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  • Created 29 Jun 2010

getting exception while running the public example files from nanohub workspace

  1. Sayan Kanungo

    Hi I was trying to run one of the given example file. After submitting my job I am getting the following exception written in the “.stderr” file:

    Got exception

    DatabaseParser the input file cannot be opened: ../../materials/all.mat application called MPI_Abort(MPI_COMM_WORLD, 1) – process 0

    Before submitting the job I have linked the “all.mat” file to my working directory in nano-hub workspace

    Any advice/guidance in this matter would be very helpful to me.

    Sayan

    the .stdout file of this simulation is attached

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  2. Sayan Kanungo

    the problem is solved, I have to use “database= ./all.mat” in the input file.

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  3. Jony Chandra Sarker

    Hi, I was trying to run a program from public_examples\NCN_summer_school_2012\Quantum_Dot_Hesam as “submit -v ncn-hub@coates -i ./all.mat -n 8 nemo-r8645 a_QD_10nm_Usman.in”. But the simulation was running for almost 18 hours and still running.

    Also another 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 it does not provide any output like other example file. Any advice/guidance in this matter would be very helpful to me.

    Thanks Jony Sarker

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  4. Hesameddin Ilatikhameneh

    Hi Jony Sarker,

    To run those 2 examples you need to have access to 8 and 24 cpus and you would be on a queue. You may want to change number of cpus (i.e -n number).

    Also you need to make sure there is a all.mat in the folder. If not please copy from other folders.

    Even if any error occurs you will get a report file. You can define a wall time (2 hours) so when it finishes you will get a log file.

    You can also take a look into Nemo5 tutorial 5b presentation on the nanohub.

    Thanks Hesam


    Emailed forum response from hesam_ilati@yahoo.com

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  5. Ross Maspero

    Hi,

    You sent that email to the wrong person

    Regards

    Ross


    Emailed forum response from r.maspero@surrey.ac.uk

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  6. Hesameddin Ilatikhameneh

    Hi,

    I just replied the email I got. I didn’t change the reciever or anything else. Should I do it another way? Please let me know.

    Thanks Hesam


    Emailed forum response from hesam_ilati@yahoo.com

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  7. James Fonseca

    Hi Hesam, Your message appeared in the correct place in the discussion forum. https://nanohub.org/groups/nemo5distribution/forum/defaultsection/job-submission/469

    I’m not really sure why Ross got it but it may have been a fluke with nanoHUB.

    @Ross, sorry about that. If you continue to get messages that aren’t for you, please submit a nanoHUB support ticket. https://nanohub.org/support/tickets

    Thanks, Jim

    On Sat, Dec 29, 2012 at 3:15 AM, nanoHUB Support Team wrote:


    Emailed forum response from jefonseca@gmail.com

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  8. RIZVI AHMED

    Considering the recent confusion about nemo5 support emails, I think that any email from support that is replied are sent to all of the nemo5 distribution and support group members. For example, I’m not involved in any discussion topics. But I’m receiving conversation emails of all the members from the day I registered for the group.


    Thanks.


    Emailed forum response from rizviahmed.ee@gmail.com

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  9. jianwei shi

    I think so, too.

    Jianwei Shi


    2012/12/30 nanoHUB Support Team


    Emailed forum response from baoxun1@gmail.com

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  10. Petrica Cristea

    Hello, everyone!

    I am not involved in the subject under consideration, however I received all messages asking for solutions on various subjects within nemo5 distribution and support group members. I have supposed that nanoHUBexperts in the field will provide appropriate solutions, and all of us have benefit from such a shared experience.

    Petrica Cristea

    On Sun, Dec 30, 2012 at 7:25 AM, nanoHUB Support Team wrote:


    Emailed forum response from pcristea@gmail.com

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  11. James Fonseca

    If anyone does not wish to receive emails, you should be able to deselect the “email forum posts” check box on the forum page: https://nanohub.org/groups/nemo5distribution/forum

    Thanks, Jim

    On Sun, Dec 30, 2012 at 3:09 AM, nanoHUB Support Team wrote:


    Emailed forum response from jefonseca@gmail.com

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  12. Gerhard Klimeck

    My apologies nanoHUB group mechanism se still evolving. We need to use available or to be implemented opt out solutions. We will follow up in the new year.


    Prof. Gerhard Klimeck Director Network for Computational Nanotechnology (765) 412 4364 http://nanoHUB.org/klimeck

    Sent from my iPhone. Pls excuse my typos.

    Am Dec 29, 2012 um 22:09 schrieb nanoHUB Support Team :


    Emailed forum response from gekco0@gmail.com

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