I am trying to run the tutorial and it keeps telling me the directory access is false.
Defect file path. Invalid path selected. /mnt/ssd/satyshur directory allowed: false,
file allowed: true glob allowed: true.
I can run nothing anymore. I recently upgraded to Rocky 9 and restarted the cryosparc without a
problem. But no one can run anything. Any ideas? Do I need to reinstall?
thanks
Probably not.
Please can you
ls -ld /mnt/ssd/satyshur
ps -eo user:12,pid,ppid,start,command | grep -e mongo -e cryosparc_
[satyshur@xingcryoem empiar_10025_subset]$ ls -ld /mnt/ssd/satyshur
drwxrwxrwx. 11 satyshur users 4096 Oct 28 14:11 /mnt/ssd/satyshur
[satyshur@xingcryoem empiar_10025_subset]$ ps -eo user:12,pid,ppid,start,command | grep -e mongo -e cryosparc_
cryosparc_u+ 2791912 1 Nov 27 /usr/lib/systemd/systemd --user
cryosparc_u+ 2791914 2791912 Nov 27 (sd-pam)
cryosparc_u+ 2792156 1 Nov 27 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/supervisord.conf
cryosparc_u+ 2804517 1 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/supervisord.conf
cryosparc_u+ 2804627 2804517 Nov 29 mongod --auth --dbpath /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_database-a2 --port 39001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
cryosparc_u+ 2804743 2804517 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
cryosparc_u+ 2804744 2804743 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
cryosparc_u+ 2804769 2804517 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
cryosparc_u+ 2804770 2804769 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
cryosparc_u+ 2804772 2804517 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
cryosparc_u+ 2804784 2804772 Nov 29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
cryosparc_u+ 2804798 2804517 Nov 29 node dist/server/index.js
cryosparc_u+ 2804816 2804517 Nov 29 /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
cryosparc_u+ 2837780 2791912 Dec 02 /usr/bin/dbus-broker-launch --scope user
cryosparc_u+ 2837781 2837780 Dec 02 dbus-broker --log 4 --controller 10 --machine-id a7230be340064b1ebc03b152b2232a9d --max-bytes 100000000000000 --max-fds 25000000000000 --max-matches 5000000000
cryosparc_u+ 2837783 2791912 Dec 02 /usr/libexec/gvfsd
cryosparc_u+ 2837788 2791912 Dec 02 /usr/libexec/gvfsd-fuse /run/user/1001/gvfs -f
cryosparc_u+ 2837862 2791912 Dec 02 /usr/libexec/xdg-desktop-portal
cryosparc_u+ 2837866 2791912 Dec 02 /usr/libexec/xdg-document-portal
cryosparc_u+ 2837869 2791912 Dec 02 /usr/libexec/xdg-permission-store
cryosparc_u+ 2837889 2791912 Dec 02 /usr/bin/pipewire
cryosparc_u+ 2837891 2791912 Dec 02 /usr/bin/wireplumber
cryosparc_u+ 2837898 2791912 Dec 02 /usr/bin/gnome-keyring-daemon --start --foreground --components=secrets
cryosparc_u+ 2837935 2791912 Dec 02 /usr/libexec/at-spi-bus-launcher
root 2844687 2410 15:37:13 sshd: cryosparc_user [priv]
cryosparc_u+ 2844691 2844687 15:37:25 sshd: cryosparc_user@pts/0
cryosparc_u+ 2844692 2844691 15:37:25 -bash
satyshur 2844769 2838080 15:42:59 grep --color=auto -e mongo -e cryosparc_
[satyshur@xingcryoem empiar_10025_subset]$
satyshur@xingcryoem empiar_10025_subset]$ ps -ax | grep cryosparc_
2792156 ? Ss 1:33 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/supervisord.conf
2804517 ? Ss 1:03 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/supervisord.conf
2804627 ? Sl 35:58 mongod --auth --dbpath /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_database-a2 --port 39001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
2804743 ? S 0:30 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
2804744 ? Sl 10:19 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
2804769 ? S 0:29 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
2804770 ? Sl 6:09 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_vis:app -n command_vis -b 0.0.0.0:39003 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
2804772 ? S 0:27 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
2804784 ? Sl 19:33 python /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn cryosparc_command.command_rtp:start() -n command_rtp -b 0.0.0.0:39005 -c /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/gunicorn.conf.py
2804816 ? Sl 5:59 /mnt/ssd/cryosparc_user/software/cryosparc/cryosparc2_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
2844687 ? Ss 0:00 sshd: cryosparc_user [priv]
2844691 ? S 0:00 sshd: cryosparc_user@pts/0
2844781 pts/1 S+ 0:00 grep --color=auto cryosparc_
rwxrwxrwx indicates that write permissions have been granted to everyone with access to this computer. You may want to change permissions and owner/group such that access is restricted to the minimum needed for proper function, for example limited to satyshur and the Linux account whose username starts with cryosparc_u (cryosparc_user?).
The . suffix suggests that an incorrectly configured selinux context might prevent CryoSPARC from functioning.
What are the outputs of the commands
/usr/sbin/getenforce
ls -Zd /mnt/ssd/satyshur
?
The simultaneous presence of two supervisord processes for the same CryoSPARC installation is not expected. You may want thoroughly shutdown CryoSPARC before starting it again.
[cryosparc_user@xingcryoem cryosparc2_master]$ /usr/sbin/getenforce
Enforcing
[cryosparc_user@xingcryoem cryosparc2_master]$ ls -Zd /mnt/ssd/satyshur
unconfined_u:object_r:unlabeled_t:s0 /mnt/ssd/satyshur
[cryosparc_user@xingcryoem cryosparc2_master]$
2024-12-03T06:00:00Z
Filesystem Size Used Avail Use% Mounted on
devtmpfs 4.0M 0 4.0M 0% /dev
tmpfs 252G 3.2M 252G 1% /dev/shm
tmpfs 101G 687M 100G 1% /run
/dev/mapper/rl_localhost–live-root 70G 19G 52G 27% /
tmpfs 252G 1.7M 252G 1% /tmp
/dev/mapper/vg_ssd-scratch 15T 6.4T 8.3T 44% /mnt/ssd
/dev/sdb1 960M 397M 564M 42% /boot
/dev/mapper/rl_localhost–live-home 164G 26G 138G 16% /home
192.168.5.1:/volume1/nas1 104T 99T 5.6T 95% /mnt/nas1
192.168.5.1:/volume2/nas2 56T 21T 36T 38% /mnt/nas2
//research.drive.wisc.edu/yxing2 90T 88T 2.8T 97% /mnt/yxlab
tmpfs 51G 60K 51G 1% /run/user/981
tmpfs 51G 52K 51G 1% /run/user/390988813
tmpfs 51G 60K 51G 1% /run/user/1001
tmpfs 51G 52K 51G 1% /run/user/715819571
tmpfs 51G 52K 51G 1% /run/user/390873633
@satyshur My initial suspicion of a permissions/access problem may be incorrect. Movies data path should be an glob pattern like, for example, /path/to/movies/*.tiff instead of a just a directory like /path/to/movies.
In your specific case (only a guess due to the truncation of the path in the screenshot), you might try:
/mnt/ssd/satyshur/tutorial_T20S/empiar_10025_subset/*.tif/mnt/ssd/satyshur/tutorial_T20S/empiar_10025_subset/norm-amibox05-0.mrcthanks. I will work with it.
kas
{
“id”: “674f8420b21d3db5371e2b58”,
“project_uid”: “P46”,
“uid”: “J1”,
“PID_main”: null,
“PID_monitor”: null,
“PID_workers”: ,
“bench”: {},
“children”: ,
“cloned_from”: null,
“cluster_job_custom_vars”: {},
“cluster_job_id”: null,
“cluster_job_monitor_event_id”: null,
“cluster_job_monitor_last_run_at”: null,
“cluster_job_monitor_retries”: 0,
“cluster_job_status”: null,
“cluster_job_status_code”: null,
“cluster_job_submission_script”: null,
“completed_at”: null,
“completed_count”: 0,
“created_at”: “2024-12-03T22:20:16.648Z”,
“created_by_job_uid”: null,
“created_by_user_id”: “5e4eda5aff7fd93e1a890751”,
“deleted”: false,
“description”: “Enter a description.”,
“enable_bench”: false,
“errors_build_inputs”: {},
“errors_build_params”: {
“blob_paths”: {
“message”: “Invalid path specified: /mnt/ssd/satyshur/tutorial_T20s/empiar_10025_subset/*.tiff directory allowed: False; file allowed: True; glob allowed: True”,
“warning”: false
}
sorry it is tif not tiff
It is amazing how much time I spend in a syntax error. Doh.