[lammps-users] My modeling is able to run with single CPU. However, it can not run under multiCPU.

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1

Hi, everyone,

I like to minimize a five chains in my simulation.
However, I found it is able to run with single CPU, but it can’t run under multi-CPU.

I like to modify this modeling to be able to run under multi-CPU, what can i do?
Enclosed please find the data file,input file, output file, and log file.

Thanks in advance.

Houyang

1.out (3.29 KB)

data.1 (9.29 KB)

in.1 (473 Bytes)

log (797 Bytes)

2

Houyang,

It has nothing to do with your model. It is sth related to how you build up the lammps with MPI version. Read the document, especially " how to build lammps " section. Or find a local parallel computing expert to help you out.

Ajing

3

Hi, Ajing,
The lammps i used was compiled by the expert of super computer center in my university.
I also asked some friend ran the job on their computer, and it was not work.

Thanks
Houyang

4

Hi Houyang,

I tested your system. Actually the one cpu minimization can run (but
no warrant to be correct) and the multiple cpus minimization cannot
run with the error:

ERROR on proc 1: Bond atoms 37 45 missing on proc 1 at step 0
ERROR on proc 2: Bond atoms 21 29 missing on proc 2 at step 0

I checked you data.1 file and found the coordinates of atoms 37 and 45
are as follows:

-15.9473 -20.6692 8.4152
-8.4382 -4.6255 -16.7348

The distance between these two atoms is ~18 angstroms (considering the
pbc), which is far from the bond length r0=1.5 angstrom in your in.1
file. I also viewed your system with vmd and found the structure is
very strange.

So please check the initial structure first and do lammps simulation
with reasonable initial configuration!!!

Dongshan

5

Hi Dongshan,

Thanks so much for your kindly reply and suggestions.
I will rewrite the initial configuration and test it again.

Thanks again.
Houyang