Sunday, August 31, 2008


Nowadays it is common to categorize goods and services, like website hosting for example, under the labels of "recognized leaders" and "low cost alternatives". In our field of NMR software, where every product does its best (and its worst too) to differentiate itself from the rest, any form of categorization is arduous. For a certain period, it was true that some products were updated irregularly, and they could be inscribed into a "low cost" category. The release of Jeol Delta as freeware seemed to break the barrier once and forever. It was a major name, it was the same program used to drive the spectrometers, and it came for free. The public, or at least most of it, ignored Delta, for a reason. It is too much different from what most of us have been used to, difficult to use and impossible to learn. The reaction of public has demonstrated that neither the brand nor the free availability are a guarantee of success.
There are no recipes, there is no known road to success (with the latter word I am only meaning the fulfillment of the desires of the public). Consider that the choice of a program is often a collective choice (a fight?). They don't like having more than one program into the same lab, or even department. It seems to be a font of confusion to use more than a single program. In some cases the members feels reassured if they are using the same program that is endorsed by the recognized expert of the department. In other cases, they just don't think that this can be an issue, because a program is already in use, and who cares if it's good or bad, science must go on.
In theory, the user should not find the most convenient program in general, but the one that was written specifically for him/her. For example, TopSpin was written for the loyal Bruker customers who required the persistence of the old UXNMR command line commands. NMRPipe was written to process multidimensional spectra of bio-polymers. In practice, however, many people prefer TopSpin over NMRPipe to process this kind of spectra. In summary, there are four factors to evaluate:
  1. the original purpose of the program
  2. the other (unexpected) virtues of it
  3. the affordability
  4. the local consensus.
I know nothing about the consensus around you, I can attempt to guess what the initial purpose of each product was.
SpinWorks wanted to solve with a single product both the daily and advanced tasks of a chemistry lab, in other words 1D processing and 1D simulations. NP-NMR, as the name says, is dedicated to natural products. Nuts and NMRnotebook are the ones that really wanted to be "low cost", although my list "today's prices" tells another story. Nuts also has a fondness for the command line, while the notebook has the opposite fondness for automatic processing. The ACD collection has been written with the large pharmaceutical companies in mind. Mnova claims to be everybody's choice, but it also has the not-so-secret ambition to substitute ACD where possible. iNMR has been written for the scientist who needs to observe the spectra on the monitor, while iNMR reader is the product for those who only need to print the spectrum (or PDF it).
The third incarnation of iNMR reader, released last week, is another program that breaks the preconceived ideas about "low-cost" software. To start with, it never belonged to this category, but to the "ultra-low-cost" instead. To continue with, version 3, just because it incorporates the same engine of iNMR 3, is the fastest NMR program in circulation. The fact that speed is important is confirmed, for example, by Bruker. I have a leaflet that says:
The Fastest Spectrometer Ever
Avance(TM) III
The new and enhanced Avance III NMR spectrometer architecture yields the fastest[...]

Now consider that iNMR reader is not just a little bit faster than the software of the Avance; it is a whole lot faster (you need no chronograph to tell which is the winner...).
If speed is not important in your case, it still means many things that you would care about. When a program is so markedly faster than the average, it means that the authors:
  1. Have a deep understanding of the organization of NMR data
  2. Have a deep understanding of the computer and the operative system
  3. Have written fresh new code to solve the old tasks

What does the last consideration imply? That when you buy a "new" program, normally half of its components are made of old (and stale?) code! That's what the speed, or the slowness, can tell.
To finish with, a completely new feature of iNMR reader 3 is automatic phase correction of 2D spectra. This is something I have never written about in my blog, despite the many pages dedicated to its 1-D counterpart. I promise to dedicate an whole article ASAP. For now I can say that the algorithm of iNMR, though unpublished and unknown, really works, at least for those I call "good-looking spectra". With this expression I mean: spectra with a tolerable amount of noise and where all the peaks can be put, simultaneously, in pure absorption.

Friday, August 29, 2008

Today's Prices

If you have no idea how much is a program for NMR, this list is for you. In one of my next articles I will explain that, in this field, there is little relation between the price and the quality.
Discovering the price of the other programs can't be easier. Just contact their sales representatives.

Friday, August 15, 2008


When I wrote my last post, I hadn't tried iNMR 3 on a new computer yet. While the performance on 6-years old machines is praiseworthy for all kinds of reasons, I can't believe my eyes when iNMR 3 runs on a modern machine. 2D processing is almost instantaneous, up to the point that I am asking myself: "Where is the trick?".
iNMR 3 is still under development. The beta version is publicly available and is highly stable, certainly usable for all purposes. A dedicated page on the web is packed with detailed info. Don't panic, there's nothing technical, everything is extremely readable.What else can be said? It's the fastest NMR application I have ever seen, and I am convinced it will remain the no. 1 for a long time. Do you know anything faster?

Thursday, August 07, 2008

My Olympic Record

I like sports, I like the olympic games, but I don't care at all about records. The competition and the gestures make the show, the records mainly remind me of Ben Johnson, doping, etc..
I like speed and the speed of computers can thrill me. It's a safe case of speed, with no doping, no danger for the health. We are rarely allowed to appreciate the real speed of our computers, because most of their potential is wasted or not exploited. When surfing the internet, I can hear the fan of my computer reaching new records of decibels. It's my CPU that is employed for a Java animation into a background window: the perfect waste! Other times, it's Acrobat Reader that activates the fan. I don't know what it's doing. I know that Acrobat Reader is an application that does a single thing, and takes 100 Mb of my hard disc for doing that single thing. I understand it wastes disc space, CPU cycles and quite likely my RAM too.
The best way to appreciate the real speed of your computer is to write a program by yourself. When I wrote the first version of iNMR, I optimized it for a CPU called PowerPC G3. It was a CPU I knew quite well. When I had only written the first few lines of code, I switched to a new computer, equipped with a G5 CPU (it's the machine I am using at this moment). I continued writing the code in the way I was used to, optimized for the old G3. When iNMR became public, everybody appreciated its speed. I knew, however, that it could have been much faster. With version 2, I substituted the FFT routine. The new one, optimized for the G4, was nearly twice as fast. Great! I knew, however, that there was another lot of room to grow. During the last couple of weeks I have been working at a new engine, that will be the heart of version 3, still optimized for the G4. The reason to exist of this new engine is that the current version of iNMR requires an amount of RAM that's the double of the size of the spectrum on the foreground. It makes the program faster, but can be a problem when the foreground spectrum is a bulky 3D.
The new engine requires much less memory. I have also worked to make it as fast as possible, without compromises. I have completely changed the order in which data points are stored and even the sign conventions. The user interface bears no trace of this revolution. The program, externally, looks exactly the same. But it's more than 3 times as fast as version 1. Gauging this performance I am not taking into account all the possible operations, but only the most frequently used ones (FFT, zero-filling, transposition, weighting, ecc.. in other words the standard flow of operations). 3 times is the global average. Some 2D drawing routines are also moderately faster. Phase correction has remained the same, I don't know how to make it faster. Simulation of spin systems can also be faster, but I haven't optimized it yet.
It's not easy for the casual user to verify this speed bump, because the existing versions are already so fast that many spectra are processed instantly. To see the difference you have to choose a large phase-sensitive 2D example.
In summary, using the same computer and OS, the new code runs more than 3 times faster. I have written this ultra-optimized code in August 2008 but since 2005 I already had all the ingredients and tools to make it. Why didn't I? I would have saved a lot of time and the customers would have saved a little of money. Let's address the last point first. They are not forced to upgrade, because version 2 is fast more than enough. Now, let me find an excuse for myself. I haven't got the perfect recipe to make a program faster. What I do is to substitute a piece of the program and measure the time taken by the modified version to process a spectrum. If the time has been reduced, I retain the change and go on changing another line. As you can see, this kind of optimization can only be done after the program is complete. There is also another explanation: number-crunching is only one if the many things that a program must do (and that a programmer should optimize). The main reason for writing this new engine was a different one. As I have said, there was the need for something less memory-hungry. It's only after years of experience that you can rank priorities like these.
Version 3 will become available in January, after a prolonged period of testing. If you have an old computer with a G4 CPU, don't throw it away: it will become 3 times faster!!!