- Actors
- cryoEM Operator is the person(s) operating the TEM at an authorised period for data acquisition
- Local Administrator Account to control login authorisation based on who should have access
- Data Acquisition Collaborator(s) are people who have SLAC accounts whom the cryoEM Operator may want to help operate the TEM
- Researchers are users who would use the compute and storage facilities at SLAC to process the data that has been acquired.
- Resources
Local Windows MachineConnected to SLAC Active DirectoryRuns MinSec (virus scanner, cyber security backdoor, centralised logging and authentication)Has RAID Storage?
- CryoEM Windows Servers
- Standard FEI and Gatan servers used for data collection and TEM control
- Data stored locally per TEM
- CryoEM Data Acquisition Servers
- Unix Docker Swarm / Kubernetes Nodes that handles data movement and processing pipelines
- Utilises Apache Airflow to orchestrate workflows
- Launches jobs on GPU and CPU farm clusters that contain required software (motioncor2, ctffind, dogpicker etc)
- Shares storage with CryoEM Windows Servers via a CIFS mount for each and every TEM.
- GPFS LTS Storage + TSM HSM Tape
- Long term data storage (multi petabyte) using clustered parallel file system
- Filesystem mounted on all (Unix) Nodes
- Automatic policies to stage unused/not-hot data to tape for cheaper storage needs
- Bullet CPU Cluster
- CPU based cluster (5,000 cores); infiniband + 10GbE
- GPU Cluster
- GPU based cluster (100 gpus)
- Interactive Login Hosts
- 'Head' nodes where Researchers log in to access compute resources
- Data Transfer Nodes
- High (network) speed nodes where Researchers log into access the data
- Researchers
- Will collect data from the CryoEM Windows Servers (using SerialEM/EPU etc) either
- Onsite: in building 6
- Remotely: connect via FastX (only available when their experiment is active)
- Once data collection sessions is in process/complete, researchers can
- submit jobs to the GPU and CPU clusters via the Interactive Login Hosts
- copy data via the Data Transfer Nodes
- Will collect data from the CryoEM Windows Servers (using SerialEM/EPU etc) either
Further Information
- Apache Airflow Single Particle Pre-Processing Pipeline
- cryoEM Data Acquisition Workflow
- Pipeline Management