[CP2K-user] Gradual slowdown in my cp2k simulation

Alv LI wt... at outlook.com
Thu Jan 17 04:11:31 CET 2019



Dear CP2K users and developers,

 

I have been running cp2k-6.1 on Linux Centos 6.8 (24 CPU cores with 32GB 
ram) with a system of 1 NaBr pair solvated in 64 water molecules in a cubic 
PBC box. Some of the simulations will slow down after running for a while. 
The average time needed for a SCF step increases from 1.0 s to 2.0 s 
gradually after a random amount of time. The cp2k binary was compiled with 
gcc-4.9.4 and openmpi-2.1.5. I have tried different combinations of mpi 
ranks and openmp threads and still observed the slowdown. The speed would 
be back to normal after cleaning the cache via /proc/sys/vm/drop_caches, 
but after a while, it slows down again. The input and arch files are 
attached. Do you have any idea what is causing the slowdown and how to fix 
the problem? Any comment will be much appreciated.


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Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    1
Core(s) per socket:    12
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 63
Model name:            Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
Stepping:              2
CPU MHz:               2500.016
BogoMIPS:              4999.30
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              30720K
NUMA node0 CPU(s):     0-11
NUMA node1 CPU(s):     12-23
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