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Jean-Olivier Irisson

Hardware recommendations

Hello everyone,

I am in the market for a desktop machine dedicated to ImageJ and I am
a bit confused regarding what hardware bits are most important for my
application. Searching for recommendations on the list archives the
only recent threads I found were about laptops. So I figured I would
ask the experts on the list again.

I want to process big stacks (1000 of 3MP color images, 700KB each in
JPEG out of the camera) so they would likely be loaded as virtual
stacks. I may do a little batch processing on them: filtering,
normalization, possibly large particles detection but the latter,
which is demanding, can also be done on smaller size grayscale
versions of the images (to load them as a real stack). The main
application will be manual detection of small objects on the full size
images so I need images to load and display at 100% zoom quickly.

On the other hand, I don't have an unlimited budget ;) Given that,
what I thought was:
- fast harddrive (SAS?) since, as I understand it, within a virtual
stack, images are progressively loaded form the harddrive and not all
stored in RAM
- decent processor but no need to go over the top. one fast processor
is probably better than 2 slower ones. all of them are multicore
anyways now.
- decent amount of RAM (4GB) but, here again, not over the top, since
the virtual stacks won't be very demanding in RAM. faster RAM is
better though.
- good 24" display with a resolution > or ~ size of my images
(1920x1200)
- firewire port for fast connection to external storage where the
images reside
- Mac OS X or Linux

The part I really don't know what to think about is the graphics card:
how important is it for ImageJ? Once I get something with dedicated
RAM would it matter to go for the lastest screamer from nVidia or not?
I got an idea in the corner of my head that graphics cards really only
make a difference in 3D stuff but I feel this is now wrong.

I am currently looking at Mac Pros (but a bit over my budget), top of
the line iMacs, and Lenovo Workstations (S10 or D10).

Any advice on this would be greatly appreciated. I don't really have
anyone locally that could give advice. Sincerely,

Jean-Olivier Irisson
---
Division of Applied Marine Physics
Rosenstiel School of Marine and Atmospheric Sciences
4600 Rickenbacker Causeway, Miami, Florida 33149-1098
+1 786 342 3410
http://jo.irisson.free.fr/work/

Gabriel Lapointe

Re: Hardware recommendations

Personnaly I would build my own Desktop. You will end up paying less for
a machine that is custom build for your needs. Small computer shop will
do it for you, if you are uncomfortable with it. In any case I would
stay away from big brand, they are often using cheap hardware and forces
you to buy stuff you don't want (like being force to buy a big graphic
card if you want more RAM). Beside, you will often get a longer warranty
on the parts than on the whole computer. As for the point you raised, my
response are interleave in your text.

> - fast harddrive (SAS?) since, as I understand it, within a virtual
> stack, images are progressively loaded form the harddrive and not all
> stored in RAM
Go for multiple fast (usually small) Sata II and put them in RAID0.
There is no security here, if one HD fail all the data will be lost.
But, you are keeping backup right? If the workstation will not be used
for long term storage, go for Raptors (Western Digital) they are the
fastest around but they have a small capacity.

> - decent processor but no need to go over the top. one fast processor
> is probably better than 2 slower ones. all of them are multicore
> anyways now.
Go for a processor with big caches (that's the on processor memory).
Big GHz and gazillion core is often overrated. Remember, ImageJ will
more often work in a serial pattern so multiple core will not help you
there. Also. if the cache is too small, the processor is always waiting
for more data from the RAM, which slows down the whole operation.

> - decent amount of RAM (4GB) but, here again, not over the top, since
> the virtual stacks won't be very demanding in RAM. faster RAM is
> better though.
Get as much RAM as you can get and as fast as possible. RAM is cheap
right now and you will eventually need it. Some plugins make copies of
you image for processing or results and those are not virtual stack. You
can always use the swap but it will impaire the performance
dramatically. Personnaly, I work on big Z stack and often use my swap
partion on top of my 8 Gig of RAM.

> - good 24" display with a resolution > or ~ size of my images (1920x1200)
> - firewire port for fast connection to external storage where the
> images reside
Get eSata (external Sata) too. You will get the speed of an internal
sata drive and the conveniance of an external drive. A lot of external
drive that support eSata also have a USB2 port so it end up being more
compatible with other computers than just firewire.

> - Mac OS X or Linux
Custom build mean Linux, it's also free, takes less resources and is
more secure than Mac-OSX. Peace of mind and better performance come
sometimes at the price of more configuration. But free also means more
money for better hardware.

>
> The part I really don't know what to think about is the graphics card:
> how important is it for ImageJ? Once I get something with dedicated
> RAM would it matter to go for the lastest screamer from nVidia or not?
> I got an idea in the corner of my head that graphics cards really only
> make a difference in 3D stuff but I feel this is now wrong.
With the new plugins that use Java3D a better graphic card *might* be
worth the investment. I haven't played with those yet, so I can't
comment. However, remember that displaying your images and zooming it
requires RAM, you either put it directly on a dedicated card or you
reduce the amount available for the system. Therefore if RAM becomes
limited a dedicated graphic card *could* be a good investment.

>
> I am currently looking at Mac Pros (but a bit over my budget), top of
> the line iMacs, and Lenovo Workstations (S10 or D10).
Personally I don't like the "I know what you want to do with your
computer" philosophy of Macs. Therefore if I was forced to chose between
those I have a very clear bias toward the Lenovo.

I hope it helps,
Gabriel Lapointe

jiho

Re: Hardware recommendations

Thanks very much for your answer.

On 2009-March-17 , at 14:05 , Gabriel Lapointe wrote:

> Personnaly I would build my own Desktop. [...]

I looked into that but since it is a university purchase we are kind
of forced into some of the big brands... The computer shop that was
doing custom things and was contracted by the university now send
ready-made Lenovo configurations :( Hence my choice for Lenovo BTW.
Otherwise we basically have the choice between Dell and Apple.
In addition, an issue I have with building it from scratch would be
compatibility of parts and support by Linux. I did that a few years
back and Linux support took 6 month to come, with the next kernel. We
don't have that kind of time. But a few years might be centuries in
Linux time and maybe the days of kernel recompiling are long gone now!

>> - fast harddrive (SAS?) [...]
> Go for multiple fast (usually small) Sata II and put them in RAID0.
> [...] not be used
> for long term storage, go for Raptors (Western Digital) they are the
> fastest around but they have a small capacity.

I was thinking about 2 SAS 15000 rpm in RAID 0 and a big external
storage. These seem faster than the Raptor (10000 rpm) or is there an
inherent difference between SAS and SATA that I am overlooking?

>> [...]
> Go for a processor with big caches (that's the on processor memory).
> Big GHz and gazillion core is often overrated. Remember, ImageJ will
> more often work in a serial pattern so multiple core will not help you
> there. [...]

OK, I felt this way about the multi processor/multi core thing and
ImageJ. I currently chose a Core 2 Duo with 6MB L2 Cache. I might
spend more and get a Quad with 8MB (12 is out of my reach).

>> - decent amount of RAM (4GB) [...]
> Get as much RAM as you can get and as fast as possible. [...]

OK, good to know thanks. I am on PC3-8500 1067MHZ and will go all the
way up to 8GB

>> - firewire port for fast connection to external storage where the
>> images reside
> Get eSata (external Sata) too.

Thanks, I overlooked that indeed.

>> - Mac OS X or Linux
> Custom build mean Linux, it's also free, takes less resources and is
> more secure than Mac-OSX. Peace of mind and better performance come
> sometimes at the price of more configuration. But free also means more
> money for better hardware.

I am OK with Linux ;)
I was kind of surprised however by how relatively "cheap" the Macs are
for what you get inside. I built some configurations identical to a
Mac Pro with Dell and Lenovo and both are more expensive than the Mac
Pro (>$4500 vs $4000 for the Mac!), while still making compromises on
some components (slower RAM, less ports, not as good monitors, etc.).

>> The part I really don't know what to think about is the graphics
>> card:
>> how important is it for ImageJ? Once I get something with dedicated
>> RAM would it matter to go for the lastest screamer from nVidia or
>> not?
>> I got an idea in the corner of my head that graphics cards really
>> only
>> make a difference in 3D stuff but I feel this is now wrong.
> With the new plugins that use Java3D a better graphic card *might* be
> worth the investment. I haven't played with those yet, so I can't
> comment. However, remember that displaying your images and zooming it
> requires RAM, you either put it directly on a dedicated card or you
> reduce the amount available for the system. Therefore if RAM becomes
> limited a dedicated graphic card *could* be a good investment.

OK I think I will pass on it this time then, and get a decent one with
256 or first price 512 Video RAM and max out the actual RAM.

>> I am currently looking at Mac Pros (but a bit over my budget), top of
>> the line iMacs, and Lenovo Workstations (S10 or D10).
> Personally I don't like the "I know what you want to do with your
> computer" philosophy of Macs. Therefore if I was forced to chose
> between
> those I have a very clear bias toward the Lenovo.

Thank you again for your precise answers. I will wait a bit for more
comments and probably go with a customization of a Lenovo then.

Jean-Olivier Irisson
---
Division of Applied Marine Physics
Rosenstiel School of Marine and Atmospheric Sciences
4600 Rickenbacker Causeway, Miami, Florida 33149-1098
+1 786 342 3410
http://jo.irisson.free.fr/work/

Gabriel Lapointe

Re: Hardware recommendations

>
>> Personnaly I would build my own Desktop. [...]
>
> I looked into that but since it is a university purchase we are kind
> of forced into some of the big brands... The computer shop that was
> doing custom things and was contracted by the university now send
> ready-made Lenovo configurations :( Hence my choice for Lenovo BTW.
> Otherwise we basically have the choice between Dell and Apple.
I was suspecting that kind of things. We suffer from the same plague.

> In addition, an issue I have with building it from scratch would be
> compatibility of parts and support by Linux. I did that a few years
> back and Linux support took 6 month to come, with the next kernel. We
> don't have that kind of time. But a few years might be centuries in
> Linux time and maybe the days of kernel recompiling are long gone now!
I never complied Linux kernel, I started using linux in 2007. It is true
that hardware support for bluetooth devices, iphone and the latest 3D
graphic cards is still a bit sketchy but for the essentials there is no
problem.

>>> - fast harddrive (SAS?) [...]
>> Go for multiple fast (usually small) Sata II and put them in RAID0.
>> [...] not be used
>> for long term storage, go for Raptors (Western Digital) they are the
>> fastest around but they have a small capacity.
>
> I was thinking about 2 SAS 15000 rpm in RAID 0 and a big external
> storage. These seem faster than the Raptor (10000 rpm) or is there an
> inherent difference between SAS and SATA that I am overlooking?
Last time I check, SAS drive and interface card were more expensive. My
understanding is that they are good for things like database server but
I'm not sure they are worth it on an imaging workstation. But I maybe
wrong. It takes only a couple of seconds to load my stacks (400-800 Mb)
from a 4 disk at 7200RPM RAID5 array (ext3). I would ask myself if it is
worth the extra cost.

>
>>> - Mac OS X or Linux
>> Custom build mean Linux, it's also free, takes less resources and is
>> more secure than Mac-OSX. Peace of mind and better performance come
>> sometimes at the price of more configuration. But free also means more
>> money for better hardware.
>
> I am OK with Linux ;)
> I was kind of surprised however by how relatively "cheap" the Macs are
> for what you get inside. I built some configurations identical to a
> Mac Pro with Dell and Lenovo and both are more expensive than the Mac
> Pro (>$4500 vs $4000 for the Mac!), while still making compromises on
> some components (slower RAM, less ports, not as good monitors, etc.).

Comparing big brand to big brand it is true that, for the quality, Mac
are often cheaper than the others.

Justin Walker-3

Re: Hardware recommendations

In reply to this post by jiho

At $4000+, you're being taken for a massive ride. You could easily build a
core i7 system with dual WD Velociraptor drives in RAID 0 + a couple slow 1
TB drives, 6GB of triple channel DDR3 1600 RAM, and mid-range (say maybe a
8800GT 512MB) video card for ~$2500. That would be ample for your needs.

I suggest looking into some of the smaller vendors. I have ordered machines
from TeamHPC before, they have a federal government contract so your school
should be able to place a no-bid order with them.

Linux compatibility has come miles in the last few years. At this point,
the only things you may have issue with are wifi devices or any
significantly unusual hardware (OEM framegrabber cards, for instance).
WinXP x64 is a very stable platform, though.

- Justin Walker
University of Maryland

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of jiho
Sent: March 17, 2009 3:58 PM
To: [hidden email]
Subject: Re: [IMAGEJ] Hardware recommendations

Thanks very much for your answer.

On 2009-March-17 , at 14:05 , Gabriel Lapointe wrote:

> Personnaly I would build my own Desktop. [...]

I looked into that but since it is a university purchase we are kind
of forced into some of the big brands... The computer shop that was
doing custom things and was contracted by the university now send
ready-made Lenovo configurations :( Hence my choice for Lenovo BTW.
Otherwise we basically have the choice between Dell and Apple.
In addition, an issue I have with building it from scratch would be
compatibility of parts and support by Linux. I did that a few years
back and Linux support took 6 month to come, with the next kernel. We
don't have that kind of time. But a few years might be centuries in
Linux time and maybe the days of kernel recompiling are long gone now!

>> - fast harddrive (SAS?) [...]
> Go for multiple fast (usually small) Sata II and put them in RAID0.
> [...] not be used
> for long term storage, go for Raptors (Western Digital) they are the
> fastest around but they have a small capacity.

I was thinking about 2 SAS 15000 rpm in RAID 0 and a big external
storage. These seem faster than the Raptor (10000 rpm) or is there an
inherent difference between SAS and SATA that I am overlooking?

>> [...]
> Go for a processor with big caches (that's the on processor memory).
> Big GHz and gazillion core is often overrated. Remember, ImageJ will
> more often work in a serial pattern so multiple core will not help you
> there. [...]

OK, I felt this way about the multi processor/multi core thing and
ImageJ. I currently chose a Core 2 Duo with 6MB L2 Cache. I might
spend more and get a Quad with 8MB (12 is out of my reach).

>> - decent amount of RAM (4GB) [...]
> Get as much RAM as you can get and as fast as possible. [...]

OK, good to know thanks. I am on PC3-8500 1067MHZ and will go all the
way up to 8GB

>> - firewire port for fast connection to external storage where the
>> images reside
> Get eSata (external Sata) too.

Thanks, I overlooked that indeed.

>> - Mac OS X or Linux
> Custom build mean Linux, it's also free, takes less resources and is
> more secure than Mac-OSX. Peace of mind and better performance come
> sometimes at the price of more configuration. But free also means more
> money for better hardware.

I am OK with Linux ;)
I was kind of surprised however by how relatively "cheap" the Macs are
for what you get inside. I built some configurations identical to a
Mac Pro with Dell and Lenovo and both are more expensive than the Mac
Pro (>$4500 vs $4000 for the Mac!), while still making compromises on
some components (slower RAM, less ports, not as good monitors, etc.).

jiho

Re: Hardware recommendations

Thanks for your answer.

On 2009-March-17 , at 17:07 , Justin Walker wrote:

> At $4000+, you're being taken for a massive ride. You could easily
> build a
> core i7 system with dual WD Velociraptor drives in RAID 0 + a couple
> slow 1
> TB drives, 6GB of triple channel DDR3 1600 RAM, and mid-range (say
> maybe a
> 8800GT 512MB) video card for ~$2500. That would be ample for your
> needs.

Oh yeah, $4000 is way too expensive for this kind of application. It's
just that my supervisor works on a PowerMac G5 so I started from this
range, to have a baseline for her. Then, after reaching the $4000, I
went on to PCs and figured that I would just downgrade a bit from the
Mac and get a much cheaper system. And I was surprised to see the
price of those supposedly cheaper machines rise up high there. So I
did the part-for-part comparison just out of curiosity.

I am looking for something around $2000 + screen and external backup
storage. Thank you for your advice, especially on the video card. I
will look into that.

> I suggest looking into some of the smaller vendors. I have ordered
> machines
> from TeamHPC before, they have a federal government contract so your
> school
> should be able to place a no-bid order with them.

Thanks very much for that, it seems to be just what we need. I'll call
them tomorrow!

Jean-Olivier Irisson
---
Division of Applied Marine Physics
Rosenstiel School of Marine and Atmospheric Sciences
4600 Rickenbacker Causeway, Miami, Florida 33149-1098
+1 786 342 3410
http://jo.irisson.free.fr/work/