after I updated from v 4.4.1 to v 4.5.0, the refinement refused to run. stopped at
License is valid.
Launching job on lane default target r16763 …
Running job on master node hostname r16763
Your help will be appreciated!
Lan
Please can you post the outputs of these commands on the CryoSPARC master node:
hostname -f
cryosparcm log update | tail -n 40
ps -eo pid,ppid,start,cmd | grep cryosparc_
cat /path/to/cryosparc_worker/version
/path/to/cryosparc_worker/bin/cryosparcw gpulist
ls -al /path/to/job/dir
Edited: corrected typo in ps command
(base) [cryosparc_user@r16763 cryosparc_master]$ hostname -f
r16763.ttuhsc.edu
(base) [cryosparc_user@r16763 cryosparc_master]$ cryosparcm log update | tail -n 40
command_vis: started
command_rtp: started
command_rtp connection succeeded
command_rtp startup successful
app: started
app_api: started
-----------------------------------------------------
CryoSPARC master started.
From this machine, access CryoSPARC and CryoSPARC Live at
http://localhost:39000
From other machines on the network, access CryoSPARC and CryoSPARC Live at
http://r16763.ttuhsc.edu:39000
Startup can take several minutes. Point your browser to the address
and refresh until you see the CryoSPARC web interface.
===================================================
Now updating worker nodes.
===================================================
All workers:
r16763 cryosparc_user@r16763
-------------------------------------------------
Updating worker r16763
Direct update
\cp -f ./cryosparc_worker.tar.gz /home/cryosparc_user/software/cryosparc/cryosparc_worker
This is a forced update. To finish updating this worker node, log onto the node and run cryosparcw
Done updating all worker nodes.
If any nodes failed to update, you can manually update them.
Cluster worker installations must be manually updated.
To update manually, copy the cryosparc_worker.tar.gz file into the
cryosparc worker installation directory, and then run
$ bin/cryosparcw update
from inside the worker installation directory.
(base) [cryosparc_user@r16763 cryosparc_master]$ ps -ep pid,ppid,start,cmd | grep cryosparc_
error: process ID list syntax error
Usage:
ps [options]
Try 'ps --help <simple|list|output|threads|misc|all>'
or 'ps --help <s|l|o|t|m|a>'
for additional help text.
For more details see ps(1).
(base) [cryosparc_user@r16763 cryosparc_master]$ cat /path/to/cryosparc_worker/version
cat: /path/to/cryosparc_worker/version: No such file or directory
(base) [cryosparc_user@r16763 cryosparc_master]$ /path/to/cryosparc_worker/bin/cryosparcw gpulist
bash: /path/to/cryosparc_worker/bin/cryosparcw: No such file or directory
(base) [cryosparc_user@r16763 cryosparc_master]$ ls -al /path/to/job/dir
I apologize for the typo in the ps command. Please can you try
ps -eo pid,ppid,start,cmd | grep cryosparc_
instead.
Please can you try
cat /home/cryosparc_user/software/cryosparc/cryosparc_worker/version
/home/cryosparc_user/software/cryosparc/cryosparc_worker/bin/cryosparcw gpulist
(base) [cryosparc_user@r16763 cryosparc_master]$ ps -eo pid,ppid,start,cmd | grep cryosparc_
4137 1 12:04:22 /sbin/mount.ntfs /dev/sdc1 /run/media/cryosparc_user/LL3 -o rw,nodev,nosuid,uid=1001,gid=1001,windows_names,uhelper=udisks2
14170 3462 15:03:27 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /home/cryosparc_user/software/cryosparc/cryosparc_master/supervisord.conf
14289 14170 15:03:31 mongod --auth --dbpath /home/cryosparc_user/software/cryosparc/cryosparc_database --port 39001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
14397 14170 15:03:35 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /home/cryosparc_user/software/cryosparc/cryosparc_master/gunicorn.conf.py
14398 14397 15:03:36 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /home/cryosparc_user/software/cryosparc/cryosparc_master/gunicorn.conf.py
14427 14170 15:03:42 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /home/cryosparc_user/software/cryosparc/cryosparc_master/gunicorn.conf.py
14428 14427 15:03:43 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /home/cryosparc_user/software/cryosparc/cryosparc_master/gunicorn.conf.py
14430 14170 15:03:43 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /home/cryosparc_user/software/cryosparc/cryosparc_master/gunicorn.conf.py
14442 14430 15:03:44 python /home/cryosparc_user/software/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /home/cryosparc_user/software/cryosparc/cryosparc_master/gunicorn.conf.py
14471 14170 15:03:50 /home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
17626 12087 16:43:39 grep --color=auto cryosparc_
(base) [cryosparc_user@r16763 cryosparc_master]$
(base) [cryosparc_user@r16763 cryosparc_master]$ cat /home/cryosparc_user/software/cryosparc/cryosparc_worker/version
v4.5.0
(base) [cryosparc_user@r16763 cryosparc_master]$ /home/cryosparc_user/software/cryosparc/cryosparc_worker/bin/cryosparcw gpulist
/home/cryosparc_user/software/cryosparc/cryosparc_worker/bin/cryosparcw: line 67: config.sh: No such file or directory
ERROR: Is cryoSPARC installed? Run install.sh to complete installation. See https://guide.cryosparc.com for full instructions.
Hi,
thanks for the help. I lost the file config.sh. I deleted the previous cryosparc_worker folder and unzip
cryosparc_worker.tar.gz to generate a new one. this way works before.
(base) [cryosparc_user@r16763 cryosparc_worker]$ bin/cryosparcw update
bin/cryosparcw: line 67: config.sh: No such file or directory
ERROR: Is cryoSPARC installed? Run install.sh to complete installation. See https://guide.cryosparc.com for full instructions.
(base) [cryosparc_user@r16763 cryosparc_worker]$
@Lan
Did you run
/home/cryosparc_user/software/cryosparc/cryosparc_worker/install.sh
with the necessary options (guide)?
This step may happen automatically during a
cryosparc_master/install --standalone installation, but has to be performed manually otherwise.
base) [cryosparc_user@r16763 cryosparc_worker]$ ./install.sh --license xxxxxxxxx --cudapath /usr/local/cuda-11.6
Unknown option: --cudapath
my cuda is under usr/local Bin and Lib64 are in the same directory
can I create one a file for install.sh?
I create the config.sh (copied from the other computer) but it works.
bin/cryosparcw update
updating the older version. now v 4.5.1.
Thank you for your time and support.
Best wishes, Lan@Lan The
cryosparc_worker/install.sh --cudapath option does not apply to CryoSPARC v4.4+.
Did you successfully run a refinement job after the update to v4.5.1?
yes. I am learning how to understand the new cFSC plot.
Thanks,
Lan
thanks for the useful information. I like this new development. would you please explain the green bars, relative frequency. it is not clear to me.
Thanks,
Lan.
Hi Lan - the green bars are a histogram, showing the relative frequency of cFSCs at the resolution indicated on the X axis. So basically a more granular version of the light/dark cFSC max/min curves on the same plot