Windows 7 on Michael’s Domain

Updating GE's Äkta Avant to Windows 10

Tue, 18 Feb 2020 00:00:00 +0000

The Avant is the flagship of GE Healthcare’s Äkta line of FPLC (fast protein liquid chromatography) devices. We use it on a regular basis and it is available to everybody from the University of Helsinki.Our University decided to play nice with Microsoft and to disallow all network traffic for Windows 7 computers. Because our Äkta (bought in 2015) is in use by many different researchers, we rely on Microsoft’s Active Directory to authenticate users and to track the device usage. When the University really did shut down Windows 7 traffic in late January, we finally updated the HP computer from Windows 7 to Windows 10 . Before we did that we contacted GE in order to be sure to have a working FPLC. Although the build number of Win10, that our University is using (Windows 10 Enterprise version 1809, build 17763.1039) was not supported by any of the Unicorn 7 versions that GE has released over the years (see this software compatibility chart, which I cannot find anymore from the GE website: https://drive.google.com/open?id=1cA33lEqfEr0MIaA8r9TyoQFcxiHWuZsp) , we were assured that the software would continue working. Unfortunately, this was not true.**In-place upgrade or clean install?**We performed an upgrade of Win7 to Win10 in place. I never liked these. Even on slightly superior operating systems like macOS and Linux , the in-place upgrades have not always been smooth. A fresh start has always been the safer (and also faster) bet.Connection problemsAfter the upgrade, Unicorn 7 started to lose the connection to the Äkta Avant during ongoing protein purification runs. We clearly could see during manual runs, that specific commands would trigger a disconnect. The Äkta LCD display would black out and the device would reboot. Naturally, we suspected that this was a consequence of the upgrade to Windows 10. Because Unicorn 7.0.2 had not been tested to work with our version of Windows 10, we first wanted to try to upgrade to a Unicorn 7 version that had been tested with our Win10 build. I had already asked in December for that update from GE, but my request had been ignored and I had many other things to do at the time and never bothered to come back to the issue (in hindsight a big mistake).Software updatesSomething that Chrome and Firefox do weekly silently in the background (without the user noticing) takes in the case of GE almost 2 weeks full-time engagement by the user. A simple download might work for Bio-Rad , but GE requires a complicated, obfuscated, non-transparent, user-unfriendly, constantly changing, GDPR-non-compliant syastem, which is in addition hosted on servers that feel so slow that you constantly wonder whether your browser tab has frozen. What it’s worth, GE’s web pages have always been like this despite multiple redesigns and GE’s digital transformation. The email thread between me and various GE support addresses comprises as of today 60 emails (starting with my first support request on December 2nd, 2019). On top of this, there are also quite a few phone calls (since email seems to be often regarded as “non-urgent” by default).Privacy concerns about GE’s handling of customer dataAfter placing an order for the download, receiving a quotation, confirming the order and receiving an order confirmation, I finally received the “permission” to download the newest version of Unicorn (which is 7.5). I logged into GE’s “eDeliveryPortal” only to realize that I could see the software entitlements and downloads for many other GE customers, but none of my own. After some back-and-forth the 7.5 version finally showed up under my downloads. My license is still missing as of today. But why bother? I could use any of the other licenses (after faking the MAC address of my computer as the software apparently is locked to specific computer via the computer’s network card’s MAC address). This is clearly a violation of the GDPR as there is absolutely no reason why my data (entitlement ids, MAC addresses, Names, e-mail addresses) should be available to other customers. It might be that GE considers the University of Helsinki as a single customer; that would be a violation of the GDPR by design.**Searching for the system configuration files (i.e. firmware)**However, we had not updated the system configuration files, because I had not been able to find them from the GE LifeScience website . We were running version 3, while version 3.6 was the newest one. Notably, these files do also contain the firmware for the individual Äkta components. It appears that this download is nicely hidden. I needed help from GE in order to locate it. The GE life science website has a search function and the search even finds the download. However, it is perhaps the last item in a list of nearly 1000 hits (10 hits/page). One tip to GE: Google knows search! If you just would let Google index your complete web site, customers would find everything via a Google search. Many companies are using Google for their internal web site search. However, GE seems to expose only their product pages to search engine crawlers, but not their support pages.**Where are our licensing files?**After updating the instrument configuration, the problem persisted. After sending a system report (and then sending a second “extended” system report), GE concluded that most likely our in-place upgrade from Win7 to Win10 was to blame, because they could see some irregularities in the SystemEventLog.xml file. I had no reason to doubt this explanation and therefore requested a clean Windows 10 install from our IT guys. I then installed Unicorn 7.5 only to see that the problem had not disappeared. Just as a side note: We had a self-inflicted issue with our license file (.lic). The Unicorn installer software requests the installation of a license file, which I have never seen for download anywhere in the eDelivery portal (we have received these license files as attachments to e-mails directly from GE support staff, why are they not available for download as these are prone to be lost?). We should have made a copy of our license file before we erased our computer for the clean Win 10 install, but we missed that and I had to dig out the license file from a system backup, which I had luckily made in 2016 from the machine. And I am still searching for our license files for different system components (Classic Evaluation and Column Handling), which were not yet installed when I did the system backup.Down-grading to Windows 7In order to be sure that we did not deal with a hardware failure, we decided to downgrade the system back to Windows 7 and Unicorn 7.0.2. That was more difficult than expected, because we cannot anymore install Windows 7 on university machines. Luckily we had still one old, unused Dell desktop, that was runninig Windows 7. Unicorn 7 requires two network cards (one to communicate with the outside world and one for a separate 10. network to communicate with the Äkta Avant). We swapped the network interface card from our default computer to this old Win 7 machine. However, installing and running Unicorn requires access to the internet because the software is “phoning home”. Exactly that is disallowed for Win7 machines at our university. Hence I needed to set up a private network via my phone to allow Unicorn 7 to communicate with GE headquarters. Even worse, I needed to clone the MAC address of our default computer, because our Unicorn 7 software is apparently locked to a specific computer via the computer’s MAC address. And wireless internet access was a no-go, because the original MAC address was from a wired NIC. It is not possible to clone MAC addresses between cabled NICs and USB wireless adapters, because MAC addresses from wireless cards have a fixed prefix. Hence, I had a complicated setup from my phone via a computer to a (cable) router to the Win7 Dell computer.Windows 10 is not to blame - F-Secure is the culpritTo my surprise, the Äkta Avant kept crashing when Unicorn 7 under Win7 issued commands like “pause” or “end”. But then I realized that - unlike our old Äkta Explorer - the Avant uses regular NICs for the device communication and the University of Helsinki Win10 version is by default “enhanced” by remote control and security software. I went to the Control panel and uninstalled all software add-ons that had been installed by the university. Most notably F-Secure’s Client Security Premium was among the programs, that I uninstalled. After a reboot, I was unable to make the Äkta Avant crash. To confirm the finding, I popped the NIC back into our original default computer, rebooted and got stuck at the Windows BitLocker screen. Changing the hardware configuration inevitably triggers Windows to refuse booting. This did slow me down because it required me to engage our university’s IT department, which is chronically overworked and difficult to find. I selectively disabled the firewall from F-Secure Client Security Premium and the crashes instantly ceased also on Windows 10. It is very difficult to argue why our university would need F-Secure’s products. Windows itself comes (since XP SP2) with a very capable firewall and also has its own anti-virus software ( Windows Security Essentials / Windows Defender ), which is at least as good as its best competitors in addition to the fact, that it is free and fully integrated into Windows (and it does not require to stick third-party hooks deeply into the OS).Windows 10 is too slow on our 2015 hardwareThe only thing left is to upgrade our default computer to newer hardware. Our faculty had replaced older Win7 computers in 2019 with new machines, but this computer was 1 day too new to be included in the upgrade. However, it is already 5 years old and especially after the Windows 10 upgrade, it is very slow. When your protein elutes during your purification, you do not want fraction collection to start after a few seconds, but you want it to start instantly.

Computer time: Windows against the rest of the world

Sat, 10 Feb 2018 00:00:00 +0000

I am not sure, but Windows seems to be the only operating system, that wants the computer clock to be set to the local time zone instead of universal standard time (UTC). Maybe that is a relic of the times when Microsoft thought that the internet was not very important for the future of computing. All other operating systems apparently use UTC: MacOS, Android, Linux, BSD, … However, if you are dual-booting your computer, you can get into trouble. Not all operating systems detect automatically a dual boot install and adjust their behaviour in order to be compatible with Windows. If this is the case, the easiest is to change the behaviour of Windows. A clear write-up how to do so is available from https://liliputing.com/2016/03/fix-time-problem-dual-boot-computers-windows-linux-android.html , but here are the steps in a nutshell:

1000 times too slow

Thu, 01 Dec 2016 00:00:00 +0000

Helsinki University has outsourced parts of its IT infrastructure to Microsoft. Even if outsourcing is cheaper in the short term than generating equivalent services locally, the net effect is likely negative due to the lost jobs, know how and independence. It doesn’t need a conspiracy to explain this self-destructive behavior, just bad decision criteria, which do not include long term and externalized costs.In its push to upgrade to newer Windows versions, Microsoft ended extended support for Windows XP on April 8, 2014 and the university obeyed by denying network access to XP machines. The argument was that XP was becoming a security risk. At the same time, Windows XP accounted still for about 20% of all Windows installations on this planet ( https://www.statista.com/statistics/218089/global-market-share-of-windows-7/ ). Even in October 2015, well above 100 Million computers did still run Windows XP ( https://en.wikipedia.org/wiki/Usage_share_of_operating_systems and https://www.statista.com/statistics/218089/global-market-share-of-windows-7/ ) without any catastrophic consequences.The ban of Windows XP was a problem, since four of our devices, that we need for research, are still running Windows XP. And there is no way to upgrade the OS without upgrading the equipment (which would cost thousands or tens of thousands of Euros and therefore is mostly impossible in the present tight financial situation of the university). And of course, the software that is needed to operate the devices is not compatible with Windows 7. As a consequence, we can neither remotely operate this machinery nor do automated backups. Even taking the data for analysis to another computer requires the Adidas network .I had contacted IT support well before the extended support of Windows XP ended and asked them to find a solution. Apparently there were different possible solutions and IT support did start to implement them, but because of personnel fluctuations, the project had to be “restarted” several times and different support professionals had different opinions on how to solve this problem. With the big “fire and hire” action at the university, the whole project disintegrated again. This autumn I again discussed our needs with the IT staff, but did not receive any concrete help so far.This Tuesday, I finally wanted to know how difficult it really is to connect a Windows XP machine to the network in a way that would not compromise security, but enable file distribution, backup and remote control. I went to the Institute’s garbage place where broken electronic equipment is gathered and took three old 10/100 NICs and a few ethernet cables. One card and one cable were still functioning and I dropped the NIC into a Ubuntu 16.04 computer and connected it via ethernet cable to one of the XP machines.After manually assigning an IP to the NIC and installing samba onto the Ubuntu machine, I was able to mount the samba share as a drive on the Windows XP machine. Then I just made the samba share available via a web page. All this took about one hour. Not being an IT professional, I spend maybe an additional three hours researching how to do it (samba setup, apache setup, configuration of a secondary NIC, which is not automatic on Ubuntu). This setup fulfills all of our requirements, didn’t cost anything and was implemented within one day.A write-up of the technical details will follow once I get around documenting what I did. Agility is perhaps what is mostly missing when I look at many of our university’s IT projects. Notably I think of switching to Drupal as content management system for the university’s web pages. Sadly, our faculty is still using Dreamweaver to create its web presence and as a consequence many web pages are never updated.

½ year and 1000+€ for Win7 & Office 2010

Mon, 02 Apr 2012 00:00:00 +0000

In the beginning of 2011 I bought a netbook ( Lenovo IdeaPad S10-3t ). I bought it with my own money. It was preloaded with Windows 7 Starter Edition. Because I prefer to use Ubuntu , I shrank the Windows 7 partition and installed Ubuntu as my primary OS. I installed the University-licensed Microsoft Office XP, for which there were still installation media around in our research program. There are only two occasions when I boot into Windows: when I needed to work on collaborative publications or grant applications at home with my co-authors using Microsoft Word or when there is a program that has no equivalent on Linux (which has rarely happened during the last years).However, last October, more and more compatibility problems appeared between the aging Office XP and the newer versions of Office, that use the new XML format (.docx). On one occasion, after my boss had opened a Word file (created by Office XP), modified it and send it back to me (using compatibility mode), it became uneditable in Office XP. Word would crash whenever I tried to edit two of the three embedded images. In fact, I spent hours of recreating an editable version of that document from scratch.That was when I decided to upgrade my privately owned computer’s Windows and Office versions. Helsinki University’s license agreement with Microsoft allows staff and students to run Windows and Office on their home PC. To university researchers, it happens all the time that they need to work from home. In fact, I wrote almost a complete research paper ( Jeltsch et al, JBC 2006 ) from home. Thus it should not be difficult and not expensive to upgrade from Windows 7 Starter to Windows 7 Ultimate and from Office XP to Office 2010, right? Helsinki University wants to get higher and higher in the [Alma intranet pages]( http://www.topuniversities.com/university-rankings/world-university-rankings/2011?page=1>international rankings. Therefore, one might think the University would have made sure their researchers have easy access for the right tools to do their job. WRONG!Helsinki University has provided instructions on their Ohjelmistojakelu page of the university. Under the <a href=) (Home Use Program) link hides the “Microsoft Home Use Program and software delivery to members of the staff”. I downloaded the file (“koodi.txt”) which is a text file cotaining a code (something like “XXX0000”). With this code I went to the Microsoft Home use Program site. I had to type in my work e-mail address and the code and I received the following error message: “We are sorry, but we are unable to complete your request. the following problem(s) exist: - Please contact your benefit administrator to learn if you are eligible and to retrieve your program code.“I phoned the helpdesk of the University to ask what is wrong. The answer: “The University and Micorsoft are negotiating a new licensing deal and the old code doesn’t work anymore and the new code is not yet there.” How long will it approximately take for the new working codes codes to appear? “A few weeks.” I waited a few weeks. To be precise: I waited six weeks. I went through the same procedure as before. But the code still did not work. Retrospectively, I suppose that the helpdesk’s first answer was wrong: The codes were probably still fine, but the instructions on the university’s pages were wrong (they sent me to the wrong page to type in the code and at the time of this writing - 5 months later - the university’s pages are still wrong).In the beginning of the new year I submitted a formal support request to the helpdesk. I received the following answer:Hi MichaelUniversity of Helsinki has made a new agreement with Microsoft (moved from MSCA to EES) starting this month and now that our agreement is changing codes won't work. I assume we get new codes to our new agreement from Microsoft after all paper work is done, and this will take approx. couple of weeks or so.All we can do now is wait, you can check in february if Home Use Program -option is working. Sorry for the inconvenience.Best regards,Tommi also send me the Alma link with the instructions . I tried several of the links in the document (which were links to sites where one could order Windows and Office installation media/downloads), but already the first link was broken: Microsoft Windows operating systems: e-Academy (no CD/DVD option, only downloadable versions). It is still broken at the time of this writing.The other option (“Microsoft Home Use Program HUP (Digital River, also installation medias)”) linked only to the instructions that I already knew (and which do not work). Because apparently nobody had ever tried before to leaglly aquire Windows and Office for home use via this program, I went in March together with my computer to our physical help desk at Meilahti campus. Iivari was very friendly, but the only thing he managed to do was to replicate the problem and to convice somebody that there is a problem that should be looked at. A few days later he sent me the link to a page from where I could order Windows and Office for 20€/DVD: https://hup.atea.fi/ .This link I have never found anywhere in the university’s online instructions (as I learned later, it is somewhere there, but almost impossible to find). I am not surprised that otherwise law-abiding citizens of this country use illegal versions of Windows/Office at home if it is so difficult to be legal.I received the DVDs via Post a week later (I had to go to the post office and to pay there the 20€/DVD).Before I installed anything, I made a disk dumpdd if=/dev/sda of=/dev/sdbof my entire hard drive (250 GB hard disk, it took 20 hours via USB). Because I had Windows 7 Starter installed on my computer, I first tried to use the anytime upgrade . For this I actually only would have needed the license key, but not the physical installation disks. When I typed in the key, it started the upgrade, but failed without any details. So I decided to run the upgrade advisor (a program from Microsoft that determines whether your computer is “good” enough for the upgrade). The only thing it found was that I was short on disk space. So I freed another 5 GB by uninstalling software (mostly the bloatware that was put there by Lenovo). The second attempt also failed without any specific error message. I had no way of knowing what was the reason.So I tried a clean custom install. First I needed to transfer the Windows 7 install DVD to a USB stick (my computer has no CD/DVD drive and I or my lab doesn’t own an external CD/DVD drive). Fortunately this is easier with Windows 7 than with Windows XP. However, not all USB sticks seem to be equal and the first USB stick I tired (Verbatim) was rejected by the tool I used. I followed these instructions . Then I booted from the 4GB stick and started the upgrade. Everything went fine until the very end, when I needed to reboot and I was greeted with “Your Windows 7 install is broken. Do you want Windows to fix it?” Then I made a bad decision: I said yes. After fixing, nothing worked anymore. Upon rebooting, there was only a blinking black cursor.OK, if I cannot upgrade, I can do a fresh install. I wiped my hard drive clean and started the install. Everything went fine until I had to type in the product key. It complained that it is not a valid product key. Of course I had not thouroughly read and understood the pages at www.atea.fi . Probably because they are only in Finnish. Apparently, the University’s deal with Microsoft does not provide the staff with full installers, but only with upgrade installers. Consequently I need to keep my old Windows version around for the install. Luckily I had my diskdump. I wrote it back to the hard drive. This took only about 6 hours.This Monday I went (together with my laptop) to the local computing support. Perttu enlightened me about the possible upgrade paths to Windows 7 and tried to do the custom install using an external DVD drive. And it worked! Hallelujah! It took several reboots, but finally I had a running Windows 7 Ultimate. Installing the drivers took also about three hours. It took an eternity to download the drivers from Lenovo’s site, despite them being akamaized. Maybe they didn’t pay their bills. Now I just needed to create an iso image from the Office 2010 DVD, move it over to the computer and start the install, which went flawlessly this time.I presume that the first time I tried the custom install, the system was somehow compromised by the failed anytime-upgrade. Who knows. 500 Million lines of code, that nobody really understands anymore. It’s close to a miracle, that Microsoft is managing to keep Windows afloat.Of course the Windows installer had screwed up my grub boot loader and I had to start the machine from a System rescue CD on a USB stick and write back the MBR from my disk dump:dd if=/dev/sda of=/dev/sdc bs=512 count=1I still don’t exaclty know now, whether the Windows 7 Starter Edition does or doesn’t qualify for an upgrade using the University licensed upgrade plan. I stupidly assumed that if a 10 year old Windows XP Home qualifies, a Windows 7 Starter edition would too.The whole procedure lastet about half a year and taken together, I spent maybe seven to ten days of work for it (about half of this time during working hours, the other half during my weekends). Let’s estimate the real costs including the hours I had to put into this Windows 7 & Office 2010 installation: conservatively at least 1000€. The system is broken and the worst thing is, that there is nobody to blame and nobody who can fix it. Maybe Helsinki University should invest some energy and time into the development and adoption of open source Operating Systems. After all, the most popular one (Linux) was started by somebody from Helsinki University .