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Ideas: Expand computational capabilities (power and/ or number of computers), increase efficiency of code, streamline workflows, etc. |
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See also
Purpose of page
Write down concerns, ideas, and efforts as understood by Chemistry IT so research group members can review and correct.
Request from group: Buy a server to process multiple Matlab calculation simultaneously
Considerations, expectations, and outstanding questions:
- Windows Server or Linux server OS?
- Past testing by researchers have yielded faster processing on servers running Linux than Windows. Some researchers only comfortable working within Windows.
- If Windows Server used, buy ~$100 software on server (free clients) to enable moving large amounts of data to server more speedily.
- If Windows Server used, Chemistry IT must work out the "how", with group's input. Examples of unknowns:
- How will user accounts and their access work? How many simultaneously? Per user accounts or shared accounts? How manage contention, if desired by group?
- There will be monthly (or maybe every 3 months) shutdown periods to ensure baseline patching and OS, file-share and hardware checking.
- Chemistry IT will coordinate with group, as we do for many other servers we manage for other research groups.
Chemistry IT expects group to purchase and maintain an adequately sized, rack-mount uninterruptible poser supply (UPS) for servers we manage.
- Approximate cost is $200-450; need to size correctly. Expect batteries to last 3-4 years easily.
- Budget about $200 (reality-check amount with Michael Hint) for hardware costs related to the rack and networking required.
- Chemistry IT can often contribute some used items "free", too, if available and of adequate quality.
Server spec suggestions and costs
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Chen Computational Server
1) Confirm support (draft)
Chemistry IT to do or figure out
Where in our 248 Baker Lab server farm? CPU and UPS. Power, switch/ networking.
Still need to confirm we can "turn off" logging into Windows using NetIDs.
- System is AD-based Windows using group's instrument account. And VNC remote access tool uses AD group to enable access by NetID, so confirm that still also works with any changes made to restricting Windows log-on.
Chen Group to do or figure out
Confirm no storage backup since can rerun computations potentially lost. If hard drive breas, Chemistry IT can re-install and configure OS and applications. But all group data and results will be lost.
Does the analogy of using the server as a "toaster" resonate and work? The only time a failure of the server impacts work is when a job is being calculated. Once the data has been analyzed, the server should no longer have a copy of the original data analysed, nor the results. Those are like the bread, in a toaster.
Chemistry IT's select roles and responsibilities
- Be responsive and respectful of requests from the Chen group, including requests for software installations. Includes:
- Installing or removing applications, configuring CPU threading.
- Conduct regular maintenance by Chemistry IT
- At least every 3 months, work requires the system be taken off-line. Usually able to accomplish updates within a morning. Scheduled for every 3 months for a specific place-holder date and reminders that all jobs will be stopped are sent 2 weeks, then 1 week, then 1 day before the maintenance. On day-of work, any remaining jobs are terminated by Chemistry IT so they can accomplish the required work.
- Chemistry IT installs and maintains the OS and application updates and upgrades. Configures and maintains remote access technology.
Chen group's select roles and responsibilities
- Be responsive and respectful of requests from Chemistry IT, including planning around maintenance or emergency technical work.
- Understand that access will require using a VPN if accessing the server from personal computers, or from eduroam/ RedRover, or from home.
- VPN is not required if server is accessed from current group's computational computers.
- Understand server is for processing data, not for on-going storage of data or results. Maintain data hygiene on server's storage drive to ensure that:
- Server never has collected data that is not primarily available elsewhere. Once data has been analyzed, that data should be deleted from the server.
- Group members do not use the server for long-term storage of results. Results should be copied elsewhere (example: Group's file share) and then deleted from the server.
2) Deciding on the final specs
This step enables Chemistry IT to get a "final" quote for Peng's review. If approved, Chemistry IT can place the order.
Below on this page is an outline on the costs and trade-offs of likely computation bottlenecks, for Peng's consideration.
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Server: Dell R440
$4,016.14 itself, plus:
- Any upgrades of the server's processors or memory (below).
- Server's storage drive (below): $100-900 (not necessarily Dell).
Other anticipated, related costs:
- Uninterruptible power supply (UPS):
- Licensing: MatLab
- Move from existing workstation (no change in annual costs), or add a license?
- Licensing: VNC
- $xx (per year?)
- Unlikely: Switch or other networking. Use existing infrastructure, paid by others.
- Unlikely: Rack or other physical provisioning costs. Use small portion of existing infrastructure, paid by others.
1) Processors
The server will have two Xeon Intel processors.
Confirm specifically which ones to invest in.
| Intel model | Cores (actual) | Clock speed (GHz) | Cache (MB) | Cost change from tested | Notes |
|---|---|---|---|---|---|
| Silver 4110 | 8 | 2.1 | 11 | (As quoted) | As tested |
| Silver 4114 | 10 | 2.2 | 14 | $350.90 | |
| Silver 4116 | 12 | 2.1 | 16 | $919.60 |
Many, many more options, for more money with gradations similar to the above, up to a 22-core (which is about $6,000 more).
- See price sheet if open to spending more for processors.
2) Memory (RAM)
| Total memory | Price | Notes |
|---|---|---|
| 64 GB | subtract: ($1,462.90) | As tested |
| 128 GB | (As quoted) |
3) Storage (hard drive)
For performance, support, and maintenance, purchase a server-class, single, larger SSD drive.
- Dell pricing: ~$0.8 to $1/GB
- Non-Dell (for same drives?): Q: $0.5 to $0.6/GB?
Strategy: To get a significant price reduction, consider buying the drive separately from Dell server. Even though more cost-effective, still will be serviced under (a non-Dell) warranty.
- Quote server with cheapest drive available (and don't use), if can't buy without a hard drive.
| Solid State (SSD) storage | Dell pricing (full price) | Price we'd likely pay elsewhere |
|---|---|---|
| 960 GB | 846.40 | ~$500? |
Many, many more options, whether for more or less storage.
- Use $/GB ratios above to estimate price for other desired sizes.
- See price sheet for specific options with Dell's pricing.
4) Warranty
Most research groups expect to use server investments for 5 years. And hope for more years, beyond the 5.
Normal warranty is for 3 years, but can instead get for 4 or 5 years.
- Question: Worth getting quotes for adding 4th and 5th year warranty, vs. base of 3 years?
Most groups take a risk for years 4 and 5, taking into account (1) rapid technological obsolesce and (2) historically low failure rates.
- Thus, groups are prepared to pay for fixes, or buy new, rather than put initial money into a more extended warranty.
- Can manage risk buy buying more years up-front, up to 5.
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Request from group: Buy a server to process multiple Matlab calculation simultaneously
Considerations, expectations, and outstanding questions:
- Windows Server or Linux server OS?
- Past testing by researchers have yielded faster processing on servers running Linux than Windows. Some researchers only comfortable working within Windows.
- If Windows Server used, buy ~$100 software on server (free clients) to enable moving large amounts of data to server more speedily.
- If Windows Server used, Chemistry IT must work out the "how", with group's input. Examples of unknowns:
- How will user accounts and their access work? How many simultaneously? Per user accounts or shared accounts? How manage contention, if desired by group?
- There will be monthly (or maybe every 3 months) shutdown periods to ensure baseline patching and OS, file-share and hardware checking.
- Chemistry IT will coordinate with group, as we do for many other servers we manage for other research groups.
Chemistry IT expects group to purchase and maintain an adequately sized, rack-mount uninterruptible poser supply (UPS) for servers we manage.
- Approximate cost is $200-450; need to size correctly. Expect batteries to last 3-4 years easily.
- Budget about $200 (reality-check amount with Michael Hint) for hardware costs related to the rack and networking required.
- Chemistry IT can often contribute some used items "free", too, if available and of adequate quality.
Server spec suggestions and costs
Dell's help for choosing processors, memory, and hard drives/ SSD's (respectively) for their R440 server, valid as of 8/9/2018:
- https://www.dell.com/learn/us/en/04/help-me-choose/hmc-processor-intel-xeon-14g
- Pricing via KFS: Dell-R440-Procs.JPG
- https://www.dell.com/learn/us/en/04/help-me-choose/hmc-memory-14g
- Pricing via KFS: Dell-R440-RAM-128GB.JPG
- https://www.dell.com/learn/us/en/04/help-me-choose/hmc-server-hard-drive
- Pricing via KFS: Dell-R440-SSD.JPG
| Minimum theoretical | Minimum proposed server | ||||||||
| Criteria | Current desktop's specs | Represents ~4 TIMES the desktop specs | Cost increase if go up a level or so | FIRST borrowed Dell Server specs, PowerEdge R430 (1 U) "CHEN-21" | July/ August 2018 SECOND borrowed Dell Server specs, PowerEdge R440 (1 U) "CHEN-23" Cost: $3,135.69 | Notes | |||
|---|---|---|---|---|---|---|---|---|---|
Cores, hyper-threading (HT) | 4 cores (one processor) i5-6500, 3.20 GHz (Not HT capable) | Total 16 cores (Two, 8-cores each) Each: Xeon Silver 4110, 2.10GHz 11MB Cache (85W) HT-capable | 16 total cores => 20 total cores
16 total cores => 24 total cores
*Availability delay, as of 12/22/17. | Dual Intel Xeon E5-2620v4 2.1ghz processors with 8 real cores / 16 virtual cores per processor More details: 20MB Cache (85W) | Dual Intel Xeon Silver 4110 2.1ghz processors with 8 real cores / 16 virtual cores per processor | Hyper-threading (HT) is useful to the group. Group tested performance between HT being turned on and off on "CHEN-21". With HT, test system showed 32 cores. 25 of these could be used without saturation, and thus without delaying processing time. Without HT, only 16 cores available so maximum much less than 25 effectively used under HT. Notes:
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Storage All SSD. | 500 GB SSD | 2TB is 4 times the space: 2.0TB Samsung 960 PRO M.2 PCIe 3.0 x4 NVMe Solid State Drive (cost is $1,499) Above configuration is the fastest option since combines OS and data on fast bus.
| If need less space, easy. Save about $375 per 500GB. Replace 2.0TB at left with:
If more space is needed, more complicated and slower, but of course doable. Please ask. | 400 GB SSD (380GB usable) | RAID-0 (striped) dual 240GB SSD drives acting as a single 480GB SSD for performance | Large amounts of data not needed to be stored on server, nor moved from server. Instead, simply deleted from server after processing. | |||
| RAM | 32 GB | 128 GB | +$1,440: 128 GB => 256 GB | 32 GB | 64GB (128GB is $880.55 more) | ||||
| Warranty | 3 year, NBD Dell on-campus "parts locker" | 3 year, Advanced Parts Replacement Warranty | Warranty upgrades (all non-NBD):
| 5 year, NBD, 5x10 on-site. | |||||
| Other | n/a | n/a | Option: Redundant power supply unit (+$224). Option: Any value in Dual and/or 10-Gigabit Ethernet? (+$150-500) | Network card: Quad-port, 1Gb. | |||||
| Total cost, approx. | ~$1,000 each (*4 => $4,000) | ~$5,500 for just the server | Easy to add $500 - $18,000 to SAME server! | ~$3,700. Compared to minimum recommendation:
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