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
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
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
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.
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
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
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
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.
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
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
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
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
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