Frequently Asked Questions
How to resolve the problems on (re)starting your own cryosparc instance?
You should check all the cryosparc related processes (i.e., supervisord, mongod, command_core, command_vis, command_rtp, webapp, app, liveapp) to be terminated successfully first on tem-cs-el7.sdfarm.kr or tem-ui-el7.sdfarm.kr server.
(log into tem-cs-el7.sdfarm.kr or tem-ui-el7.sdfarm.kr server first on which the CryoSPARC is running)
(example) userid@tem-[cs|ui]-el7 $> cryosparcm stop
CryoSPARC is running.
Stopping cryoSPARC
app: stopped
command_core: stopped
command_rtp: stopped
command_vis: stopped
liveapp: stopped
webapp: stopped
database: stopped
Shut down
(example) userid@tem-[cs|ui]-el7 $> ps aux | grep <userid> | grep cryosparc
userid 2449 0.0 0.0 152792 17480 ? Ss Jun24 0:18 python /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/supervisord.conf
userid 2472 1.2 0.0 1429268 57412 ? Sl Jun24 13:19 mongod --dbpath /tem/scratch/<GroupDir>/.cryosparc/cryosparc_database --port 39031 --oplogSize 64 --replSet meteor --nojournal --wiredTigerCacheSizeGB 4
userid 2900 0.2 0.0 860572 83028 ? Sl Jun24 2:23 python -c import cryosparc_command.command_core as serv; serv.start(port=39032)
userid 4332 0.1 0.1 854192 236396 ? Sl Jun24 1:53 python -c import cryosparc_command.command_vis as serv; serv.start(port=39033)
userid 4378 0.4 0.0 1190536 196316 ? Sl Jun24 4:59 python -c import cryosparc_command.command_rtp as serv; serv.start(port=39035)
userid 5586 0.1 0.0 1331136 116972 ? Sl Jun24 1:17 /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/cryosparc_webapp/nodejs/bin/node ./bundle/main.js
userid 5625 0.1 0.0 1049868 97640 ? Sl Jun24 1:22 /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
userid 5690 0.2 0.0 1326136 81432 ? Sl Jun24 2:12 /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/cryosparc_liveapp/nodejs/bin/node ./bundle/main.js
(example) userid@tem-[cs|ui]-el7 $> ps aux | grep <userid> | grep -E "cryosparc|node" | awk '{print $2}' | xargs -I{} kill -9 {}
Second, find your own cryosparc unix socket files on /tmp directory, and if exists, delete the files using rm command.
userid@tem-[cs|ui]-el7 $> cd /tmp
(example) userid@tem-[cs|ui]-el7 $> ls -al | grep <userid> | grep sock
srwx------. 1 userid userid 0 Jun 24 16:39 cryosparc-supervisor-627a9991e2f2f069094732dfd78d1696.sock
srwx------. 1 userid userid 0 Jun 24 16:39 mongodb-39031.sock
(example) userid@tem-[cs|ui]-el7 $> rm cryosparc-supervisor-627a9991e2f2f069094732dfd78d1696.sock
(example) userid@tem-[cs|ui]-el7 $> rm mongodb-39031.sock
Then, start your cryosparc instance.
(example) userid@tem-[cs|ui]-el7 $> cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
command_core connection succeeded
command_core startup successful
command_vis: started
command_rtp: started
command_rtp connection succeeded
command_rtp startup successful
webapp: started
app: started
liveapp: started
-----------------------------------------------------
CryoSPARC master started.
From this machine, access cryoSPARC at
http://localhost:39030
and access cryoSPARC Live at
http://localhost:39036
please note the legacy cryoSPARC Live application is running at
http://localhost:39037
From other machines on the network, access cryoSPARC at
http://tem-[cs|ui]-el7.sdfarm.kr:39030
and access cryoSPARC Live at
http://tem-[cs|ui]-el7.sdfarm.kr:39036
Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
How to repair cryosparc database corruption?
With duplicated mongod executions, cryosparc database can be corrupted resulting in “database: ERROR (spawn error)” on (re)starting cryosparc instance. To address this abnormal case, you can try to repair the database with followings:
First, stop all the cryosparc processes and delete the unix socket files. See how to resolve the problems on (re)starting your own cryosparc instance for more details.
Second, try to repair the cryosparc database i.e., mongodb.
userid@tem-[cs|ui]-el7 $> cryosparcm env
userid@tem-[cs|ui]-el7 $> cd /tem/scratch/<GroupDir>/.cryosparc
userid@tem-[cs|ui]-el7 $> tar cvfz cryosparc_database.backup.tar.gz cryosparc_database
userid@tem-[cs|ui]-el7 $> eval $(cryosparcm env)
userid@tem-[cs|ui]-el7 $> cd cryosparc_database
userid@tem-[cs|ui]-el7 $> mongod --dbpath ./ --repair
How to upgrade (or downgrade) to the specific version of cryosparc softwares?
The following update guides summarize the procedure for cryosparc’s master and worker software updates. For more details, please refer to https://guide.cryosparc.com/setup-configuration-and-management/software-updates.
1. Checking for updates
Log into the tem-cs-el7.sdfarm.kr or tem-ui-el7.sdfarm.kr server where the cryosparc master is installed using ssh. Then, run this command if you want to check updates.
userid@tem-[cs|ui]-el7 $> cryosparcm update --check
CryoSPARC current version v4.0.0
update starting on Wed Mar 18 12:09:52 EDT 2021
current version v4.0.0
new version v4.1.0
Update available!
Also, you can use this command cryosparcm update –list to get a full list of available versions.
userid@tem-[cs|ui]-el7 $> cryosparcm update --check
CryoSPARC current version v4.0.0
update starting on Wed Mar 18 12:09:52 EDT 2021
Available versions:
v2.0.18
v2.0.20
v2.0.23
v2.0.27
v2.1.0
v2.2.0
v2.3.0
v2.3.2
v2.4.0
v2.4.2
v2.4.5
v2.4.6
v2.5.0
v2.5.2-locref-mask-patch
v2.8.0
v2.8.1
v2.8.2
v2.8.3
v2.9.0
v2.11.0
v2.12.0
v2.12.2
v2.12.4
v2.13.0
v2.13.2
v2.14.0
v2.14.2
v2.15.0
v3.0.0
v3.0.1
v3.1.0
v3.2.0
To install a specific version, use
$ cryosparcm update --version=vXX.YY.ZZ[-branchname]
2. Before you update: complete or kill running jobs
Before you update the cryosparc softwares, you must wait for all the running cryosparc jobs completed (or kill your jobs). You also must check all the cryosparc related processes (i.e., supervisord, mongod, command_core, command_vis, command_rtp, webapp, app, liveapp) to be terminated successfully.
(example) userid@tem-[cs|ui]-el7 $> cryosparcm stop
CryoSPARC is running.
Stopping cryoSPARC
app: stopped
command_core: stopped
command_rtp: stopped
command_vis: stopped
liveapp: stopped
webapp: stopped
database: stopped
Shut down
(example) userid@tem-[cs|ui]-el7 $> ps aux | grep <userid> | grep cryosparc
userid 2449 0.0 0.0 152792 17480 ? Ss Jun24 0:18 python /tem/home/userid/.cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /tem/home/userid/.cryosparc/cryosparc2_master/supervisord.conf
userid 2472 1.2 0.0 1429268 57412 ? Sl Jun24 13:19 mongod --dbpath /tem/home/userid/.cryosparc/cryosparc_database --port 39031 --oplogSize 64 --replSet meteor --nojournal --wiredTigerCacheSizeGB 4
userid 2900 0.2 0.0 860572 83028 ? Sl Jun24 2:23 python -c import cryosparc_command.command_core as serv; serv.start(port=39032)
userid 4332 0.1 0.1 854192 236396 ? Sl Jun24 1:53 python -c import cryosparc_command.command_vis as serv; serv.start(port=39033)
userid 4378 0.4 0.0 1190536 196316 ? Sl Jun24 4:59 python -c import cryosparc_command.command_rtp as serv; serv.start(port=39035)
userid 5586 0.1 0.0 1331136 116972 ? Sl Jun24 1:17 /tem/home/userid/.cryosparc/cryosparc2_master/cryosparc_webapp/nodejs/bin/node ./bundle/main.js
userid 5625 0.1 0.0 1049868 97640 ? Sl Jun24 1:22 /tem/home/userid/.cryosparc/cryosparc2_master/cryosparc_app/nodejs/bin/node ./bundle/main.js
userid 5690 0.2 0.0 1326136 81432 ? Sl Jun24 2:12 /tem/home/userid/.cryosparc/cryosparc2_master/cryosparc_liveapp/nodejs/bin/node ./bundle/main.js
(example) userid@tem-[cs|ui]-el7 $> kill -9 2449 2472 2900 4332 4378 5586 5625 5690
Find your own cryosparc unix socket files on /tmp directory, and if exists, delete the files using rm command.
userid@tem-[cs|ui]-el7 $> cd /tmp
(example) userid@tem-[cs|ui]-el7 $> ls -al | grep <userid> | grep sock
srwx------. 1 userid userid 0 Jun 24 16:39 cryosparc-supervisor-627a9991e2f2f069094732dfd78d1696.sock
srwx------. 1 userid userid 0 Jun 24 16:39 mongodb-39031.sock
(example) userid@tem-[cs|ui]-el7 $> rm cryosparc-supervisor-627a9991e2f2f069094732dfd78d1696.sock
(example) userid@tem-[cs|ui]-el7 $> rm mongodb-39031.sock
3. Back-up cryosparc databases
We also highly recommend making a backup of your database as described below.
userid@tem-[cs|ui]-el7 $> cryosparcm backup
Backing up to /tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive
CryoSPARC is not already running.
Starting the database in case it's not already running.
database: started
Executing mongodump.
2021-04-20T15:00:42.606+0900 writing admin.system.version to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.608+0900 done dumping admin.system.version (1 document)
2021-04-20T15:00:42.609+0900 writing meteor.events to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.617+0900 writing meteor.fs.files to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.617+0900 writing meteor.notifications to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.618+0900 writing meteor.fs.chunks to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.661+0900 done dumping meteor.notifications (315 documents)
2021-04-20T15:00:42.661+0900 writing meteor.jobs to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.692+0900 done dumping meteor.fs.files (8386 documents)
2021-04-20T15:00:42.692+0900 writing meteor.cache_files to archive '/tem/scratch/<GroupDir>/.cryosparc/cryosparc_database/backup/cryosparc_backup_2021_04_20_15h00.archive'
2021-04-20T15:00:42.693+0900 done dumping meteor.jobs (166 documents)
... (omit)
2021-04-20T15:00:42.751+0900 done dumping meteor.file_index (0 documents)
2021-04-20T15:00:42.755+0900 done dumping meteor.exposures (0 documents)
2021-04-20T15:00:42.770+0900 done dumping meteor.events (25676 documents)
2021-04-20T15:00:45.182+0900 [####....................] meteor.fs.chunks 1535/8386 (18.3%)
2021-04-20T15:00:48.182+0900 [########................] meteor.fs.chunks 3048/8386 (36.3%)
2021-04-20T15:00:51.182+0900 [###############.........] meteor.fs.chunks 5475/8386 (65.3%)
2021-04-20T15:00:53.903+0900 [########################] meteor.fs.chunks 8386/8386 (100.0%)
2021-04-20T15:00:53.905+0900 done dumping meteor.fs.chunks (8386 documents)
Complete!
After backing up your cryosparc database, you should check the status of cryosparc daemons and stop them again.
userid@tem-[cs|ui]-el7 $> cryosparcm status
userid@tem-[cs|ui]-el7 $> cryosparcm stop
4. Cryosparc master updates
To begin automatic master updates with the newest available version of cryoSPARC, just run
userid@tem-[cs|ui]-el7 $> cryosparcm update
CryoSPARC current version v4.0.0
update starting on Tue Apr 20 15:36:12 KST 2021
No version specified - updating to latest version.
=============================
Updating to version v4.1.0.
=============================
CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
Removing previous downloads...
Downloading master update...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 785M 100 785M 0 0 2072k 0 0:06:27 0:06:27 --:--:-- 3897k
Downloading worker update...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 1807M 100 1807M 0 0 2312k 0 0:13:20 0:13:20 --:--:-- 7988k
Done.
Update will now be applied to the master installation,
followed by worker installations on other nodes.
Deleting old files...
Extracting...
Done.
===================================================
Installing latest master dependencies.
===================================================
Checking dependencies...
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
Installing anaconda python...
------------------------------------------------------------------------
PREFIX=/tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Solving environment: done
## Package Plan ##
environment location: /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/deps/anaconda
added / updated specs:
- _libgcc_mutex==0.1=main
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py37_0
- cffi==1.14.0=py37he30daa8_1
- chardet==3.0.4=py37_1003
- conda-package-handling==1.6.1=py37h7b6447c_0
- conda==4.8.3=py37_0
- cryptography==2.9.2=py37h1ba5d50_0
- idna==2.9=py_1
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.3=he6710b0_1
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1g=h7b6447c_0
- pip==20.0.2=py37_3
- pycosat==0.6.3=py37h7b6447c_0
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py37_0
- pysocks==1.7.1=py37_0
- python==3.7.7=hcff3b4d_5
- readline==8.0=h7b6447c_0
- requests==2.23.0=py37_0
- ruamel_yaml==0.15.87=py37h7b6447c_0
- setuptools==46.4.0=py37_0
- six==1.14.0=py37_0
- sqlite==3.31.1=h62c20be_1
- tk==8.6.8=hbc83047_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py37_0
- wheel==0.34.2=py37_0
- xz==5.2.5=h7b6447c_0
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0
certifi pkgs/main/linux-64::certifi-2020.4.5.1-py37_0
cffi pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0
idna pkgs/main/noarch::idna-2.9-py_1
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
pip pkgs/main/linux-64::pip-20.0.2-py37_3
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/linux-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-46.4.0-py37_0
six pkgs/main/linux-64::six-1.14.0-py37_0
sqlite pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0
wheel pkgs/main/linux-64::wheel-0.34.2-py37_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
------------------------------------------------------------------------
Done.
anaconda python installation successful.
------------------------------------------------------------------------
Extracting all conda packages...
------------------------------------------------------------------------
............................................................................
------------------------------------------------------------------------
Done.
conda packages installation successful.
------------------------------------------------------------------------
Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for mongodb
Dependencies for mongodb have not changed.
Completed dependency check.
===================================================
Successfully updated master to version v4.1.0.
---
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
command_core connection succeeded
command_core startup successful
command_vis: started
command_rtp: started
command_rtp connection succeeded
command_rtp startup successful
webapp: started
app: started
liveapp: started
-----------------------------------------------------
CryoSPARC master started.
From this machine, access cryoSPARC at
http://localhost:39030
and access cryoSPARC Live at
http://localhost:39036
please note the legacy cryoSPARC Live application is running at
http://localhost:39037
From other machines on the network, access cryoSPARC at
http://tem-cs-el7.sdfarm.kr:39030
and access cryoSPARC Live at
http://tem-cs-el7.sdfarm.kr:39036
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:
---------------------------------------------------
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.
Or, you can update the master with a specific version.
userid@tem-[cs|ui]-el7 $> cryosparcm update --version=vXX.YY.ZZ
After updating the master of your cryosparc instance, you should check the status of cryosparc daemons and stop them again in order to re-install the worker softwares.
userid@tem-[cs|ui]-el7 $> cryosparcm status
userid@tem-[cs|ui]-el7 $> cryosparcm stop
5. Cryosparc worker updates
Since we adopt the clustered installation method for cryosparc instances, we shoud manually update the cryosparc worker. But simply with cryosparc worker updates (guided from cryosparc official site), you might face up with the version mismatch problem of CUDA SDK runtime libraries (the root cause is unknwon now). So we decide to newly install all the cryosparc worker softwares to address this issues.
If you successully update the cryosparc master softwares above, you must find cryosparc_worker.tar.gz tar ball in ~/.cryosparc/cryosparc_master directory.
userid@tem-[cs|ui]-el7 $> cd /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master
userid@tem-[cs|ui]-el7 $> ls -al *.tar.gz
-rw-r-----. 1 userid userid 823226956 Apr 20 15:42 cryosparc_master.tar.gz
-rw-r-----. 1 userid userid 1895278500 Apr 20 15:56 cryosparc_worker.tar.gz
First, modity the name of the previous worker directory to that with .orig postfix and copy/uncompress the worker tar ball to .cryosparc directory.
If your master installation directory is “cryosparc_master”, use these commands.
userid@tem-[cs|ui]-el7 $> cd /tem/scratch/<GroupDir>/.cryosparc
userid@tem-[cs|ui]-el7 $> mv cryosparc_worker cryosparc_worker.orig
userid@tem-[cs|ui]-el7 $> cp /tem/scratch/<GroupDir>/.cryosparc/cryosparc_master/cryosparc_worker.tar.gz /tem/scratch/<GroupDir>/.cryosparc
userid@tem-[cs|ui]-el7 $> tar xvfz cryosparc_worker.tar.gz
Then, re-install all the cryosparc worker softwares with the followings (note that cryosparc version 4.3.0+ has self-contained CUDA SDK, so you don’t have to select the host directory path of CUDA SDK while installing the cryosparc worker):
userid@tem-[cs|ui]-el7 $> cd /tem/scratch/<GroupDir>/.cryosparc/cryosparc_worker
userid@tem-[cs|ui]-el7 $> eval $(cryosparcm env)
userid@tem-[cs|ui]-el7 $> ./install.sh --license $CRYOSPARC_LICENSE_ID
******* CRYOSPARC SYSTEM: WORKER INSTALLER ***********************
Installation Settings:
License ID : xxxxxxxxxxxx
Root Directory : /tem/scratch/<GroupDir>/.cryosparc/cryosparc_worker
Standalone Installation : false
Version : v4.1.0
******************************************************************
CUDA check..
Found nvidia-smi at /bin/nvidia-smi
CUDA Path was provided as /usr/local/cuda-11.8
Checking CUDA installation...
Found nvcc at /usr/local/cuda-11.8/bin/nvcc
The above cuda installation will be used but can be changed later.
******************************************************************
Setting up hard-coded config.sh environment variables
******************************************************************
Installing all dependencies.
Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
Checking dependencies...
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
Installing anaconda python...
------------------------------------------------------------------------
PREFIX=/tem/scratch/<GroupDir>/.cryosparc/cryosparc_worker/deps/anaconda
Unpacking payload ...
Solving environment: done
## Package Plan ##
environment location: /tem/scratch/<GroupDir>/.cryosparc/cryosparc_worker/deps/anaconda
added / updated specs:
- _libgcc_mutex==0.1=main
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py37_0
- cffi==1.14.0=py37he30daa8_1
- chardet==3.0.4=py37_1003
- conda-package-handling==1.6.1=py37h7b6447c_0
- conda==4.8.3=py37_0
- cryptography==2.9.2=py37h1ba5d50_0
- idna==2.9=py_1
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.3=he6710b0_1
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1g=h7b6447c_0
- pip==20.0.2=py37_3
- pycosat==0.6.3=py37h7b6447c_0
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py37_0
- pysocks==1.7.1=py37_0
- python==3.7.7=hcff3b4d_5
- readline==8.0=h7b6447c_0
- requests==2.23.0=py37_0
- ruamel_yaml==0.15.87=py37h7b6447c_0
- setuptools==46.4.0=py37_0
- six==1.14.0=py37_0
- sqlite==3.31.1=h62c20be_1
- tk==8.6.8=hbc83047_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py37_0
- wheel==0.34.2=py37_0
- xz==5.2.5=h7b6447c_0
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0
certifi pkgs/main/linux-64::certifi-2020.4.5.1-py37_0
cffi pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0
idna pkgs/main/noarch::idna-2.9-py_1
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
pip pkgs/main/linux-64::pip-20.0.2-py37_3
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/linux-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-46.4.0-py37_0
six pkgs/main/linux-64::six-1.14.0-py37_0
sqlite pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0
wheel pkgs/main/linux-64::wheel-0.34.2-py37_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
------------------------------------------------------------------------
Done.
anaconda python installation successful.
------------------------------------------------------------------------
Extracting all conda packages...
------------------------------------------------------------------------
------------------------------------------------------------------------
Done.
conda packages installation successful.
------------------------------------------------------------------------
Preparing to install all pip packages...
------------------------------------------------------------------------
Processing ./deps_bundle/python/python_packages/pip_packages/pycuda-2020.1.tar.gz
Skipping wheel build for pycuda, due to binaries being disabled for it.
Installing collected packages: pycuda
Running setup.py install for pycuda ... done
Successfully installed pycuda-2020.1
------------------------------------------------------------------------
Done.
pip packages installation successful.
------------------------------------------------------------------------
Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for ctffind
Dependencies for ctffind have changed - reinstalling...
------------------------------------------------------------------------
ctffind 4.1.10 installation successful.
------------------------------------------------------------------------
Completed.
Currently checking hash for cudnn
Dependencies for cudnn have changed - reinstalling...
------------------------------------------------------------------------
cudnn 8.1.0.77 for CUDA 11 installation successful.
------------------------------------------------------------------------
Completed.
Currently checking hash for gctf
Dependencies for gctf have changed - reinstalling...
------------------------------------------------------------------------
Gctf v1.06 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
******* CRYOSPARC WORKER INSTALLATION COMPLETE *******************
In order to run processing jobs, you will need to connect this
worker to a cryoSPARC master.
******************************************************************
6. Running the new cryosparc instance
All the cryosparc master and worker updates has completed. So, you need to re-execute cryosparc instance daemons (assume userid’s CRYOSPARC_BASE_PORT is 39030).
userid@tem-[cs|ui]-el7 $> cd ~/
userid@tem-[cs|ui]-el7 $> cryosparcm env
userid@tem-[cs|ui]-el7 $> cryosparcm status
userid@tem-[cs|ui]-el7 $> cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
command_core connection succeeded
command_core startup successful
command_vis: started
command_rtp: started
command_rtp connection succeeded
command_rtp startup successful
webapp: started
app: started
liveapp: started
-----------------------------------------------------
CryoSPARC master started.
From this machine, access cryoSPARC at
http://localhost:39030
and access cryoSPARC Live at
http://localhost:39036
please note the legacy cryoSPARC Live application is running at
http://localhost:39037
From other machines on the network, access cryoSPARC at
http://tem-[cs|ui]-el7.sdfarm.kr:39030
and access cryoSPARC Live at
http://tem-[cs|ui]-el7.sdfarm.kr:39036
Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.