Problems during installation on workstation; [database spawn ERROR]

open

#1

Hi developers!

I’m trying to install cryoSparc as standalone; everything goes smooth at first but I’m stacked when the master process starts to complete the standalone installer.

I paste below the error point… any ideas?


*********** CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

  The installer will now download, install and connect the worker
  package on this machine. The worker package will allow cryoSPARC
  to run compute jobs.

******************************************************************

 Starting cryoSPARC...

Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/casdanie/tools/cryosparc/s5/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 1149, in database_names
    "listDatabases")["databases"]]
  File "/home/casdanie/tools/cryosparc/s5/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/casdanie/tools/cryosparc/s5/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/casdanie/tools/cryosparc/s5/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/casdanie/tools/cryosparc/s5/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/casdanie/tools/cryosparc/s5/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/casdanie/tools/cryosparc/s5/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
    address))
  File "/home/casdanie/tools/cryosparc/s5/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
~/.bashrc has been executed

#2

Hi @Daniel_Castano,

Any chance you’re running on CentOS? You need to ensure ports 39000 to 39005 are not blocked by the firewall. Please refer to this: https://stackoverflow.com/questions/24729024/open-firewall-port-on-centos-7

- Suhail


#3

Hi Suhail,

Thanks! No, my setting is an Ubuntu 16.04…
Actually, if I run
netstat -an | grep 39000 | grep -i listen

I get nothing. Any advice on how to proceed from here?
Daniel


#4

Hi Daniel,

Hmm, interesting. Can you try running cryosparcm status and pasting the output? I’d also recommend cryosparcm restart to stop and start the instance - sometimes that solves the problem.

- Suhail


#5

Hi Suhail,

thanks for your answer… found a weird effect. cryosparc reports that there is a missing folder:

>     casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s5/cryosparc2_master[0]>  bin/cryosparcm status
>     bin/cryosparcm: line 25: cd: /home/casdanie/tools/cryosparc/s5/cryosparc2_master/bin
>     /home/casdanie/tools/cryosparc/s5/cryosparc2_master/bin/../: No such file or directory

… but the folder is actually there:

casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s5/cryosparc2_master[1]> ls /home/casdanie/tools/cryosparc/s5/cryosparc2_master/bin/…/
bin cryosparc2_webapp install.sh
check_install_deps.sh deps run
config.sh deps_bundle setup_client_ipython.py
cryosparc2_command deps_bundle_hashes supervisord.conf
cryosparc2_compute deps_hashes version

Does it mean that I cannot use the “cryosparcm” command directly providing the path from a higher directory (i.e., from cryosparc2_master writing “bin/cryosparcm XXX”)? Is it necessary to explicitely include the “bin” in the PATH?

In any case, after including the bin path, restarting with “cryosparcm restart”, I got the report that I paste below

casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s5/cryosparc2_master[0]>  cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/casdanie/tools/cryosparc/s5/cryosparc2_master
Current cryoSPARC version: v2.9.0
----------------------------------------------------------------------------

cryosparcm process status:

command_core                     STOPPED   Jul 15 09:43 AM
command_proxy                    STOPPED   Jul 15 09:43 AM
command_vis                      STOPPED   Jul 15 09:43 AM
database                         STOPPED   Jul 15 09:43 AM
watchdog_dev                     STOPPED   Not started
webapp                           STOPPED   Jul 15 09:43 AM
webapp_dev                       STOPPED   Not started

----------------------------------------------------------------------------

global config variables:

export CRYOSPARC_LICENSE_ID=""
export CRYOSPARC_MASTER_HOSTNAME="bs-dalc03.ethz.ch"
export CRYOSPARC_DB_PATH="/home/casdanie/tools/cryosparc/s5/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

#6

Well… I keep trying to install cryosparc. The error I land on most frequently is the one I paste here:

******* CRYOSPARC WORKER INSTALLATION COMPLETE *******************

 In order to run processing jobs, you will need to connect this
 worker to a cryoSPARC master.

******************************************************************

******************************************************************

 Connecting the cryoSPARC worker to the master...

bin/cryosparcw: line 30: cd: /home/casdanie/tools/cryosparc/s6/cryosparc2_worker/bin
/home/casdanie/tools/cryosparc/s6/cryosparc2_worker/bin/../: No such file or directory
~/.bashrc has been executed
casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s6/cryosparc2_master[0]> ls /home/casdanie/tools/cryosparc/s6/cryosparc2_worker/bin/../
bin		       cryosparc2_compute  deps_bundle_hashes  version
check_install_deps.sh  deps		   deps_hashes
config.sh	       deps_bundle	   install.sh
casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s6/cryosparc2_master[0]> 

I cannot interpret the reported error, as the offending path is clearly in the file system.
In any case; is there a way that I can complete the connection of the worker to the master manually? What I mean is that this problem with the folders uncorrectly seen as missing by cryosparc persists when trying to use “cryosparcw connect”

casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s6/cryosparc2_worker[1]> bin/cryosparcw connect --worker bioem-gpu03 --master bioem-gpu03 --ssdpath /local0/tmp/cryosparc/scratch
bin/cryosparcw: line 30: cd: /home/casdanie/tools/cryosparc/s6/cryosparc2_worker/bin
/home/casdanie/tools/cryosparc/s6/cryosparc2_worker/bin/../: No such file or directory
casdanie@d.ethz.ch@bs-dalc03:~/tools/cryosparc/s6/cryosparc2_worker[1]> ls /home/casdanie/tools/cryosparc/s6/cryosparc2_worker/bin/../
bin		       cryosparc2_compute  deps_bundle_hashes  version
check_install_deps.sh  deps		   deps_hashes
config.sh	       deps_bundle	   install.sh

#7

Hi @Daniel_Castano,

Are you using bash? If possible, can you switch to that shell and then run the script?

- Suhail


#8

Yep… I always use bash:
casdanie@d.ethz.ch@bs-dalc03:~/.ssh[0]> echo $0
-bash