8/23/2021

Pacific Northwest Download

PNCC Offers 3 Methods to Get Data:

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  • Globus (required on all applications)

  • ARIA2

  • EMSL User Portal

PNCC data sets are very large, with some of them comprising multiple terabytes. Distance matters a great deal when transferring such large quantities of data across geographical distances on a wide area network. The speed of network transfers has to be taken into account, as they can cause transfer times to vary by factors of 1000! Transfer rates of 100-400 Mbps are typical when transferring data from PNCC if your network connection is well-tuned.

To work around some of the inherent problems of transferring large quantities of data across long distances, PNCC recommends that you:

1. Ensure that machines at your institution are well-configured for long-distance data transfer.

2. Choose a file transfer tool that can perform well.

3. Test your transfers end-to-end from EMSL to troubleshoot any problems prior to taking data at PNCC.

Frequently Asked Questions and Tips for Tuning Data Transfer

How do I get my data?

PNCC processes data and distributes it to users via the EMSL Computing facility (https://www.emsl.pnl.gov) at Pacific Northwest National Laboratory in Richland, Washington (PNNL). The EMSL computing facility features parallel HPC systems, petabytes of data storage, and dedicated high-speed data transfer capability. We offer three routes for you to access your PNCC data.

  1. The fastest transfer option is using Globus. This is the preferred method because you can get near real-time access to the data as it streams off the microscope and detector. Globus also provides a single point of access for you to see old and new data using a single endpoint rather than needing separate download links for each dataset. However, not all institutions permit Globus transfers inbound. PNCC now requires each proposal to list the Globus ID for at least one team member at time of proposal submission. Once your project is approved the PNCC data transfer team will reach out to the principle investigator and team to do a test transfer via a shared endpoint to confirm if GLOBUS works for you and to establish expected transfer speeds to your local storage. Setting up Globus access is pretty straightforward and is completely free for academics and non-profits. To get the ID go to https://www.globusid.org/create where you can register for a Globus basic account if your institution doesn’t already have an institutional license.
  2. The second fastest transfer option to download PNCC data is to use the ARIA2 parallel download manager. For every dataset collected an autogenerated email will be sent to members of the team to notify that data is available for download. However, this option is only available after a microscope session is complete and the full dataset has been uploaded to the archive. Installation of ARIA2 is straightforward with options to compile from source or direct download of binaries for OS X and Windows. Once installed, the use of ARIA2 is very easy. At the bottom of each PNCC autogenerated dataset email is a link for specific use with ARIA2 which points to the particular dataset. Simply copy this link and launch it with the ARIA2 command line to initiate the transfer. Similar to Globus, if your local connection is intermittent or the download gets halted, ARIA2 will automatically resume after disruption. ARIA2 parallelized download options are particularly helpful for big files or when data transfer rates are slow between your institution and the PNCC archive.
  3. The slowest but most accessible transfer option is via the Environmental Molecular Sciences Laboratory'sUser Portal “Get Data” tab. To access the datasets, login to the EMSL User Portal then either migrate to the “Get Data” tab or click the MyEMSL data download link provided in the autogenerated email mentioned above. Note: The portal login gives you a token needed to see the data and the token can time out after awhile. If you have problems seeing the data, try logging in to the portal on another browser page then refreshing the data portal page.

If you have any issues or difficulties, please contact our Data Teamdirectly by email. None of these tools will perform well if you are distant from the Pacific Northwest United States and have not addressed the tuning issues described in 'Configure and check your machines' below.

How will I know when I have data ready?

If using Globus, you will usually see your data on the our Globus Endpoint within 30 minutes of your session starting on the microscope. You will not be notified automatically about the start of the session but your SPOC may contact you if you have a pre-scheduled reservation. Whether or not you are using Globus to download your data, an auto-generated email will be sent to the project team members when the complete dataset is archived and available for download. This occurs after the end of the session and can take extra time depending on the archival queue. The auto-generated email will have a subject line of “MyEMSL Notification - Data Uploaded for Project XXXXX” and the message will contain direct links to your data in the EMSL data portal and a metalink that may be used to download your data with ARIA2. Note: You may receive multiple copies of this is your dataset was incomplete upon archiving.

The automated pre-processed data will be separately uploaded automatically to the archive and an auto-generated email will again be sent to the project team when that data is available for download. Depending on the queue size, the pre-processed data may appear in the archive later than the raw data. However, the pre-processed data will be visible via Globus as soon as each file is created.

Please contact our Data Teamdirectly by email if you still don't see your dataset more than 24 hours after the end of your session.

What is Globus? Why are we using it?

Globus is widely used in the scientific research community for sharing and transferring large quantities of data. It is designed to provide secure, reliable, high performance data access across multiple sites in a single interface. GLOBUS is used day in and day out to transfer PNCC data from OHSU to EMSL and moves multiple terabytes of data per day.

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Introductory information about GLOBUS is available here.

How do I to obtain a Globus ID?

In order to use Globus, you will need a Globus ID. The Globus ID identifies you to Globus, and allows you to access Globus endpoints (see below), including the EMSL Data Transfer Node (emsl#dtn) that hosts PNCC user data. Additional information about getting started with Globus is available here.

What are the minimum technical requirements for running Globus?

The normal Globus mode of operations is to use endpoints at either end of a data transfer. An endpoint is usually a dedicated data storage system with high performance network interfaces and disk storage, tuned for long distance data transfers.

It is also possible to set up a personal computer as a Globus endpoint by installing Globus Connect Personal software on it. Note: that this will probably not perform as well as a dedicated, tuned endpoint. If you have a local server-class Globus endpoint at your institution, it will likely be better to transfer data to that endpoint, then make a local copy down to your own machine.

What should I do if Globus doesn't work for me?

As mentioned above in the 'How do I get my data' section, PNCC has 2 other options for data transfer. Please contact our Data Teamdirectly if you have any questions about the other access mechanisms. Note, the auto-generated emails that you will receive when every dataset is available in the archive will also have specific instructions and links to the particular dataset.

What are typical data transfer speeds?

The average data collection results in 2TB+ of data. At 1Gbps transfer speeds (ie: a common internal wired networking) it would take 6+ hours to transfer that amount of data locally from start to finish. The further your location is from our site, the slower data transfer rates are likely to be. The emsl#msc Globus endpoint available to PNCC users has been observed sending data via Globus to Arizona as fast as 275 megabytes/second. At that rate, one terabyte can be transferred in about an hour. In comparison, a poor cross-country connection has been seen to perform as badly as 250 kilobytes/second, in which case that same terabyte would take a month and a half to transfer demonstrating the need to tune network connections at the user institution.

Configure and check your machines.

In order to get good data transfer rates from PNCC, your receiving machine(s) must have:

  1. A reliable network connection that does not experience errors or dropped packets
  2. A fast-wired network interface (10 gigabit/second is recommended). Do not use wireless for these data transfers!
  3. Tuning of the operating system (Linux, Windows, or MacOS) that dedicates extra system memory to data transfer
  4. Fast disk or SSD storage (capable of at least 100 megabyte/second) that is large enough to hold your data set(s)

The farther you are from the Pacific Northwest in the United States, the more important #1, #2, and #3 are. See here for instructions on #3.

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Background info: At long distances, many megabytes of data can be “in the wire” between computers that are far apart even when taking the speed of light in a cable into account. The computers at either end must be tuned to dedicate at least a “cable full” of their memory to each active data transfer, or they will drop data that will then have to be re-sent. This problem is noticeable at distances of about 500 miles, and can slow down transfers by a factor of 1,000 on cross-country connections. Almost no computer is tuned for this “out of the box,” but fortunately tuning guidelines are available here.

How do I test my data transfer rate?

To perform a data transfer rate test, please contact our Data Teamdirectly through email with the subject line: Test Dataset.

When a new Globus Shared Endpoint is created for your project, a large file named 'testdata' containing random data will be placed in it. You should download that file to test transfer rates to your institution.

If you want to test with known high-performance servers, or compare the speed of distant vs. local transfers, The Energy Sciences Network (ESNet) maintains a set of machines for such testing. They use the GridFTP protocol (which Globus uses) for maximum performance. See https://fasterdata.es.net/performance-testing/DTNs.

What is ARIA2?

ARIA2 is a multi-protocol data download tool that is available at https://aria2.github.io. ARIA2 has several useful features, including the ability to transfer multiple data streams simultaneously to improve performance. It can use the metalink to your data that is in the “MyEMSL Notification - Data Uploaded for Project XXXXX” email message. It can also resume an interrupted data transfer without having to restart.

What is the MyEMSL data portal?

The simplest but least performant way to download data is from the EMSL User Portal at https://eus.emsl.pnnl.gov/Portal. Log in to the portal with your EMSL-assigned email address and password. Click on the “Get Data” tab to see a list of instruments that have data available to you. You can navigate to the data set of interest, select the files and folders that you want to download, and then click on the “Queue Selected Files for Download.” The portal will then prepare a downloadable set of files for you anywhere from several minutes to hours. You may leave the page and return to it later; the portal will continue preparing your data.

Notes:

  1. A “Project Team Access” banner across the corner of the Upload pane indicates that the data set has not yet been released to the public. This means it is available only to approved members of the project and authorized EMSL staff. As an authorized member of the project, you should be able to download this data.
  2. If you do not see any instruments or data sets on the portal pages, make sure you go to https://eus.emsl.pnnl.gov/Portal and log in, then reload the pages. Also, select the appropriate date range for the data you are looking for.
  3. Once a downloadable file set (a “cart”) has been prepared you may download it with your web browser, or use a tool like wget, curl, or ARIA2.
Can we use rsync?

Unfortunately, rsync is prohibited by an institutional firewall on our end, so is not an option. ARIA2 is available as a command line based parallel download manager. See the 'How do I get my data' section above for details about ARIA2 and contact the Data Teamdirectly if you have questions with its implementation.

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Can we send hard drives?

Yes, but this must be approved by schedulingbefore shipping hard drives to our facility. We prefer data to be transferred via one of the options listed above, but do make exceptions for projects where the institution is far from the center, has very poor transfer rates and has large datasets.

What are my imaging parameters?

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For all DATA COLLECTION sessions, a 'METADATA_INFO.txt' file is automatically created within 30 minutes of the session data appearing on PNCC compute resources. This 'METADATA_INFO.txt' contains all relevant parameters including Cs value, accelerating voltage, pixel size, exposure dose, etc. Keep in mind, that the pixel size value is coming from the cross-grating grid and can be a few % off, contact your SPOC before processing the data to get an accurate value (calibrated on the standard protein dataset). The metadata file can be found at the same directory level where you will find the 'frames/' folder and the 'relion3_preprocess/' folders containing your raw images and preprocessed data. Open the 'METADATA_INFO.txt' file with any text editing program. Please contact your SPOCwith any questions about the specific parameters or the Data Teamdirectly if the file can not be found for some reason in your data directory. Note, the metadata file is not created for screening sessions.

Pacific Northwest or PNW from ORBX’s North American scenery series. How good is it and how to get the most of this scenery?

FTX Pacific Northwest

Pros and cons

What I like in FTX Pacific Northwest?

  • autogen – perfect placement and good density
  • mesh (10m resolution)
  • accurate coastlines, lakes and rives
  • photoreal areas
  • mountain peaks (mesh + photoscenery)
  • three high quality airports/airfields for free
  • Portland cityscape
  • Seattle city
  • additional airfields, seaplane bases and helipads
  • AI Traffic
  • large number of high quality payware airports available for this scenery
  • freeware RTMM sceneries available

What I do not like in PNW?

  • landclass (in some places)
  • vector roads (in some places)
  • autogen density (in some large cities)

What can be improved?

  • large airports (although I should remember that this is not an airport scenery)
  • upgraded airports

FTX Pacific Northwest by ORBX

What am I dealing with in this review? FTX Pacific Northwest scenery covers coastal areas of Washington and Oregon states in U.S. and the south-western corner of British Columbia in Canada including cities like Eugene, Portland, Tacoma, Seattle, Vancouver and the whole Vancouver Island.

It’s one of ORBX’s area sceneries that combine custom landclass, vector data and mesh. Additionally FTX sceneries include upgraded airports, new airfields and seaplane bases, photoreal areas in several cities, glaciers and mountains. This scenery also features fire towers and helipads.

Reviewer’s note

I review FTX Pacific Northwest with all additional ORBX freeware products that can be downloaded and installed to improve the quality of this product.

Vashon Island

Purchase

ORBX FTX Pacific Nothwest pageredirects to the FlightSimStore where PNW can be purchased for just 29,95 Australian Dollars – that makes 19 Euro or 22 U.S. Dollars at current rates (September 2015). The price is 10 dollars lower than in 2013 when I bought this scenery.

Installation

ORBX wrapper requires the order number, date and your email to run the installer. Then it is an automated process that will install FTX scenery into ORBX folder in your main FSX folder.

Northwest

After installation you should download updated libraries (and FTX Central software) from ORBX website.

To activate the scenery – run FTX Central.

Documents

Press PDF button next to the scenery name in FTX Central (current version) to open the manual. Like with all FTX products – the manual will guide you through installation and configuration process. It also explains what is included in this scenery and how to get the most of it. If you have add-ons that cover the same area – read compatibility notes.

Apart from this PDF manual there is a very useful Google Earth .kmz file that shows the area covered by this scenery and all it’s features. You can download this file from ORBX website before you decide on buying this scenery – https://www.fullterrain.com/product/pnw.

Airports (5******)

Reviewer’s note:

This is a 5-star rating for airports of the area scenery. It should not be confused with a 5-star rating of a single airport scenery.

There are 4 kinds of airports in Pacific Northwest scenery.

First we have large airports like Seattle, Portland or Vancouver. Just like the default airports in FSX – they suck big time. That’s ok – this is not an airport scenery and nobody promised us KSEA in HD.

The second group is made of small airports, landing strips and seaplane bases. The quality among these vary. There are some awesome places with 3d grass and objects like hangars, buildings, radio or lights towers, cars and smaller items from ORBX libraries. There are also many basic airports (and especially – sea plane bases) where there is nothing but a runway (or “spawn” places in case of water runway). I should be said that there are such a basic places in real world so it is not necessarily a mistake.

Upgraded airport

There are also helipads next to the fire towers. Actually these are platforms made of wooden logs, not a proper helipads – so be aware and do not take a large and heavy helicopter there. I really enjoy looking for them – sometimes in a helicopter, more often in a plane when I am cruising just above mountain tops. In case you are lost – GPS will help you find this places.

Helipad…

The fourth kind consists of three freeware airports that ORBX gives for free on their Freeware page:

  • KHQM Bowerman Airport
  • 2S1 Vashon Island Airport
  • 7WA3 West Wind Airport

Bowerman

Technically these airports are separate (freeware) products but I decided to include them in this review. Bowerman on the Pacific coast is a small airport with an asphalt runway and published IFR procedures. Smaller Vashon Municipal is located close to Seattle on an island in Puget Sound. It’s perfect for a sightseeing flight in Cessna 172. Remember to keep your chart at hand – airspace around Seattle is a complicated one. West Wind is a small private strip owned by Douglas Davis. Placed near Bellingham is a perfect place to take-off for a mountain flight – Mt. Baker (10800 ft.) is just 20 miles east.

Compared to ORBX’s payware add-on airports for this scenery – these three look just a little outdated. When compared to other payware sceneries available on the market they could easily compete with many of them.

Vector scenery (4****)

What I like most about ORBX FTX sceneries are the shorelines and rivers. It’s crucial to have good reference points on the ground when flying planes like Piper Cub and this scenery gives exactly what is expected when I compare my map with a peninsula or a small island I am flying over.

Roads are ok. I never got lost following them (I would be surprised if I did – high quality vector data for this region is easily available) but on the other hand… I do not like what I see when I am flying over highly populated regions – roads look messy when there are to many of them on a small area and they do not mix well with landclass textures in the background.

Autogen (4****)

Tree density is nice but It’s not on the level of FTX Southern Alaska or FTX Scotland. Here I clearly see that this is an older scenery.

If you have not tried the new FTX sceneries – I can say that the autogen keeps the standard density of a good payware area sceneries of other developers. That is good… but not good enough. (one more note – for me forest density is one of the most important features in area sceneries).

Building autogen is correct and very close to what I desire. It’s perfect in small towns. Bit sparse in large cities (but Portland).

Seattle

Portland (6*****)

I’m in autogen-heaven… and then my FSX crashes because of OOM error. Ok – partly my fault – no system will be ok with extremely dense autogen settings (+autogen improving tweaks) and a city like this. With FSX settings adjusted correctly – this is a beautiful city to fly above in a helicopter or a slow plane.

My favorite flights were in a police or medevac helicopter – low over the river, barely above beautifully crafted bridges.

Portland Cityscape is (similarly to previously mentioned airports) a freeware add-on downloaded from ORBX Freeware page.

Portland

Landclass (4****)

This scenery (like all FTX) uses a custom landclass – both LC placement and textures are designed for this scenery. The improvement over the default FSX is great. When compared to other FTX sceneries – it seems a little inferior. But I still like it.

Floatplane in Canada

PNW

Photoreal areas (5*****)

Seattle and several mountains are covered with aerial or satellite imagery. I rarely flown above Seattle. Trying to follow real rules I find it challenging for a small plane pilot because of complex airspace around Seattle-Tacoma Airport. Although KSEA is a decent airport I do not have much time to admire the view when approaching in an airliner.

What I like most is to fly above mountains that are covered with photoscenery – like Mt. St. Helens, Mt. Adams and other prominent peaks of Cascade Range. I do not have technical information about the resolution of this photoscenery but it is sufficient to fly low above it in a small plane or a helicopter.

Seattle

Mesh (5*****)

I did a test. Actually – I made a mistake. I was sure that FTX NA is activated and took off from one of small airports near Mt. Rainier. The default FSX scenery (+ freeware STRM mesh) looked ugly but nevertheless I tried to navigate around valleys connecting Packwood with Ranger Creek. And I got lost…

Then I restarted my FSX with FTX NA properly activated. Everything changed. I could easily name mountains, passes and valleys when I looked around. This scenery uses 10m mesh and it works well.

Scenery compatibility (5******)

I already described freeware ORBX airports and Portland Cityscape. There are also 22 ORBX payware airports for Pacific Northwest (you will find reviews of some of them in C-Aviation.net soon).

If bush flying is your thing – there are plenty small sceneries at Return to Misty Moorings. Free of charge.

Vancouver payware scenery was published by FSAddon.

If you need more space to fly – Pacific Fjords, Rockies and Northern California sceneries published by ORBX extend this scenery in every direction.

Flying over Pacific Northwest

I did most of my flights in small planes. The pleasure of flying a Cessna, Piper or Beechcraft at low altitude never fades with a scenery this good. But this is not all that the scenery has to offer.

Flying around Seattle

Sometimes I fly military aircraft and this scenery is handling low-level high speed flights very well (that is an advantage of a landclass scenery over high resolution photoscenery). Take a look at sectional chart and find yourself a MOA to fly into and have a little fun. I recommend Chinook MOA south of Whidbey Island NAS (Naval Air Station) – that is an air base belonging to U.S. Navy – they fly F-18s, P-3s and EA-6s from Whidbey.

RAF having fun in MOA… or maybe it was outside of MOA? Clearly too low ;)

When I want to fly large airliners – I mostly use Seattle Tacoma airport for my Boeing 777. It’s not that nice as a payware airport but among PNW large airports – it’s the best. For smaller airliners (I fly Beech 1900 turboprop) – the small airports with paved runways seem best. Unfortunately – there is a gap in between Seattle and small airports – large airports are terrible (I hate Portland – although I flown from this airport several times to admire the city). As I said – this is area scenery, not an airport scenery.

Summary (5*****)

5-stars. Same as Norway (soon to be translated and published)… but very different. Let me compare this scenery with FTX Norway or FTX Southern Alaska. It’s worse. And better.

If I had to review this scenery just as it is – with no additional sceneries installed – it would be rated 4****. It’s older then Alaska and Norway and it’s age already shows. But this 4 star rating would be useless for you. It’s about a product and I would like to rate the experience. Additional sceneries are clearly a part of this experience and I feel that a scenery that encourages people (and companies) to build upon deserves appreciation. That is why this is a 5-star scenery.

Look at this vector roads

Pacific Northwest Downloadable Map

If you ask me – what to choose – Southern Alaska or Pacific Northwest? My answer will be – both. But if you have to make a choice – let me put it like this. If you have no other ORBX FTX scenery – go with PNW. It’s a cheaper and you will get an idea how ORBX payware airports may improve your experience. If you already know what FTX is about – make your choice based on the region that you prefer.

Quality to price – great

For 29.95 Australian Dollars (19 Euro) you get a large, high quality area scenery and 3 small airports. That’s not much for what they give.

West Wind freeware airport

Add-ons used in this review:

  • Sky and clouds – REX 4 Texture Direct
  • Clouds – REX Soft Clouds
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5