*Hi,*
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
flog1.log
For 100 ps it took about 1 hr (as I can see from the log file)
Time: 47060.494 3923.274 1199.5
1h05:23
(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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