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

[jkrieger at mrc-lmb.cam.ac.uk]

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 	      
 16GB 	hs21
fmb34 - fmb42 	        9 	IBM HS22 	8 	        2.4 GHz Xeon E5530 	       
16GB 	hs22
fmb43 - fmb88 	        45 	Dell PE M610 	8 	        2.4 GHz Xeon E5530 	  
     16GB 	m610
fmb88 - fmb90 	        3 	Dell PE M610+ 	12 	        3.4 GHz Xeon X5690 	 
      48GB 	m610+
fmb91 - fmb202 	        112 	Dell PE M620 	24 (HT) 	2.9 GHz Xeon E5-2667 	
       64GB 	m620
fmb203 - fmb279 	77 	Dell PE M620 	24 (HT) 	3.5 GHz Xeon E5-2643 v2 	64GB
	m620+
fmb280 - fmb359 	80 	Dell PE M630 	24 (HT) 	3.4 GHz Xeon E5-2643 v3 	64GB
	m630

I could only run GROMACS 4.6.2 on the last three node types and I believe
the same is true for 5.0.4

Best wishes
James

> I have found that only some kinds of nodes on our cluster work for gromacs
> 4.6 (the ones we call m620, m620+ and m630 but not others - I can check
> the details tomorrow). I haven't tested it again now I'm using 5.0 so
> don't know if that's still an issue but if it is it could explain why your
> restart failed even and the initial run didn't.
>
>> 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 Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> 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 simulation immadiately based on checkpoint file
>>>> with
>>>> the remaining 2 nodes. does gromacs support such case ?
>>>> I need help.
>>>>
>>>
>>> Have you tried it?  It should work.  You will probably get a note about
>>> the continuation not being exact due to a change in the number of
>>> cores,
>>> but the run should proceed fine.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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