Ideas: Expand computational capabilities (power and/ or number of computers), increase efficiency of code, streamline workflows, etc.
Purpose of page
Write down concerns, ideas, and efforts as understood by Chemistry IT so research group members can review and correct.
Chen Computational Server
Warranty for 3 years, expect to us it for 5 years. And hope for more years beyond the 5.
- Can manage risk buy buying more years, up to 5. Historically not an issue, but no guarantees, obviously.
1) Confirm support (draft)
Chemistry IT's role and responsibilities
- Be responsive and respectful of requests from the Chen group, including requests for software installations.
- Conduct regular maintenance by Chemistry IT
- At least every 3 months, require the system to be taken off-line. Usually able to accomplish updates within a morning. Scheduled for every 3 months and reminders that all jobs will be stopped are sent 1 week and 1 day before the maintenance.
- Chemistry IT installing OS and application updates and upgrades
- Installing or removing applications, configuring CPU threading.
On-request changes by Chen's group
- Be responsive and respectful of requests from Chemistry IT, including planning around maintenance or emergency technical work.
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.
Server
Dell R440
$4,016.14, plus:
- storage drive (below): $500-1,000.
- Any upgrades (below)
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.
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 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:
|
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:
|
Core prices snap-shot
- Prices taken 12/22/2017
- Prices go up dramatically with both core-count and processor speeds.
- Cache sizes and power consumption also increase with capabilities.
- This chart of estimated marginal costs is a sub-set of options pulled from <https://www.thinkmate.com/system/rax-xs4-21s1-sh> and <https://www.thinkmate.com/system/rax-xs4-21s1-10g>, focusing on SLOWEST procs to reduce costs. Other, more expensive-per-proc (faster) options available.
Approximate price increase buying TWO processors compared to 8-core Xeon Silver 4110 NOTE: Can also get a server with just ONE processor (at half the marginal cost), if core-count is sufficient. | Processor (all Intl Xeon) | Actual core count EACH processor Obtain total count by multiply by 2 since 2 procs. All HT-capable | Other specs |
|---|---|---|---|
| $0 (base-line, for price comparison) | Silver 4110 | 8-core => 16 | 2.10GHz 11.00MB Cache (85W) (Same price as 4-core 2.60GHz 8.25MB Cache (85W) version) |
| +460 | Silver 4114 | 10-core => 20 | 2.20GHz 13.75MB Cache (85W) |
| +1,200 | Silver 4116 | 12-core => 24 | 2.10GHz 16.50MB Cache (85W) |
| +1,628 | Gold 5115 | 10-core => 20 | 2.40GHz 13.75MB Cache (85W) |
| +1,960 (availability delay) | Gold 5118 | 12-core => 24 | 2.30GHz 16.50MB Cache (105W) |
| +3,060 (availability delay) | Gold 6126 | 12-core => 24 | 2.60GHz 19.25MB Cache (125W) |
| +3,280 | Gold 6130 | 16-core => 32 | 2.10GHz 22.00MB Cache (125W) |
| +5,060 | Gold 6138 | 20-core => 40 | 2.00GHz 27.50MB Cache (125W) |
| +7,560 | Gold 6152 | 22-core => 44 | 2.10GHz 30.25MB Cache (140W) |
| +6,560 (availability delay) | Platinum 8153 | 16-core => 32 | 2.00GHz 22.00MB Cache (125W) |
| +15,660 (availability delay), and +$400 chipset | Platinum 8158 | 12-core => 24 | 3.00GHz 24.75MB Cache (150W) |
| +10,160, and +$400 chipset | Platinum 8160 | 24-core => 48 | 2.10GHz 33.00MB Cache (150W) |
| +13,560, and +$400 chipset | Platinum 8164 | 26-core => 52 | 2.00GHz 35.75MB Cache (150W) |
| +16,660, and +$400 chipset | Platinum 8170 | 26-core => 52 | 2.10GHz 35.75MB Cache (165W) |
| +19,760, and +$400 chipset | Platinum 8176 | 28-core => 56 | 2.10GHz 38.50MB Cache (165W) |
Why server with 2 processors? Why not one or four, for example?
No savings buying just a one-processor server, especially if want more cores. JUST the price of the process jumps by the cost of an entire server!
- +$5,080: 16 total cores => 24 total cores (one proc)
Consider four processors only if needed and can afford many more cores. Option is not cost-effective for the core-counts we are currently looking at. Other considerations:
- Currently, only older processors are currently as an option with four-processor servers.
- Server prices START at about $12,000, for 32 total cores.
- Core counts and price upgrades are "times 4", not "times 2".
What if need more than 2TB total storage?
If need more than 2TB total, likely must use more complicated, multiple storage option.
- We can dig deeper to confirm this, if necessary to decision-making.
- More storage likely will be slower, even is sticking to SSDs.
An example of an option to get more than 2TB storage:
First: Choose boot drive, which can be small. For example:
- OS only: 512GB Samsung 960 PRO M.2 PCIe 3.0 x4 NVMe Solid State Drive (cost is $399).
THEN: Choose a single main storage drive. Some examples and their costs:
- Data ONLY fast SSD:
- 3.84TB => $1,500 - 2,100
- 7.68TB => $3,000
- Data ONLY slow spinning, compared to current desktop's much faster SSD:
- 4TB => $200
- 8TB => $350
- 12TB => $650
Status
10/5/17: Oliver met with Mahdi <mh2356> and Kushal <ks2285>. Action steps to have Peng review and refine:
(1) Group: Decide if worth having (select?) Matlab code reviewed by experts at CAC, focused primarily to increase efficiency. Secondary outcomes include:
- May result in the ability to run older code on current version of Matlab, expanding where code could run on non-group computers.
- May result in clarifying computational bottlenecks so the best fitted computational hardware is purchased. What does one prioritize when faced with choice to invest in: better processors, number of processors, number of cores per processors, bus speeds, SSD drives, and/ or RAM?
- May result in a confirmation whether or not problem lends itself to parallelization. If so, can increase efficiency with the right hardware and expands the locations to efficiently run the code (RedCloud, etc.).
(2) Oliver: Have group test their code on test server in 248, initially by-passing using the network to get the data to the server.
- Time comparisons of both single runs and simultaneous runs. Does the server reduce computational time for a single job, as compared to current workstations? To what degree does the server's performance drop as more jobs are added? Again, compare to current workstations.
(3) Oliver: Optimize getting data to test server in 248 via the network.
Other thoughs from Oliver:
- Confirm if any campus computing is a good fit for the group: CISER, RedCloud (likely only if code can be and is parallelized), David Botsh's cluster(?), others?
- Group may benefit from optimizing workflow at various workstations.