[gmx-users] MD Simulation Time Is Slow

Ahmed dojjan9 at gmail.com
Fri Jun 14 23:07:17 CEST 2019


I am using gromacs and I  would like to enhance my MD simulations time run
on the servers. I execute the following command:

gmx mdrun -nt 24 -s full.tpr -e full1.edr -o full1.trr -c p4iw_full1.gro -g

For 100 ps it took about 1 hr (as I can see from the log file)

       Time:    47060.494     3923.274     1199.5


                 (ns/day)    (hour/ns)

Performance:        2.202       10.898

Please let me know if I can make the run faster? Since I am going to do MD
simulations run for 100 ns. (Protein with 750 amino acids in water)

I appreciate your help and time,
A. Dojjan

The server features is here

Architecture:        x8:6_64

CPU op-mode(s):      32-bit, 64-bit

Byte Order:          Little Endian

CPU(s):              12

On-line CPU(s) list: 0-11

Thread(s) per core:  1

Core(s) per socket:  1

Socket(s):           12

NUMA node(s):        2

Vendor ID:           GenuineIntel

CPU family:          6

Model:               62

Model name:          Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz

Stepping:            4

CPU MHz:             2600.000

BogoMIPS:            5200.00

Hypervisor vendor:   VMware

Virtualization type: full

L1d cache:           32K

L1i cache:           32K

L2 cache:            256K

L3 cache:            20480K

NUMA node0 CPU(s):   0-5

NUMA node1 CPU(s):   6-11

Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush dts mmx fxsr sse sse2 ss syscall nx rdtscp lm
constant_tsc arch_perfmon pebs bts nopl xtopology tsc_reliable nonstop_tsc
cpuid pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 x2apic popcnt
tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm cpuid_fault
pti fsgsbase tsc_adjust smep arat

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