Re: [gmx-users] Tabulated potentials and performance

2010-08-04 Thread João M . Damas
Hi guys, >From what I've tested, it seems that performances decreases linearly with the amount of tables used, exactly the opposite of what Lanyuan has said. I've tested this for GROMACS 4.0.4 and from 1 to 190 tables. Near 190 tables, it seems that a threshold in performance starts to form, but n

Re: [gmx-users] Tabulated potentials and performance

2010-07-20 Thread ms
On 19/07/10 23:18, Lanyuan Lu wrote: From our group's experience, there is a critical point for dramatic performance drop when one uses two many tables. The possible reason is that the size of tables exceeds the cache size. However, this only happens when the number of tables is beyond something

Re: [gmx-users] Tabulated potentials and performance

2010-07-19 Thread Lanyuan Lu
>From our group's experience, there is a critical point for dramatic performance drop when one uses two many tables. The possible reason is that the size of tables exceeds the cache size. However, this only happens when the number of tables is beyond something like 50. The total table size for the

Re: [gmx-users] Tabulated potentials and performance

2010-07-19 Thread ms
On 19/07/10 18:32, Da-Wei Li wrote: I remember the manu states that it won't cost too much compared with standard potential function form. Well, I find in the manual exactly the opposite: "Note that table lookup is significantly slower than computation of the most simple Lennard-Jones and Coulo

Re: [gmx-users] Tabulated potentials and performance

2010-07-19 Thread Da-Wei Li
I remember the manu states that it won't cost too much compared with standard potential function form. dawei On Mon, Jul 19, 2010 at 1:22 PM, ms wrote: > On 19/07/10 17:32, Da-Wei Li wrote: >> >> It will be very little from my experience. Remember that the dominate >> part is the non-bonded forc

Re: [gmx-users] Tabulated potentials and performance

2010-07-19 Thread ms
On 19/07/10 17:32, Da-Wei Li wrote: It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. Well, that's exactly what I tabulate. dawei On Mon, Jul 19, 2010 at 12:22 PM, ms wrote: Hi, Do you know where can I find some information on

Re: [gmx-users] Tabulated potentials and performance

2010-07-19 Thread Da-Wei Li
It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. dawei On Mon, Jul 19, 2010 at 12:22 PM, ms wrote: > Hi, > > Do you know where can I find some information on how using tabulated > potential affects gmx performance, and how? I have to

[gmx-users] Tabulated potentials and performance

2010-07-19 Thread ms
Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing listg