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
Marawan
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Received on Sat Sep 22 2012 - 20:00:02 PDT
