Questions about UltraScan-in-a-Box (USiaB):

Index:

  1. What is UltraScan-in-a-Box (USiaB)?
  2. What hardware is required for USiaB?
  3. What network configurations are needed for USiaB?
  4. How do I obtain USiaB system information from the Linux command line about the hardware?
  5. What makes USiaB so secure?
  6. How does data flow in USiaB?
  7. What is USiaB light?
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  1. What is UltraScan-in-a-Box (USiaB)? -  UltraScan-in-a-Box is a Linux server that provides all UltraScan components, including the Optima AUC integration and data acquisition module, in a server environment that is remotely accessed via ssh and VNC using Windows, Macintosh, Linux, Android and Iphone clients. There are two types of USiaB solutions available: A high-end server or cluster solution with large storage, high memory and at least 128 core CPU capability that includes parallel computing, LIMS service and batch mode operation all in one server. USiaB is commercially supported by AUC Solutions, please visit AUC Solutions on the web for additional information. This version is appropriate for installation in corporate environments and cGxP laboratories. The second version does not include supercomputer hardware or LIMS service inside of the USiaB server, but insteads connects to the cloud and HPC services from AUC Solutions and NSF Access, respectively. The second version will work with an ordinary PC or a modest VM with a minimum of 4 cores and 16 GB of RAM, or more if multiple users access the system simultaneously. All USiaB servers are accessed via ssh (port 22), which must be opened to the users. In addition, for the second USiaB server type, outgoing ports 3306 and 443 need to be unblocked to communicate with the remote infrastructure.
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  2. What hardware is required for USiaB? The USiaB server hardware requirements depend on the number and types of analyses you are planning to perform. We currently recommend a AMD Epyc with 128 real compute cores and 256 GB of RAM. Such a system is capable of supporting up to 2-3 Optimas, allowing up to 16 2DSA or 4 genetic algorithm analyses to run concurrently. An entire analysis refinement workflow, including Monte Carlo analysis, will typically take 1-3 hours, depending on datasize, and up to 16 samples could be processed simultaneously. If you are willing to wait for jobs by processing them sequentially, fewer cores and smaller memory configurations will suffice by linearly scaling the number of cores with the number of jobs that can be performed (provided the job type is the same). This does not hold when switching to a chipset that has more limited memory bandwidth than the Epyc line of servers, such as ThreadRippers. Performance details change all the time, so check with your hardware vendor. These performance metrics are from a AMD Epyc 7742 chipset with a dual socket configuration. If you want to run very large global analyses, with multiple velocity datasets included, additional memory could be helpful, depending on the size of the globally fitted data. Some UltraScan users have USiaB servers set up using virtual machines configured to provide scalable resources depending on user load. As long as the necessary network connections are available in the data center, this solution may also work well.
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  3. What network configurations are needed for USiaB? If you are planning to install USiaB at your organization, check with your IT group on the network requirements for USiaB. Due to the critical timing of data acquisition with the Optima AUC, it is important that the network supporting the Optima-USiaB connection is reliable and fast. Connectivity over long distances may be an issue due to network latency. In addition, a private VLAN or VPN is required between the Optima and the USiaB server to assure data safety. A detailed discussion of network requirements and a list of pre-installation questions can be found here.
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  4. How do I obtain USiaB system information from the Linux command line about the hardware?

    • Total storage, free storage and used storage available on the system: 'df -h'
    • Total number of drives installed on the system (if not part of a hardware RAID): 'cat /proc/diskstats'
    • Software RAID devices, RAID levels, RAID status, and participating drives: 'cat /proc/mdstat'
    • Processor details: 'cat /proc/cpuinfo'
    • RAM (total/used/free/shared/buffered/cached/available): ‘free’
    • Operating System: ‘cat /etc/redhat-release’
    • Kernel version: ’uname -a’
    • Network interface information: ’/sbin/ifconfig’
    • Mounted drives, including networked mounted shares: ’mount’

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  5. What makes USiaB so secure? - USiaB is designed to be more secure than your tyical Windows computer. First, the USiaB system is typically installed within a secure laboratory environment, where physical access is well controlled. The server is installed on a private network, internal to the company, and not in the cloud. All components are executing on the server itself, not on a remote system outside of your control. Second, USiaB uses two separate networks. The first is used by the user to connect to the server, the second is a private, non-routable network to communicate with the Optima AUC whose operating system is no longer up-to-date with the latest security standard. The second network is directly firewalled by USiaB to prevent unauthorized access even from within your organization. Communications on all networks are encrypted, and the first network can only communicate over port 22 (secure shell), and uses a multi-factor authentication: 1. username, 2. public/private RSA digital key pairs, 3. source IP address validation, and 4. optionally a passpharase. VNC is used to transport the GUI information efficiently even over a slower network, but the connection is end-to-end encrypted by forcing the connection through a ssh tunnel. Similarly, the remote maintenance by AUC Solutions is performed using a reverse ssh tunnel to AUC Solution's secure server, which avoids opening any ports on the outside of the corporate firewall - the server is therefore invisible on the Internet. Additional information is available through the UltraScan-in-a-Box overview video
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  6. How does data flow in USiaB? - After logging into their account, the user starts their USiaB desktop environment and starts the UltraScan software. Here, the first step is to select the GMP Data Acquisition" module from the GMP menu. A experimental protocol is created and stored in the MySQL database in read-only format, and submitted to the target Optima AUC. An operator selects the protocol from the touchscreen on the Optima and initiates an experiment. The Beckman data acquisition software consumes the Optima-specific portions of the protocol and executes an experiment, saving data into the Optima's PostgreSQL database. The UltraScan Optima data acquisition service monitors the ongoing experiment, providing status updates to the UltraScan software running on the USiaB server. At the end of the experiment, UltraScan transfers a binary copy of the data into the MySQL database on the USiaB server, and performs data editing and passes the data to the MPI module for analysis. Any manual steps are documented by collecting necessary electronic signatures. After analysis is complete, data analysis reports, spreadsheets, plots, etc. are stored in the MySQL database and a GMP report is generated, which is signed and also stored in the MySQL database. On a user-configurable schedule in the crontab service, the MySQL database and selected directories on the USiaB server are pushed to the network attached storage unit using appropriate rsync logic for archival long-term storage. Original data as well as any metadata analysis result can be recalled and retrieved from the MySQL database at will. A data flow diagram is available here.
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  7. What is USiaB light? - USiaB light refers to a version of USiaB which is identical to USiaB except that it does not include high-performance computing, and instead leverages the U.S. or Canada-based public computing infrastructure. In Canada, this is provided through the Canadian Center for Hydrodynamics, and in the U.S. through the NSF-funded ACCESS infrastructure. While these resources are available for free, at this time, these resources are only available to academic and not-for-profit users in the U.S. and Canada. Please contact AUC Solutions for more information on this solution.
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