Am 19.03.2014 um 16:28 schrieb Abhinav Mittal: >>>>>> <snip> >>>>>> hostlist abhnav
Is there an "i" missing? -- Reuti >>>>>> seq_no 0 >>>>>> load_thresholds np_load_avg=1.75 >>>>>> suspend_thresholds NONE >>>>>> nsuspend 1 >>>>>> suspend_interval 00:05:00 >>>>>> priority 0 >>>>>> min_cpu_interval 00:05:00 >>>>>> processors 2 >>>>> >>>>> Most likely this should be set to UNDEFINED unless you are running one of >>>>> the supported OS for this option. >>>>> >>>>> Please have a look at `man queue_conf` for an explanation. >>>>> >>>>> -- Reuti >>>>> >>>>> >>>>>> qtype BATCH INTERACTIVE >>>>>> ckpt_list NONE >>>>>> pe_list make >>>>>> rerun FALSE >>>>>> slots 1 >>>>>> tmpdir /tmp >>>>>> shell /bin/csh >>>>>> prolog NONE >>>>>> epilog NONE >>>>>> shell_start_mode posix_compliant >>>>>> starter_method NONE >>>>>> suspend_method NONE >>>>>> resume_method NONE >>>>>> terminate_method NONE >>>>>> notify 00:00:60 >>>>>> owner_list NONE >>>>>> user_lists arusers >>>>>> xuser_lists NONE >>>>>> subordinate_list NONE >>>>>> complex_values NONE >>>>>> projects NONE >>>>>> xprojects NONE >>>>>> calendar NONE >>>>>> initial_state default >>>>>> s_rt INFINITY >>>>>> h_rt INFINITY >>>>>> s_cpu INFINITY >>>>>> h_cpu INFINITY >>>>>> s_fsize INFINITY >>>>>> h_fsize INFINITY >>>>>> s_data INFINITY >>>>>> h_data INFINITY >>>>>> s_stack INFINITY >>>>>> h_stack INFINITY >>>>>> s_core INFINITY >>>>>> h_core INFINITY >>>>>> s_rss INFINITY >>>>>> h_rss INFINITY >>>>>> s_vmem INFINITY >>>>>> h_vmem INFINITY >>>>>> >>>>>> On Wed, Mar 19, 2014 at 6:54 PM, Reuti <[email protected]> >>>>>> wrote: >>>>>>> Am 19.03.2014 um 14:02 schrieb Abhinav Mittal: >>>>>>> >>>>>>>> -------------------------------------------------------------------------------------------------------------------------------- >>>>>>>> abhinav@abhnav:~$ qconf -sel >>>>>>>> abhnav >>>>>>>> abhinav@abhnav:~$ qconf -sql >>>>>>>> New >>>>>>>> abhinav@abhnav:~$ qconf -sconf >>>>>>>> #global: >>>>>>>> execd_spool_dir /var/spool/gridengine/execd >>>>>>>> mailer /usr/bin/mail >>>>>>>> xterm /usr/bin/xterm >>>>>>>> load_sensor none >>>>>>>> prolog none >>>>>>>> epilog none >>>>>>>> shell_start_mode posix_compliant >>>>>>>> login_shells bash,sh,ksh,csh,tcsh >>>>>>>> min_uid 0 >>>>>>>> min_gid 0 >>>>>>>> user_lists none >>>>>>>> xuser_lists none >>>>>>>> projects none >>>>>>>> xprojects none >>>>>>>> enforce_project false >>>>>>>> enforce_user auto >>>>>>>> load_report_time 00:00:40 >>>>>>>> max_unheard 00:05:00 >>>>>>>> reschedule_unknown 00:00:00 >>>>>>>> loglevel log_warning >>>>>>> >>>>>>> This I suggest to change to: >>>>>>> >>>>>>> loglevel log_info >>>>>>> >>>>>>> >>>>>>>> administrator_mail root >>>>>>>> set_token_cmd none >>>>>>>> pag_cmd none >>>>>>>> token_extend_time none >>>>>>>> shepherd_cmd none >>>>>>>> qmaster_params none >>>>>>>> execd_params none >>>>>>>> reporting_params accounting=true reporting=false \ >>>>>>>> flush_time=00:00:15 joblog=false >>>>>>>> sharelog=00:00:00 >>>>>>>> finished_jobs 100 >>>>>>>> gid_range 65400-65500 >>>>>>>> max_aj_instances 2000 >>>>>>>> max_aj_tasks 75000 >>>>>>>> max_u_jobs 0 >>>>>>>> max_jobs 0 >>>>>>>> auto_user_oticket 0 >>>>>>>> auto_user_fshare 0 >>>>>>>> auto_user_default_project none >>>>>>>> auto_user_delete_time 86400 >>>>>>>> delegated_file_staging false >>>>>>>> reprioritize 0 >>>>>>>> rlogin_daemon /usr/sbin/sshd -i >>>>>>>> rlogin_command /usr/bin/ssh >>>>>>>> qlogin_daemon /usr/sbin/sshd -i >>>>>>>> qlogin_command /usr/share/gridengine/qlogin-wrapper >>>>>>>> rsh_daemon /usr/sbin/sshd -i >>>>>>>> rsh_command /usr/bin/ssh >>>>>>> >>>>>>> Did you set this up? The default is to use the builtin tools for the >>>>>>> commands above. >>>>>>> >>>>>>> >>>>>>>> jsv_url none >>>>>>>> jsv_allowed_mod ac,h,i,e,o,j,M,N,p,w >>>>>>> >>>>>>> Fine. >>>>>>> >>>>>>> >>>>>>>> abhinav@abhnav:~$ qstat -f >>>>>>>> queuename qtype resv/used/tot. load_avg arch >>>>>>>> states >>>>>>>> --------------------------------------------------------------------------------- >>>>>>>> New@abhnav BIP 0/0/1 0.68 lx26-amd64 >>>>>>>> >>>>>>>> ############################################################################ >>>>>>>> - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING >>>>>>>> JOBS >>>>>>>> ############################################################################ >>>>>>>> 3 0.75000 emt0.0.0.t abhinav qw 03/16/2014 00:54:30 1 >>>>>>>> 5 0.75000 emt0.0.0.t abhinav qw 03/16/2014 07:44:02 1 >>>>>>>> 6 0.75000 emt0.0.0.t abhinav qw 03/16/2014 07:46:05 1 >>>>>>>> 7 0.75000 emt0.0.0.t abhinav qw 03/18/2014 22:16:49 1 >>>>>>>> 9 0.75000 emt0.0.0.t abhinav qw 03/18/2014 22:23:41 1 >>>>>>>> 10 0.75000 emt0.0.0.t abhinav qw 03/18/2014 22:25:11 1 >>>>>>>> 11 0.75000 emt0.0.0.t abhinav qw 03/18/2014 22:27:40 1 >>>>>>>> 12 0.75000 emt0.0.0.t abhinav qw 03/18/2014 22:47:21 1 >>>>>>>> 13 0.75000 emt0.0.0.t abhinav qw 03/18/2014 23:14:14 1 >>>>>>>> 14 0.75000 emt0.0.0.t abhinav qw 03/18/2014 23:14:48 1 >>>>>>>> 15 0.75000 emt0.0.0.t abhinav qw 03/19/2014 16:06:01 1 >>>>>>>> 16 0.25000 script.sh abhinav qw 03/19/2014 17:03:34 1 >>>>>>>> 17 0.25000 script.sh abhinav qw 03/19/2014 17:04:14 1 >>>>>>>> 18 0.25000 script.sh abhinav qw 03/19/2014 17:04:54 1 >>>>>>>> 19 0.25000 script.sh abhinav qw 03/19/2014 17:07:08 1 >>>>>>> >>>>>>> So, what does the queue look like: >>>>>>> >>>>>>> $ qconf -sq New >>>>>>> >>>>>>> -- Reuti >>>>>>> >>>>>>> >>>>>>>> abhinav@abhnav:~$ hostname >>>>>>>> abhnav >>>>>>>> >>>>>>>> On Wed, Mar 19, 2014 at 5:24 PM, Reuti <[email protected]> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> Am 19.03.2014 um 12:37 schrieb Abhinav Mittal: >>>>>>>>> >>>>>>>>>> Not working >>>>>>>>>> >>>>>>>>>> abhinav@abhnav:~$ qconf -ss >>>>>>>>>> abhnav >>>>>>>>>> localhost >>>>>>>>>> abhinav@abhnav:~$ hostname >>>>>>>>>> abhnav >>>>>>>>>> abhinav@abhnav:~$ qsub script.sh >>>>>>>>>> Unable to run job: warning: abhinav your job is not allowed to run >>>>>>>>>> in any queue >>>>>>>>>> Your job 18 ("script.sh") has been submitted. >>>>>>>>>> Exiting. >>>>>>>>>> >>>>>>>>>> Same for qsub -b y as well >>>>>>>>>> >>>>>>>>>> On Wed, Mar 19, 2014 at 4:30 PM, Reuti <[email protected]> >>>>>>>>>> wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Am 19.03.2014 um 11:45 schrieb Abhinav Mittal: >>>>>>>>>>> >>>>>>>>>>>> I am trying to run a software called >>>>>>>>>>>> "Segway"(http://noble.gs.washington.edu/proj/segway/doc/1.1.0/segway.html) >>>>>>>>>>> >>>>>>>>>>> Before looking into any application specific problems: is a simple >>>>>>>>>>> script echo'ing "Hello World" working? Can you submit a binary with >>>>>>>>>>> `qsub -b y hostname` too? >>>>>>>>>>> >>>>>>>>>>> -- Reuti >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> and getting an error "your job is not allowed to run in any que". >>>>>>>>>>>> submit host : localhost , abhnav >>>>>>>>>>>> hostname : abhnav >>>>>>>>>>>> Still I am getting this error >>>>>>>>>>>> Please help. >>>>>>>>>>>> >>>>>>>>>>>> ----------------------------------------------------------------------------------------------------------------- >>>>>>>>>>>> >>>>>>>>>>>> abhinav@abhnav:~$ segway --num-labels=4 train test.genomedata >>>>>>>>>>>> traindir >>>>>>>>>>>> traindir/observations/chr21.0000.float32 (9411193, 9595548) >>>>>>>>>>>> ____ PROGRAM ENDED SUCCESSFULLY WITH STATUS 0 AT Wednesday March 19 >>>>>>>>>>>> 2014, 16:06:01 IST ____ >>>>>>>>>>>> Traceback (most recent call last): >>>>>>>>>>>> File "/home/abhinav/arch/Linux-x86_64/bin/segway", line 9, in >>>>>>>>>>>> <module> >>>>>>>>>>>> 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 2899, in run_train_round >>>>>>>>>>>> round_index, **kwargs) >>>>>>>>>>>> File "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/run.py", >>>>>>>>>>>> line 2770, in queue_train_parallel >>>>>>>>>>>> res.queue(restartable_job) >>>>>>>>>>>> File >>>>>>>>>>>> "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/__init__.py", >>>>>>>>>>>> line 174, in queue >>>>>>>>>>>> self._queue_unconditional(restartable_job) >>>>>>>>>>>> File >>>>>>>>>>>> "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/__init__.py", >>>>>>>>>>>> line 164, in _queue_unconditional >>>>>>>>>>>> jobid = restartable_job.run() >>>>>>>>>>>> File >>>>>>>>>>>> "/home/abhinav/arch/Linux-x86_64/lib/python2.7/segway/cluster/__init__.py", >>>>>>>>>>>> line 116, in run >>>>>>>>>>>> res = self.session.runJob(job_template) >>>>>>>>>>>> File >>>>>>>>>>>> "/home/abhinav/arch/Linux-x86_64/lib/python2.7/drmaa-0.7.6-py2.7.egg/drmaa/session.py", >>>>>>>>>>>> line 314, in runJob >>>>>>>>>>>> c(drmaa_run_job, jid, sizeof(jid), jobTemplate) >>>>>>>>>>>> File >>>>>>>>>>>> "/home/abhinav/arch/Linux-x86_64/lib/python2.7/drmaa-0.7.6-py2.7.egg/drmaa/helpers.py", >>>>>>>>>>>> line 299, in c >>>>>>>>>>>> return f(*(args + (error_buffer, sizeof(error_buffer)))) >>>>>>>>>>>> File >>>>>>>>>>>> "/home/abhinav/arch/Linux-x86_64/lib/python2.7/drmaa-0.7.6-py2.7.egg/drmaa/errors.py", >>>>>>>>>>>> line 151, in error_check >>>>>>>>>>>> raise _ERRORS[code - 1](error_string) >>>>>>>>>>>> drmaa.errors.DeniedByDrmException: code 17: warning: abhinav your >>>>>>>>>>>> job >>>>>>>>>>>> is not allowed to run in any queue >>>>>>>>>>>> Your job 15 ("emt0.0.0.traindir.43308e4eaf5211e3a4741803736f5e43") >>>>>>>>>>>> has >>>>>>>>>>>> been submitted >>>>>>>>>>>> abhinav@abhnav:~$ hostname >>>>>>>>>>>> abhnav >>>>>>>>>>>> abhinav@abhnav:~$ qconf -ss >>>>>>>>>>>> abhnav >>>>>>>>>>>> localhost >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> users mailing list >>>>>>>>>>>> [email protected] >>>>>>>>>>>> https://gridengine.org/mailman/listinfo/users >>>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> users mailing list >>>>>>>>> [email protected] >>>>>>>>> https://gridengine.org/mailman/listinfo/users >>>>>>> >>>>> >>> _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
