Kirk, et al
The Dell site is tricky to navigate at times as different computers are offered depending on how you enter the site (academic, government, personal, etc.) I can tell you that I found the T3500n (with RH5.3) via the higher education portal (at least here in the states) While I didn't have the chance to respond to your initial request, I will be doing the exact same thing with our INOVA system in the coming months as well. Nice to see that T3500/RH5.3 out of the box may work with VJ w/o the full os/VJ supplied by Varian. In addition, I believe Dell automatically supplies the first ethernet card, so the choice (way down the list below the monitors) is for the second card.
Cheers!
Neal
Neal J Stolowich, PhD
NMR Facilities Manager
Department of Chemistry
University of Louisville
Louisville, KY 40292
(502) 852-7894
-------------------------------------------------------------
>>> "Kirk Marat" <kirk_marat_at_umanitoba.ca> 09/04/09 2:31 PM >>>
Thanks to everyone who responded to my request for experiences with upgrading an INOVA to a Dell
computer with a newer release of VnmrJ.
The overall opinion seems to be that this is a good move, and that you can buy the computer directly
from Dell. But:
- Make sure you get the exact computer configuration specified by Varian.
- Install the RHEL 5.1 version supplied by Varian.
- If you have a PPC acquisition computer (we do), there are some minor tweaks (documented in the
Varian newsletter) required to get the console to boot
- Follow the instructions carefully! (here's where many of us seem to mess-up :-) )
Now, as I was preparing this summary I received an email from Rolf Kyburz at Varian informing me
that the Dell T3400 is about to become obsolete and will be replaced by the T3500, which Varian will
be supporting. This Dell model will require RHEL 5.3 and Varian will no longer provide the RHEL 5.1
disk, nor will it be needed. Varian will also not be providing a RHEL 5.3 disk, so the plain
vanilla RHEL 5.3 installation may require some tweaks. However, Varian supplies a tool called
"sysprofiler" will should tell you exactly what you need to do before installing VnmrJ. (Thanks
Rolf!)
I think I will go for the T3500 RHEL 5.3 option, and will let everyone know how I make out. One of
the difficulties may be getting the exact Dell configuration that Varian specifies through the Dell
ecommerce site. For instance, I can see no way to specify that I want two ethernet cards. Although
some of the Dell literature mentions RHEL, I can see no option for either RHEL or "no OS" on the web
site.
Thanks!
-Kirk
--------------------------------------------
We're still testing out VNMRJ2.2D on a Dell T3400 running an Inova 500.
The issue was the operating system that VNMRJ2.2D requires: it's RHEL5.1
Dell preloads (and our local IT supports) RHEL5.3 which won't work, so you
have to take a step back in terms of the operating system to get things
running. There's a special OS DVD that Varian sells that will load
RHEL5.1 properly; my IT guy took a look at it, and thinks he's figured out
what the "special sauce" is. Let me know if you want this info.
I have bought several computers directly from Dell and turned put
Varian software on them. The most recent purchase was a T3400, then
I used to upgrade our Mercury Vx-300.
The most important thing is that you make sure that it is EXACTLY as
Varian specificies, then get the media kit from Varian -- Red Hat and VNMRJ.
-----------------------------------------
Then---when I went to install red hat, you put the Varian DVD in and
you use a kickstart file that they suggest, by manually typing a boot
command that starts the installation: linux
ks:cdrom:/Varian755RH51.cfg But the first time that I tried this,
it couldn't partition the disk and kicked me out of the installation,
so I did a generic red hat installation off of the same Varian dvd.
VNMRJ wouldn't install correctly, so I went back and tried to install
Red Hat again using the kickstart command per the Varian
instructions, it worked fine this time through.
Then, the trick to getting VNMRJ to install seems to be that it now
won't install off the media, you have to copy the DVD into a
temporary directory on /home (be sure to copy it via tar commands -
or it messes up the symbolic links), then after you extract it, run
the ./load.nmr script (as root) and it works fine
--------------------------------------
Yes this is a tempting option and one I have done many times. I have not
done it with the T3400 specificly. The only gotchas that I have run into
are you have to reinstall redhat this has to be a complete/full install. I
do not know why but you have to do this. Then make sure that the /
partition is atleast 10GB. Finally on one system this was a totally
differnet computer system then what Varian says use I had to install some
seperate packages to get Vnmrj to install. But i was getting errors and so
I just found what those files went to on the internet and got the package.
Hopw that helps! I say if you can follow the Redhat install instructions
then you can do it.
----------------------------------------
As, I write this e-mail, I am in the process of ordering two T3500 PCs directly from Dell. The
T3400 is outdated and will be replaced as an option by Varian quite soon. Thanks to Rolf Kyburz for
informing me about this. I am having more luck configuring the T3500 appropriately according to
Varian specs, but I don't know how easy it will be to install and use VNMRJ as yet. I could not
purchase the specified T3400 or 755N from Dell when I attempted to get them. I tried to get the
755N a few months ago, and the T3400 yesterday. I'll keep you posted as to how it goes if you would
like.
----------------------------------------
As, I write this e-mail, I am in the process of ordering two T3500 PCs directly from Dell. The
T3400 is outdated and will be replaced as an option by Varian quite soon. Thanks to Rolf Kyburz for
informing me about this. I am having more luck configuring the T3500 appropriately according to
Varian specs, but I don't know how easy it will be to install and use VNMRJ as yet. I could not
purchase the specified T3400 or 755N from Dell when I attempted to get them. I tried to get the
755N a few months ago, and the T3400 yesterday. I'll keep you posted as to how it goes if you would
like.
-----------------------------------------
We bought our Dell through Varian, already loaded with Linux Enterprise 4. It was not loaded with
the Varian
software, though we asked for this in the quote. The Linux configuration isn't usually the problem,
though at the time
Varian was suggesting not to use SELinux. We had to reload VnmrJ2.1b 3-4 times before each problem
was caught
and diagnosed. Christine Hofstetter at Varian was very helpful. There are plenty of "gotchas" in
this upgrade. It isn't a
2 hour job, more like a 1 week job (OK, 2-3 days). Make sure the Dell configuration is correct.
I am very pleased with how the Dell functions and I like it tons better than the Blade150. I'm an
all Linux lab, which makes
life a little easier on networking and security. It was a painful task to get to this point.
----------------------------------------
Buy the _exact_ same computer (memory, memory type, video card etc.) or
else Varian will shrug its collective shoulder if you have any problems
with the installation. Do a clean Linux install from the Varian DVD. I
bought Varian spec Dell 755N's and tried installing Linux from Cornell's
Red Hat 5.1 distribution. Vnmrj didn't run. I ended up having to pay
Varian for their version of "free" Linux. Once I had that, installation
went mostly fine, BUT:
1. Do NOT change the hostname after you install vnmrj or vnmrj will die
trying to initialize. It took me three #%$_at_# days to figure this out.
2. I had problems with the console not getting the correct boot file
that could easily be solved by renaming a few files (see Software FAQ ->
Acquisition/Network Communications -> Installing VnmrJ on UnityINOVA on
the Varian User pages).
-----------------------------------------
First, Kirk, I strongly advise buying exactly the Dell that Varian tells you to, down to the last
megahertz and disk rpm. Doing otherwise (even when we know it doesn't matter) gives Varian a free
pass to tell you that you're on your own.
Second, I wonder how many people think that once Agilent acquires Varian, we'll be seeing H-P host
computers running either linux or HPUX.
Third, when I migrate my Merc Plus from a Blade 1500 to a Dell Precision 390n, I wonder what I have
to consider regarding the ProTune parts of the software.
------------------------------------------
I purchased 4 Dell Optiplex 755 PCs directly from Dell. It was a
nightmare to get Red Hat 5 and VnmrJ 2.2D to load correctly. It took 3
weeks for Varian's marketing department to provide me with a RetHat5
DVD. Once I finally got the software to load on one machine I found it
easier to clone the harddrive than to try to load from scratch on the
other PCs. One for the four "identical" PCs loads OK the other 3 do not.
These PCs have the same configuration, purchased at the same time, they
even have sequential serial numbers.
Dell does not support RedHat on the 755, so they were no help. I was
able to find out that Dell preloads a custom software package
specifically for Varian. It is not available to anyone else.
I do not know about the T3400, but if I had the choice I would spend the
extra money and buy direct from Varian. The first thing I would do is
create a back-up image of the new harddrive.
--------------------------------------
I recently upgraded our INOVA systems (750, 400, 200) and two Mercury 300 to the latest VNMRJ 2.2D
on Dell Linux systems I purchased directly from Dell. If you are not familiar enough with Linux I
would recommend purchasing the Varian RHEL 5.1 install DVD. I did this to see what extras they
included then made my own installation DVD based on RHEL 5.3. But in hind sight it wasn't necessary,
I could have downloaded the extras or copied from my RHEL 4.3 NMRS systems. A VERY helpful tool
when configuring your own install is sysprofiler, available for download from Varian's user library.
All my issues were covered by sysprofiler's report and the bug lists for 2.2D & RHEL 5.3.
Dell config:
T3400
3.0 GHz
4 GB RAM
250 GB HD
NVIDIA FX 570 Graphics card
24" LCD
-----------------------------------
upgraded the computers here by buying from Dell directly (755N) and
getting the 5.1 restore DVD from Varian. Dell Canada does not sell
nVidia Quatro video cards so I bought the 570 card and extra Ethernet
card from tiger direct. I upgraded VnmrS and Mercury this way.
-----------------------------------
We've done this for two of our Inovas. We added the older 390N Dells
with RHL 4.0u3. The only problem we had was a communications problem
with the older Inova (1997) and the Motorola console CPU but this was
fixed in about an hour with a patch that I overlooked.
One strong suggestion. I HIGHLY recommend that you get the Linux media
DVD kit from Varian. It installs the base copy of RHL as required to
operate the spectrometer. Also, I used the upgrade quote to reproduce
EXACTLY the hardware that Varian offered.
Overall I had no problem with this upgrade that a phone call and email
didn't solve in a matter of hours.
-------------------------------------------
We upgraded our 2 inovas and 2 mercurys 4 years ago without problems.
We got our computers direclty from Dell. They are now running vnmrj
2.2D under rhel 5.3.
-------------------------------------------
I started this conversion on my INOVA400 about a year ago. I bought the Dell computer and the LINUX
software directly from the manufacturers, and also bout the VNMRJ software from Varian. I started
the installation and ran into a problem with the vnnmj recognizing the serial ports and other
control issues with the SMS sample changer. After spending a lot of time and getting some help from
AMMRL, I finally resolved some of the problems, but still could not run the instrument. I finally
gave up and asked Varian to come in and do the install. They of course blamed the problem on the way
LINUX was configured and not the vnmrj. So I bought another version of LINUX configured by Varian
and the app person tried for several day to get the system working right, but could not do it. So, I
still don't have a working system. Varian has sent me a newer version of vnmrj which is supposed to
take care of the problem, but have not come back to try to install it again. I may go ahead and try
it again myself and see if I can get it working. In the meantime, if you get any good hints from the
rest of the group, please let me know.
Sorry that I was not much help, but I thought you may want to know about my experience anyway. I
suggest that, if you have the time and patience, to go ahead and try it yourself first and see if
you can make it work. Then contact Varian, although as it was in my case they may not have a good
solution for you either.
-------------------------------------------
I upgraded our Inova 500 and did so straight from the quote. I regret
doing so, as the computer was delivered without the VNMRJ software
installed. This was in contrast to a similar upgrade on our Bruker 500,
where the computer arrived with the TopSpin software installed,
basically ready to hookup to the spectrometer.
On the positive side, I had no trouble installing VNMRJ on the Dell with
RHEL5 preloaded. Therefore, a service visit was not required to complete
the upgrade.
In retrospect, I could have saved a lot of money buying the computer
directly from Dell. I wouldn't anticipate any additional problems for
you if you were to do so.
------------------------------------------
I'm in a similar situation, except that I'm still running VNMR 6.1C on
Sun-Blades for my Inovas. Now that I've installed a RedHat LINUX-based
Bruker Avance-III system in the lab, getting everything switched over to
Dells/VNMRJ seems a little more appealing. Of course, re-training over
300 users from more than 50 different research groups is a daunting task
(and a major contributor to my activation energy barrier thus far). But,
considering the limited lifetimes of the Sun-Blades, my hand will be forced
at some point.
I can tell you that we have "upgraded" all of our Biomolecular NMR systems
(2 500s and our 600) to Dells running VNMRJ 2.1B, and that seems to have
gone quite smoothly; however, all of these Dells systems were purchased (at
a premium) directly from Varian... so this doesn't exactly answer your
question.
The bottom line is that I'm very interested to receive the benefit of any
wisdom you might gain from your posting. Please post a summary if you learn
anything useful because I'm sure many would appreciate it.
-------------------------------------------------
None that I know of --- but gotchas can come from anywhere.
Be sure you are up to date with the quote before going off to buy something
- Dell computer names and our recommended models change fast.
You will need to install a Disk Image so as to have Varian approved
configuration for Red Hat - we supply that.
The recommended software in VJ2.2D. If you try to use anything but Red Hat
- be aware that we can't help you directly. People do
customize and upgrade their Red Hat after initial configuration - but be
aware that adding subtracting software may have surprising results for VJ.
That is the last upgrade for INOVA
2.2D is designed to have the same look and feel as our current 2.3A
software for VNMRS.
SolidsPack is the recommended software and it works with 2.2D ... you are
now using it with 2.1B - not much will change. You know the SolidsPack
Caveats for INOVA.
2.2D allows direct control of the MAS controller through the RS232
interface -- ACC goes away. There are some useful debugging/control
features in ACC that are not in 2.2D -- so keep your Sun to occasionally
use ACC. ACC does not run on Linux.
Your current controller cable is 24 pin at the Sun? You will need to
adapt it to 9-pin on the Dell - or we will quote you the right cable.
------------------------------------------
I have purchased the T3400 directly from Dell it works just fine with
VnmrJ 2.1D. I've gotten VnmrJ to work on several other variations of
non-Dell hardware as well as Red Hat 5.3 and Centos 5.3.
We are currently running our Inova 600 from a clone PC running Centos 5.3.
I tried to configure the clone similarly to the Dell..., but there seems
to be quite a bit of leeway.
Let me know if you want more advice or specifics from our experiences at
stretching the envelope.
If you'd like, I can send the Dell configuration that we actually ordered.
---------------------------------------------
I did this last year, moving all of my systems (Inova, Mercury)
from Sun/Solaris/VnmrX6.1c to Dell/redHat/VnmrJ2.2D. It went
very smoothly. I specified and purchased Varian's exact specified
system at the time (Optiplex 755) with exact the configuration they
specified. I did add memory for my workstations, and got a couple
flat panels displays that were better than those Varian used, but the
basic configuration was according to Varian's book. I then used their
OS DVD to install the RedHat (systems were purchased with Vista
since they did not offer them with no Operating System. There was
a minor hiccup in installing the OS - the Varian disk did not allow for
overwriting non-Linux partitions. I had to do a dummy install to make
the partitions linux partitions, and then run the Varian kickstart config
to get the official Varian version installed. After a year, I have had no
problems with the hardware platform.
------------------------------------------
We went with the more expensive Varian Dells (optiplex 755n) with Redhat
preinstalled and I installed VNMRJ. Went smoothly, and after the initial
hair-pulling over why I couldn't find things that I wanted in the software
interface I am quite happy with VNMRJ 2.2D.
Whatever way you do the Dells, I think it is worth moving onto 2.2D.
--------------------------------------------
I have installed 2.2C on Dell Optiplex 755 without any problem. But now, the 755 is not available
any more. I am ordering T3400 and trying to install 2.2C to replace other host computer. I guess
that there is no any problem to install vnmrj software from my previous experience. Please order the
exatly computer as Varian request, otherwise you may have some problem. (e.g. display for different
Video card).
-------------------------------------------
I have upgraded two Inova from Solaris 9 computers to Optiplex Dell's
running 2.2D. Here are my $0.02
1) I have had no problems with the hardware, I made sure to get
exactly the same hardware that Varian recommended.
2) Purchase the OS from Varian. I mistakenly had my IT department
install the standard RHEL OS, which resulted in several months of
working with the IT office and Rolf Kyburz trying to get RHEL 5.3
working with VnmrJ 2.2D... In the end I have got things working
beautifully (with several more months of work I even have the
computers playing nicely with our LDAP network). So, unless you enjoy
"getting under the hood" and tweaking your OS, I would suggest paying
the money and purchasing the special RHEL 5.1 disks from Varian to
ensure that the OS simply works out of the box.
3) Be careful about what type of Inova you have. I got my 300 MHz
"almost working" the first day we started playing around with stuff.
After several months of polishing the non-standard installation I was
ready to upgrade our 500 MHz in one day - BUT, it turns out that
particular instrument needs the PPC version of VxWorks and the
installer doesn't seem to have a way of recognizing this... after a
week of reinstalling and tweaking everything multiple times a friend
remembered the PPC issue and we got things working and submitted the
bug to Rolf - so you can now find this in the Varian news.
----------------------------------------------
We have two Varian nmr systems, INOVA AS500 & AS400. Both of them were upgraded to Linux on the
year 2006.
We bought two PCs in our local market with the following configurations.
Dell 380N PC, Red Hat Linux Kit
Dell Precision 380n Mini-Tower
Intel Pentium 4 Processor, 3.20GHz
1.0 GB, 533MHz DDR2 SDRAM memory
Dell 19 inch UltraSharp 1905FP Flat Panel
64MB PCIe x16 nVidia Quadro NVS 285
80GB SATA, 7200 RPM Hard Drive
1.44 MB Floppy Drive
16X DVD+/-RW Data Only
Dell USB 2-Button Mouse, Scroll
Keyboard
2 x 10/100/1000 Gigabit Ethernet controller
There were problems on the communication between console and workstation. Finally, two PCs'
motherboard were replaced by Dell.
---------------------------------------------------
I just upgraded two Varian Mercury Vx instruments running VNMR 6.1C to
VNMRJ 2.2D on Dell T3400 computers . Although Varian says that the
software runs under RedHat 5.1 I found it very difficult to install a
generic 5.1 and get the software running properly. After three week of
working on this I gave up and purchased the OS recovery DVD from Varian
(01-921736-00). Using this disk the everything installed easily and and
the software runs fine.
---------------------------------------------------
Kirk Marat, Ph. D., NMR Facility Manager
Dept. of Chemistry
University of Manitoba
Winnipeg, MB, R3T 2N2, CANADA
C#, What C++ should have been
ph. (204) 474-6259 FAX: (204) 474-7608
kirk_marat_at_umanitoba.ca
ALL SPAM forwarded to Spam Cop
Received on Fri Sep 04 2009 - 10:09:48 MST