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Re: [lammps-users] Problem with compute cluster/atom
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Re: [lammps-users] Problem with compute cluster/atom

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 14 Jun 2017 08:27:09 -0400

On Wed, Jun 14, 2017 at 6:37 AM, <1132033@...3237...> wrote:
Dear all,

I am using lammps-31Mar17 MPI version. With the script file listed below, I found mpirun -np 1 could produce good result, however, running with more threads like -np 20, the error message comes up like "*** Error in `./lmp_mpi': malloc(): memory corruption (fast): 0x0000000002167da0 ***".

My computer have two processors "Intel® Xeon(R) CPU E5-2698 v4 @ 2.20GHz × 16" with 40 cores, and the number of threads usually didn't effect the outcome without computing the cluster ID. So I guess the problem has something to do with the compute cluster/atom command.
I wonder if this error is due to a mistake on my side, or a problem in lammps. Please shed some light on this error. Testing the script file and posting your results would also be very helpful.

​sorry, i cannot​ reproduce the error you are seeing with the 19May2017 version of LAMMPS with gcc 6.3 and MPICH 3.2 using the unmodified mpi makefile
please let us know what compiler, compiler version, compiler flags, MPI library etc. you are using.



Best regards,



dimension       3
boundary        p p p
atom_style      atomic
neighbor        0.3 bin
neigh_modify    delay 5

lattice         fcc 1.5
region          box block -10 10 -10 10 -10 10
region          init block -5 5 -5 5 -5 5
create_box      1 box
create_atoms    1 region init
mass            * 1.0
velocity        all create 1.0 19880503 loop geom

pair_style      lj/cut 1.2
pair_coeff      * * 1.0 1.0 1.2

fix             1 all nve/limit 0.001
timestep        0.003
thermo          100
compute         clusterID all cluster/atom 1.2
dump            monitor all custom 500 dump.lammps    id type x y z     c_clusterID

run             10000
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Dr. Axel Kohlmeyer  akohlmey@...92......
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.