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  • Created 29 Jun 2010

Not getting any output from the simulation while running a Public_examples

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  1. Jony Chandra Sarker

    Hi, I was running an example from NCN_summer_school_2012\Quantum_Dot_Yuling—- i have submitted the job as “submit -v ncn-hub@rossmann -i ./all.mat -n 24 nemo-r8645 Usman_new.in”. But i didnot get any output form the simulation. For this problem material file specified in global solve portion as “database = /home/ba01/u139/hsuehy/2012/prototype/materials/all.mat” My question is why we can not define the material database as (database = ./all.mat) like other examples. Also i got massage in log file as “NEMO 5 logfile. NEMO 5 Compiled on Oct 25 2012 at 17:37:34 on coates-fe02.rcac.purdue.edu Current time: Thu Dec 27 14:53:02 2012 , master process: rossmann-a145.rcac.purdue.edu Nemo logfile for process 0: qd.log Nemo finished reading input deck after 0.113382 s.”

    I have tried to run that program a several time and failed to get any output. Any advice/guidance in this matter would be very helpful to me.

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  2. Hesameddin Ilatikhameneh

    Hello,

    Actually you need to change that database path to ./all.mat and copy all.mat file from other folder to that folder.

    This change was part of summer school presentation.

    Moreover, you are trying to get 24 cpus (-n 24) which may lead to a long wait in the queue for your task to start.

    Let us know if you still have the problem. Thanks Hesam


    Emailed forum response from hesam_ilati@yahoo.com

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  3. Jony Chandra Sarker

    Dear Hesam, I have followed your suggestion related to all.mat file and tried to simulate (public_examples\NCN_summer_school_2012\Quantum_Dot_Yuling\Usman_new.in). But i have again failed to get any output from the simulation. I got the massage in the log file as “NEMO 5 logfile. NEMO 5 Compiled on Oct 25 2012 at 17:37:34 on coates-fe02.rcac.purdue.edu Current time: Sat Jan 5 20:55:19 2013 , master process: rossmann-a118.rcac.purdue.edu Nemo logfile for process 0: qd.log Nemo finished reading input deck after 0.681858 s. Nemo/PetscMatrixDouble Initializing DOUBLE SLEPc… Nemo/PetscMatrixComplex Initializing COMPLEX SLEPc… Nemo NEW database parsed okay Nemo finished reading material database after 2.06245 s. Running NEMO on 24 nodes.

    ==============================================
    =

    Nemo initializing Material regions…

    ==============================================
    =

    Material creating GaAs

    Crystal initializing…

    Material creating GaInAs

    Crystal initializing…
    for binary com the tag is ? stress_reducing_layer

    Material creating InAs

    Crystal initializing…
    for binary com the tag is ? stress_reducing_layer

    Material creating GaAs

    Crystal initializing…

    Material creating InAs

    Crystal initializing…

    Nemo Material regions were initialized in 0.101752 seconds. SimpleShapes creating shapes… SimpleShapes shape creation is done. SimpleShapes creating shapes… SimpleShapes shape creation is done. Nemo Geometry was initialized in 1.46523 seconds.

    ==============================================
    =

    Nemo initializing Domains…

    ==============================================
    =

    Domain atomic_structure initializing… inside initPseudomorphicDomain building conventional cell… Crystal calculating conventional cell… done. Crystal calculating cell bonds… done.

    PseudomorphicDomain building block has been created. Crystal calculating conventional cell… done. Crystal calculating conventional cell… done. Crystal calculating conventional cell… done. Crystal calculating conventional cell… done. Crystal calculating conventional cell… done.

    PseudomorphicDomain creating atoms…St9bad_alloc


    Please, let me know how can i solve this problem. Thanks

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  4. Jony Chandra Sarker

    I also get to know from STDOUT file relating to not to get any output from Usman_new.in file

    PseudomporphicDomain: cannot build atoms. Probably out of memory” This massege has shown after creating the atom.


    Please, let me know how can i solve this problem. Thanks

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  5. Hesameddin Ilatikhameneh

    Dear Jony,

    The input-deck you are trying to run (Usman_new.in) needs hundreds of cpus since it has very large size (more than 10M atoms). You can find geometry, by looking into domain dimensions and Regions min and max (in nano meter) in the input-deck.

    As error message suggests, memory of 24 nodes was not sufficient for such a huge geometry.

    Please run other input decks in that folder which have smaller geometry.

    We are working on the solvers to reduce memory usage.

    Thanks Hesam


    Emailed forum response from hesam_ilati@yahoo.com

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  6. Jony Chandra Sarker

    Dear Hesam, Thanks. I have already run the others programs(InAs_dome_QD.in or a_QD_10nm_Usman.in) which have smaller geometry and they are working well. However input files such as Usman_new.in or Usman_schrodi.in is not working due to very large size as you mentioned earlier. Can i use hundreds of cpus in this purpose? Will they work if i submit the job as “submit -v ncn-hub@rossmann -i ./all.mat -n 100 nemo-r8645 Usman_new.in” ?

    Thanks . Jony

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  7. Hesameddin Ilatikhameneh

    Actually for that specific example we used 300-800 cpus (on different clusters). You can try to use such number of cpus but I am not sure how many cpus you are allowed to use.

    Are you sure that you need to run such a huge geometry? Usually it is possible to reduce geometry by using correct bounday condition.

    Thanks Hesam


    Emailed forum response from hesam_ilati@yahoo.com

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  8. Jony Chandra Sarker

    Dear Hesam,

    Thanks a lot. Surely i will try to reduce the geometry by using suitable boundary condition and the domain. Again thanks for your kind concern.

    Jony sarker

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