Re: [gmx-users] Simulation runs on iMac but explodes on cluster

> > I'd still be skeptical. 15000 steps is a long time for the trajectories to > diverge. If you can run to 14550 with SSE and stop, and then show that > continuing with SSE explodes and unoptimized kernels do not, then you have > serious evidence of a bug. Diagnosing the cause of such a bug will n

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Mark, Thanks for the information and help. OK, but that can be just lucky - how lucky depends on your preparation > protocol, which you haven't told us about. You are not actually doing the > same calculation on both machines - the processes are chaotic even if > everything seems equivalent. >

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

On 13/07/2011 7:32 PM, Luke Goodsell wrote: Hi Per, I did as you suggested and it's just reached step 15000 and is still going. Many thanks indeed! I'd still be skeptical. 15000 steps is a long time for the trajectories to diverge. If you can run to 14550 with SSE and stop, and then show th

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Per, I did as you suggested and it's just reached step 15000 and is still going. Many thanks indeed! Is there something I can do to extract useful debugging information to submit to redmine? Luke On Wed, Jul 13, 2011 at 10:00, Per Larsson wrote: > Hi! > > Could you try running with GMX_NOO

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

On 13/07/2011 7:01 PM, Luke Goodsell wrote: Hi Mark, Perhaps your simulation is intrinsically unstable, and you haven't gotten unlucky enough yet on the iMac. Check out http://www.gromacs.org/Documentation/Terminology/Blowing_Up The simulation on the iMac reaches a stable equilibriu

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Mark, Perhaps your simulation is intrinsically unstable, and you haven't gotten > unlucky enough yet on the iMac. Check out http://www.gromacs.org/** > Documentation/Terminology/**Blowing_Up > The simulation on the iMac reaches a sta

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi! Could you try running with GMX_NOOPTIMIZEDKERNELS=1, to see if this could potentially be a bug in the sse code (I noticed nb_kernel410_x86_64_sse in your error message. Thanks /Per 13 jul 2011 kl. 09.35 skrev Luke Goodsell: > As the subject suggests, I have a simulation that runs corre

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

Hi Emanuel, What kind of compounds are you simulating? > > ~1800 atom protein > What size of box are you using? > Not sure of specifics, since the tpr file was provided by a collaborator, but it appears to be ~ 7nm in each dimension > > > Do you run on multiple thread when you run i

Re: [gmx-users] Simulation runs on iMac but explodes on cluster

On 13/07/2011 5:35 PM, Luke Goodsell wrote: Hi, As the subject suggests, I have a simulation that runs correctly on my iMac, but fails when I try to run it on a cluster, and I am hoping someone may be able to suggest which things to try first to resolve the issue. Background: The simulation

RE: [gmx-users] Simulation runs on iMac but explodes on cluster

bject: [gmx-users] Simulation runs on iMac but explodes on cluster Hi, As the subject suggests, I have a simulation that runs correctly on my iMac, but fails when I try to run it on a cluster, and I am hoping someone may be able to suggest which things to try first to resolve the issue.

[gmx-users] Simulation runs on iMac but explodes on cluster

Hi, As the subject suggests, I have a simulation that runs correctly on my iMac, but fails when I try to run it on a cluster, and I am hoping someone may be able to suggest which things to try first to resolve the issue. Background: The simulation proceeds perfectly well on the iMac (OS X 10.5) w