Dear Colleagues,
First I apologize for the delay to send in the feedback information and
thank all my colleagues who gave me their kind help. I waited for my
computer coming then I could give my hands-on experience. Unfortunately
it is still not here yet.
My question:
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I am considering to replace our old Sun workstation (host to an Inova)
with a more powerful Linux or Solaris box. Since Varian removed Sun from
their website, I assume they will no longer provide upgrade for Solaris
in future. In addition, Blade1500 is not available from market place any
more. The best thing to go now is probably a Dell.
Unfortunately Varian doesn't have any thing about Dell computer in their
website. I wonder if anybody did this upgrade to a Dell on their own
(purchasing computer directly from Dell instead of Varian)? If so, what
additional hardware needs to be ordered from Varian, for instance,
another (special) network interface card to communicate with
spectrometer? Your experience with purchasing Dell PC from Varian is
also welcome.
Your response is highly appreciated. I will summarize to AMMRL list.
Hopefully it will be helpful for others too.
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Following is the summary of feedback I received with confidentiality:
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I've attached the system configuration that I have. I had a ridiculous
time with the DVD drive, even after having it exchanged, so in the end I
just used a USB CD-RW, which worked fine (Iomega CD-RW 52x24x52x, Model#
CDRW55292EXT). I got RHEL WS 4 and installed that as per the Varian
manual (although I did make some mistakes and had to reinstall a couple
of times). One thing I noticed was that I had to have all the font
packages installed to make everything work okay. I had a font problem,
and installing all the font packages (I don't know which one was the
critical one) solved that. You'll probably have to transfer the probe
files by hand, that's what I had to do (but that's a known bug with any
VnmrJ upgrade). I would also recommend doing a full recalibration
(indirect, gradients, pw90, etc.) just so you know that everything is
written correctly.
Bad news is that I still have printing problems. I can print without
incident, but I 'm running in automation and it always prints out a page
for every specrta. I don't want that, and I've done EVERYTHING I know
how. I've pretty much done the same print setup I had in Solaris 9, and
tried variations on that, and it still prints a page automatically after
every sample is done. We process all our data using ACD/labs or MesteC
offline of the NMR anyway, so I just turned the printer off (should go
to /dev/null now, or the Linux equivalent of that file). There's only
one user that prefers the Varian software, so I just NFS the data
directory (read-only and wrapped to our network, of course) for him to
process on another computer. Frankly, I probably should have queried
the AMMRL to find out how to get it to stop printing, but since it's not
relevant to us I haven't done that yet.
As for the network cards, you can run as a console host with only one
card, but since we need to connect to the network/internet/etc. I had to
order an extra one. I've attached my configuration, although please
don't spread it around as is, I prefer not to ruffle any feathers. Cheers,
P.S. Be sure and check out all the known VnmrJ and VnmrJ Linux bugs on
the Varian buglist, is could save you a lot of trouble later.
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We bought the computer from Dell ourselves and installed Linux
and VnmrJ 1.1D. I think the Varian cost was ~4500, and we paid ~1500.
It took a little while to get everything right, so if time is an issue I
would just purchase it ready-to-go from Varian. Especially if this is
your main NMR, you wouldn't want any more downtime than absolutely
necessary. There are still a couple of minor issues in automation, but
otherwise things work okay now. Having said that, I don't know what the
Dell from Varian provides as far as software configuration and what
you'll have to do yourself.
We didn't purchase anything special, we just ordered the Varian
configuration with extra RAM and a faster chip direct from Dell (the
Varian configuration lists the type of network cards, etc. that you
need). So far people are pretty happy with it, we had a Sun Blade 150
in automation (intolerably slow) and since we've put it on the Linux box
we've had no issues. On a side note, I've seen a reasonably
priced Sun Blade 2000 on ebay and anysystem.com (2*900MHz, 2GB RAM,
2*36GB HDD for $995), so if you want to stick with Sun you should be
able to get a fairly powerful used system. Sun hardware lasts a long
time (at least it used to, I don't know about now) so this may still be
a safe bet. If you're very comfortable with Sun this may be a deciding
factor; but the Linux that Varian recommends (RHEL Workstation 4) is
MUCH easier to work with than Solaris, at least comparing Solaris CDE to
the Linux Gnome.
Hope this helps,
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ask me next week - I am in the process of installing vnmrJ for Linux on
a Dell, to control an Inova.
Varian does sell a Dell computer that they support. (Don't assume that
the absence of an item from web site means that it doesn't exist - any
more than the absence of an NOE could prove that two protons are not in
proximity.)
An important issue is whether your RF cabinet is controlled by a
Motorola or a PowerPC. (An Inova controlled by a Motorola is not
currently supported, but some savvy users have gotten it to work. They
are helping me now. )
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After visiting Palo Alto and talking to some of the Varian software
people, they want to phase the SUN systems out and don't really want to
support Solaris 10, although they have been including Solaris 10 info in
their newsletters.
If you still want to use a SUN system, Otter Creek Systems
http://www.ottersun.com/ sells used & refurbished systems. I have done
business with them for years and they've always been helpful. Also,
Triangle Analytical
http://www.triangleanalytical.com/ has purchased
some used SUN computers and preloaded them with VNMR.
The Dell systems that shipped with our new instruments are standard Dell
Precision workstations with Redheat Enterprise Linux. Two standard NICs
can be use or one NIC and a Linksys router. I prefer not having to deal
with the router so I recommend the 2 NICs. You can get other versions
of Linux to work but Varian only supports RedHat Enterprise Linux.
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Despite extensive effort, I have not been able to get linux to work on our
own Dells. I highly recommend you purchase from Varian and get them to
guarantee that it work.
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You are correct about the fact that Varian is phasing out support for Sun
hardware and the Solaris operating system. However, there have been several
Varian users who have figured out how to make VNJRJ run under Solaris 10
(even though Varian officially does not support Solaris 10). Sun no longer
sells any new computers that are designed to operate below Solaris 10;
however, there is one person who got a new Ultra-25 (or Ultra-45.. I'm no
sure) to function under Solaris-9.
I will forward you a recent "VNMR NEWS" that clearly outlines how some of
our colleagues (including Jack Howarth, at Cincinatti) got VNMRJ 2.1 to run
under Solaris 10.
Of course, the LINUX route works also. My colleague at our 900 facility
recently got a Dell LINUX box configured to run our 900, and it works great.
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We tried, as suggested there, to go with a Blade 1500 to upgrade our
spectrometer, but could not find a Blade 1500 for resell. So we are
currently in the process of upgrading with a Dell 380+Red Hat. It seems
the Linux version is ok, as suggested by many other users. And we'll
have moved forward to the place Varian is definitely forcing users to
go, so that is a positive.
Even so, if I had access to a Blade 1500, I would still go that
direction for a Mercury console. The current limitation of VNMRJ 1.1d
still persists for that console, and I am still much more confortable
with Solaris (and I like having the classic interface available). But
going either direction is almost certainly ok, and again, going with a
Linux PC is more progressive for the future.
Hope that helps, but let me know if you have more questions.
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Call your Varian sales rep and have a chat with them. Varian probably
won't offer much support if you buy a PC on your own. The Dell system
that works on the Varian is fairly specific and you must get exactly the
right combination of hardware if it's going to go as smoothly as
possible.
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I am very interested in this same question. I recently asked our
service engineer and this is the email reply he sent me back:
/Yes, it is possible to switch the Inova Sun base to the PC host. It
involves buying new computer and monitor from Varian (the Dell was
custom configured for VNMR application), loading a new software(I think
this is included when the PC was bought from Varian), transferring
calibration files and automation files. I do not see any downside
except that you will use VNMRJ exclusively. The classic VNMR (6.1C)
will not be available anymore. I will suggest for you to get in touch
with your salesman (Margaret or Cory). They could provide you
information regarding what you need to buy as well as answer your
questions regarding application-wise transition from the old VNMR to the
new PC base system./
Not sure if this helps any, but I would be interested in what you learn.
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Varian has addressed this in their VnmrNews. I recommend that you
search for information about this on the Users Only section of their
web-site, &/or that you chat with your Varian rep. I think that they
only guarantee the systems they sell, and I think they discourage going
straight to Dell.
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I bought a Dell directly from Varian bundled with VnmrJ. You could
potentially do this yourself if you are comfortable installing Red Hat
Enterprise Linux 4 (it requires the 64 bit version) on that specific Dell
configuration, assuming Varian will sell you the software without a
computer (I had the impression they wouldn't).
Contrary to Varian's recommendations, I have installed all the Red
Hat updates as they have become available. There are only a couple of the
hundreds of updates that interact with the Varian software in any way.
The fixes are very minor and they were incorporated in an article in the
VNMR email newsletter several months ago.
I have also loaded RHEL 4 on 3 Dell computers for my Bruker Avance
systems, in addition to 2 HP workstations I have that were supplied
directly by Bruker. The HP's and an older Dell never presented any
problems. Two newer Dells I bought for Bruker instruments and the Dell
Precision 380N on the Varian have identical problems in that they refuse
to boot any kernel newer than the 2.6.9-5 kernel on the RHEL CD's. The
error messages from trying to boot newer kernels are fairly generic and
many fixes for these error messages have been suggested in Linux forums.
I have never found one that works on the newer Dells. I think there is
some evidence that there is bad juju between the Dell BIOS and RHEL boot
configuration options. There are some problems with the older kernel,
particularly some whining at boot time about the display driver wasting a
lot of CPU cycles. The display does do some flaky things e.g. if you have
VnmrJ and Firefox open at the same time. I would be delighted to hear of
a successful fix for this problem.
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There is a problem. Dell workstations are not uniform: they have
slightly different parts, different BIOS, so the software support
department at Varian has to adjust components of the operating system
for every new batch. As a result, the price for the Varian validated
workstation is $3,000 plus ~$2,000 for the software and license. On the
other hand, if you buy the workstation from Dell (~$1,300) you will have
to rub off your pants fiddling with multiple Linux files before it
communicates smoothly with the console. And it is not about the graphics
because a stand-alone workstation is running vnmrj just fine.
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The answer to your question is complex and success on getting a Dell PC
running on an Inova depends on several factors:
a. version of vnmrj you plan to run
b. version of RedHat linux
c. type of Dell computer and it's associated internal hardware (graphics
cards, hard drives, chip set etc.).
d. vintage of the Inova (PowerPC or older Motorola CPU)
We've had both success and failure attempting to put Dell PC's on our
Inova's. We were able to get two systems (Motorola vintage Inova's)
running perfectly using Dell 270's with Red Hat 3 and Vnmrj 1.1D. Our
attempt to get a much faster Dell GX620 running with VNMRJ 2.1b and Red Hat
4 on a similiar vintage inova was less sucessful. There are several issues
which require the setacq script and boot sequence to be modified. Even
after the system is modified enough to get it to run there is a more
serious issue with interactive communication where the system appears to
hang during shimming. My thought is that the PC is simply too fast for
this older acquisition CPU and there are timing issues. We're still
working on the GX620 so it may be possible to solve the problems, but I'm
not certain.
I do know that Varian's currently shipping PC is a Dell 380 with Red Hat 4.
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We are running both the Dell/Linux boxes here and in fact we are using
new Sun Ultra 45 computers running Solaris 10 as well. We used Open
Technologies to buy and install the computers. They do some NMR service
here as well from time to time. I have included his info below. Good
luck.
Open Technologies, Inc.
donfrank_at_opentech.biz
www.opentech.biz
(269) 288-0273
(269) 288-0274 (fax)
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--
WCAS Structural Biology NMR facility manager
Northwestern University
Phone: 847-467-1222
TECH, KG88
2145 Sheridan Rd.
Evanston, IL 60208
Received on Wed Oct 25 2006 - 19:32:51 MST