On Sat, Sep 22, 2012 at 10:53 PM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Hi Jason,
> You are right, when i tried to use the (#PBS -l nodes=8:ppn=8) the PBS
> output file contains the line (Num Procs is 64)....
>
> Now, this way didn't give me out files at all even after the job finished,
> i mean no md.out or md.mdcrd files etc...
> I tried to trace the location of these files by viewing the full
> job specifications using the (qstat -f jobid) command, i thought the job
> output files may be placed somewhere such as in a scratch folder, but the
> output should be directed to the same directory as given by the output of
> the previous command:
>
> Job Id: 57991.pbs.hpc.swin.edu.au
> Job_Name = m8_npt
> Job_Owner = mahmed.g2.hpc.swin.edu.au
> job_state = R
> queue = gstar
> server = pbs.hpc.swin.edu.au
> Checkpoint = u
> ctime = Sun Sep 23 12:51:54 2012
> Error_Path = g2.hpc.swin.edu.au:/home/mahmed/amber_test/m8_npt.e57991
> exec_host =
> gstar058/8+gstar058/7+gstar058/6+gstar058/5+gstar058/4+gstar05
> 8/3+gstar058/2+gstar058/0+gstar053/7+gstar053/6+gstar053/5+gstar053/4+
> gstar053/3+gstar053/2+gstar053/1+gstar053/0+gstar052/8+gstar052/7+gsta
> r052/6+gstar052/5+gstar052/4+gstar052/3+gstar052/2+gstar052/1+gstar051
> /7+gstar051/6+gstar051/5+gstar051/4+gstar051/3+gstar051/2+gstar051/1+g
> star051/0+gstar050/7+gstar050/6+gstar050/5+gstar050/4+gstar050/3+gstar
> 050/2+gstar050/1+gstar050/0+gstar047/7+gstar047/6+gstar047/5+gstar047/
> 4+gstar047/3+gstar047/2+gstar047/1+gstar047/0+gstar046/7+gstar046/6+gs
> tar046/5+gstar046/4+gstar046/3+gstar046/2+gstar046/1+gstar046/0+gstar0
> 45/7+gstar045/6+gstar045/5+gstar045/4+gstar045/3+gstar045/2+gstar045/1
> +gstar045/0
> Hold_Types = n
> Join_Path = n
> Keep_Files = n
> Mail_Points = a
> mtime = Sun Sep 23 12:52:11 2012
> Output_Path = g2.hpc.swin.edu.au:/home/mahmed/amber_test/m8_npt.o57991
> Priority = 0
> qtime = Sun Sep 23 12:51:54 2012
> Rerunable = True
> Resource_List.mem = 4gb
> Resource_List.nodect = 8
> Resource_List.nodes = 8:ppn=8
> Resource_List.pmem = 1024mb
> Resource_List.walltime = 01:10:00
> session_id = 20012
> Variable_List = PBS_O_QUEUE=gstar,PBS_O_HOST=g2.hpc.swin.edu.au,
> PBS_O_HOME=/home/mahmed,PBS_O_LANG=en_US.UTF-8,PBS_O_LOGNAME=mahmed,
> PBS_O_PATH=/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/to
> rque/bin:/opt/moab/bin:/opt/sgi/sgimc/bin:/home/mahmed/bin,
> PBS_O_MAIL=/var/spool/mail/mahmed,PBS_O_SHELL=/bin/bash,
> PBS_SERVER=pbs.hpc.swin.edu.au,PBS_O_WORKDIR=/home/mahmed/amber_test
> etime = Sun Sep 23 12:51:54 2012
> submit_args = m8_npt
> start_time = Sun Sep 23 12:51:54 2012
> Walltime.Remaining = 4176
> start_count = 1
> fault_tolerant = False
> submit_host = g2.hpc.swin.edu.au
> init_work_dir = /home/mahmed/amber_test
>
>
>
>
> could you please comment
>
Did you set your working directory (via "cd")? Typically, my PBS job files
have the command:
cd $PBS_O_WORKDIR
before running the actual program. This changes to the directory from
which the job was submitted. I'm not sure what the default working
directory is (you can determine it by using the pwd command and just
reading it from the stdout file.
This is described on my wiki site a little:
http://jswails.wikidot.com/using-pbs#toc10
I would suggest reading through that page to help understand PBS a little
better.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Sep 22 2012 - 20:30:02 PDT
