************************** Frequently Asked Questions ************************** * 1. `how to resolve the problems on (re)starting your own cryosparc instance`_ * 2. `how to repair cryosparc database corruption caused by duplicated mongod executions`_ * 3. `how to update cryosparc softwares`_ .. _how to resolve the problems on (re)starting your own cryosparc instance: 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. .. code-block:: bash (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 | grep cryosparc userid 2449 0.0 0.0 152792 17480 ? Ss Jun24 0:18 python /tem/scratch//.cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /tem/scratch//.cryosparc/cryosparc_master/supervisord.conf userid 2472 1.2 0.0 1429268 57412 ? Sl Jun24 13:19 mongod --dbpath /tem/scratch//.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//.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//.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//.cryosparc/cryosparc_master/cryosparc_liveapp/nodejs/bin/node ./bundle/main.js (example) userid@tem-[cs|ui]-el7 $> ps aux | grep | 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. .. code-block:: bash userid@tem-[cs|ui]-el7 $> cd /tmp (example) userid@tem-[cs|ui]-el7 $> ls -al | grep | 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. .. code-block:: bash (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 caused by duplicated mongod executions: 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. .. code-block:: bash userid@tem-[cs|ui]-el7 $> cryosparcm env userid@tem-[cs|ui]-el7 $> cd /tem/scratch//.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 update cryosparc softwares: 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. .. code-block:: bash 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. .. code-block:: bash 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. .. code-block:: bash (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 | 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. .. code-block:: bash userid@tem-[cs|ui]-el7 $> cd /tmp (example) userid@tem-[cs|ui]-el7 $> ls -al | grep | 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. .. code-block:: bash userid@tem-[cs|ui]-el7 $> cryosparcm backup Backing up to /tem/scratch//.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//.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//.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//.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//.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//.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//.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//.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. .. code-block:: bash 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 .. code-block:: bash 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//.cryosparc/cryosparc_master/deps/anaconda Unpacking payload ... Solving environment: done ## Package Plan ##   environment location: /tem/scratch//.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. .. code-block:: bash 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. .. code-block:: bash 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. .. code-block:: bash userid@tem-[cs|ui]-el7 $> cd /tem/scratch//.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. .. code-block:: bash userid@tem-[cs|ui]-el7 $> cd /tem/scratch//.cryosparc userid@tem-[cs|ui]-el7 $> mv cryosparc_worker cryosparc_worker.orig userid@tem-[cs|ui]-el7 $> cp /tem/scratch//.cryosparc/cryosparc_master/cryosparc_worker.tar.gz /tem/scratch//.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): .. code-block:: bash userid@tem-[cs|ui]-el7 $> cd /tem/scratch//.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//.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//.cryosparc/cryosparc_worker/deps/anaconda Unpacking payload ... Solving environment: done ## Package Plan ##   environment location: /tem/scratch//.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). .. code-block:: bash 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.