Job sits in queue

open

#1

Dear Experts,
My job is just sitting in queue and not running. I have enough RAM. I tried even a simple import of 3D map. Still not working.
Any suggestions?
Thanks!


#2

Hi @slee,

When you navigate to the resource manager (button on the bottom panel of the screen), what is the message you see for that job?

- Suhail


#3

Dear Suhail,
Resource manager is blank, no message.
Thanks!

Sukyeong


#4

Hi @slee,

Can you please post the joblog as well as any logs from command_core?
cryosparcm joblog PX JX
cryosparcm log command_core


#5

Hi,
Please see the following joblog and command_core log. Many thanks!
Sukyeong

JOBLOG

Traceback (most recent call last):
File “/data1/people/slee/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 174, in _run_module_as_main
main”, fname, loader, pkg_name)
File “/data1/people/slee/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 72, in _run_code
exec code in run_globals
File “/data1/people/slee/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 83, in
print eval(“cli.”+command)
File “”, line 1, in
File “/data1/people/slee/cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 57, in func
assert False, res[‘error’]
AssertionError: {u’message’: u"OtherError: argument of type ‘NoneType’ is not iterable", u’code’: 500, u’data’: None, u’name’: u’OtherError’}


COMMAND_CORE log is

COMMAND CORE STARTED === 2019-06-13 10:17:12.288286 ==========================
*** BG WORKER START
Indexing $HOME ----
Base path: $HOME
Indexing $HOME/sp ----
Base path: $HOME/sp
Indexing $HOME/sp ----
Base path: $HOME/sp
Indexing $HOME/Desktop ----
Base path: $HOME/Desktop
Indexing $HOME/Desktop ----
Base path: $HOME/Desktop
Indexing $HOME/Desktop/ATPase ----
Base path: $HOME/Desktop/ATPase
Indexing $HOME/Desktop/ATPase/batch1_relion ----
Base path: $HOME/Desktop/ATPase/batch1_relion
Indexing $HOME/Desktop/ATPase/batch1_relion/Extract ----
Base path: $HOME/Desktop/ATPase/batch1_relion/Extract
Indexing $HOME/Desktop/ATPase/batch1_relion/Extract/job014 ----
Base path: $HOME/Desktop/ATPase/batch1_relion/Extract/job014
Indexing $HOME/Desktop/ATPase/batch1_relion/Extract/job014/particles.star ----
Base path: $HOME/Desktop/ATPase/batch1_relion/Extract/job014
particle_meta_path path
Setting parameter J1.particle_meta_path with value $HOME/Desktop/ATPase/batch1_relion/Extract/job014/particles.star of type <type ‘str’>
accel_kv number
Setting parameter J1.accel_kv with value 300 of type <type ‘int’>
cs_mm number
Setting parameter J1.cs_mm with value 1 of type <type ‘int’>
amp_contrast number
Setting parameter J1.amp_contrast with value 0.1 of type <type ‘float’>
psize_A number
Setting parameter J1.psize_A with value 1.05 of type <type ‘float’>
failed to connect link
[JSONRPC ERROR 2019-06-13 10:44:40.780861 at get_job ]

Traceback (most recent call last):
File “cryosparc2_command/command_core/init.py”, line 106, in wrapper
res = func(*args, **kwargs)
File “cryosparc2_command/command_core/init.py”, line 2627, in get_job
return sanitize_id(com.get_job(mongo.db, project_uid, job_uid, *args, **kwargs))
File “cryosparc2_command/command_core/init.py”, line 156, in sanitize_id
if ‘_id’ in obj:
TypeError: argument of type ‘NoneType’ is not iterable

[JSONRPC ERROR 2019-06-13 10:44:40.809161 at get_job_dir_abs ]

Traceback (most recent call last):
File “cryosparc2_command/command_core/init.py”, line 106, in wrapper
res = func(*args, **kwargs)
File “cryosparc2_command/command_core/init.py”, line 3368, in get_job_dir_abs
job_doc = get_job(project_uid, job_uid, ‘job_dir’)
File “cryosparc2_command/command_core/init.py”, line 115, in wrapper
raise e
TypeError: argument of type ‘NoneType’ is not iterable

[JSONRPC ERROR 2019-06-13 10:44:40.809346 at get_job_log_path_abs ]

Traceback (most recent call last):
File “cryosparc2_command/command_core/init.py”, line 106, in wrapper
res = func(*args, **kwargs)
File “cryosparc2_command/command_core/init.py”, line 3374, in get_job_log_path_abs
job_dir_abs = get_job_dir_abs(project_uid, job_uid)
File “cryosparc2_command/command_core/init.py”, line 115, in wrapper
raise e
TypeError: argument of type ‘NoneType’ is not iterable