Re: [gmx-users] Domain decomposition error with -rerun

Hi, Thanks for the reply. I am only doing a rerun of a trajectory that has already evolved without any dynamic load balancing problems. -rerun only recalculates energies right. I don't understand why the same trajectory is giving decomposition error now. On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SU

Re: [gmx-users] Domain decomposition error with -rerun

Hi. That indicates a problem with dynamic load balancing. Try to build different sizes of the box. On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer wrote: > Hi, > > I am trying to calculate interaction between specific residues using gmx > mdrun -rerun flag. The trajectory was in a dcd format

[gmx-users] Domain decomposition error with -rerun

Hi, I am trying to calculate interaction between specific residues using gmx mdrun -rerun flag. The trajectory was in a dcd format, which I converted to a trr file. I get the following error - Domain decomposition has not been implemented for box vectors that have non-zero components in direction

[gmx-users] Force fields

Dear all, I have the Gromos-54A7 force fields (FF) for the molecule number 1 in the below link, using thoes how I can have the FF for the molecules number 2,3 and 4 in the same link without doing extra calculations? What could be the relation between the FF of other molecule with the FF of molecule

Re: [gmx-users] strange GPU load distribution

I see. :) I will check again when I am back at work. Thanks! Alex On 4/27/2018 2:16 PM, Mark Abraham wrote: Hi, What you think was run isn't nearly as useful when troubleshooting as asking the kernel what is actually running. Mark On Fri, Apr 27, 2018, 21:59 Alex wrote: Mark, I copied

Re: [gmx-users] strange GPU load distribution

Hi, What you think was run isn't nearly as useful when troubleshooting as asking the kernel what is actually running. Mark On Fri, Apr 27, 2018, 21:59 Alex wrote: > Mark, I copied the exact command line from the script, right above the > mdp file. It is literally how the script calls mdrun in

Re: [gmx-users] strange GPU load distribution

Mark, I copied the exact command line from the script, right above the mdp file. It is literally how the script calls mdrun in this case: gmx mdrun -nt 2 -nb cpu -pme cpu -deffnm On 4/27/2018 1:52 PM, Mark Abraham wrote: Group cutoff scheme can never run on a gpu, so none of that should matte

Re: [gmx-users] strange GPU load distribution

Group cutoff scheme can never run on a gpu, so none of that should matter. Use ps and find out what the command lines were. Mark On Fri, Apr 27, 2018, 21:37 Alex wrote: > Update: we're basically removing commands one by one from the script that > submits the jobs causing the issue. The culprit

Re: [gmx-users] strange GPU load distribution

Update: we're basically removing commands one by one from the script that submits the jobs causing the issue. The culprit is both EM and the MD run: and GPUs are being affected _before_ MD starts loading the CPU, i.e. this is the initial setting up of the EM run -- CPU load is near zero, nvidia-smi

Re: [gmx-users] strange GPU load distribution

As I said, only two users, and nvidia-smi shows the process name. We're investigating and it does appear that it is EM that uses cutoff electrostatics and as a result the user did not bother with -pme cpu in the mdrun call. What would be the correct way to enforce cpu-only mdrun when coulombtype =

Re: [gmx-users] Box size to be considered in editconf

On 4/27/18 1:36 PM, SHYANTANI MAITI wrote: Dear all, What should be the size of a cubic box in the command editconf for simulating a protein-protein complex consisting of 500 residues altogether? Depends entirely upon the geometry of the protein itself. The box size for a globular protein wi

Re: [gmx-users] strange GPU load distribution

No. Look at the processes that are running, e.g. with top or ps. Either old simulations or another user is running. Mark On Fri, Apr 27, 2018, 20:33 Alex wrote: > Strange. There are only two people using this machine, myself being one of > them, and the other person specifically forces -nb cpu

Re: [gmx-users] strange GPU load distribution

Strange. There are only two people using this machine, myself being one of them, and the other person specifically forces -nb cpu -pme cpu in his calls to mdrun. Are any other GMX utilities (e.g. insert-molecules, grompp, or energy) trying to use GPUs? Thanks, Alex On Fri, Apr 27, 2018 at 5:33 A

[gmx-users] Box size to be considered in editconf

Dear all, What should be the size of a cubic box in the command editconf for simulating a protein-protein complex consisting of 500 residues altogether? Thanks in advance. -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

Re: [gmx-users] strange GPU load distribution

The second column is PIDs so there is a whole lot more going on there than just a single simulation, single rank using two GPUs. That would be one PID and two entries for the two GPUs. Are you sure you're not running other processes? -- Szilárd On Thu, Apr 26, 2018 at 5:52 AM, Alex wrote: > Hi