Re: [gmx-users] Loosing partly the available CPU time

Hi Szila I tried more more OpenMP threads, (-ntomp 4), however, the performance dropped down drastically so that an NVT simulation which just took 3 hours to be finished in "-ntomp 1", now takes more thank 16 hours! Cheers, Alex On Mon, Aug 15, 2016 at 6:34 PM, Szilárd Páll

Re: [gmx-users] Loosing partly the available CPU time

Hi, Although I don't know what exactly is the system you are simulating, one thing is clear: you're pushing the parallelization limit with - 200 atoms/core - likely "concentrated" free energy interactions. The former that alone will make the run very sensitive to load imbalance and the latter

Re: [gmx-users] Loosing partly the available CPU time

Hi Szilárd, Thanks for your response, please find below a link containing required files.log files. https://drive.google.com/file/d/0B_CbyhnbKqQDc2FaeWxITWxqdDg/view?usp=sharing Thanks, Cheers, Alex On Mon, Aug 15, 2016 at 2:52 PM, Szilárd Páll wrote: > Hi, > > Please

Re: [gmx-users] Loosing partly the available CPU time

Hi, Please post full logs; what you cut out of the file will often miss information needed to diagnose your issues. At first sight it seems that you simply have an imbalanced system. Not sure about the source of the imbalance and without knowing more about your system/setup and how is it

[gmx-users] Loosing partly the available CPU time

Dear gromacs user, My free energy calculation works well, however, I am loosing around 56.5 % of the available CPU time as stated in my log file which is really considerable. The problem is due to the load imbalance and domain decomposition, but I have no idea to improve it, below is the very end