Switching from windows to mac for research

I have switched my productive research computer from PC to Mac about one month ago.
My old dell latitude D630 was outdated and needed a replacement.
Having been influenced by the impressions during my stay as a visiting scientist at Caltech last summer, I decided to finally switch over to apple for my productive working environment when the new macs would be released in July 2012. I had already been impressed by the manufacturing and engineering quality of apple for a while and honestly, I was not by the quality of dell. The price of the systems to chose from were in the same range. However, there was one reason which had influenced me before. Here in Germany, I don’t know many people, doing research on a mac. Most of the systems run on windows, some people also work on linux. Therefore I was not really sure wether the necessary standard programs were available and if they were, possible to use easily without relearning, productively and quickly.

It took me a while to figure everything out and to find what works well and how and what does not. After about one month of using my new MacBook Pro 13“ Core i7 I can preliminarily conclude that I am generally quite happy. I must mention, I am not using the computer in the lab. There I am still using our standard windows PCs with the usual mess of proprietary and open drivers of a multitude of scientific hardware mixed and VisualBasic, Labview etc. installed. I have also no plans to switch these systems to Mac. Never touch a running system, might be true for this case, or perhaps I am just not curageous enough yet to try this as well, as I have already made the experience how difficult it can be to get all drivers and lab hardware running after a windows version update.

I got the MacBook Pro just when it was released. Therefore it initially came with Mac OS X Lion preinstalled but with a free upgrade to Mountain Lion which was available soon after I got it and which I therefore installed effectively immediately.[important] Due to this, the notes refer to my experience with Mac OS X Mountain Lion (10.8), the currently newest version. I mention features and programs in decending order of perceived importance. My aim is to give you a user’s impression and provide some useful workarounds and software tips in case you are in the same situation, considering switching from PC to Mac. May my findings save you time.[/important]

Included Mac OS X Features with Research Relevance

  • TimeMachine: I like it a lot. I have been using the backup features of MS Windows 7, which I had been missing in earlier windows versions. In research, backups are very important, most importantly to provide good archiving for documentation of my research. Windows 7 has not done a bad job, but TimeMachine is unbeaten. It works in the background and hardly ever shows itself, taking a full snapshot of everything I work on every hour. With Mac OS X Mountain Lion now it even supports more than one backup drive. Unfortunately, it does not work well with other drive formats than the mac format HFS+ and it does not natively support NAS, unless you buy a proprietary Apple TimeCapsule, although there are workarounds. The workarounds do not seem very convincing to me. The whole backup system bases on the journaled file system approach of HFS+ with its advantages and disadvantages. 
    Summarizing, now I feel much more secure: I always have an up-to-date backup in my office, wherever I take the laptop. And as Apple finally integrated USB 3.0 into the current lineup of MacBook Pros helps a lot. It makes large backups really fast.
  • Very short boot-times. More exactly, I hardly ever restart my mac, I just send it to sleep and wake it up again, both of which only takes a few seconds. I always had to switch my old windows PC completely off and this took more than a minute. If I did not, it simply refused restart often enough, if it did not, it took much longer. Now, when I open the lid of the mac, it is on nearly instantly, with a typical delay time of just a few seconds, even with matlab, office and some finders open. And I do not have a mac with SSD, just a standard hard disk. It is true, I do not restart often, but it is worth mentioning, that when I do, there is an annoying sound from the optical disk drive every time. I cannot understand this design bug. If it were my choice, I had skipped the optical disk drive alltogether anyway. I hardly ever need it for a long time already. 
  • The Mac finder is quite different than the windows explorer. It took me a while to get acquainted. Now I got used to some of its nice features, partifularly its sliding panes and integrated preview. I ended up missing some mac features on windows computers and some windows features on mac computers.
  • The Mac gestures: Simply great. I liked gestures on my smart phone for a while. I think they make things really easy. The nice multitouch glass trackpad together with the very nice keyboard are really nice to use. For heavy number work, I am quite happy to have an external keyboard as well with an extra number block.
  • Multiple desktops, called „spaces“ on Mac OS X save me a lot of time searching, closing, opening, minimizing and maximizing windows all the time. I use this feature a lot and I already liked it on linux, but Mac brings it to a new level. I really miss this feature on windows. The multiple desktops come in particularly useful when I am working on one or more remote machines via remote desktop in parallel. The other desktop is just one swipe with four fingers away and all my windows stay where they were.
  • The Mac preview function is really great. I do not like Adobe Acrobat. This always was one of the most laggy programs on my PC and it always had this terrible background process started which should speed it up. I hate programs which do not work as expected. Now I also have Acrobat Pro for Mac installed, but I hardly ever need it unless I need very fancy functions. Just for viewing PDFs, images or other stuff, I rely on the Mac OS X integrated preview viewer and it works great, including multitouch gestures, zooming, very good rendering, until a number of about 10 open documents with a reasonable size of below or about 50 pages.
  • Remote network drives (NAS): It was astonishing for me. When I tried to mount our institute’s network storage drives, I found out that older ones, based on the industry standard SMB protocol, simply did not connect. There seems to be a workaround, which in my case does not work reliably and is a bit cluttered. New drives, supporting newer versions of the protocol work with mac flawlessly.
  • NTFS, the standard windows file system, is not supported by Mac OS X for writing. I have found a workaround, which is depreciated by apple themselves and a few extra programs, which promise to solve the problem. But honestly, for a file system I do not want to fiddle around with third party programs. On the other hand, HFS+ from apple is of course not supported natively by windows. Also there seem to be a few workarounds, but you cannot ever expect a windows user to adapt to a mac file system only for you. I now had to reformat my bigger external drives, which I want to be still able to read with a windows computer to the relatively new exFAT, which seems to work quite well up to now, but of course it was some extra work.
  • Printers and peripherals: I was positively astonished how nicely mac works with the network printers. All the driver-stuff, which I was used to from windows, is just gone. The only thing I did not find, was a mac replacement for a driver which allows us to use the workgroup’s lexmark printer / copier as a remote network scanner. I think I won’t miss that functionality anyway, as I have found out the lexmark software to be unstable on windows and as the printer also supports scanning to email.
  • It is nice that Mac OS X has a good pocket calculator app. I mentioned that I got used to using matlab for nearly everything. Maybe this is not entirely true. The calculator is at least as good as the eventually released calculator in windows 7, after the previous versions have been more toys than applicable for science. Now, the Mac OS X Mountain Lion calculator even allows for very fast and simple unit conversions, which are, remark, sorted by type, physically correctly. Nice work. Additionally there seem to be a bunch of apps on the Mac OS X app store, which I have not yet tried.

Licensed and Open Source Programs for Research on the Mac

  • Matlab looks nearly as it looks on windows. It runs nicely, also with the multithreading support etc. You can install the linux installation of matlab on a Mac. I use it all the time, even for replacing my pocket calculator and for programming, as I did on windows.
    However, I realized that different than on Mac OS X Lion, in Mountain Lion the Java runtime is not included any more. You have to download it from Oracle manually and install it before you install matlab. Like on windows, Matlab for Mac is based on Java for all high-level functions.
    Also in my case, it was necessary to download and install XQuartz (2.7.2), which seems as it was also included in Mac OS X Lion and has been dropped for Mountain Lion. It provides the necessary interface environment.
  • Gwyddion is a good, platform independent program to analyze AFM scan data. I also use it to analyze NSOM data and other scanning microscopy measurement data. It turned out that my version which I had installed under Mac OS X Lion did not run any more on Mountain Lion. It simply did not give me any error message. After some searching, I found that after installing X11, it started again. Same problem as with Matlab, as it seems. To install it, I decided to install MacPorts, a project which ports Linux programs to Mac, as it is described on the Gwyddion website.
  • Virtual Private Network: We have an enterprise VPN, based on OpenVPN and I use it to access papers and to work via remote desktop. As a side effect it also allows for a secure connection whenever I am out of the institute walls. I recommend you the free open-source client „Tunnelblick„. It works great. A nice, reliable, unobtrusive program, residing as a small icon in the Mac status bar, showing its status by color, details by hovering and connects me with one click to a selection of adjustable VPNs. It seems that for Mountain Lion you must use the latest beta.
  • MS Office for Mac 2011 speaks for itself. Microsoft is our standard working environment, including word, excel, powerpoint and in my case also outlook. Things look a bit different. The basic functionality is quite similar. However, I have switched from MS Office 2010 on Windows 7. The two most important differences which I would consider relevant are in this case, powerpoint has lost its abilities, which it has newly gained on windows Office 2010, to include nice formulas into a presentation. I was quite happy about this addition. The bad thing is, even opening a presentation with such formulas in Office 2011 on Mac leads not even to image-like presentation, but to a completely wrong display. Also embedded videos do not work as expected. Trying to play them leads to the download of some obscure software stuff and I have not yet followed up, but for such things I now simply turn on Office 2010 on a virtual Windows 7 on parallels. Another thing which is quite strange is, MS Outlook 2011 for Mac seems not to support the good old way MS Outlook 2010 and earlier versions on Windows saved data in PST files. I have not yet fully decided how to work around this efficiently. I rely a lot on Outlook and the nice exchange server integration, including calendars, email, tasks etc. and I have not yet been convinced to switch to any of the alternative products, also being influenced by our institute providing an exchange server infrastructure. 
    Unfortunately I found out that if a program has crashed on my mac, there is a very high probability that it is from the MS Office suite and probably it is even the microsoft „crash handler“, which in my case, sometimes consumes 100%+ CPU resources, leading to running cooling fans. 
  • Remote Desktop which I use extensively to log into remote windows servers/workstations in our institute for large numeric calculations and some administrative tasks. The virtual desktop environment which comes with MS Office for Mac comes in quite handy and solves my demands well. I had also been recommended the open source virtual desktop app Cordt, but I hardly ever use it.
  • Git is a distributed version control system. I use it quite extensively to manage my self-written code in matlab and some other stuff. I found that after the update from Lion to Mountain Lion it stopped working, when I called it from the command line.
    The reason lies at the Mac programming environment XCode, which is available via the OS X integrated app store or on the apple websites for free. However, I had to apply a device connectivity update to XCode and then manually tell it to redownload and install the command line tools by opening XCode -> Preferences -> Downloads and select install command line tools. Alternatively, of course, you can directly download only git from the git websites. I also found a very nice git interface from the makers of bitbucket, SourceTree and another one, GitX. I am currently trying both but I have not yet decided which one I prefer. I like a clean and quick graphical overview  over a pure command line environment.
  • Parallels with Windows 7 First I had installed a bootcamp dual boot windows installation, which I mounted into a virtual parallels machine. But I soon realized that I never used it as a bootcamp OS and that I had to reinstall the windows anyway because I underestimated the huge amounts of space for the installed programs only. Therefore I now have a purely virtual Windows 7 installation running on parallels. Of course it runs not quite as smoothly as real apps in the native OS, but it works well enough for just a few programs which I still cannot use on mac natively. The nice thing is, it offers a mode where you can simply open single windows windows and mix them with your mac windows. It also mounts your mac own documents folders into the virtual windows, including read and write support from windows programs. This makes it really useful for me for those windows programs which I still need.
  • Adobe products just work. It seems to me, they are made more for mac than for windows.
  • Corel Draw has been our institute standard. This program package is even completely free to students here, which I think is a good markeding decision. Unfortunatel it is also a pity as I found out that I would be really happy to be able to work as well with Adobe Illustrator as I can work with all shortcuts and tricks with Corel Draw. Now, that there is no Corel Draw for Mac OS X, I am trying to convert completely to Adobe Illustrator for vector graphics, graph postprocessing, poster design and all little graphics tasks and to Adobe Photoshop for pixelstuff. However, it has proven to be quite complicated to convert CorelDraw files (.cdr) to Adobe Illustrator. Both programs pretend to be able to speak each others language, but when it comes to real conversion of e.g. a scientific poster, all texts end up shreddered and verctor graphics internally mixed up. This makes a mixed environment difficult. I am sure, it is partly intended by both, Adobe and Corel. Therefore now I had to decide to keep a backup version of CorelDraw installed on my virtual windows. There are just too many complex CorelDraw documents which I have one made and it is too unreliable to convert them automatically.
  • Mendeley works well on Mac. I have been using it to sort and keep track my local library of papers for several years now and I really like it. However, the integration into MS Word 2011 on Mac is by far not as good as on Windows with Word 2010.
    You have to search for the mendeley functions in a script menu. Then, whatever you change, it always parses through the document incredibly slowly. This disturbs productive working quite a bit! It feels a bit like compiling a LaTeX document, but in word. As soon as you have a lot of citations in a document (about 10 at least) it feels very laggy. Also, with the transition, I remembered a big disadvantage of Mendeley again, which always came into my mind when I had to move my library to a new computer. In principle, mendeley just installs and pulls your library from their server. 
    However, in reality, I have a big number of papers saved as PDFs, organized by mendeley on my disk. It is too much to upload within the free account space, offered by mendeley. Usually this is no problem at all. I do not need my PDFs to be all hosted in the cloud. But when I move, it is really difficult to get all the PDFs synced and integrated in the library again.
    I had to reimport the PDFs and after that I had to re-eliminate all duplicates, which for several hundreds of them is definitely no fun.
    I still hope, Mendeley will integrate a function to simply move local PDF libraries soon.
    Another fact which I had to realize is, that mendeley on my Mac feels like one of the more crash-prone apps. Perhaps it simply attacts more attention, not being hidden between loads of windows junkware, crashing over and over again. But I already had to cancel the program forcibly via the mac task manager.
    Also, before, while I was on windows, I was locked out from mekentosj’s Papers, which, as far as I know, is even older than Mendeley, but only exists for Mac OS X. Now, I would have the chance to try it. It always seemed very tempting on their website. I am now already fully in Mendeley and CiteuLike, but still, trying would be nice. Currently, I am hold back by the fact that Papers costs a more than neglectable amount of money.
  • LaTeX is essential for my work. Of course there is a package for Mac, which turned out to be very easy to install as the quite large, but concise package MacTex, which bases on TeXLive. But the important thing about LaTeX is the editor you chose to use as it is the piece of software you interact with most of the time. On windows I am a big fan of the nice editor WinEdt. The name already says it. It is a pure windows program. Therefore I had to search for something new for Mac. Some people told me, I should try TextMate. The software looks quite OK. I think, I will have to get used to it. I actually found out this one has now recently even been released as a OpenSource software on GitHub. This is a nice step by the developer. However, I ended up not being able to compile the program properly and the downloaded binary I got started and worked but gave me some strange error messages whenever I tried to compile a LaTeX document. It seems, as I do not find help via google for this problem, I am possibly the only one experiencing this problem. It might work well for you. I have to find a workaround when I have a bit more time than now. Currently I am simply too busy to care for stuff as peripheral as this. I also found a big fan community of an editor named SublimeTeX. However, in principle there is a reason why I do simply not like working with eMacs e.g. SublimeTeX looks much less Mac-like. I testwise installed it, but did not really dive into its specific strengths.
  • Lumerical FDTD solutions is a nice commercial FDTD solver package for Maxwell’s equations/optics, which I use a lot. It works out of the box on my mac. Nice work.
  • Keka is an open-source program to compress and decompress files. On windows I am always using 7zip, which does not exist for mac. There seem to be some 7zip-surrogatives, but they did not look as appealing as keka. Keka supports all standard compression formats, including .zip, .rar and .tar.gz, .7zip, .gzip, .bzip but it also supports .iso and the mac image format .dmg. It is simple, unobtrusive, seems to be relatively fast and for me has never crashed yet. It just does its job, extracting with a double click on any archive and archives when a file is dragged on the program icon.
  • Some other stuff I use, VLC player, Firefox and Chrome, Skype just work out of the box as expected. 

[notice]This list is for sure not complete and concise. I just wrote my first impressions and tips down for others to use. I might update the article at a later time, when I am a bit less busy than now.[/notice]