Submitting R jobs using PBS
- by Tony
I am submitting a job using qsub that runs parallelized R. My
intention is to have R programme running on 4 different cores rather than 8 cores. Here are some of
my settings in PBS file:
#PBS -l nodes=1:ppn=4
....
time R --no-save < program1.R > program1.log
I am issuing the command "ta job_id" and I'm seeing that 4 cores are listed. However, the job occupies a large amount of memory(31944900k used vs 32949628k total). If I were to use 8 cores, the jobs got hang due to memory limitation.
top - 21:03:53 up 77 days, 11:54, 0 users, load average: 3.99, 3.75, 3.37
Tasks: 207 total, 5 running, 202 sleeping, 0 stopped, 0 zombie
Cpu(s): 30.4%us, 1.6%sy, 0.0%ni, 66.8%id, 0.0%wa, 0.0%hi, 1.2%si, 0.0%st
Mem: 32949628k total, 31944900k used, 1004728k free, 269812k buffers
Swap: 2097136k total, 8360k used, 2088776k free, 6030856k cached
Here is a snapshot when issuing command ta job_id
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
1794 x 25 0 6247m 6.0g 1780 R 99.2 19.1 8:14.37 R
1795 x 25 0 6332m 6.1g 1780 R 99.2 19.4 8:14.37 R
1796 x 25 0 6242m 6.0g 1784 R 99.2 19.1 8:14.37 R
1797 x 25 0 6322m 6.1g 1780 R 99.2 19.4 8:14.33 R
1714 x 18 0 65932 1504 1248 S 0.0 0.0 0:00.00 bash
1761 x 18 0 63840 1244 1052 S 0.0 0.0 0:00.00 20016.hpc
1783 x 18 0 133m 7096 1128 S 0.0 0.0 0:00.00 python
1786 x 18 0 137m 46m 2688 S 0.0 0.1 0:02.06 R
How can I prevent other users to use the other 4 cores? I like to mask somehow that my job is using 8 cores with 4 cores idling.
Could anyone kindly help me out on this? Can this be solved using pbs?
Many Thanks
