Re: failure in RATTLE

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Dec 16 2008 - 13:26:09 CST

On Tue, 16 Dec 2008, Sangamesh B wrote:

SB> Hello NAMD users,
SB>
SB> I'm running NAMD-2.6 built with MPICH2 & GNU compilers on Rocks-5
SB> Linux cluster. There were no errors during compilation.
SB> The examples given with NAMD distribution were also working.
SB>
SB> For one of the input file, the following error is appearing:

for one the the input files from where?
are they provided by a user, did you write
them or did you download them?
 
SB> /opt/apps/namd26_gnu/Linux-amd64-MPI/charmrun +p4
SB> /opt/apps/namd26_gnu/Linux-amd64-MPI/namd2 npt02.inp | tee
SB> npt_result_out_ll

you obviously didn't read the documentation well enough.
when you compile with MPI, you _have_ to use mpirun and
_not_ charmrun. howeve, if you simply run over GigE, there
is no need to recompile, but you can use the provided
precompiled binaries (and _with_ charmrun).

SB> ..
SB>
SB> ERROR: Atom 3601 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 3602 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 3603 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 20926 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 20927 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 20928 velocity is nan nan nan (limit is 10000)

as an HPC consultant you should know that "nan" is an
sign of indication of invalid math and that can either
mean and invalid or bad input or a miscompiled binary.

SB> ERROR: Atoms moving too fast; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 60!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 60!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 60!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 60!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 277!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 277!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 277!
SB> ERROR: Constraint failure; simulation has become unstable.
SB>
SB> ..
SB> ERROR: Atom 30757 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 30758 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 30759 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 34330 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 34331 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atom 34332 velocity is nan nan nan (limit is 10000)
SB> ERROR: Atoms moving too fast; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 480!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 480!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 480!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 480!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 1082!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 1082!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 1082!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 1082!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 703!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Constraint failure in RATTLE algorithm for atom 703!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Exiting prematurely.
SB> ==========================================
SB> WallClock: 4.136847 CPUTime: 4.136847 Memory: 128778 kB
SB> End of program
SB> ERROR: Exiting prematurely.
SB> ==========================================
SB> WallClock: 4.144087 CPUTime: 4.144086 Memory: 128778 kB
SB> End of program
SB> ERROR: Constraint failure in RATTLE algorithm for atom 703!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Exiting prematurely.
SB> ==========================================
SB> WallClock: 4.156466 CPUTime: 4.156467 Memory: 128778 kB
SB> End of program
SB> ERROR: Constraint failure in RATTLE algorithm for atom 703!
SB> ERROR: Constraint failure; simulation has become unstable.
SB> ERROR: Exiting prematurely.
SB> ==========================================
SB> WallClock: 4.164990 CPUTime: 4.164990 Memory: 128778 kB
SB> End of program
SB>
SB> I'm not understanding why these errors are appearing.

simple: garbage in, garbage out.
 
SB> Are these errors due to wrong parameters in the input file or NAMD not
SB> installed properly or else due to lower memory on the computer? (4 Gb
SB> mem, run on single node)

classical MD does not require a lot of memory. please also note,
that the quoted output indicates that you are running 4 (serial)
copies instead of a proper parallel run (it should be even more
obvious from the first part of the output, that you didn't quote).

for the reason, see above.

SB>
SB> Thanks in advance,
SB> Sangamesh,
SB> Consulatnt - HPC

please note the typo. ;-)

cheers,
   axel.

 

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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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