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This is a new feature of the website!

The previous FAQ is still posted as a PDF file here.  We are migrating that information into this FAQ.

As always, you can reach us at support@nmrbox.org with any questions or suggestions you have.

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When connecting to NMRbox via RealVNC for the first time, or after a reboot of the server, the screen resolution will likely be smaller than you desire. The NMRbox team has built a tool to allow for quick screen resolution changes which works without affecting any ongoing processes. The tool can be launched in a few different manners:

  1. By going to the Xfce menu bar (in the upper left hand corner of the screen by default) and selecting "nmrbox-util" and then "Resolution Changer"
  2. By going to the Xfce menu bar and selecting "Settings" "Display"
  3. By running "resolution_changer.py" from a Terminal window

Once launched simply select the desired resolution and press "Apply". The window will stay open for easy adjustment to a different resolution if desired. Press "Exit" whey you are finished.

It is sometimes desirable to have the screen resolution be slightly smaller your monitors resolution, in those cases select the "Scale resolution by 90%" radial button.

If you plan on spanning your RealVNC window over two monitors you should select the "Double Horizontal Width" radial button. Note that by default the RealVNC window will only be displayed on a single monitor. Please read the FAQ on how to have RealVNC span two monitors.

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Acknowledging and referencing NMRbox is important for continuing financial support from NIH. If you use NMRbox for any data processing or analysis for a published study, please cite our Biophysical Journal article and acknowledge the NMRbox Center as shown below: 

NMRbox: A Resource for Biomolecular NMR Computation. Maciejewski, M.W., Schuyler, A.D., Gryk, M.R., Moraru, I.I., Romero, P.R., Ulrich, E.L., Eghbalnia, H.R., Livny, M., Delaglio, F., and Hoch, J.C., Biophys J., 112 1529-1534. PMID: 28445744, DOI: 10.1016/j.bpj.2017.03.011

"This study made use of NMRbox: National Center for Biomolecular NMR Data Processing and Analysis, a Biomedical Technology Research Resource (BTRR), which is supported by NIH grant P41GM111135 (NIGMS)."

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No! Once the VNC Server session is started it will remain running until it is either explicitly closed or the NMRbox server is power cycled. You can connect and disconnect to the same VNC session multiple times and from multiple devices. Calculations that are being performed continue to execute even when the VNC Viewer is disconnected. This can be convenient when using NMRbox from different locations such as work and home.

Note that you can connect to your NMRbox VNC Session multiple times concurrently from the same or different devices. In this case the Desktop environment is shared (all connections will view the exact same screen, including mouse movements).

If your VNC session is not behaving properly you can explicitly kill it by opening a terminal and entering the command "kill-vnc-server" and then selecting the server to kill (generally there will only be one selection).

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If the graphical windows in a VNC session start behaving oddly, the easiest fix is to stop your current session and create a new one by reconnecting with the VNC viewer. Note that merely disconnecting your VNC viewer leaves the graphical session running so you can just pick up where you left off. To stop a VNC session, open a Terminal window and type: kill-vnc-server. You'll be presented with a list of sessions; if you're executing kill-vnc-server within a VNC session, the current session will be annotated. Just select the desired session to close and press Enter. If you run kill-vnc-server from a VNC session the VNC connection will be disconnected and you will need to reconnect via Real VNC Viewer.

Note that running kill-vnc-server is akin to logging out and back into a computer and thus any currently running jobs will be lost.

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You can use the password reset form at https://nmrbox.org/forgot-password to reset your password.

It is important that you do not attempt to login with the wrong password over and over again. Too many failures will cause your account to be blacklisted for a period of time. 

Alternatively, email us at support@nmrbox.org for assistance.

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If the VNC Viewer cannot connect to username.nmrbox.org there are four likely possibilities;

1. Your internet connection is not functioning or you are mistyping the server name, username, or password.

2. The username.nmrbox.org VM is not functioning properly.

3. Your institution is blocking the outgoing port which RealVNC is attempting to use to connect to our servers.

4. You attempted to login repeatedly with the wrong password and your computer has been blacklisted by the VNC server.

Troubleshooting: After verifying that you have an active internet connection attempt to login to the NMRbox website (https://nmrbox.org) from the "Sign In". If you can login to the website your username and password are correct. To test the NMRbox VM try to ssh into the server. From OSX or Linux open a terminal and type “ssh username.nmrbox.org”, without the quotes where username is your username. If you are prompted for a password then the NMRbox VM is alive. From Windows you will need to download a ssh client program if you do not already have one installed. BitVise Tunnelier is a good choice, but there are many others as well. If you cannot ssh to the NMRbox VM please contact the NMRbox team via email at support@nmrbox.org so that we may help fix the issue.

If you can ssh successfully, but cannot connect via VNC, then it may be possible that your computer is blacklisted due to too many failed logins or your institution is possibly blocking the outgoing port that VNC is using. If you can connect from a different computer in your institution it is likely that your computer has been blacklisted. Send an email to support@nmrbox.org to have the blacklist removed. To test if your institution is blocking VNC attempt to connect via VNC from outside your institution, such as from your home. You can also send the NMRbox team an email at support@nmrbox.org and we will test the connectivity.

If your institution is blocking the port that VNC is using there are two fixes. The preferred fix is to contact your IT department and ask that they open port 5900 for outbound traffic for your computers. If your IT department is not amendable to this then contact the NMRbox team at support@nmrbox.org and we will work out a solution for you.


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You have several options:

  1. scp
    You can connect to your named NMRbox VM (username@username.nmrbox.org) via ssh and use scp.

  2. Globus
    See our Globus guide.

  3. DropBox
    Open a terminal and type: dropbox start -i
    This will launch the DropBox installer.
    Follow the instructions to install and login.

  4. RealVNC

            > To SEND files from local computer to NMRbox    

                    hover mouse near top center of VNC window
                    click on “File transfer” icon                    
                    follow directions

            > to FETCH files from NMRbox to local computer

                    click VNC icon in status bar (top right, next to username)
                    click menu icon in top right of pop-up window
                    select “File transfer…” menu item
                    follow directions

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You must use Real VNC Viewer - no other VNC Viewer will connect to NMRbox!

NMRbox utilizes a commercial VNC server from the company RealVNC. The commercial version of RealVNC provides several benefits as outlined here, but the only way to connect to NMRbox is with a VNC Viewer from RealVNC. The good news is that the NMRbox team has purchased licenses for RealVNC server and NMRbox Users only need to download the free VNC Viewer from RealVNC which runs on almost any device.

Note that you only need to install the RealVNC Viewer and not the server portion named RealVNC Connect.

  • Mac users: Download RealVNC Viewer from here and install.
  • Windows users download RealVNC Connect from here and install. During the installation de-select the VNC server checkbox.

Benefits of RealVNC server:

  • Free. RealVNC Viewer is free for all platforms and runs on almost all devices.
  • Full encryption. All connections with NMRbox are fully encrypted.
  • Single sign-on. Your NMRbox username and password are used to logon, unlike open-source VNC servers which require the User to create a separate, unsecure, login which resides in the users Home folder.
  • Daemon mode. There is no need to login via ssh and start a vncserver session manually. VNC server sessions are started automatically when you login via RealVNC Viewer.
  • Built-in file transfer. Files can be transferred into and out of your NMRbox account from within the RealVNC Viewer program.
  • Local printing. The default printer on your local computer is mapped to your NMRbox account allowing Users to print from within NMRbox to your local printer.
  • Full screen mode and multiple monitors. RealVNC supports Full Screen mode with and without scaling and allows the display to span multiple monitors.
  • Performance. The commercial RealVNC Viewer / Server combination has excellent performance.
  • Persistent sessions. Once started the VNC server session will remain alive allowing the User to connect and disconnect as often as they like from any location or device.

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We will make every effort to not shut-down services to NMRbox VM PaaS, but occasionally the systems will need to be powered off for maintenance. We will make every effort to notify users ahead of time with any scheduled outages. When possible our preferred time for maintenance will be on Monday’s at 7:30 AM Eastern Time (New York), but reserve the right to handle maintenance at other times as well.

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The use of a Terminal Emulator (often called “shell”, “terminal”, or “command line”) is critical to utilize many of the programs within NMRbox. We have created a document on how to use the terminal which can be found on the Documentation page of the NMRbox website. In addition, the sites below are good sources of information and Ryans’s Tutorials has some good tutorials.

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Newer laptops often have very high resolution screens - even 4k displays!. On Windows and OSX the size of menus, icons, and fonts are scaled to be larger so they are readable on such high resolution screens. However, when connecting NMRbox VM PaaS the menus, icons, and fonts may be so small they are unreadable. To fix this issue open a terminal and run “resolution-changer.py” and choose a reasonable resolution for your screen size, which may be considerably less than the actual screen resolution, such as 1920x1080 when using a Retina or 4K laptop. The NMRbox window will be small and hard to read at this point on your high resolution screen. Then go to the RealVNC Viewer Toolbar and select Full Screen or play with the scaling setting to stretch the screen size larger and hence make things easier to view. Note that you may need to select / deselect the “Scale to window size” and “preserve aspect ratio” from the Options window under the “Advanced” window and “Display” tab to optimize your window. With a bit of playing around you should be able to find settings that suit for laptop.

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Go to https://nmrbox.org and press “Sign up for an account” and fill out the form. You will receive a confirmation email. NMRbox accounts are manually verified and can take up to 2 business days to process. Once your account is validated you will receive an email with instructions on how to access your account and connect to NMRbox.

Note, if you have any questions or do not receive any of the emails referenced above, please contact us at support@nmrbox.org to ensure that your account request is properly handled. 

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Well, the obvious answer is that either the username is not correct or the password is incorrect. However, figuring out which or whether there is another issues can be difficult. Here are some guidelines on how to resolve the situation.

First, do not continue to login repeatedly with the wrong username or password. After 8 straight unsuccessful login attempts the computer you are using will be blacklisted and it will take a while for the blacklist to be lifted.

Attempt to login to the NMRbox website by going to https://nmrbox.org and selecting "Sign In". If you can sign-in via the NMRbox website then your username and password are correct and there is another issue. If you cannot login to the NMRbox website then attempt to reset your password from https://nmrbox.org/password-reset

Check that the “Username:” and “Password:” in the VNC Viewer – Authentication dialog box, which appears after entering the “VNC Server:” in the VNC Viewer dialog box, is correct. By default the “Username:” is set to the username of the current account on your local computer and is generally not your NMRbox username and thus needs to be changed.

Attempt to ssh into the computer to verify the username and password. From Linux or OSX enter the following command from a terminal “ssh username@username.nmrbox.org”. From Windows you will need a ssh program such as BitVise Tunnelier. Note that too many unsuccessful ssh attempts can also cause your computer to be blacklisted, thus don’t try the same wrong username and password over-and-over again.

Attempt to make a VNC connection from another computer. If your computer was blacklisted the connection will be possible from another computer with a different IP address. The blacklist starts with a 10 second lockout after 8 unsuccessful logins and then grows geometrically. Thus if you wait a while your computer will be removed from the blacklist automatically.

If you are unable to resolve the issue send an email to support@nmrbox.org for further assistance and provide as much detailed information as possible.


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In Linux there is a search path that can be shown by opening a terminal window and entering the command “echo $PATH”. The output will be a series of directories that are searched when you enter a command. For example, when you type “ls” from a terminal, locations in the path are searched until the command “ls” is found and then it is executed (no further searching is done). In the case of “ls” the command is located in /bin/ls.

When you create shell scripts for processing data you may simply try to type the name of the script to have the script run. For example, let’s say you create a script called nmrpipe.com. From a terminal you type “nmrpipe.com” and you get a “command not found” error. This is because the current working directory is not in the search path and hence the command nmrpipe.com is not found. To resolve this issue add a “./” in front of the script name, “./nmrpipe.com”. The “.” is mapped to the current working directory so typing “./nmrpipe.com” is equivalent to typing the explicit path “/home/nmrbox/username/…/nmrpipe.com” just in a shorthanded way. As a note “..” is mapped to the parent of the current working directory. That is why the command “cd ..” moves up one directory.

In the past many users would add the current working directory to their path. However, we would discourage anyone from doing this for a few reasons.

It is very easy to type “./” in front of your scripts so very little is gained.

It ensures you are running the script you think you are running. Imagine a scenario where there is a script called nmrpipe.com in the search path and it is searched before the current working directory. Now when you type nmrpipe.com you end up running the nmrpipe.com script from a different location than the expected current working directory.

It is security risk. Imagine you accidentally download a malicious program called “ls” which performs some undesirable task and ends by running the real ls command. If you perform an ls command from a current working directory where the malicious ls command was located you would be running the malicious code accidentally, and because it masks itself by running the real ls command you may not even realize what you did.

If you accidentally create a file with the same name as a system command then the system command may not run properly from the directory. Imagine if you accidentally created a file called mkdir and the current working directory was in the path. Now when you try to run the command mkdir from that directory you would simply get a returned prompt without anything happening making it appear that the mkdir command was not working properly.


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No! With the commercial version of RealVNC that NMRbox is utilizing the VNC server runs as a daemon and a VNC server session is started when the User logs in from the RealVNC Viewer. You should never run the command “vncserver” from within NMRbox. With free versions of VNC that many users are familiar with the general procedure was to ssh and then start a VNC server with vncserver :XX where XX was the display port. Then the user would connect with a VNC Viewer to servername:XX. With the commercial version of RealVNC implemented in NMRbox the user never runs "vncserver" and never enters the display port number, both are handled by the daemon.

In addition, your VNC session stays alive even when you disconnect disconnect the RealVNC Viewer. In this way any calculations or open programs will remain running. When you connect again the VNC daemon will route you to the correct session.

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First, the instructions below are for version 6 and up of RealVNC Viewer. We recommend upgrading if you are using an older version.

When the VNC Viewer is running there will likely be a menu at the top/middle of the window that is mostly hidden and all that may be visible is the very bottom of the Toolbar. To reveal the Toolbar hover the mouse over the area and the Toolbar will reveal itself. It is also possible that the Toolbar is set to not be present from the VNC Viewer Options. If this is the case open the VNC Viewer Options by pressing "F8 (On Macs use the fn key along with F8" from within a active VNC session and select "Properties" from the menu that appears.

To turn the Toolbar back on follow the directions above to open the Properties Dialog box and select the Expert Tab. Type EnableToolbar in the Filter window and then change the Value to "True"

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Yes! When RealVNC Viewer establishes a connection to NMRbox the default printer on your computer when the connection is created is mapped and set as the default printer inside NMRbox. You can then print to your local printer even though what you are printing is on the remote NMRbox VM server.

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Yes, you can have an NMRbox VNC connection use two monitors, but there are a few restrictions. First, the NMRbox display will span two monitors, but they are treated as a single display, not as separate dual displays as is common in Windows and OSX. The other restriction is that the VNC Viewer must be in Full Screen Mode for the display to span multiple monitors.

To setup your NMRbox VNC connection to use two monitors follow these instructions.

Step 1: Use RealVNC Viewer to connect to username.nmrbox.org and login.

Step 2: Open a terminal and run “resolution-changer.py”. Select the desired resolution for a single monitor and then check the "Double Horizontal Width" under Variations. Note, the window will shrink to fit the window on a single screen at this time and may make font sizes small.

Step 3: Open the VNC Viewer Options dialog box by hitting "F8" from the VNC window and then selecting "Properties", or from the top Toolbar at the top center of the screen and select "Properties". From the Properties dialog box select the "Expert" tab and type "UseAllMonitors" in the Filter and change the value to "True"

Step 4: From the VNC Viewer Options select Full Screen mode and your NMRbox display should now span across both monitors. Note that you may want to play with the “Scale to Window Size” selection under the “Display” tab for optimal results. You will want to change the “UseAllMonitors” setting back to “False” when only using a single monitor.


Answer

In late 2017 NMRbox will be offered as a downloadable version. However, the NMRbox Team believes strongly in the benefits of the PaaS version which are outlined here:

Ease of installation. The only thing a User needs to install is a lightweight program called RealVNC Viewer or a ssh client. For a downloadable VM the User must install a hypervisor, such as VirtualBox, install the NMRbox VM, and configure file storage so that it is robust (not always an easy task). Additionally the local VM will share resources with your personal computer.

Security. User files are stored on Enterprise class file servers with significant redundancy and Home folders are backed up regularly.

Performance. NMRbox VMs are housed on dedicated VM servers with 36 compute cores and 256 GB of physical RAM with six 10 GB network cards. The data center housing NMRbox servers has a 100 GB network connection to the outside world and 40 GB network fabric between the switches and redundant 10 GB network connections to the VM hosts and storage.

Cost. The use of NMRbox is FREE, including the computational resources and file storage. No need to have your own high-end computers for NMR data processing.

Portability. With the use of RealVNC Viewer a User can connect and disconnect to their NMRbox account while calculations are on-going and Users can connect from wherever they have a network connection. No need to be tied to a Workstation in the lab.

Easy migration. When a new version of NMRbox is released all that is needed to upgrade is a simple reboot of the our systems.


Answer

There are several answers to this question depending on perspective as described here:

Is the data safe from a mechanical (disk) failure? NMRbox User Home folders are stored on an Enterprise class file server with redundancy to deal with failures of multiple hard drives. In addition, backups of the Users Home folders occur on a regular basis and snapshots of the NMRbox home folders is performed daily. While we have confidence in the file server housing Users Home folders and our backup solution we do encourage Users to copy their important files “off-line” as well. Users can also store their files on /nmr/archive/username. This can be treated as a second home folder and is a private cloud file system with a very high level of redundancy and has data stored in three different physical locations and rivals the protection that Fortune 500 companies use to store their data. The downside of the private cloud file system is that the performance could be somewhat slower than the system where Users Home folders are located, but users should not notice much of a difference.

Is the data safe from other NMRbox users? By default no other NMRbox user has access to your NMRbox Home folder. However, if you change the permissions of your Home folder (something we strongly advise Users not to do) then other NMRbox Users may have access to your files. Likewise, the majority of NMRbox team members do not have access to Users Home folders except the IT professionals that are in charge of maintaining the infrastructure.

Is the data safe from hackers? The NMRbox team takes protecting the NMRbox VMs from hackers seriously and several mechanisms have been put in place to ensure that the NMRbox VMs are protected. However, we cannot guarantee that a breach will not occur. The best protection we can do is to make sure that we have backups of data (which we do) and to encourage Users to not share login information and to use strong passwords (which we are trying to enforce).

Is the data safe from myself? Unlike Windows and OSX, when files are deleted from a terminal they are gone for good and do not end up in a Trash or Recycle Bin. The NMRbox team is creating backups of Users Home folders on a regular basis which may be used to restore data if a User accidentally deletes their files. We have also enabled file system snapshot which will provide a mechanism to restore files that are accidentally deleted. However, these backups and snapshots are designed to recover from catastrophic failures of the system and will require significant effort of the NMRbox team to restore. Thus, the NMRbox team will be happy to help a User who accidentally deletes their files, but the restoration may take a day or two and hopefully should not become a regular occurrence. There is also a limited time that a given backup will be kept before it is over-written (likely 3 days) so it is imperative that you contact the NMRbox team at support@nmrbox.org immediately if you need to restore accidentally deleted files.


Answer

Users can store files in a few different locations each with different reliability and convenience.

Home folder (/home/nmrbox/username) - Of course the most common location to store files is the your home folder, but you also have access to a archive folder as well. Your home folder is located at /home/nmrbox/username and resides on a high performance file server with fault tolerance for failed components such as hard drive failures. As of now the NMRbox team is not implementing a quota on user storage capacity, but we reserve the right to do so in the future if we run low on high performance storage capacity. However, in this case we will not force files to be deleted, but rather migrate files to your "second home folder" on our archive system (see next point for more information). By default users home folders are set so no other user has read access.

Archive folder (/nmr/archive/username) - Each NMRbox user has access to a archive folder which can be better thought of as a second home folder located at /nmr/archive/username on a private cloud run by the University of Connecticut. The private cloud storage system is Geo-dispersed across three physical locations and has extreme fault tolerance due to mechanical failures. The performance may be modestly slower than your home folder on /home/nmrbox/username, but you should not notice too much of a difference between the systems. We are not planning on using a quota system for storage on /nmr/archive/username, but we reserve the right to do so if the amount of storage from a single user becomes too large for us to handle. By default users archive folders are set so no other user has read access.

Public folder (/public) - Users home and archive folders are, by default, set so no other user has read access and we encourage users to leave the default setting as-is. To share files with other NMRbox users, or the NMRbox team for troubleshooting, we have created a /public folder which is writable by all. Feel free to COPY files into /public for sharing. NOTE: The /public folder is designed for sharing and SHOULD NOT be treated as a long term solution for storing files. The NMRbox team reserves the right to remove very old files from /public if needed and no provision for backups on the /public folder have been put in place. We encourage users to COPY their files to /public so that the files still exist in the the users home or archive folder and not to use /public as a "working directory".

Dropbox -