Regarding installation of version 3.2

PRIYANKA · April 29, 2021, 6:28am

Hi,
I am facing problem when doing installation of version3.2.
Previously,I was working with version2.4 and it was working fine.Due to some problem,I have to start reinstall but now that 2.4 version is not available.
I have pasted the error which I am facing while installation of version 3.2.Can someone provide me the procedure of installation as I am stuck from last two months. Every-time there is error.I have tried to follow every solution mentioned in discussion forum posted by other.
Please help me for the same.

cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: ERROR (spawn error)

cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/priyanka/cryosparc3/cryosparc_master
Current cryoSPARC version: v3.2.0
----------------------------------------------------------------------------

CryoSPARC process status:
app                              STOPPED   Not started
app_dev                          STOPPED   Not started
command_core                     FATAL     Exited too quickly (process log may have details)
command_rtp                      STOPPED   Not started
command_vis                      STOPPED   Not started
database                         RUNNING   pid 75997, uptime 0:00:38
liveapp                          STOPPED   Not started
liveapp_dev                      STOPPED   Not started
webapp                           STOPPED   Not started
webapp_dev                       STOPPED   Not started

nfrasser · April 30, 2021, 6:39pm

Hi @PRIYANKA can you end me the output of the following command?

cryosparcm log command_core | tail -n 100

PRIYANKA · May 1, 2021, 5:58am

Hi,
This is the error it is showing when I am typing cryosparcm log command_core | tail -n 100

run_simple(host, port, self, **options)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1052, in run_simple
    inner()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1005, in inner
    fd=fd,
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 848, in make_server
    host, port, app, request_handler, passthrough_errors, ssl_context, fd=fd
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 740, in __init__
    HTTPServer.__init__(self, server_address, handler)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 452, in __init__
    self.server_bind()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py", line 137, in server_bind
    socketserver.TCPServer.server_bind(self)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 466, in server_bind
    self.socket.bind(self.server_address)
OSError: [Errno 98] Address already in use
COMMAND CORE STARTED ===  2021-05-01 11:12:21.174653  ==========================
*** BG WORKER START
 * Serving Flask app "command_core" (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: off
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/priyanka/cryosparc3/cryosparc_master/cryosparc_command/command_core/__init__.py", line 272, in start
    app.run(host="0.0.0.0", port=port, threaded=True, passthrough_errors=False)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/flask/app.py", line 990, in run
    run_simple(host, port, self, **options)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1052, in run_simple
    inner()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1005, in inner
    fd=fd,
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 848, in make_server
    host, port, app, request_handler, passthrough_errors, ssl_context, fd=fd
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 740, in __init__
    HTTPServer.__init__(self, server_address, handler)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 452, in __init__
    self.server_bind()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py", line 137, in server_bind
    socketserver.TCPServer.server_bind(self)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 466, in server_bind
    self.socket.bind(self.server_address)
OSError: [Errno 98] Address already in use
COMMAND CORE STARTED ===  2021-05-01 11:12:24.127947  ==========================
*** BG WORKER START
 * Serving Flask app "command_core" (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: off
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/priyanka/cryosparc3/cryosparc_master/cryosparc_command/command_core/__init__.py", line 272, in start
    app.run(host="0.0.0.0", port=port, threaded=True, passthrough_errors=False)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/flask/app.py", line 990, in run
    run_simple(host, port, self, **options)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1052, in run_simple
    inner()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1005, in inner
    fd=fd,
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 848, in make_server
    host, port, app, request_handler, passthrough_errors, ssl_context, fd=fd
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 740, in __init__
    HTTPServer.__init__(self, server_address, handler)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 452, in __init__
    self.server_bind()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py", line 137, in server_bind
    socketserver.TCPServer.server_bind(self)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 466, in server_bind
    self.socket.bind(self.server_address)
OSError: [Errno 98] Address already in use
COMMAND CORE STARTED ===  2021-05-01 11:12:28.060212  ==========================
*** BG WORKER START
 * Serving Flask app "command_core" (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: off
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/priyanka/cryosparc3/cryosparc_master/cryosparc_command/command_core/__init__.py", line 272, in start
    app.run(host="0.0.0.0", port=port, threaded=True, passthrough_errors=False)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/flask/app.py", line 990, in run
    run_simple(host, port, self, **options)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1052, in run_simple
    inner()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 1005, in inner
    fd=fd,
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 848, in make_server
    host, port, app, request_handler, passthrough_errors, ssl_context, fd=fd
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/werkzeug/serving.py", line 740, in __init__
    HTTPServer.__init__(self, server_address, handler)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 452, in __init__
    self.server_bind()
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/http/server.py", line 137, in server_bind
    socketserver.TCPServer.server_bind(self)
  File "/home/priyanka/cryosparc3/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/socketserver.py", line 466, in server_bind
    self.socket.bind(self.server_address)
OSError: [Errno 98] Address already in use

Thanks,

Regards,
Priyanka

PRIYANKA · May 1, 2021, 6:08am

Hi,
Thanks for your concern.Please help me.My work is completely stuck.I want to resolve this problem.

Thanks,

Regards,
Priyanka

nfrasser · May 3, 2021, 10:07pm

Hi @PRIYANKA , this error indicates that there is already another cryoSPARC instance running that is conflicting with the current one.

To fix this, first completely stop your current instance from the command line with the following commands:

cd /home/priyanka/cryosparc3/cryosparc_master
./bin/cryosparcm stop

If you have another folder with cryoSPARC installed (say, at /home/priyanka/cryosparc2), navigate to that directory, navigate to the inner cryosparc2_master directory and run this command to stop it:

./bin/cryosparcm stop

Look inside the /home/priyanka/cryosparc3/cryosparc_master/config.sh command with this command:

cat /home/priyanka/cryosparc3/cryosparc_master/config.sh

Look for the line that begins with export CRYOSPARC_BASE_PORT= and find the base port number you used when you first installed cryoSPARC (for example 39000).

To ensure no remaining cryoSPARC processes are running, I suggest restarting your machine.

If you can’t do that, look for any processes that are bound to the first few ports starting from that number. For example:

lsof -i :39000
lsof -i :39001
lsof -i :39002
lsof -i :39003
lsof -i :39004
lsof -i :39005
lsof -i :39006
lsof -i :39007

If each command has no output, then nothing is bound to that port. If there is, you’ll see output that looks like this:

$ lsof -i :39002                                                                                                                                           [21/05/3| 5:04PM]
COMMAND    PID     USER   FD   TYPE     DEVICE SIZE/OFF NODE NAME
python  704982 nfrasser    4u  IPv4 3991296075      0t0  TCP *:39002 (LISTEN)

Find the process ID (PID) of each process (704982 in the above example) and kill it with the following command:

kill <PID>

Once you’ve done all the steps above, try starting your cryoSPARC instance with this command:

cd /home/priyanka/cryosparc3/cryosparc_master
./bin/cryosparcm start

If that still doesn’t work, send me the output of the following commands (be sure to omit your license ID from the output of the status command before posting):

cd /home/priyanka/cryosparc3/cryosparc_master
./bin/cryosparcm status
./bin/cryosparcm log command_core | tail -n 100

PRIYANKA · May 4, 2021, 7:31am

Hi,
Thanks for your help and concern. It fixed my issue. Now,I am able to conitnue my work.

Thanks,

Regards,
Priyanka