output files. To my
>>> >> surprise, the older output files had amber 11 at the top. Even though
>>> >> my new simulations won't run, they do write the header, which says
>>> >> amber 12.
>>> >>
>>> >> I did see that it is possible to have some combination of amber 11 and
>>> >> amber 12, but I never installed amber 11 and do not have the tar files
>>> >> to do so. Is there any way to install amber 11 with amber 12 tar files
>>> >> (accidentally)? My hypothesis is that some requirement, such as my
>>> >> version of gnu, was out of date during my previous installation,
>>> >> preventing the complete installation of amber 12. I have tried to
>>> >> recreate the mistake, since I didn't think I could make files meant
>>> >> for amber 11 to work with amber 12, without success. The only solution
>>> >> I can think of right now is to purchase amber 11 and create a hybrid
>>> >> form of amber 11 and amber 12 that will hopefully run my simulations
>>> >> once more.
>>> >>
>>> >
>>> > When Amber 12 was released, it actually still said "Amber 11" at the top.
>>> > That was updated in bugfix.2 for Amber 12. Do you have all bug fixes
>>> > applied?
>>> >
>>> > What error messages are you getting? And what exactly are you doing?
>>> The
>>> > better way forward, IMO, is to fix Amber 12... What kind of REMD are you
>>> > doing?
>>> >
>>> > All the best,
>>> > Jason
>>> >
>>> > --
>>> > Jason M. Swails
>>> > Quantum Theory Project,
>>> > University of Florida
>>> > Ph.D. Candidate
>>> > 352-392-4032
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org <javascript:;>
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org <javascript:;>
>>> 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
>
> _______________________________________________
> AMBER mailing list
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> 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 Fri Mar 15 2013 - 09:00:04 PDT
