[gmx-users] Dyn. Load Balance changes Cut off

[Johnny Lu]

I don't see things like that on every machine that I used.

The machine that made that log file has 4 Tesla K40, and 16 Xeon CPU.

Using 4 MPI threads
Using 8 OpenMP threads per tMPI thread

Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz
Family:  6  Model: 45  Stepping:  7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc
pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
tdt x2apic
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256


4 GPUs detected:
  #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
  #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
  #2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
  #3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible

4 GPUs auto-selected for this run.
Mapping of GPUs to the 4 PP ranks in this node: #0, #1, #2, #3

Will do PME sum in reciprocal space.


On Fri, Nov 7, 2014 at 1:21 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi.
>
> When I read the log file, I see:
>
>  PP/PME load balancing changed the cut-off and PME settings:
>            particle-particle                    PME
>             rcoulomb  rlist            grid      spacing   1/beta
>    initial  1.000 nm  1.090 nm      64  64  64   0.117 nm  0.320 nm
>    final    1.302 nm  1.392 nm      48  48  48   0.156 nm  0.417 nm
>  cost-ratio           2.08             0.42
>  (note that these numbers concern only part of the total PP and PME load)
>
> So, the cut off that I typed in the mdp file was changed.
>
> Will that affect the result of the simulation? I'm using gromacs 4.6.7.
> Or any cut off will be fine, as long as I use a cut off that is long
> enough?
>
> The force field paper for Amber99SB-ILDN used 1.0 nm for both VdW and PME
> electrostatic cut off.
>
> Thanks again.
>