Includes all release notes from previous patch 250811
See installation instructions here (CryoSPARC v4.7.1):
This patch fails to install on my master, while the worker was patched correctly the first time. I’ve tried downloading the file first and then installing it, and I’ve tried the --force flag, but still no success. The output doesn’t indicate any problem:
$ cryosparcm patch --force
A cryoSPARC patch is available
Current Version: v4.7.1
Current Patch: None
New Patch: 250814
Released On: 2025-08-14 20:14:16
Requires Restart: Yes
Patch Notes:
- Fixed: Ab-Initio Reconstruction no longer fails with a NaN error when one or more densities become completely empty.
- Fixed: Subset Particles by Statistic job no longer fails when manual thresholds are specified in the job builder.
- Fixed: Select Volume job now produces passthrough outputs consistently based on input connections.
Install patch? (y/n): y
Downloading...
Downloading cryosparc_master_patch.tar.gz...
Downloading cryosparc_worker_patch.tar.gz...
Patching... checking versions
Done.
Gathering worker info...
Patch worker xxx? (y/n): n
Skipped worker patch.
To patch workers:
1. Upload the worker patch cryosparc_master/cryosparc_worker_patch.tar.gz onto each worker node
2. Log into each worker node and run "cryosparcw patch"
e.g.,
cp -f cryosparc_worker_patch.tar.gz /opt/bioxray/programs/cryosparc2/cryosparc2_worker/cryosparc_worker_patch.tar.gz
/opt/programs/cryosparc2/cryosparc2_worker/bin/cryosparcw patch
Finishing...
Done.
Patch v4.7.1+250814 applied!
To complete installation, restart cryoSPARC with the following command:
cryosparcm restart
I see the “version” file in the master installation folder, but a “patch” file isn’t generated. It is there in the worker installation folder. I have restarted the cryosparcm service. I’ve also tried to launch a job, which fails with the error that the master and worker isn’t the same version.
Any ideas for how to fix this?
@boggild Please can you post the outputs of these commands, which should help rule out some possible causes of the issue:
which cryosparcm
type cryosparcm
ls -al $(dirname $(which cryosparcm))
/opt/cryosparc2/cryosparc2_master/bin/cryosparcm
cryosparcm is /opt/cryosparc2/cryosparc2_master/bin/cryosparcm
total 100
drwxr-xr-x 3 anbog anbog 4096 Jun 19 16:12 .
drwxrwx--- 15 anbog anbog 4096 Aug 19 13:28 ..
-rwxr-xr-x 1 anbog anbog 76613 Jun 19 16:12 cryosparcm
-rwxr-xr-x 1 anbog anbog 761 Jun 19 16:12 gitmulti
-rw-r--r-- 1 anbog anbog 2065 Jun 19 16:12 minicurl.py
drwxrwxr-x 2 anbog anbog 4096 Jun 20 15:44 __pycache__
-rw-r--r-- 1 anbog anbog 2511 Jun 19 16:12 watch_restart_command.py
The installation has gone through patches and updates successfully many times before.
I’ve just tried downgrading to 4.7.0, then updating and finally patching again, but I still end up with only the worker patched and the master stuck at 4.7.1.
Thanks @boggild for posting the command outputs. Please can you also post the output of the commands
ls -l /opt/cryosparc2/cryosparc2_master/cryosparc_tools/
ls -l /opt/cryosparc2/cryosparc2_master/
ls -l /opt/cryosparc2/cryosparc2_master/cryosparc_tools/
total 36
drwxr-xr-x 4 anbog anbog 4096 Aug 20 12:53 cryosparc
-rw-r--r-- 1 anbog anbog 1488 Jun 19 16:12 LICENSE
-rw-r--r-- 1 anbog anbog 285 Jun 19 16:12 MANIFEST.in
-rw-r--r-- 1 anbog anbog 1676 Jun 19 16:12 pyproject.toml
-rw-r--r-- 1 anbog anbog 206 Jun 19 16:12 pyrightconfig.json
-rw-r--r-- 1 anbog anbog 41 Jun 19 16:12 revision
-rw-r--r-- 1 anbog anbog 1574 Jun 19 16:12 setup.py
drwxr-xr-x 3 anbog anbog 4096 Jun 19 16:12 typings
-rw-r--r-- 1 anbog anbog 153 Jun 19 16:12 vercel.json
and
ls -l /opt/cryosparc2/cryosparc2_master/
total 4735808
drwxr-xr-x 3 anbog anbog 4096 Jun 19 16:12 bin
drwxrwxr-x 3 anbog anbog 4096 Aug 31 2023 build
-rwxr-xr-x 1 anbog anbog 5458 Jun 19 16:12 check_install_deps.sh
-rw-r----- 1 anbog anbog 641 Dec 8 2022 config.sh
drwxrwxr-x 5 anbog anbog 4096 Aug 20 12:53 cryosparc_app
drwxr-xr-x 11 anbog anbog 4096 Aug 20 12:53 cryosparc_command
drwxr-xr-x 15 anbog anbog 4096 Aug 20 12:53 cryosparc_compute
-rw-rw-r-- 1 anbog anbog 661648812 Aug 20 12:47 cryosparc_master.tar.gz
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:16 cryosparc_tools
-rw-rw-r-- 1 anbog anbog 4187660038 Aug 20 12:53 cryosparc_worker.tar.gz
drwxr-x--- 4 anbog anbog 4096 Sep 11 2024 deps
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:30 deps_bundle
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:30 deps_bundle_hashes
drwxr-x--- 4 anbog anbog 4096 May 27 2019 deps_hashes
-rw-rw-r-- 1 anbog anbog 6170 Aug 31 2023 environment.yml
-rw-r--r-- 1 anbog anbog 288 Jun 19 16:12 gunicorn.conf.py
-rw-r----- 1 anbog anbog 9053 May 27 2019 install-output.txt
-rw-r--r-- 1 anbog anbog 3128 Jun 19 16:12 install.py
-rwxr-xr-x 1 anbog anbog 14290 Jun 19 16:12 install.sh
lrwxrwxrwx 1 anbog anbog 43 Jun 19 16:12 lib -> deps/anaconda/envs/cryosparc_master_env/lib
-rw-r--r-- 1 anbog anbog 15621 Jun 19 16:12 patch.py
drwxrwxr-x 2 anbog anbog 4096 Aug 20 12:54 __pycache__
drwxr-x--- 3 anbog anbog 4096 Aug 20 12:53 run
-rw-r--r-- 1 anbog anbog 4072 Jun 19 16:12 setup_client_ipython.py
-rw-r--r-- 1 anbog anbog 4294 Jun 19 16:12 supervisord.conf
drwxr-xr-x 2 anbog anbog 4096 Jun 19 16:12 systemd
-rw-r--r-- 1 anbog anbog 7 Jun 19 16:30 version
Thanks @boggild . What about the outputs of these commands (some of which may fail, or produce no output):
ls -al /opt/bioxray/programs/cryosparc2/cryosparc2_master/
ps -eo user,pid,ppid,start,cmd | grep cryosparc_
Output for the last command:
ps -eo user,pid,ppid,start,cmd | grep cryosparc_
anbog 263055 2520 Aug 20 python /opt/cryosparc2/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /opt/cryosparc2/cryosparc2_master/supervisord.conf
anbog 263268 263055 Aug 20 python /opt/cryosparc2/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 /opt/cryosparc2/cryosparc2_master/gunicorn.conf.py
anbog 263270 263268 Aug 20 python /opt/cryosparc2/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 /opt/cryosparc2/cryosparc2_master/gunicorn.conf.py
anbog 263307 263055 Aug 20 python3.10 /opt/cryosparc2/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/flask --app cryosparc_command.command_vis run -h 0.0.0.0 -p 39003 --with-threads
anbog 263342 263055 Aug 20 python /opt/cryosparc2/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 /opt/cryosparc2/cryosparc2_master/gunicorn.conf.py
anbog 263343 263342 Aug 20 python /opt/cryosparc2/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 /opt/cryosparc2/cryosparc2_master/gunicorn.conf.py
anbog 263380 263055 Aug 20 /opt/cryosparc2/cryosparc2_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
anbog 406641 406331 15:28:16 grep --color=auto cryosparc_
The second command points to a non-existing folder, but perhaps you meant one of the following?
ls -al /opt/cryosparc2/cryosparc2_master/
total 4735816
drwxrwx--- 15 anbog anbog 4096 Aug 20 12:53 .
drwxr-x--- 7 anbog anbog 4096 Aug 12 2024 ..
drwxr-xr-x 3 anbog anbog 4096 Jun 19 16:12 bin
drwxrwxr-x 3 anbog anbog 4096 Aug 31 2023 build
-rwxr-xr-x 1 anbog anbog 5458 Jun 19 16:12 check_install_deps.sh
-rw-r----- 1 anbog anbog 641 Dec 8 2022 config.sh
drwxrwxr-x 5 anbog anbog 4096 Aug 20 12:53 cryosparc_app
drwxr-xr-x 11 anbog anbog 4096 Aug 20 12:53 cryosparc_command
drwxr-xr-x 15 anbog anbog 4096 Aug 20 12:53 cryosparc_compute
-rw-rw-r-- 1 anbog anbog 661648812 Aug 20 12:47 cryosparc_master.tar.gz
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:16 cryosparc_tools
-rw-rw-r-- 1 anbog anbog 4187660038 Aug 20 12:53 cryosparc_worker.tar.gz
drwxr-x--- 4 anbog anbog 4096 Sep 11 2024 deps
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:30 deps_bundle
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:30 deps_bundle_hashes
drwxr-x--- 4 anbog anbog 4096 May 27 2019 deps_hashes
-rw-rw-r-- 1 anbog anbog 6170 Aug 31 2023 environment.yml
-rw-r--r-- 1 anbog anbog 288 Jun 19 16:12 gunicorn.conf.py
-rw-r----- 1 anbog anbog 9053 May 27 2019 install-output.txt
-rw-r--r-- 1 anbog anbog 3128 Jun 19 16:12 install.py
-rwxr-xr-x 1 anbog anbog 14290 Jun 19 16:12 install.sh
lrwxrwxrwx 1 anbog anbog 43 Jun 19 16:12 lib -> deps/anaconda/envs/cryosparc_master_env/lib
-rw-r--r-- 1 anbog anbog 15621 Jun 19 16:12 patch.py
drwxrwxr-x 2 anbog anbog 4096 Aug 20 12:54 __pycache__
drwxr-x--- 3 anbog anbog 4096 Aug 20 12:53 run
-rw-r--r-- 1 anbog anbog 4072 Jun 19 16:12 setup_client_ipython.py
-rw-r--r-- 1 anbog anbog 4294 Jun 19 16:12 supervisord.conf
drwxr-xr-x 2 anbog anbog 4096 Jun 19 16:12 systemd
-rw-r--r-- 1 anbog anbog 7 Jun 19 16:30 version
or
ls -al /opt/bioxray/programs/cryosparc2/cryosparc2_worker/
total 68
drwxrwxr-x 9 anbog anbog 4096 Aug 20 12:54 .
drwxr-xr-x 3 cryosparc2 cryosparc2 4096 Dec 9 2022 ..
drwxr-xr-x 2 anbog anbog 4096 Jun 19 16:12 bin
-rwxr-xr-x 1 anbog anbog 5437 Jun 19 16:12 check_install_deps.sh
-rw-r--r-- 1 anbog anbog 283 Nov 8 2023 config.sh
drwxrwxr-x 15 anbog anbog 4096 Aug 20 13:08 cryosparc_compute
drwxrwxr-x 4 anbog anbog 4096 Aug 20 12:54 cryosparc_tools
drwxr-xr-x 4 anbog anbog 4096 Sep 11 2024 deps
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:30 deps_bundle
drwxr-xr-x 4 anbog anbog 4096 Jun 19 16:30 deps_bundle_hashes
drwxr-xr-x 4 anbog anbog 4096 Dec 10 2020 deps_hashes
-rw-rw-r-- 1 anbog anbog 7122 Aug 31 2023 environment.yml
-rwxr-xr-x 1 anbog anbog 4859 Jun 19 16:12 install.sh
lrwxrwxrwx 1 anbog anbog 43 Jun 19 16:12 lib -> deps/anaconda/envs/cryosparc_worker_env/lib
-rw-r--r-- 1 anbog anbog 7 Jun 19 16:30 version
Thanks for posting these outputs. I am unfortunately still not able to tell what is causing the problems during patching.
Please can you run the following commands
csm="/opt/cryosparc2/cryosparc2_master/bin/cryosparcm"
cd $(mktemp -d)
(
$csm patch --download
ls -l $(dirname $(dirname $csm))/cryosparc_master_patch.tar.gz
bash -x $csm patch --install
$csm status
) 2>patch.err | tee patch.out
pwd # note path to retrieve out an err files
and email us the patch.out and patch.err files.
I manage an instance running the CUDA12 branch (v4.7.1-cuda12) and by mistake I patched it with patch 250814, but now I saw that I should have applied patch 250811 instead. What should I do now?
@daniel.s.d.larsson If you used the standard the standard CryoSPARC patch procedure, there is no harm in applying the (-cuda12-specific) 250814 patch to a v4.7.1-cuda12 installation.