Cryosparc install always fails on reinstall

[lsweezy]

Hello,

I have been trying to rebuild cryosparc standalone installation on a machine where the the previous install had been wiped (the directory containing it was rm -rf’d). This included the files for cryosparc_master, cryosparc_worker, and cryosparc_database. Whenever I try to reinstall, it breaks at the same step, when trying to create the initial cryosparc user.

Creating the initial cryoSPARC user…

Creating user USERNAME with email: USERNAME@EMAIL.edu password: PASSWORD
Traceback (most recent call last):
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 174, in _run_module_as_main
“main”, fname, loader, pkg_name)
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 72, in _run_code
exec code in run_globals
File “/home/USER/cryosparc2/cryosparc2_master/cryosparc2_compute/client.py”, line 57, in
print eval(“cli.”+command)
File “”, line 1, in
File “/home/USER/cryosparc2/cryosparc2_master/cryosparc2_compute/client.py”, line 31, in func
assert False, res[‘error’]
AssertionError: {u’message’: u’OtherError: [HOSTNAME]:39001: [Errno 111] Connection refused’, u’code’: 500, u’data’: None, u’name’: u’OtherError’}

I’m assuming there must be something leftover from the previous install but I cannot tell where that would be. Any help with this issue would be greatly appreciated !

[user123]

Hey lsweezy,

I am getting a very similar message when trying to install Cryosparc2. I didn’t remove the cryosparc1 files and was assuming I could install and run them in parallel.

I’ll be making a new post for this, since the beginning of our errors differ.

Creating the initial cryoSPARC user…

Creating user User123 with email: asdf@gmail.com password: asdf
/home/user/SoftwareA/Cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/requests/init.py:80: RequestsDependencyWarning: urllib3 (1.23) or chardet (3.0.4) doesn’t match a supported version!
RequestsDependencyWarning)
Traceback (most recent call last):
File “/home/user/SoftwareA/Cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 174, in _run_module_as_main
“main”, fname, loader, pkg_name)
File “/home/user/SoftwareA/Cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/runpy.py”, line 72, in _run_code
exec code in run_globals
File “/home/user/SoftwareA/Cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 57, in
print eval(“cli.”+command)
File “”, line 1, in
File “/home/user/SoftwareA/Cryosparc/cryosparc2_master/cryosparc2_compute/client.py”, line 31, in func
assert False, res[‘error’]
AssertionError: {u’message’: u’OtherError: user-desktop:39001: [Errno 111] Connection refused’, u’code’: 500, u’data’: None, u’name’: u’OtherError’}

[stephan]

Hi @lsweezy & @user123,

Can you report the status of cryosparc?

cryosparcm status

It is possible the rebuild didn’t work successfully. If so, check out this post:

Update failure from 2.2 --> 2.3

Hi @Elad, It looks like the update process couldn't delete the directory properly (cryosparc was still somehow running/ another user had a session open?) You data should be fine, but I'd recommend stopping cryoSPARC completely (cryosparcm stop), ensuring any processes aren't alive (ps -ax | grep "supervisord", kill any cryoSPARC 2 PID's) manually deleting only the cryosparc2_master directory, and then reinstalling cryoSPARC.

[lsweezy]

Hi!

Thanks for the help !

running cryosparcm status returns the following

---

CryoSPARC System master node installed at
/home/USER/cryosparc2/cryosparc2_master
Current cryoSPARC version: v2.3.2

cryosparcm process status:

command_core STOPPED Not started
command_proxy STOPPED Not started
command_vis STOPPED Not started
database FATAL Exited too quickly (process log may have details)
watchdog_dev STOPPED Not started
webapp STOPPED Not started
webapp_dev STOPPED Not started

---

global config variables:

export CRYOSPARC_LICENSE_ID=“ID_NUMBER”
export CRYOSPARC_MASTER_HOSTNAME=“HOSTNAME”
export CRYOSPARC_DB_PATH="/home/USER/cryosparc2/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

I tried what was suggested in the following link, but there didn’t appear to be any sort of leftover processes running. I did notice that first time I would try an install that would fail, I would get a slightly different error, about the database not starting properly, which I have pasted below:

Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
File “”, line 1, in
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 1149, in database_names
“listDatabases”)[“databases”]]
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/database.py”, line 491, in command
with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 859, in _socket_for_reads
with self._get_socket(read_preference) as sock_info:
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py”, line 17, in enter
return self.gen.next()
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py”, line 823, in _get_socket
server = self._get_topology().select_server(selector)
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py”, line 214, in select_server
address))
File “/home/USER/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py”, line 189, in select_servers
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused

[user123]

Hi @stephan

Thanks for your help! Turns out I had a capital Cryosparc in one of my paths when it should have been lowercase. I think cryosparcm started running when I tried and failed the first installation attempt. “Cryosparcm stop” plus fixing the path seemed to allow installation

I am a bit concerned that I need to remove some files from the previous installation and possibly reinstall. The cryosparc2_database folder has some files that show modified Oct8, the date of the failed installation. There’s multiple index-wt files for a few numbers. Should I rm-rf the whole cryosparc folder and restart?

Thanks!

Here’s what I got with the status command for reference.

---

CryoSPARC System master node installed at
/home/user/SoftwareA/Cryosparc/cryosparc2_master
Current cryoSPARC version: v2.3.2

cryosparcm process status:

command_core RUNNING pid 27650, uptime 1 day, 5:37:35
command_proxy RUNNING pid 27682, uptime 1 day, 5:37:31
command_vis RUNNING pid 27669, uptime 1 day, 5:37:33
database EXITED Oct 08 05:13 PM
watchdog_dev STOPPED Not started
webapp RUNNING pid 27688, uptime 1 day, 5:37:30
webapp_dev STOPPED Not started

---

global config variables:

export CRYOSPARC_LICENSE_ID=""
export CRYOSPARC_MASTER_HOSTNAME=“user-desktop”
export CRYOSPARC_DB_PATH="/home/user/SoftwareA/Cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

[user123]

Hi @stephan
I now get an error “Error connecting to cryoSPARC license server. Checking local license file. Could not find local license file. Please re-establish your connection to the license servers.”
I deleted the whole cryosparc folder and reinstalled and it still occurs.

cryosparcm status

CryoSPARC System master node installed at
/home/user/SoftwareA/Cryosparc/cryosparc2_master
Current cryoSPARC version: v2.3.2

cryosparcm process status:

command_core RUNNING pid 2018, uptime 0:05:11
command_proxy RUNNING pid 2049, uptime 0:05:08
command_vis RUNNING pid 2038, uptime 0:05:09
database RUNNING pid 1898, uptime 0:05:13
watchdog_dev STOPPED Not started
webapp RUNNING pid 2055, uptime 0:05:07
webapp_dev STOPPED Not started

---

global config variables:

export CRYOSPARC_LICENSE_ID="<##-##-##-##-##>"
export CRYOSPARC_MASTER_HOSTNAME=“user-desktop”
export CRYOSPARC_DB_PATH="/home/user/SoftwareA/Cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

[lsweezy]

I managed to clear up the issue. There were some .sock files (mongodb-39001 & cryosparc-supervisor-(something)). Deleting these and then reinstalling fixed the issue !