Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi all, After spending time for troubleshooting, I found that gromacs checkpoint/restart feature is working well. The failure occurred because I use root user to submit restart job (using slurm resource manager). After switching to non root user, the restart process is running. The reason why I

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

ok thanks > Hi, > > Yes, that's one way to work around the problem. In some places, a module > subsystem can be used to take care of the selection automatically, but you > don't want to set one up for just you to use. > > Mark > > On Sun, May 15, 2016 at 11:48 AM

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, Yes, that's one way to work around the problem. In some places, a module subsystem can be used to take care of the selection automatically, but you don't want to set one up for just you to use. Mark On Sun, May 15, 2016 at 11:48 AM wrote: > Thanks Mark, > > My

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Thanks Mark, My sysadmins have let me install my own GROMACS versions and have not informed me of any such mechanism. Would you suggest I qrsh into a node of each type and build an mdrun-only version on each? I'd then select a particular node type for a submit script with the relevant mdrun.

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, On Sat, May 14, 2016 at 1:09 PM wrote: > In case it's relevant/interesting to anyone, here are the details on our > cluster nodes: > > nodes # model # cores cpu model > RAM node_type > fmb01 - fmb33 33

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

In case it's relevant/interesting to anyone, here are the details on our cluster nodes: nodes # model # cores cpu model RAM node_type fmb01 - fmb33 33 IBM HS21XM 8 3 GHz Xeon E5450

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

On 5/14/16 3:48 AM, Husen R wrote: Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount of processes from 24 to 16 processes.

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

thanks a lot for your fast response. I have tried it, and it failed. I ask in this forum just to make sure. However, there was something in my cluster that probably make it failed. I'll handle it first and then retry to restart again. Regards, Husen On Sat, May 14, 2016 at 7:58 AM, Justin

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

On 5/13/16 8:53 PM, Husen R wrote: Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager. On Sat, May 14, 2016 at 7:53 AM, Husen R wrote: > Dear all > > Does simulation able to be restarted from checkpoint file with fewer nodes > ? > let's say, at the first time, I run simulation with 3 nodes. At running

[gmx-users] Restart simulation from checkpoint file with fewer nodes

Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that simulation immadiately based on checkpoint