Hi,
Thanks for your patience. Here is the second letter I want to send to you.
When I tried the cryosparcw connect, it failed with the following error.
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ /mnt/data/cryosparc_worker/bin/cryosparcw connect
Traceback (most recent call last):
File "/mnt/data/cryosparc_worker/bin/connect.py", line 65, in <module>
assert master_hostname is not None, "--master is required"
AssertionError: --master is required
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ find /mnt/data/cryosparc_worker -name config.sh
/mnt/data/cryosparc_worker/config.sh
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ /mnt/data/cryosparc_worker/bin/cryosparcw connect --master cryosparc_master
Traceback (most recent call last):
File "/mnt/data/cryosparc_worker/bin/connect.py", line 66, in <module>
assert worker_hostname is not None, "--worker is required"
AssertionError: --worker is required
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ /mnt/data/cryosparc_worker/bin/cryosparcw connect --master cryosparc_master --worker cryosparc_worker01
---------------------------------------------------------------
CRYOSPARC CONNECT --------------------------------------------
---------------------------------------------------------------
Attempting to register worker cryosparc_worker01 to command cryosparc_master:39002
Connecting as unix user jk4882
Will register using ssh string: jk4882@cryosparc_worker01
If this is incorrect, you should re-run this command with the flag --sshstr <ssh string>
---------------------------------------------------------------
/mnt/data/cryosparc_worker/cryosparc_tools/cryosparc/command.py:135: UserWarning: *** CommandClient: (http://cryosparc_master:39002/api) HTTP Error 503 Service Unavailable; please check cryosparcm log command_core for additional information.
Response from server: b'<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" http://www.w3.org/TR/html4/loose.dtd>\n<HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">\n<TITLE>ERROR: The requested URL could not be retrieved</TITLE>\n<STYLE>\n\nbody {\n display: block;\n font-family: \'Helvetica Neue\', Helvetica, Arial, sans-serif;\n text-rendering: optimizelegibility;\n text-align: center;\n}\n\n#sign {\n color: #5A5A5A;\n font-weight: 600;\n margin: 60px 0 20px 0;\n}\n\n#headline {\n color: #5A5A5A;\n font-size: 48px;\n font-weight: 200;\n min-height: 48px;\n letter-spacing: -1px;\n line-height: 48px;\n margin: 0 0 10px 0;\n}\n\n#byline {\n color: #999999;\n font-size: 20px;\n font-weight: 300;\n min-height: 25px;\n line-height: 25px;\n margin: 0 0 30px 0;\n}\n\n#details {\n color: #5A5A5A;\n font-size: 16px;\n height: 24px;\n line-height: 24px;\n margin: 20px 0 0 0;\n}\n .icon,\n .icon::before,\n .icon::after\n {\n position: relative;\n padding: 0;\n margin: 0;\n }\n\n .icon {\n font-size: 88px;\n color: transparent;\n }\n .icon.warning {\n display: inline-block;\n\n top: 0.225em;\n width: 1.15em;\n height: 1.15em;\n overflow: hidden;\n border: none;\n background-color: transparent;\n border-radius: 0.625em;\n }\n\n .icon.warning::before {\n content: "";\n display: block;\n top: -0.08em;\n left: 0.0em;\n position: absolute;\n border: transparent 0.6em solid;\n border-bottom-color: #5a5a5a;\n border-bottom-width: 1em;\n border-top-width: 0;\n box-shadow: #999 0 1px 1px;\n }\n\n .icon.warning::after {\n display: block;\n position: absolute;\n top: 0.3em;\n left: 0;\n width: 100%;\n padding: 0 1px;\n text-align: center;\n Xfont-family: "Garamond";\n font-family: "Arial";\n content: "!";\n font-size: 0.65em;\n font-weight: bold;\n color: #FFFFFF;\n }\n</STYLE>\n</HEAD><BODY>\n<div id="error-container" class="container">\n <div style="align: center; padding-bottom: 10px;">\n <span id="sign" class="icon warning"></span>\n <h1 id="headline">The requested URL could not be retrieved.</h1>\n <p id="byline">Unable to determine IP address from host name for <I>cryosparc_master</I></p>\n </div>\n</div>\n</BODY>\n</HTML>\n'
system = self._get_callable("system.describe")()
Traceback (most recent call last):
File "/mnt/data/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 105, in func
with make_json_request(self, "/api", data=data, _stacklevel=4) as request:
File "/mnt/data/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/contextlib.py", line 135, in __enter__
return next(self.gen)
File "/mnt/data/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 226, in make_request
raise CommandError(error_reason, url=url, code=code, data=resdata)
cryosparc_tools.cryosparc.errors.CommandError: *** (http://cryosparc_master:39002/api, code 503) HTTP Error 503 Service Unavailable; please check cryosparcm log command_core for additional information.
Response from server: b'<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" http://www.w3.org/TR/html4/loose.dtd>\n<HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">\n<TITLE>ERROR: The requested URL could not be retrieved</TITLE>\n<STYLE>\n\nbody {\n display: block;\n font-family: \'Helvetica Neue\', Helvetica, Arial, sans-serif;\n text-rendering: optimizelegibility;\n text-align: center;\n}\n\n#sign {\n color: #5A5A5A;\n font-weight: 600;\n margin: 60px 0 20px 0;\n}\n\n#headline {\n color: #5A5A5A;\n font-size: 48px;\n font-weight: 200;\n min-height: 48px;\n letter-spacing: -1px;\n line-height: 48px;\n margin: 0 0 10px 0;\n}\n\n#byline {\n color: #999999;\n font-size: 20px;\n font-weight: 300;\n min-height: 25px;\n line-height: 25px;\n margin: 0 0 30px 0;\n}\n\n#details {\n color: #5A5A5A;\n font-size: 16px;\n height: 24px;\n line-height: 24px;\n margin: 20px 0 0 0;\n}\n .icon,\n .icon::before,\n .icon::after\n {\n position: relative;\n padding: 0;\n margin: 0;\n }\n\n .icon {\n font-size: 88px;\n color: transparent;\n }\n .icon.warning {\n display: inline-block;\n\n top: 0.225em;\n width: 1.15em;\n height: 1.15em;\n overflow: hidden;\n border: none;\n background-color: transparent;\n border-radius: 0.625em;\n }\n\n .icon.warning::before {\n content: "";\n display: block;\n top: -0.08em;\n left: 0.0em;\n position: absolute;\n border: transparent 0.6em solid;\n border-bottom-color: #5a5a5a;\n border-bottom-width: 1em;\n border-top-width: 0;\n box-shadow: #999 0 1px 1px;\n }\n\n .icon.warning::after {\n display: block;\n position: absolute;\n top: 0.3em;\n left: 0;\n width: 100%;\n padding: 0 1px;\n text-align: center;\n Xfont-family: "Garamond";\n font-family: "Arial";\n content: "!";\n font-size: 0.65em;\n font-weight: bold;\n color: #FFFFFF;\n }\n</STYLE>\n</HEAD><BODY>\n<div id="error-container" class="container">\n <div style="align: center; padding-bottom: 10px;">\n <span id="sign" class="icon warning"></span>\n <h1 id="headline">The requested URL could not be retrieved.</h1>\n <p id="byline">Unable to determine IP address from host name for <I>cryosparc_master</I></p>\n </div>\n</div>\n</BODY>\n</HTML>\n'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/mnt/data/cryosparc_worker/bin/connect.py", line 78, in <module>
cli = client.CommandClient(host=master_hostname, port=command_core_port, service="command_core")
File "/mnt/data/cryosparc_worker/cryosparc_compute/client.py", line 38, in __init__
super().__init__(service, host, port, url, timeout, headers, cls=NumpyEncoder)
File "/mnt/data/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 97, in __init__
self._reload() # attempt connection immediately to gather methods
File "/mnt/data/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 135, in _reload
system = self._get_callable("system.describe")()
File "/mnt/data/cryosparc_worker/cryosparc_tools/cryosparc/command.py", line 108, in func
raise CommandError(
cryosparc_tools.cryosparc.errors.CommandError: *** (http://cryosparc_master:39002, code 503) Encounted error from JSONRPC function "system.describe" with params ()
I tried to debug but I failed to pinpoint the problem… In case these information has some value…
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ cryosparcm status | grep -v LICENSE
cryosparcm: command not found
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ /mnt/data/cryosparcm status | grep -v LICENSE
0817/ cryosparc_database/ cryosparc_worker/ .Trash-290217128/
CryoSPARC_data/ cryosparc_master/ master-v4.5.3.tar.gz worker-v4.5.3.tar.gz
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ /mnt/data/cryosparc_master/bin/cryosparcm status | grep -v LICENSE
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/mnt/data/cryosparc_master
Current cryoSPARC version: v4.5.3
----------------------------------------------------------------------------
CryoSPARC process status:
app RUNNING pid 54965, uptime 2 days, 3:52:33
app_api RUNNING pid 54986, uptime 2 days, 3:52:31
app_api_dev STOPPED Not started
command_core RUNNING pid 54915, uptime 2 days, 3:52:45
command_rtp RUNNING pid 54951, uptime 2 days, 3:52:37
command_vis RUNNING pid 54937, uptime 2 days, 3:52:39
database RUNNING pid 54810, uptime 2 days, 3:52:49
----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------
global config variables:
export CRYOSPARC_MASTER_HOSTNAME="icrc4lcga001"
export no_proxy=localhost,::1,127.0.0.1,${CRYOSPARC_MASTER_HOSTNAME},.columbia.edu
export CRYOSPARC_DB_PATH="/mnt/data/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000
export CRYOSPARC_INSECURE=false
export CRYOSPARC_DB_ENABLE_AUTH=true
export CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10
export CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000
export CRYOSPARC_PROJECT_DIR_PREFIX='CS-'
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_CLICK_WRAP=true
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ hostname -f
icrc4lcga001
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ host $(hostname -f)
icrc4lcga001 has address 127.0.1.1
jk4882@icrc4lcga001:/mnt/data/cryosparc_worker$ cd ..
I wondered if you could shed some light on these problem. If I need to delete cryosparcw and re-install it, I would like to know how to complete delete it?
Thanks for your time and help again!
Best,
Junqing