Error after updating

Install, Configure and Update
1

We recently updated cryosparc and are now receiving the following error after trying to start cryosparc.

Starting CryoSPARC master services...

⚠ Unable to access \`ip_unprivileged_port_start\`. Continuing without \`ip_unprivileged_port_start\` check.

CryoSPARC is not already running.

Configuring database... OK

database: started

Checking database... OK

cache: started

    ✓ cache connection succeeded

api:0: started

api:1: started

api:2: started

    ✓ api connection succeeded

    ✓ api startup succeeded

scheduler: started

command_vis: started

✕ ExecError: supervisorctl -c /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/config/supervisord.conf start 'app:\*': Command failed (code 7)

    Output: app: ERROR (spawn error)

    Error:
2

@ragusam Please can you try the extended CryoSPARC shutdown procedure. If afterward you still cannot restart CryoSPARC, please post the output of the command

ps -eo user,pid,ppid,start,cmd | grep -e cryosparc_ -e mongo -e node
3

Thank you. I followed the extended shutdown procedure but the program did not start. I have run the command you suggest and I get the following.

root      1690     1 08:54:20 /usr/sbin/mcelog --ignorenodev --daemon --syslog

cryospa+ 53248     1 12:40:09 python /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/supervisord -c /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/config/supervisord.conf

cryospa+ 53324 53248 12:40:19 mongod --auth --dbpath /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_database --port 61001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all --networkMessageCompressors snappy

cryospa+ 53400 53248 12:40:28 python3.12 /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/uvicorn api.main:app --fd 0 --log-config /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/config/log.conf

cryospa+ 53401 53248 12:40:28 python3.12 /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/uvicorn api.main:app --fd 0 --log-config /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/config/log.conf

cryospa+ 53402 53248 12:40:28 python3.12 /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/uvicorn api.main:app --fd 0 --log-config /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/config/log.conf

cryospa+ 53992 53248 12:41:55 python3.12 /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/flask --app command.command_vis:start() run -h 0.0.0.0 -p 61003 --with-threads

cryospa+ 53994 51767 12:41:56 grep --color=auto -e cryosparc\_ -e mongo -e node
4

Thanks @ragusam . Please can you also post the outputs of the commands

cryosparcm log supervisord | tail -n 30
cryosparcm log app | tail -n 10
5

Here is the output of the first command for log supervisord

2026-05-28 13:20:53,447 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:20:56,530 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:20:57,533 INFO spawned: ‘command_vis’ with pid 62594
2026-05-28 13:20:58,535 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:01,638 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:02,641 INFO spawned: ‘command_vis’ with pid 62611
2026-05-28 13:21:03,644 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:06,765 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:07,769 INFO spawned: ‘command_vis’ with pid 62627
2026-05-28 13:21:08,771 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:11,876 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:12,879 INFO spawned: ‘command_vis’ with pid 62643
2026-05-28 13:21:13,881 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:17,007 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:18,010 INFO spawned: ‘command_vis’ with pid 62659
2026-05-28 13:21:19,012 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:22,244 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:23,248 INFO spawned: ‘command_vis’ with pid 62675
2026-05-28 13:21:24,250 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:27,352 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:28,355 INFO spawned: ‘command_vis’ with pid 62691
2026-05-28 13:21:29,357 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:32,495 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:33,498 INFO spawned: ‘command_vis’ with pid 62707
2026-05-28 13:21:34,500 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:37,606 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:38,609 INFO spawned: ‘command_vis’ with pid 62731
2026-05-28 13:21:39,611 INFO success: command_vis entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2026-05-28 13:21:42,854 WARN exited: command_vis (exit status 2; not expected)
2026-05-28 13:21:43,858 INFO spawned: ‘command_vis’ with pid 62762

Here is the output for the second command log app

node: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127) node: /lib64/libm.so.6: version `GLIBC_2.27’ not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127)
node: /lib64/libc.so.6: version `GLIBC_2.27' not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127) node: /lib64/libc.so.6: version `GLIBC_2.28’ not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127)
node: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127) node: /lib64/libc.so.6: version `GLIBC_2.27’ not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127)
node: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127) node: /lib64/libm.so.6: version `GLIBC_2.27’ not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127)
node: /lib64/libc.so.6: version `GLIBC_2.27' not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127) node: /lib64/libc.so.6: version `GLIBC_2.28’ not found (required by /mnt/data0/cryosparc_user/software/cryosparc2/cryosparc_master/.pixi/envs/master/bin/../lib/libnode.so.127)
6

Interesting. Is your OS compatible with CryoSPARC v5?
What is the output of the command

cat /etc/*release

?

7

That seems to be the issue. The operating system is scientific linux which is no longer supported and needs to be replaced. I will replace the operating system and reinstall cryosparc

NAME=“Scientific Linux”
VERSION=“7.9 (Nitrogen)”
ID=“scientific”
ID_LIKE=“rhel centos fedora”
VERSION_ID=“7.9”
PRETTY_NAME=“Scientific Linux 7.9 (Nitrogen)”
ANSI_COLOR=“0;31”
CPE_NAME=“cpe:/o:scientificlinux:scientificlinux:7.9:GA”
HOME_URL=“http://www.scientificlinux.org//”
BUG_REPORT_URL="mailto:scientific-linux-devel@listserv.fnal.gov"

REDHAT_BUGZILLA_PRODUCT=“Scientific Linux 7”
REDHAT_BUGZILLA_PRODUCT_VERSION=7.9
REDHAT_SUPPORT_PRODUCT=“Scientific Linux”
REDHAT_SUPPORT_PRODUCT_VERSION=“7.9”
Scientific Linux release 7.9 (Nitrogen)
Scientific Linux release 7.9 (Nitrogen)
Scientific Linux release 7.9 (Nitrogen)

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