EricR86
commented
10 years ago From hoffman...@gmail.com on March 20, 2014 03:55:16
Are you able to get the standard tests in segway/test to work?
Closed EricR86 closed 10 years ago
EricR86
commented
10 years ago From hoffman...@gmail.com on March 20, 2014 03:55:16
Are you able to get the standard tests in segway/test to work?
EricR86
commented
10 years ago From apocalyp...@gmail.com on March 20, 2014 04:52:52
Same problem!
abhinav@abhnav:~/Downloads2/test$ bash ./test.sh
traindir/observations/chr21.0000.float32 (9411193, 9595548)
PROGRAM ENDED SUCCESSFULLY WITH STATUS 0 AT Thursday March 20
2014, 17:18:28 IST
queued 49: emt0.0.0.traindir.8c9c2632b02511e39ca61803736f5e43
(mem_requested=2048M h_vmem=2048M h_stack=8M)
^CTraceback (most recent call last):
File "/home/abhinav/arch/Linux-x86_64/bin/segway", line 9, in
EricR86
commented
10 years ago From hoffman...@gmail.com on March 20, 2014 07:15:20
It looks like the job is queuing up just fine, what is happening to it? What are the results of qstat while your Segway job is running and you're waiting.
EricR86
commented
10 years ago From apocalyp...@gmail.com on March 20, 2014 07:58:08
abhinav@abhnav:~/Downloads2/test$ bash test.sh traindir/observations/chr21.0000.float32 (9411193, 9595548) PROGRAM ENDED SUCCESSFULLY WITH STATUS 0 AT Thursday March 20 2014, 20:26:26 IST queued 54: emt0.0.0.traindir.cfa38e24b03f11e3a8591803736f5e43 (mem_requested=2048M h_vmem=2048M h_stack=8M)
abhinav@abhnav:~/Downloads2$ qstat job-ID prior name user state submit/start at
54 0.50000 emt0.0.0.t abhinav qw 03/20/2014 20:26:26
11
Working for small script containing "Hello World"
abhinav@abhnav:~$ qsub script.sh Your job 53 ("script.sh") has been submitted abhinav@abhnav:~$ ls | grep script script.sh script.sh.e53 script.sh.o53
EricR86
commented
10 years ago From hoffman...@gmail.com on March 20, 2014 11:54:42
OK, "qw" means your job has been submitted but not started for some reason. What does qstat -j 53 get you? This should explain the reason.
EricR86
commented
10 years ago From apocalyp...@gmail.com on March 20, 2014 14:12:57
scheduling info: (-l h_stack=8M,h_vmem=2048M,mem_requested=2048M) cannot run at host "abhnav" because it offers only hc:mem_requested=1.801G
EricR86
commented
10 years ago From apocalyp...@gmail.com on March 21, 2014 05:46:02
Problem is basically I have 2GB RAM and machine is able to allocate 1.8 GB whereas Segway requires 2048 MB = 2GB RAM.
On Fri, Mar 21, 2014 at 2:42 AM, Abhinav Mittal apocalypse.mittal@gmail.com wrote:
EricR86
commented
10 years ago From hoffman...@gmail.com on March 21, 2014 06:12:32
Try --mem-usage-progression=1,1.8. Then it will only allocate 1 GB, and 1.8 if that doesn't work. http://noble.gs.washington.edu/proj/segway/doc/1.1.0/segway.html#memory-usage I'm closing this since it isn't a bug. If you have further questions on this, please email segway-users@uw.edu. Thanks!
Summary: segway train queuing job that never starts (was: segway train not responding)
Status: Invalid
From apocalyp...@gmail.com on March 20, 2014 01:25:40
abhinav@abhnav:~$ qhost -F mem_requested
HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS
global - - - - - - - abhnav lx26-amd64 4 0.18 1.8G 913.0M 1.9G 301.5M Host Resource(s): hc:mem_requested=1.801G localhost
abhinav@abhnav:~$ segway --num-labels=4 train test.genomedata traindir4 traindir4/observations/chr21.0000.float32 (9411193, 9595548) PROGRAM ENDED SUCCESSFULLY WITH STATUS 0 AT Thursday March 20 2014, 10:46:02 IST queued 48: emt0.0.0.traindir4.ba32aef4afee11e3b8541803736f5e43 (mem_requested=2048M h_vmem=2048M h_stack=8M)
on interruption
^CTraceback (most recent call last): File "/home/abhinav/arch/Linux-x86_64/bin/segway", line 9, in
load_entry_point('segway==1.1.0', 'console_scripts', 'segway')()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3592, in main
return runner()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3429, in call
self.run(_args, *_kwargs)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3407, in run
self.run_train()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3038, in run_train
instance_params = run_train_func(num_segs_range)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 3056, in run_train_singlethread
res = [self.run_train_instance()]
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 2937, in run_train_instance
self.run_train_round(instance_index, round_index, kwargs)
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", line 2900, in run_train_round
restartable_jobs.wait()
File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/init**.py", line 192, in wait
sleep(MIN_JOB_WAIT_SLEEP_TIME)
KeyboardInterrupt
qmon queue control->running tab (empty) listed in pending jobs
Original issue: http://code.google.com/p/segway-genome/issues/detail?id=30