New Research Lab and Resources

I have a new research lab! As space has tightened requiring the repurposing of previous spaces, my former lab which had plumbing and the requisite safety shower and eye-wash is being taken over by one of my colleagues – it is now being renovated to install a sink, bench space, and other things you would need in a wet lab. As a computational chemist, all I need is power and ports for my workstations. So I’ve moved into a new space that does not have the plumbing lines. Renovations started in late June and were completed last week!

On Thursday, with the help of colleagues, we moved in furniture and a number of workstations and a local Linux server. By the end of the day we had the server and four client machines up and running, which is sufficient to get my research students started. Classes start this coming week, and my students are returning this weekend. Besides returning research students, I have one new student joining my lab who is coming in bright and early on Monday morning at 8am to start learning the ropes!

As with any move, there are always a few hitches. The server has some sort of display problem – it boots up fine, and then at some point in the process the screen goes blank on the attached monitor. Also one of the hard drives on the server failed, but because I have RAID, everything still runs fine. I will need to replace the hard drive otherwise another failure could cause some problems. Some of the new ports were inactive, which was a bit annoying because we had to plug into each one to check those that can be used. The very helpful IT person is working with the networking and telecom folks to make sure all those get activated.

On Friday I was able to set up an account for my new student on three different systems. Besides the local server and clients in my lab, I have access to two other computational clusters located in a server room in a different building. The local machines are mainly terminals for my students to work although it does have one useful piece of software (Spartan) for students to build molecules. It is very user-friendly and we also use it throughout the curriculum starting from the very first semester of college chemistry. Students need a molecular perspective! (We have exercises that utilize molecular modeling on the computer, but students also construct hand-held molecules with kits.)

The two other clusters are the main workhorse programs. Students connect (ssh) to them for production runs. One of the clusters was first built when I started my tenure track position. I started with a server and four nodes, and over the years added more nodes (1U servers into a rack mount), and maybe six years ago I got a new server with more disk space. It’s not fancy, but it was economical and gets the job done. For the newer cluster started I partnered with the IT department – we pooled funds to start a blade server system. The plan is for this to be a university-wide resource where we the users pool our resources. That system came up in January, and we will be doubling our hardware resources this upcoming semester.

So the other thing I had to do on Friday was update the training materials for my new student who is starting on Monday. Most things are the same – we start with a Unix tutorial, followed by learning a text editor (vi), and then move on to using the specific computational software. However, the job submission process for the two clusters is different. On my older cluster, exclusively used by my group (and paid for by my grants), we don’t have a queueing system. Everyone gets in the habit of checking the load across the nodes, and not submitting more jobs then there are processors on a single node. The new one uses Torque/Moab so students will have to get used to that too. (I have job submission scripts written.) The other thing a new student finds confusing is keeping track of where they are now that they have three accounts (rather than two), one for each cluster system, including the local one in the lab.

Anyway, I’m excited for the new semester research-wise. I’m in the midst of writing an NSF RUI proposal, although I still have funding on another award through the end of 2017. For me, proposal writing starts off as a drag, and then after a few days I get excited about the new things I’m proposing. I’m not sure why it’s a drag when I start off. Probably because I don’t write them often enough (a side-benefit of not needing as many resources and having landed almost all the grants I’ve submitted, fingers crossed for this next one!) so it feels a bit “unproductive” because I’m not churning out results. Then again, I get a similar feeling when writing papers, which I do much more often than grants, so maybe it’s a productivity thing. Or maybe there’s a secret fear of being “judged” by one’s peers. (I certainly don’t feel a conscious fear.) Or maybe it’s because I’m not working directly with the students when I’m writing. Or maybe because I’m not a good writer. Well, part of starting this blog was to try and improve. We’ll see if that works!