Job sits in queue

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(Sukyeong Lee) #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!


(Suhail Dawood) #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


(Sukyeong Lee) #3

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

Sukyeong


(Stephan Arulthasan) #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


(Sukyeong Lee) #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 <module>
    print eval("cli."+command)
  File "<string>", line 1, in <module>
  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
-----------------------------------------------------