NMR Facility - Chemistry Department

Exciting news!
The long-anticipated upgrade to the 500-2 computer is here!

Main differences

  • Two monitors (see photo)
  • Log in with your “new” username/password (the ones provided as part of reapplication)
  • CentOS 7 operating system
    • Logging in and out is slightly different – see below
    • Operating system is no longer obsolete! Yay!
  • MNova is installed, enabling analysis while conducting intensive experiments
  • Two new “folders” appear on the desktop that facilitate file transfer:
    • “my_files” = a link to your data folder in the file browser
    • “dataXfer” = a link to your home folder on the data transfer computer, nmr15/50
    • With both folders open, you can simply drag your data to dataXfer to move it to the data transfer computer, where you can see it with Filezilla, WinSCP, or other programs. No need to use the command line!
  • New command on nmr15/50: “get500-2“. If you do log in to the data transfer computer with a command line, you can now type “get500-2”, provide your password, and your new data will copy from 500-2 to your current location on nmr15/50.

NOTE: 500-3 and 500-1 will also operate this way (though I don’t think we have enough spare screens to give 500-1 a second monitor)

Practical things you MUST know

Logging in/out

  • The default login screen lists all the users, but you’ll find it easier to click the small “Not listed?” text at the bottom. This gives you a normal text-entry box for your username.
  • When logging out, it is VERY important to click the button in the LOWER LEFT CORNER of your screen. Select “Leave”…then choose “Log Out”.
  • DANGER: There’s a handy-looking “Leave” button in the upper-right corner of the screen. DO NOT CLICK IT!!! It shuts down the computer entirely. I’m investigating how to disable it, but in the meantime, just don’t touch the menu in the upper-right corner.

Accessing dataXfer

  • When using the link “dataXfer” to access nmr15, you’ll probably get a dialog about a “KDE wallet” for storing your login information. The wallet feature isn’t sufficiently enabled, so please just click “cancel” and ignore it. You’ll still get to your folder on nmr15.

Weird one-time warnings and messages

When requesting “ssh” or file transfer access between computers, you may see some strange messages that end in a question that ends in “yes/no”. Go ahead and say “yes”. These messages usually mention something about an “RSA key” or some other security protocol. These systems do that any time you request access from one computer to a specific other computer for the first time. The system then remembers that you said it’s OK, then won’t ask you any more. To enable some of these new features, some of those memories had to be erased. All will be fine if you just respond “yes”.

MNova license activation

The first time you use MNova on 500-2, you’ll need to install the licenses. This is very easy, since they’ve been put in a fairly obvious location in your account directory.

  • Click on the MestReNova icon on your desktop. You’ll get a pop-up message about installing your license.
  • Click “install” – the choice on the left.
  • MNova will give you a file browser so you can find your license file. You’ll see a folder named “mnova_licenses”.
    • Click the “mnova_licences” folder to enter it.
    • Select the only file inside, “licenses.zip”, and click “install”
    • Close Mnova and start it again
  • You should be able to run MNova essentially forever.

New data location

Bruker’s more current setups, like on 400-2, use a new data directory that reduces complexity and typing labor:

  • OLD: /opt/topspin/data/<username>/nmr/<spectra>
  • NEW: /opt/nmrdata/<username>/<spectra>

Your own directory in /opt/nmrdata is your default when setting up new experiments with the START / CREATE DATASET button.

When you type “get500-2” on nmr15/50, it executes a command that looks for new data in your /opt/nmrdata/<username> directory.

Previous data

All data collected prior to this upgrade (before August 4, 2020) are still available in /opt/topspin/data/<username>. This is a little tricky since the new system is on a new hard drive, and the old data are on the old hard drive, but a linux symbolic link makes the magic happen.

Who has access?

Today, August 5, 2020, all users who had reapplied by July 1 have active accounts on 500-2 if they were trained in manual operation. A small number of people have reapplied since then, and they will be activated shortly. The recent NMR census identified a number of people who should be returning to lab soon, and accounts for them will be set up in anticipation of their reapplication; they will just not get their new passwords until they reapply.

New working modes

The addition of the second monitor affords some new ways of working.

  • Consider maximizing your Topspin window in the left-hand monitor.
  • In the right-hand monitor, you can place:
    • The lock window and BSMS control panel (the one with all the lock and shim buttons). This way, you can see it more easily, and it will be out of the way.
    • MNova. When performing, for example, reaction monitoring or multiple 2D experiments, you can process and analyze data using Mnova in the right-hand monitor while keeping an eye on data collection on the left.
    • Bruker’s PDF experiment guides, which provide handy step-by-step instructions on how to perform various experiments like 1D NOE and DOSY. (I’ll add these files to everyone’s desktops soon.)
    • A Terminal window (Konsole) or file browser (Dolphin. Don’t ask me why the linux people call it “Dolphin” instead of “File Browser”).

The need for the upgrade

Why was an operating system upgrade necessary? Why did it take so long to implement?

First, know that the previous OS was CentOS 5, and it had two big problems. First, it was obsolete. The last time a software update was provided for CentOS 5 was March 31, 2017. Second, there is a well-known security hole in CentOS 5, and it will never be fixed; it was discovered after RedHat (the creator of RedHat and CentOS Linux) declared it would no longer update or fix that version, so they left it alone. Our systems should have been upgraded earlier, but upgrading Linux systems is difficult, rendering it hard to make the move.

Second, CentOS/Linux systems cannot be simply “upgraded” like PCs or Macs. Once needs to start with a fresh, blank hard drive with no operating system, no software, no file system, no nothing. The system has to be created and configured from scratch, including every user account. Fortunately our helpful Bruker support engineer Peter Demou provided a disk image I used to install the correctly-configured CentOS 7 with Topspin. But Bruker does not provide any means for migrating existing user accounts to a new computer. This must be done with either an extremely labor-intensive process or by using a set of custom-made scripts, development of which is also extremely labor-intensive.

Third, identifying the user accounts that needed to be re-created took a fair amount of effort. Historically, user accounts on the facility computers (nine of them), were managed in some coordination with one another, but there were many conflicts between systems. Old systems like the old 400-2 had almost 600 active user accounts, some of which dated back to 2003, but new systems like 400-1 had fewer accounts. Most active users had accounts on all systems, but not everyone did. Many data folders had been kept, copied from one computer to another, though they were more tan 15 years old and had no clear owner. So determining who needed a new account was rather a headache.

Fourth, there have been difficulties at the admin level in managing the Linux account and group identifiers. Ideally, each research group would have one group ID number that would be used on all computers. But here that was only true from most groups. Some were unrepresented on some computers. Others were present on all system, but used different identifying numbers on one or two instruments. Our system was in desperate need of harmonization so we could move forward with a new holistic management scheme.

After months of analyzing user accounts, assisted by the reapplication process and the NMR census of active users, a map was developed that described a trajectory for each user’s and group’s old information to new information. This set of new user information was fed to a series of scripts in the GCIS lab to create new accounts on 400-2. 500-2 needed a somewhat different set of scripts and information, but that was developed and it was implemented in mid-July.

Though the new computer was working with new accounts, and could run the spectrometer, that system configuration was not released to users right away. If it had been, there would be no easy way to get data from the spectrometer to users’ laptops. The data transfer computer, nmr15, thus needed to be fixed, too, making adjustments and additions to all the user accounts via a new set of scripts.

Bright new holistic future

The successful upgrade of 500-2 will soon be replicated on 500-3, then 500-1, then the offline data processing computers (for whenever we’ll be able to use them again). When done, we’ll have a facility featuring:

  • The same operating system, CentOS 7, on every facility computer.
  • The same version of Topspin, TS3.6.2, running on every spectrometer and data processing computer.
  • MNova on every 500 and data processing computer.
  • Every trained user will have an account on every spectrometer and data processing computer.
    • Users with only Level1 training will have placeholder accounts with admin-only passwords on the 500s. Once they pass Level2 training, their passwords will be changed so they can access all the 500s.
  • Simplified data access

A primary aim of this scheme is creating an environment where every user accesses the instrument that best suits their needs, not just the one they are accustomed to because of the software interface. For example,

  • If 400-1 is backlogged, you can go to 400-2 and operate it easily.
  • If you need a long 13C 1D experiment, you’ll be comfortable using 500-2, even if you work in GCIS.
  • If you need extra 1H sensitivity and spectral dispersion, like with a DOSY or polymer sample, you’ll feel comfortable using 500-3. (there are plan for switching in a different probe that has better 1H sensitivity)

Now that the user and group databases have been created, and the scripts have been succesfully developed and used, we should expect completion of the transformation in the next few weeks.

Enjoy the new 500-2!