AMD Threadripper and (1-4) NVIDIA 2080Ti and 2070 for NAMD Molecular Dynamics

AMD Threadripper and (1-4) NVIDIA 2080Ti and 2070 for NAMD Molecular Dynamics

GPU acceleration results
In my recent experience with AMD Threadripper 2990WX I was impressed with processor-based performance using the NAMD. Of course adding the NVIDIA GPU to the system gives a dramatic improvement since NAMD has a good GPU acceleration. I love NAMD for many reasons and one of them is that it makes a good standard renderer to look at the performance of the CPU / GPU. NAMD requires a balance between the CPU and the GPU to achieve the best results. It is also not very sensitive to the acceleration of AVX vector units. NAMD is measured well with lots of cores (or a lot of cluster nodes). After some discussion, I decided it was good to look at the performance of multiple graphics processing units with NAMD in the Threadripper program. The assumption is that there will be enough cores to keep up with the new GPU at the powerful NVIDIA.

Last Post My AMD Threadripper 2990WX 32-core vs Intel Xeon-W 2175 14-core - Linpack The NAMD and Kernel Build Time are good backgrounds for this post and have an interesting comparison with the Xeon-W Intel® 14-core system.

I spent a long afternoon on the same platform I used at the last post. I've been able to get a few tests using the 29 -Worked 24-core Threadbar program, but most of the results use a 32-core 2990WX processor.

I had a 2 Side Fan cooling NVIDIA RTX 2070 GPU. It is impractical to use more than two of these types of cards in a system because of the problems of heat choke (very bad), see the NVIDIA Dual-Fan GeForce RTX Coolers Ruining Multi-GPU Performance. Two days after the test, we got the first batch of RTX 2070 with blower fans! You should be able to configure the systems with these tools now.

We have fan blower versions of RTX 2080Ti so I managed to test 1 to 4 of these brilliant cards.

Test systems: AMD 2990WX and Intel Xeon-W 2175
The AMD Threadripper system you used was a test structure with the following key components,

AMD hardware
AMD Ryzen Threadripper 2990WX 32-Core @ 3.00GHz (4.2GHz Turbo)
AMD Ryzen Threadripper 2970WX 24-Core @ 3.00GHz (4.0GHz Turbo)
Gigabyte X399 AORUS XTREME-CF motherboard
128GB DDR2 2666 MHz memory
Samsung 970 PRO 512GB M.2 SSD
Ubuntu 18.04 see, the best way to install Ubuntu 18.04 with NVIDIA drivers and any desktop flavor

NAMD, NAMD_2.13_Linux-x86_64-multicore, and NAMD_2.13_Linux-x86_64-multicore-CUDA

Test results
When I sat in front of the system it had 24-core TR 2970WX processors in that I did a few tasks however before I exchanged the 2990WX. The first job I run was the CPU only. The results were very satisfactory in that the measurement with increasing number of threads was very homogeneous. Interestingly, the performance of NAMD has been uniformly improved with SMT "super chains". This is not always the case and often you see that only "real" cores are improving performance.

CPU results

The graph shows how successful SMT threads are with NAMD. Note that Lower is better! What is reported is the default NAMD performance output on day / ns, ie, the days required to perform 1 nano-second of simulation. Yes, this is a very intense task. Large jobs can last for weeks or months. My job was run for 500 steps of simulation.


This is a very good CPU performance to run this post! In an earlier publication, NAMD performed on the Xeon-Scalable 8180 and 8 GTX 1080Ti processing units, using the dual Xeon 8180 system with a total of 56 CPUs, which was 2.93 days / day with 32 heart. These processors cost more than $ 10,000 each. So the 32-core Threadripper is a bargain compared. [Using all 56 cores on this Intel system I got 1.68 days / ns]. Note: If you look at that oldest share, you will see that I took the inverse of the natural NAMD output and the ns / n mentioned in the report. Keep this in mind if you make a comparison. (Sorry about that)

GPU acceleration results

The first thing I have to say about the GPU's results is that, even with the good performance of the 32-core of the 2990WX, it is not enough just to keep up with more than 1 or 2 NVIDIA's new RTX GPU. The worst result range with 1 2070 to the best result with 4 2080Ti is the only 1.6 acceleration.

I'm not saying that these results are bad! It is actually very good and clearly shows how much performance it gains by adding a "modest" graphics processing unit such as the RTX 2070 which provides speeds up to about 5 CPU results only. However, by the time you add 2 RTX of 2070 or 2080Ti you are restricted by the CPU.

In the earlier release I mentioned above, the Xeon 8180 dual-core processor provided sufficient CPU capacity for 0.438 days / second with 1 GTX 1080Ti and the use of 2 1080Ti gave 0.248 days / day. The additional GPU only made the performance improvement smaller, more limited again by the CPU. (I
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How to switch from a Microsoft account to a local user in Windows 10

How to switch from a Microsoft account to a local user in Windows 10

How to switch from a Microsoft account to a local user in Windows 10

Why should I do this?
When you receive your Puget computer, during the setup process, if you accidentally linked your Microsoft account and no longer want to keep in touch, we can help you return to a standard local account only. Many users do not need additional services bundled with a Microsoft account such as OneDrive or Office 365, or the device synchronizes to the device.

How to return to the local account from a Microsoft account

If you are not using MS services, it is possible to return to a standard local account only. This will retain all documents, settings, applications, and user files, but it will disable the MS link and features.

1. Open Settings> Accounts and select "Your information"

2. On the next screen, if you see this or similar, this computer is registered in your Microsoft account, select "Sign in with a local account instead"

3. Now enter your Microsoft Account password. This verifies that you are authorized to make the modification

4. In the new window labeled "Switch to Local Account", please enter a new Local User Name, Password and Tip, then select "Next" - be sure to write this information somewhere where access will only be to The Puja computer

5. The screen will prompt you to save your work and "Sign out and finish". The system will now log off and you will need to sign in using the information you just provided

If any apps are installed directly from the Windows Store, you'll need to sign in again; however, they will not be uninstalled during this process.

Different types of accounts
When you create a new local account, you will have the option to set "Administrator," "Standard," "Child," or "Guest."

This administrator account will give the user full access to everything on the computer without having to enter any additional passwords or credentials.

A standard account can access most computers but will not be able to make important changes, install new applications, or run them even though applications that are already installed can run.

The child's account is similar to the standard account but provides additional family safety settings by default.

The guest account can use the computer to a limited extent, similar to the standard account, but without privacy where anyone can sign in to the guest account and there can be only one account. No applications can be installed, but existing applications can be run. This is mostly restricted to browsing the web and files stored within the guest account.

Create an additional user (local account)

You may want to create a secondary account for a friend or family, or you may want to have a second account for testing purposes, and in either case guide you through creating a new (local) account on your computer.

1. Open the Settings app from the Start menu

2. Select "Accounts"

3. Select "Add another person to this computer"

4. In "How this person logs in" as we create a local account, please select "I do not have this person's login information"

5. Microsoft will try to help you create a Microsoft account, but we will click "Add a user without a Microsoft account" instead

6. Create your username, password and hint if you want and then select "Next" - Make sure you type these credentials down for later use.

Once the account is created, sign out of the current user and log on using the credentials that you typed in the last step. Windows will start to create user folders and "Exit Setup Things" which may take some time. Once complete, the new user account will be fully activated.

Create a Microsoft account

Creating a Microsoft account on your Puget computer follows the same steps as the local account, but when you access step 4 instead of selecting "I do not have this user login information," you will only enter an e-mail address. Creating a Microsoft account synchronizes settings between computers as well as helping to migrate data from Outlook, OneDrive, and other Office 365 applications. We found that many of our users prefer to use local accounts but have the option. Additionally, you can switch from a local account to a Microsoft account simply by selecting "Log on with a Microsoft account instead of" in Accounting in the settings list.

Is contained
I've finished everything! We hope this explains some of the things about your account settings for your Puget system.
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Trying to fix Puget systems: What you can expect

Trying to fix Puget systems: What you can expect

All Puget Systems come with work and lifetime support. This means that you will never have to pay for the work or support involved with solving problems that arise with your computer. It is very important that we resolve your issues quickly and thoroughly so that you can return to doing the work that interests you.

We put a strong effort to resolve issues that arise in this area, while the system is still in your care, to help you avoid having to part with your computer for any length of time. We recognize that sending your system is not always a good option. However, there are some situations that may require you to send your system to be diagnosed and repaired here in our facility. This article aims to help those who are in such a situation understand what to expect when sending their computers for repair. 

Initiate a repair

Once the Puget Systems support technician has exhausted all the possibilities of solving the problem you are experiencing in the field, you may be asked to send your system to our source for repair. The first step to getting your computer to fix the support technician involves adding the fix to our schedule. The schedule scheduler maintains a fixed calendar for your system on one of our seats and helps protect against unexpected delays in the repair experience. Once the repair process is scheduled, you will receive an email from us containing shipping instructions to send the system to our facility and confirm the start date of the repair. The message will also include a link to a form that needs to be filled in to ensure we have full access to the system and recharged to the correct location. Please fill out as soon as possible, because it lists the information without which we can not complete the fix.

When the system arrives here at Puget Systems and receives a repair technician, you will receive a follow-up email confirming your arrival. The second email will also include a link to your repair ticket on our website, where you can check the status of your system as it makes its way despite our process.

If we have not yet received your responses to the repair form - including confirmation of the sender's shipping address and password for your operating system, if you choose to submit it - the start of the fix may be delayed. In most cases, the repair process takes five to seven business days to complete. It is important to note that this estimate does not include transit time to or from our facility.

Your system arrives at our facility

Once it reaches our repair department, the technician will carefully remove the system and check for damage. Although our systems and original packaging materials are specifically designed to minimize damage caused by shipping, it is important for us to inspect computers as soon as they arrive because, in rare cases, the carrier may have caused damage beyond what our containers can carry. If we find evidence of improper handling of the shipment during transportation to our facility, we will notify you immediately and process a claim with the carrier. We strongly recommend that all system shipments be shipped to our facility for their full value or shipped with a card provided by us. All labels provided by Puget Systems include automatic insurance. If you do not fill your order properly according to our instructions, or ship the system yourself without having to secure it, you may be liable for any costs in case of damage to the shipment. Again, shipping damage is rare but for transparency and due diligence, we feel it is important to provide this information here.

As long as your system reaches its scheduled repair date, it will run on the seat and will begin working on the date the system was scheduled to begin the repair. If the system arrives before the scheduled fix date, it will be marked and placed in our queue. If the system reaches after the scheduled repair date, the fix may be delayed.

Once the system reaches a repair seat, we will check the system and fill out updates in the repair ticket, visible to you via the repair tracking link we sent by email when the system arrived at our facility. After you verify, the next step is to repeat the problem (s) that you are experiencing. If we can not reliably reproduce the issues you originally reported, we may contact you for additional information.

If and when we are able to access the operating system, we will create a test user account. We do this for several reasons. First, this allows us to work in the environment of your program without interacting with your personal data or changing any of your settings. Second, this also allows us to upload our own tools and then remove them without leaving any trace behind you.

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Cyber ​​classes are popular in traditional high schools

Cyber ​​classes are popular in traditional high schools

E-Charter or e-Academies is no longer the only online choice for basic education students. Traditional schools now offer more online programs and blending (classes combining online and school courses) where technology transforms education at all levels.
Cyber ​​classes are popular in traditional high schools

"Students want to do this"
Downing town Area School District in Chester County, Pennsylvania, began offering Internet options in 2011 and was mixed up with courses in 2014. Christie Burke, the region's digital education coordinator, says the province can not ignore this request. . Last year, more than 1,200 secondary students were enrolled in Blended Downing Town; 37 took all their lessons online. She says there are many reasons why there are cyber students.

Here are some reasons:

Flexibility for athletes and working students

For example, cyber options attract athletes, who may need periods of 7 or 8 or a group of athletes who travel, train or compete in other parts of the country. Online courses serve students with medical problems, from irritable bowel syndrome to Lyme disease or depression.

Students in the Allied Health Training Program in Downing town, which takes students off campus during the first and second periods, can schedule online courses that they miss.

Online coursework helps to mix students who need to work in jobs where shifts overlap with traditional school hours.

Helps students in alternative ED programs

Douglas School is an alternative school in the Christina school district of Delaware, whose primary purpose is to support students as they prepare to return from Douglas to their geography school, said James Daniels, director of education. Douglas provides counseling and behavior components in small and mixed classrooms. Academic content is cataloged through online platforms and targeted to fill gaps in the student's path. Digital maps help students find out where they are in their program and allow them to develop their education. They can, for example, quickly track what they missed in order to graduate in time. Daniels says the students told him, "If that were not the case, I would not have graduated."

Homework, classroom roles

Saig Gregor, an administrative director, says school principals in Washington (Sewell, New Jersey), assistant school supervisor for curriculum and education, Jack McGee, and director of secondary education and corporate technology. Cyber ​​lessons provide introductory and back-to-back materials for students at home, at the doctor's office, or anywhere; students can then re-introduce them as needed to understand the entire material.

Cyber ​​Lessons Face Teacher Role as Lecturer. Group sessions can be used for deeper investigation, problem solving and applications, explains Wendy Morales, Digital Media Arts Supervisor and Technology Supervisor at the Middletown Township Public Schools in Leonardo, New Jersey. Teachers facilitate online conversations, classroom links, and interviews with experts in the field. They can interact with students online as well as at school.

An example of the inverse approach comes from McGee and Gregor. For homework, students may watch a video about the conditions of the north and south before the civil war. Chapter time is then used to apply this information in small groups and to strategize for economic, political and military objectives. Helps the teacher guide the process and works with the classroom to analyze how they compare their expectations with what actually happened.

The result is greater participation by all students (rather than controlling the time of the semester by a few) in addition to individual students' ownership of learning, achieving greater achievement and retention.

Personal education

Many areas, such as Middletown and Washington, offer students in grades 3 to 12 with digital devices. With the information at their fingertips 24/7, students can explore the technical or engineering aspects of the material that excites them, says Morales. She adds that with this access and allocation of Middletown's time for students to follow their individual concerns (the so-called Genius Clock), non-traditional learners can shine.

In this rich electronic environment, instruction meets the student at his or her own level, says McGee. The ability to accelerate special lessons over one week reduces stress while building students' time management skills. Discordant students who may not "get" the traditional lecture have online options for multiple approaches as well as access to area teachers. Students say they feel less stressful.

Digital devices also help bridge the digital divide and allow employees to track student progress, including AP points, and the greater participation of traditionally underrepresented voices.

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Designed by Jide Ogunsanya.