Change default port number

kortal · June 13, 2020, 9:05pm

Hi,

Is there any easy way to change port number instead of reinstalling the software?

Thank you!

nfrasser · June 15, 2020, 6:55pm

Hi @kortal, you can change the default port number in cryosparc_master/config.sh file.

Stop cryoSPARC with cryosparcm stop
Edit cryosparc_master/config.sh and look for the line that looks like export CRYOSPARC_BASE_PORT=xxxxx. Change xxxxx to the desired port value
Exit/log out of the current terminal and log back in
Restart cryoSPARC with cryosparcm start

Let me know how that goes.

Nick

wonderful · October 16, 2020, 7:22am

command_vis: started command_proxy: started command_rtp: ERROR (spawn error)

- List item

nfrasser · October 16, 2020, 1:53pm

Hi @wonderful, this means a component that runs cryoSPARC Live failed to start. Can you send me the logs for it via this command?

cryosparcm log command_rtp

(Afterwards press Ctrl+C to exit)

wonderful · October 17, 2020, 7:49am

hi

*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 1 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 2 of 3
*** client.py: command (http://localhost:39006/api) did not reply within timeout of 300 seconds, attempt 3 of 3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "cryosparc2_command/command_rtp/__init__.py", line 32, in <module>
    rc.connect(os.environ['CRYOSPARC_MASTER_HOSTNAME'], int(os.environ['CRYOSPARC_COMMAND_CORE_PORT']))
  File "cryosparc2_compute/jobs/runcommon.py", line 82, in connect
    cli = client.CommandClient(master_hostname, int(master_command_core_port))
  File "cryosparc2_compute/client.py", line 33, in __init__
    self._reload()
  File "cryosparc2_compute/client.py", line 61, in _reload
    system = self._get_callable('system.describe')()
  File "cryosparc2_compute/client.py", line 50, in func
    res = r.json()
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/models.py", line 897, in json
    return complexjson.loads(self.text, **kwargs)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 364, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/tommy/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py", line 382, in raw_decode
    raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded
2020-10-16 15:24:43,932     RTP                   INFO      === STARTED === 
2020-10-16 15:24:43,932     RTP.BACKGROUND_WORKER INFO      === STARTED === 
2020-10-16 16:29:57,094     RTP                   INFO      === STARTED === 
2020-10-16 16:29:57,095     RTP.BACKGROUND_WORKER INFO      === STARTED === 
2020-10-16 19:15:54,969     RTP                   INFO      === STARTED === 
2020-10-16 19:15:54,983     RTP.BACKGROUND_WORKER INFO      === STARTED === 
2020-10-16 19:30:46,148     RTP                   INFO      === STARTED === 
2020-10-16 19:30:46,148     RTP.BACKGROUND_WORKER INFO      === STARTED === 
2020-10-16 20:24:06,487     RTP                   INFO      === STARTED === 
2020-10-16 20:24:06,502     RTP.BACKGROUND_WORKER INFO      === STARTED ===

nfrasser · October 21, 2020, 2:58pm

@wonderful from the logs it looks like this is working now, can you confirm? If not, please restart your machine. Then run these two commands and send me the output:

cryosparcm restart
cryosparcm status

wonderful · October 23, 2020, 11:17am

CryoSPARC is running.
Stopping cryosparc
command_rtp: stopped
command_proxy: stopped
command_vis: stopped
webapp: stopped
command_core: stopped
database: stopped
Shut down
Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: started

500 Internal Server Error

Internal Server Error

The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.

command_vis: started
command_proxy: started
command_rtp: ERROR (spawn error)

wonderful · October 25, 2020, 9:19am

hi,@nfrasser,above is the output that when I change the port and as your way to restart cryosparc.it seems didn’t work,so I change the port back.

nfrasser · October 26, 2020, 2:27pm

@wonderful ah I see, this indicates that there is another process running on one of ports that cryoSPARC requires. To fix this, stop cryoSPARC and run these commands (substitute the port numbers with the correct port - e.g., if your base port is 40000, instead of 39000, 39001, etc; use 40000, 40001, 40002, etc.):

lsof -i :39000
lsof -i :39001
lsof -i :39002
lsof -i :39003
lsof -i :39005
lsof -i :39006

If you’ll see output like this for one of the commands:

lsof -i :39000
COMMAND   PID     USER        FD   TYPE     DEVICE SIZE/OFF NODE NAME
node    27752 cryosparcuser   15u  IPv4 2206290935      0t0  TCP *:39000 (LISTEN)
node    27752 cryosparcuser   16u  IPv4 2321775470      0t0  TCP localhost:39000->localhost:52142 (ESTABLISHED)

This means there is a process bound to that port so that cryoSPARC can’t use it (in this case node with process ID 27752). Kill that process and re-run the lsof commands until there is no more output.

Then start cryoSPARC. Send me any output you’re not sure about. Hope that helps!

Nick

nfrasser · November 2, 2020, 3:05pm

Hi @wonderful, any update on this? Did this resolve your issue?

wonderful · November 4, 2020, 5:03am

hi@nfrasser,I have some job didn’t finish in cryosparc .So I still didn’t update them.When I finish my job,I will try it as soon as possible.Then,I will report it.Thank you.