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Re^9: Regarding FIREFLY-8.1.0 running speeds on Cluster with IntelMPI

Siddheshwar Chopra
sidhusai@gmail.com



Dear Alex,
I feel happy to inform you that my first o/p has completed on cluster. It took 36 hours with nprocs=32. There were 40 atoms.

Regards,




On Sat Apr 19 '14 6:36pm, Siddheshwar Chopra wrote
--------------------------------------------------
>Dear Alex,
>Alex the program started just yesterday. All thanks to the queuing process. I will inform you as it gets over. I too need to learn many things regarding fine tuning of inputs to speed up the calculations.

>Regards,

>On Sat Apr 19 '14 1:08am, Alex Granovsky wrote
>----------------------------------------------
>>Dear Siddheshwar,

>>Did you finally get the output file from the cluster?
>>If yes, could you please share it? If no, could you please explain
>>how exactly you ran Firefly on that cluster? We would be glad to
>>help you but we need this information to be able to help.

>>Kind regards,
>>Alex Granovsky
>>
>>
>>On Tue Apr 15 '14 1:18pm, Siddheshwar Chopra wrote
>>--------------------------------------------------
>>>Dear Alex,
>>>Thank you so much for clearing this doubt about multiple executables..
>>>Sir, truly said by you, use of -o command is needed here. But unfortunately I realized it after I had queued some programs already. I will definitely do this next run onwards. Could you give me some tips on how to get my script run faster from the queue or get started faster? I mean the combinations of node and ppn and so on?

>>>Regards,

>>>On Tue Apr 15 '14 11:07am, Alex Granovsky wrote
>>>-----------------------------------------------
>>>>Dear Siddheshwar,

>>>>I'd suggest you to use -o command line option to redirect output
>>>>to file. Are you using it? If you are not, then most likely output
>>>>gets redirected by the batch system on the cluster. This way batch
>>>>system may wait for job completion before creating output file for
>>>>you. With -o option you get output in a real time.

>>>>>Alex Sir, do I need to have MULTIPLE executables of FIREFLY, if I need to run several scripts parallely?

>>>>No you do not need to have multiple copies. A single copy is enough.

>>>>Kind regards,
>>>>Alex Granovsky
>>>>
>>>>
>>>>
>>>>On Tue Apr 15 '14 7:02am, Siddheshwar Chopra wrote
>>>>--------------------------------------------------
>>>>>Dear Alex,
>>>>>No Sir. It is not that I didn't get the output. I get the o/p of short programs. The Temp Dir has root access and ONLY the o/p that completes moves in to the user folder. The configuration is fine, it is just that the program is taking more time than my expectation.
>>>>>Alex Sir, do I need to have MULTIPLE executables of FIREFLY, if I need to run several scripts parallely?

>>>>>Regards,

>>>>>On Tue Apr 15 '14 0:58am, Alex Granovsky wrote
>>>>>----------------------------------------------
>>>>>>Dear Siddheshwar,

>>>>>>if you have not gotten output files thus far then you most likely
>>>>>>misconfigured or misused Firefly on the cluster.

>>>>>>Kind regards,
>>>>>>Alex Granovsky
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Sat Apr 12 '14 6:57am, Siddheshwar Chopra wrote
>>>>>>--------------------------------------------------
>>>>>>>Dear Alex,
>>>>>>>I would need some time to provide the o/p from cluster. Actually it is giving me o/p ONLY when it is completed. But I seem to add less walltime everytime..And that my concern.. It needs more than 2 days atleast..So I slowly increasing it.

>>>>>>>Regards,

>>>>>>>On Fri Apr 11 '14 4:33pm, Alex Granovsky wrote
>>>>>>>----------------------------------------------
>>>>>>>>Hello,

>>>>>>>>could you please send me two outputs, one when running on cluster
>>>>>>>>and second from your laptop.

>>>>>>>>Kind regards,
>>>>>>>>Alex Granovsky
>>>>>>>>
>>>>>>>>
>>>>>>>>On Fri Apr 11 '14 12:35pm, Siddheshwar Chopra wrote
>>>>>>>>---------------------------------------------------
>>>>>>>>>Dear Alex and Firefly users,
>>>>>>>>>I am working with Intel MPI version of Firefly-8.1.0 on a cluster. I have run say a OPT+HESSIAN job of around 45 atoms of Silicon on my laptop (with i3, 2.2GHz,2GB DDR3 RAM) and also on a cluster (with 2 nodes and ppn=16 (max support),64GB RAM).
>>>>>>>>>The program ends in around 7 days on my laptop, but the cluster also takes more than 3 days for the same. The commands in the i/p file are:

>>>>>>>>> $SYSTEM MEMORY=34459319 aoints=dist TIMLIM=5295600 KDIAG=0 $END
>>>>>>>>> $CONTRL INTTYP=HONDO ICUT=11 ITOL=30 RUNTYP=OPTIMIZE SCFTYP=RHF $END
>>>>>>>>> $CONTRL DFTTYP=B3LYP COORD=UNIQUE NZVAR=114 $END
>>>>>>>>> $CONTRL MAXIT=10000 MOLPLT=.t. PLTORB=.t. $END
>>>>>>>>> $BASIS GBASIS=N31 NGAUSS=6 $END
>>>>>>>>> $STATPT opttol=10E-8 NSTEP=200 Method=GDIIS HSSEND=.TRUE. $END
>>>>>>>>> $SMP CALL64=.t. HTTFIX=.f. $END
>>>>>>>>> $p2p p2p=.t. mxbuf=2048 dlb=.t. $END
>>>>>>>>> $SCF dirscf=.t. fdiff= .f. diis=.t. $END �
>>>>>>>>> $DFT HFX(1)=0.15 LMAX=41 NRAD=99 $end
>>>>>>>>> $ZMAT DLC=.t. AUTO=.t. $END
>>>>>>>>> $SCF NCONV=8 $END
>>>>>>>>>
>>>>>>>>>Could anyone help me out in explaining what wrong is being done or how to optimize the program speeds on cluster? It has become very essential to understand this issue to progress further.

>>>>>>>>>Regards,


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