I am trying to run many small serial jobs with GNU Parallel on a PBS cluster, each compute node has 16 cores, as I intended to use multiple compute nodes therefore I passed the option -S $SERVERNAME to GNUParallel, however what confuses me is that the number of jobs started on the node using -S $SERVERNAME does not equal to the number of jobs I specified when I intended to spawn more than 9 jobs, below are my observations:
[fchen14@shelob001 ~]$ parallel --version
GNU parallel 20160922
Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016
Ole Tange and Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
GNU parallel comes with no warranty.
Web site: http://www.gnu.org/software/parallel
When using programs that use GNU Parallel to process data for publication
please cite as described in 'parallel --citation'.
[fchen14@shelob001 ~]$ hostname # this shows my hostname
shelob001
When use GNUParallel as local host without -S $SERVERNAME, there is no problem, I intended to spawn 10 jobs, and GNUParallel started 10 jobs:
[fchen14@shelob001 ~]$ parallel --progress echo ::: `seq 1 10`
Computers / CPU cores / Max jobs to run
1:local / 16 / 10 # 10 jobs spawned, no problem
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
local:10/0/100%/0.0s 1
local:9/1/100%/0.0s 2
local:8/2/100%/0.0s 3
local:7/3/100%/0.0s 4
local:6/4/100%/0.0s 5
local:5/5/100%/0.0s 6
local:4/6/100%/0.0s 7
local:3/7/100%/0.0s 8
local:2/8/100%/0.0s 9
local:1/9/100%/0.0s 10
local:0/10/100%/0.0s
When I use GNUParallel to spawn less than 10 jobs using the -S $SERVERNAME, still no problem.
[fchen14@shelob001 ~]$ parallel -S shelob001 --progress echo ::: `seq 1 1`
Computers / CPU cores / Max jobs to run
1:shelob001 / 16 / 1 # When the number of jobs is less than 10, no problem
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
shelob001:1/0/100%/0.0s 1
shelob001:0/1/100%/1.0s
[fchen14@shelob001 ~]$ parallel -S shelob001 --progress echo ::: `seq 1 8`
Computers / CPU cores / Max jobs to run
1:shelob001 / 16 / 8 # When the number of jobs is less than 10, no problem
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
shelob001:8/0/100%/0.0s 1
shelob001:7/1/100%/1.0s 7
shelob001:6/2/100%/0.5s 3
shelob001:5/3/100%/0.3s 8
shelob001:4/4/100%/0.2s 5
shelob001:3/5/100%/0.2s 2
shelob001:2/6/100%/0.2s 6
shelob001:1/7/100%/0.1s 4
shelob001:0/8/100%/0.1s
[fchen14@shelob001 ~]$ parallel -S shelob001 --progress echo ::: `seq 1 9`
Computers / CPU cores / Max jobs to run
1:shelob001 / 16 / 9 # When the number of jobs is less than 10, no problem
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
shelob001:9/0/100%/0.0s 1
shelob001:8/1/100%/1.0s 5
shelob001:7/2/100%/0.5s 8
shelob001:6/3/100%/0.3s 2
shelob001:5/4/100%/0.2s 6
shelob001:4/5/100%/0.2s 9
shelob001:3/6/100%/0.2s 3
shelob001:2/7/100%/0.1s 4
shelob001:1/8/100%/0.1s 7
shelob001:0/9/100%/0.1s
Here is what confuses me, when I try to use a job number >=10, the number of jobs spawned is always one less than wanted, here I want to spawn 10, only started 9 jobs:
[fchen14@shelob001 ~]$ parallel -S shelob001 --progress echo ::: `seq 1 10` # I want to start 10 jobs
Computers / CPU cores / Max jobs to run
1:shelob001 / 16 / 9 #why here "Max jobs to run" is 9?
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
shelob001:9/0/100%/0.0s 2
shelob001:9/1/100%/3.0s 1
shelob001:8/2/100%/1.5s 7
shelob001:7/3/100%/1.0s 4
shelob001:6/4/100%/0.8s 9
shelob001:5/5/100%/0.6s 8
shelob001:4/6/100%/0.5s 3
shelob001:3/7/100%/0.4s 5
shelob001:2/8/100%/0.4s 6
shelob001:1/9/100%/0.4s 10
shelob001:0/10/100%/0.4s
[fchen14@shelob001 ~]$ parallel -S shelob001 --progress echo ::: `seq 1 11`
Computers / CPU cores / Max jobs to run
1:shelob001 / 16 / 10 # it seems the jobs started is one less than I specified
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
shelob001:10/0/100%/0.0s 1
shelob001:10/1/100%/3.0s 2
shelob001:9/2/100%/1.5s 8
shelob001:8/3/100%/1.0s 3
shelob001:7/4/100%/0.8s 4
shelob001:6/5/100%/0.6s 5
shelob001:5/6/100%/0.5s 7
shelob001:4/7/100%/0.4s 10
shelob001:3/8/100%/0.4s 9
shelob001:2/9/100%/0.3s 6
shelob001:1/10/100%/0.4s 11
shelob001:0/11/100%/0.4s
[fchen14@shelob001 ~]$
I checked the status of the compute node using "top", it does show that only 9 Cpus are used when I use seq 1 10. Hopefully I have made my problem clear, could anyone point out the possible cause of this problem? Any suggestion is welcome.
Thank you very much!
Looks like you found a bug. Workaround: -j+1