[Octopus-users] Any tips for big systems (protein)?

[Cheng. W]

Dear Nicola and Xavier,

Thank you very much for reply. Now the calculation can pass the Hartree 
part now.

What I am very curious is that the memory usage seems to be very huge, 
the following is the error output of PBS

* O    891.972994            0.000367 4308616 | ..|projector.projector_end
* I    891.973335   1216089039.856874 4308616 | 
..|submesh.submesh_init_sphere
* O    892.130911            0.157592 4338120 | 
..|submesh.submesh_init_sphere
* I    892.131247   1216089040.014791 4338120 | ..|projector.projector_init
* O    892.131502            0.000251 4338120 | ..|projector.projector_init
* I    892.131730   1216089040.015268 4338120 | 
..|submesh.submesh_init_sphere
* O   1011.367826          119.254781 4367624 | 
..|submesh.submesh_init_sphere
* I   1011.619627   1216089159.503184 4367624 | ..|projector.projector_end
* I   1011.619725   1216089159.503260 4367624 | ..|..|submesh.submesh_end
* O   1011.619778            0.000054 4367624 | ..|..|submesh.submesh_end
* O   1011.619825            0.000181 4367624 | ..|projector.projector_end
* I   1011.619867   1216089159.503402 4367624 | ..|submesh.submesh_copy
/var/spool/pbs/mom_priv/jobs/4667.cudran.SC: line 14:  5582 
Killed                  octopus_mpi >gs.out

To Nicola:
I found the memory usage depend on the Boxshape and radius,  The radius 
is the minimum (16.) I can use, otherwise there are warning messages 
that some atoms are out of the radius if the radius are set smaller than 
16.  I am testing other boxshape and see what happened.

Cheers,
Cheng



Nicola Spallanzani wrote:
> Hi,
>
> Cheng:
> only now I notice that you have setted a radius too much large.
> I suggest you to find the bigger volume that allow you to run the gs, 
> then find the smaller volume that go to convergence.
>
> Xavier:
> I was able to run the gs with a parallelization both in states and in 
> domains, and to run the td only with a parall. in domains.
> Do you know why for you it is opposite?
>
> Cheers,
> Nicola
>
>
>
> Xavier Andrade wrote:
>> Hi,
>>
>> Actually the input file that Cheng mentions has a lot of input 
>> variables that you should not normally use, as the default is fine. 
>> In particular, as Nicola said, do not use parallelization in states 
>> (for the moment it only works for the time propagation) and leave the 
>> default poisson solver (isf). With the default parameters I have been 
>> able to make test runs (non-converged spacing) up to one thousand atoms.
>>
>> What could be problematic is the SCF convergency. First of all add 
>> some few extra states and if still your SCF iteration is not 
>> converging you may want to put a finite electronic temperature.
>>
>> Cheers,
>>
>> Xavier
>>
>> On Mon, 14 Jul 2008, Nicola Spallanzani wrote:
>>
>>> Hi Cheng,
>>> I was able to do a gs/td calculation of a big molecule of 207 atoms. I
>>> can suggest you to use the "isf" PoissonSolver and to make a
>>> parallelization only in domains.
>>> This was right for me... I hope the same for you!
>>>
>>> Cheers,
>>> Nicola
>>>
>>>