the runI-TASSER.pl script (and others) use qstat in the parallel mode, but SGE's qstat seems to be not quite compatible with PBS. Since I don't have a PBS system to try this on, it is hard to see what the problem is. Could somebody with a PBS system with jobs running please post the output of:
"qstat -u username" and "qstat -f"? For SGE these are (reduced to one instance of each type of result):
qstat -u mathog
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
1527 0.55500 test_on_co mathog r 05/23/2014 12:29:10 all.q@compute-0-21.local 1
1528 0.55500 spu_000100 mathog r 05/23/2014 12:29:25 all.q@compute-0-18.local 1
and
qstat -f
queuename qtype resv/used/tot. load_avg arch states
---------------------------------------------------------------------------------
all.q@compute-0-5.local BIP 0/1/1 0.98 lx26-amd64
1540 0.55500 spu_000100 mathog r 05/23/2014 12:29:25 1
---------------------------------------------------------------------------------
all.q@compute-0-6.local BIP 0/0/1 0.00 lx26-amd64
---------------------------------------------------------------------------------
The jobname is being truncated to 10 characters (in this case out of 40, see example below) and I think that is why on a clean run the master job exited while waiting for the threading jobs to complete. As far as I know the only way to get the complete job name on SGE is with qstat -r:
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
1527 0.55500 test_on_co mathog r 05/23/2014 12:29:10 all.q@compute-0-21.local 1
Full jobname: test_on_compute-0-1.sh
Master Queue: all.q@compute-0-21.local
Hard Resources:
Soft Resources:
Hard requested queues: all.q@compute-0-21.local
1528 0.55500 spu_000100 mathog r 05/23/2014 12:29:25 all.q@compute-0-18.local 1
Full jobname: spu_000100.1_on_compute-0-21.localsim_2A
Master Queue: all.q@compute-0-18.local
Hard Resources:
Soft Resources:
Thanks.