[gmx-developers] how to extend a run using tpbconv?

[Berk Hess]

Hi,

The problem was that the number of pme nodes, which is read from the 
checkpoint file,
was only set on the master node and not on all the other nodes.
I have fixed it.

Thanks for reporting this bug,

Berk

Berk Hess wrote:
> Hi,
>
> I have fixed problems like this a few weeks ago.
> Is this with the newest CVS code?
>
> If not could you try it with the newest code.
> If it still you can mail me your new tpr file and your cpt file.
>
> Berk
>
> spitaleri.andrea at hsr.it wrote:
>> Hi Berk,
>> thanks for your reply. I followed your suggestion but I did not work.
>> Basically:
>> 1. tpbconv -s old -extend (or until) -o new -> it does not work (it ask
>> for trr)
>>
>> 2. tpbconv -s old -nsteps -o new 2a. mdrun -s new -cpi file.cpt it 
>> crashes with this error:
>>
>> Program mdrun, VERSION 4.0_beta1
>> Source code file: domdec.c, line: 5627
>>
>> Fatal error:
>> The size of the domain decomposition grid (12) does not match the number
>> of nodes (24). The total number of nodes is
>>  24
>>
>> The only way to get to work it is in the old fashion:
>> tpbconv -s -extend -o new -f -e
>> mdrun -s new (without file.cpt)
>>
>> I am just wondering wheter the last procedure is still correct.
>>
>> Thanks in advance
>>
>> andrea
>>
>> Andrea Spitaleri PhD
>> Dulbecco Telethon Institute c/o DIBIT Scientific Institute
>> Biomolecular NMR, 1B4
>> Via Olgettina 58
>> 20132 Milano (Italy)
>> Tel: 0039-0226434348/5622/3497/4922
>> Fax: 0039-0226434153
>>
>> ----- Original Message -----
>> From: Berk Hess <hessb at mpip-mainz.mpg.de>
>> Date: Tuesday, September 16, 2008 5:00 pm
>> Subject: Re: [gmx-developers] how to extend a run using tpbconv?
>>
>>  
>>> Hi,
>>>
>>> Extending is only required if you want more steps then you initially 
>>> set in your mdp file.
>>>
>>> The procedure is to first modify only nsteps in your tpr file and 
>>> then continue from the checkpoint file:
>>> 1 tpbconv -s old -extend (or -until or -nsteps) -o new
>>> 2 mdrun -s new -cpi file.cpt
>>>
>>> Berk
>>>
>>> andrea spitaleri wrote:
>>>    
>>>> Hi then,
>>>> I see that now gromacs can read checkpoint file. Which is now       
>>> the    
>>>> right procedure to extend a simulation using tpbconv?
>>>>
>>>> 1. tpbconv -s file.tpr -f file.cpt -extend 1000 -o new
>>>> or
>>>> 1. tpbconv -s file.tpr -f file.trr -extend 1000 -o new
>>>>
>>>> 2. mdrun -s new
>>>> or
>>>> 2. mdrun -s new -cpi file.cpt
>>>>
>>>> Then, do I need to keep the same number of cpus of the previous       
>>> run or    
>>>> I can change?
>>>>
>>>> thanks in advance
>>>>
>>>> Regards,
>>>>
>>>> andrea
>>>>
>>>>       
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