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Thread: submission of program with at does not work

  1. #1
    Join Date
    May 2010
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    137

    submission of program with at does not work

    Hi!
    when starting the following program:

    mpirun -n 3 xmipp_mpi_ml_refine3d -i ml_1245.sel -vol 3ref.sel -ang 10 -o ref -iter 20

    from the bash shell it runs without problems

    when writing these same commands into the file "job" and running

    at -f job now

    I get the message that the job has been submitted but nothing happens:

    atq does not show anything and top shows that nothing runs

    when I submit a bash script that e.g. copies files it works well

    what is wrong? I spent hours trying out a number of things but did not get it to run in batch mode

    Thanks for hints, D-E

  2. #2
    wojox is offline I Ubuntu, Therefore, I Am
    Join Date
    Apr 2009
    Beans
    8,628

    Re: submission of program with at does not work

    Try

    Code:
    sudo at -f job now
    Then

    Code:
    man at

  3. #3
    Join Date
    May 2010
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    137

    Re: submission of program with at does not work

    Hi wojox,
    thanks, but sorry, it does not work! I do neither need sudo when submitting a bash script as this works well!
    D-E

  4. #4
    wojox is offline I Ubuntu, Therefore, I Am
    Join Date
    Apr 2009
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    8,628

    Re: submission of program with at does not work

    Okay specify when you want it

    Code:
    at now + 2 minutes -f job now

  5. #5
    Join Date
    May 2010
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    137

    Re: submission of program with at does not work

    Thanx, but why should it run when I specify 'now + 2 minutes' instad of 'now'? Would it need some time to get it started? As I wrote before, it works fine with a file containing e.g.:

    z=z
    for i in *.spi
    do
    cp $i $i$z
    done

    but it does not when submitting the program I specified!

  6. #6
    Join Date
    Feb 2010
    Location
    Silicon Valley
    Beans
    1,898
    Distro
    Xubuntu 12.04 Precise Pangolin

    Re: submission of program with at does not work

    What shows up /var/log/syslog when it runs?

    Also, make sure you have a Mail Transfer Agent installed, like postfix. The output of any commands (or errors) will be emailed to you.
    Last edited by gmargo; November 29th, 2010 at 07:30 PM.

  7. #7
    Join Date
    May 2010
    Beans
    137

    Re: submission of program with at does not work

    Well, I do not see anything relevant in the syslog. There is nothing referring to at! I have the impression that the problem is the transfer of the parameters. Commands not having parameters seem to work. E.g. command xyz > x works, while command -i xyz -o x do not. Neither does it help to give the complete path. The program has to run in directory which it is being started in and take the input from the parameters given. I have tried to enclose the whole command into ' ' or ` ` and many other things. Sofar no avail. Help ist greatly appreciated!

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