Cluster installation issue(s)

Install, Configure and Update
1

First off, I noticed an issue with the database not being happy with our Lustre file system. I’m guessing this is an issue with the file-locking, as we’ve seen it with other databases like SQLite. The work-around was just to put the database directory on a separate, non-Lustre file system.

The second issue is on that I can’t seem to get around. I have trouble “connecting” to our cluster:

[cryosparc_user@login02 config_files]$ cryosparcm cluster connect
Traceback (most recent call last):
File “”, line 5, in
File “/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/json/init.py”, line 291, in load
**kw)
File “/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/json/init.py”, line 339, in loads
return _default_decoder.decode(s)
File “/home/cryosparc_user/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/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py”, line 380, in raw_decode
obj, end = self.scan_once(s, idx)
ValueError: Expecting , delimiter: line 5 column 5 (char 159)

I don’t believe this is a syntax error in my configuration files as I get the same error even when I use the example configuration files:

[cryosparc_user@login02 foo]$ ~/cryosparc2_master/bin/cryosparcm cluster example pbs
Writing example cluster_info.json and cluster_script.sh to current dir
[cryosparc_user@login02 foo]$ cryosparcm cluster connect Traceback (most recent call last):
File “”, line 5, in
File “/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/json/init.py”, line 291, in load
**kw)
File “/home/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/json/init.py”, line 339, in loads
return _default_decoder.decode(s)
File “/home/cryosparc_user/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/cryosparc_user/cryosparc2_master/deps/anaconda/lib/python2.7/json/decoder.py”, line 380, in raw_decode
obj, end = self.scan_once(s, idx)
ValueError: Expecting , delimiter: line 5 column 5 (char 159)

Things appear to be running properly:

[cryosparc_user@login02 examples]$ cryosparcm status ----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/cryosparc_user/cryosparc2_master
Current cryoSPARC version: v2.1.0

cryosparcm process status:

command_core RUNNING pid 6745, uptime 0:12:13
command_proxy RUNNING pid 7406, uptime 0:11:43
command_vis RUNNING pid 7400, uptime 0:11:46
database RUNNING pid 6393, uptime 0:12:38
watchdog_dev STOPPED Not started
webapp RUNNING pid 7418, uptime 0:11:40
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=“3557a562-b5fd-11e8-b46f-47917e63cf05”
export CRYOSPARC_MASTER_HOSTNAME=“login02”
export CRYOSPARC_DB_PATH="/home/cryosparc_user/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

Any help will be greatly appreciated.

2

The issue is related to a missing , at the end of "cache_path" json entry (line 5). Once you dumped an example, please edit the cluster_info.json file and add a comma. It should fix the issue. If you want to completely fix the issue, you need to edit cryosparc2_master/bin/cryosparcm and add comma at the end of line 800 and 861 where a sample json is dumped for PBS and SLURM by running cryosparcm cluster example pbs

Hope this helps

3

The missing comma did indeed fix the issue. Thanks!