prerequisite black fingernail polish. I don't
remember how or why, but during the interview I claimed that SGI
was doomed because of the rising power of PCs and their graphics
cards. He seemed to take this personally and the interview ended.
I didn't get the job.
Cordially,
J
nteractive processes so the desktops' users (hardly) noticed.
Sure, it wasn't as fast or pretty as a real cluster, but it falls into
the computational category I invented called Pretty High Performance
Computing (PHPC).
Cordially,
Jon Forr
need for what I call
"pretty high performance computing", which is the highest performance
computing you can achieve, given practical limits like funding, space,
time, ... Sure there will always people who can figure out how to go
faster, but PHP
y can build
gcc and other large packages very quickly.
The scientists who run single process simulations
also like them but they're not real picky about
how long it takes for something to run. They also
generally spend close to no time at all optimizing
anything.
--
Jon Forrest
Research Comp
ow do you
figure out which memory module to
replace?
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
___
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physical
machine using VirtualBox. I call this Rocks-in-the-Box.
You'd never want to use this method for production
work but doing things this way makes it very easy
to create test clusters. You could also use these
test clusters to dabble in parallel programming.
Cordially,
--
Jon Fo
risk of using up too much RAM if a program
gets out of hand writing to /tmp.
Right. I don't think this is a good idea for scratch
space for the reasons you mention. It does make sense
for things like compilers and other programs that
create very transient and small files.
Cordially,
--
ople base their opinions on the manufacturer's
claims, and some people base their opinions
on the famous papers from Google and CMU that
came out a couple of years ago that described
how very large numbers of drives really work.
It's an interesting topic, no doubt.
Cordially,
--
Jon Forrest
R
lved in the research projects seemed
like they would have promising commercial
value, such as RAID, RISC, Postgres, and NOW.
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jl
low us to accept the equipment.
Things are different now, but space and people
are still more expensive than most equipment.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jl
x27;t come up with Twin boxes, I might
be forced to follow your advice. I'm not concerned
about sysadmin work, because I'm using Rocks. I'm more
concerned about ending up in the Twilight Zone where
things aren't as they appear.
--
Jon Forrest
Research Computing Support
College o
come out but my problem is that
I have money to spend that has to be spent soon,
maybe before the Twin boxes come out. So, I'm trying
to decide what to do. (I only want 1U boxes because
I have to pay for rack space).
Any advice?
Cordially,
--
Jon Forrest
Research Computing Support
College
ent
most of you run in, but it does present
interesting issues.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
___
Beowu
are to
create a cluster. Maybe later you'll find some commercial
products that solve specific problems, but one of the nice
things about modern clusters is that there's so much
good quality free software available.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
1
ou can buy a PCI card for not much money.
Once USB 3 is ubiquitous this problem (e.g USB 2.0 vs eSATA)
will go away.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@be
nt page of
the paper.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
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is?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
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999308 errors:0 dropped:0 overruns:0 frame:0
TX packets:27468315 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:24225053296 (22.5 GiB) TX bytes:73313582546 (68.2 GiB)
Interrupt:74 Base address:0x2000
Any advice on what to do?
es will have to be rewritten anyway, why
write them in a language which would require
purchasing yet another compiler?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-
evel which could
benefit molecular dynamics simulations?
Of course, but at what price? I'm talking both about
both the price in dollars, and the price in non-standard
directives.
I'm not a chemist so I don't know what would speed up MD calculations
more than a good GPU.
Cordially
at the s1070 is ~6k$ so you are talking at most two to three
machines here with your budget.
Ha, ha!! ~$6K should get me two compute nodes, complete
with graphics cards.
I appreciate everyone's comments, and I welcome more.
Cordially,
--
Jon Forrest
Research Computing Support
College of
CPUs - only on the GPUs).
Even if GPUs can be time shared, given the expense
of copying between main memory and GPU memory,
sharing GPUs among several processes will degrade
performance.
Are there any other issues I'm leaving out?
Cordially,
--
Jon Forrest
Research Computing Support
College of C
ed
cluster might be easier to deal with from a central management
point of view.
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
_
caused by the virtualization
is a factor, but it's decreasing as time goes
on due to better hardware support of virtualization
and cleverer software.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-14
D (if any)
justify its expense. Of course, in any production system
you'll want a few extra RAID cards lying around just
in case.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
08:41:08 frank kernel: []
:xfs:xfs_create+0x237/0x45c
Sep 28 08:41:08 frank kernel: []
:xfs:xfs_attr_get+0x8e/0x9f
Sep 28 08:41:08 frank kernel: []
:xfs:xfs_vn_mknod+0x144/0x215
Sep 28 08:41:08 frank kernel: [] vfs_create+0xe6/0x158
Cordially,
--
Jon Forrest
Research Computing Support
College of
ed on the dual-motherboard Supermicro cases.
Since each motherboard can hold 2 processors, and each AMD
Istanbul processor has 6-cores, I can get 24 cores per rack
unit. That's pretty dense.
I believe that SuperMicro also makes similar motherboards
for Intel processors.
Check it out!
Cordial
I'll have to figure out how to force IB when
using OpenMPI.
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
___
Beowulf m
the strange way the OFED
was installed, I can't easily run over just ethernet.
Thanks for your help
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
Bill Broadley wrote:
My first suggest sanity test would be to test latency and bandwidth to insure
you are getting IB numbers. So 80-100MB/sec and 30-60us for a small packet
would imply GigE. 6-8 times the bandwidth certainly would imply SDR or
better. Latency varies quite a bit among impleme
about IB.
How would you test your IB network
to make sure all is well?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
___
University Ingres database for this. When the database
became corrupt this was very embarrassing since I was using
this HSM system for work that the Postgres database group
was doing. This was the same group that had originally developed
Ingres.
I hope HSMs have become better since then.
Cordial
d the fact that my office is
cooler than our computer room - this is a sad fact
about the financial state of the Univ. of Calif. these days.
Anyway, thanks for all the suggestions.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkele
nodes are working fine
in the computer room.
I'm not convinced the problem is actually
the memory. Other than opening the node
to spray cooling liquid when it's in the warm
room, what approach would you use to figure out which
component(s) is(are) failing?
Cordially,
--
Jon Forrest
Resear
l times while you're
learning. This is normal.
Once you have more knowledge, and you've tried running
the actual program you want to run in the future, then
start thinking about the best hardware to get.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
Uni
Joe Landman wrote:
Imagine you are a processor, and you have written to a location in ram.
So now your cache line is dirty, and waiting in queue to be flushed
out. In your parallel program, along comes someone else who really,
really wants to read that cache line. Ok, so this forces you to
good
thing, because then all the benefits of caching would kick in.
There would be no cache coherence overhead since text is read-only.
Why is this a bad thing?
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
ch-only?
I did my test for both Alpha OSF/1 a while back, and modern
Intel x86.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
__
alize that this limit exists, and unless
we get much smarter, isn't likely to go away.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
___
On Mon, Apr 6, 2009 at 4:13 AM, Geoff Galitz wrote:
Can anyone recommend a good tex editor for the Windows Vista platform?
There are a lot of options out there on the web, but many of them seem
squirrely to me (too many required additional components or limited
usability).
Someone pointed ou
though my
job is mainly to manage Unix machines. The "vim" editor,
which is what you get on Linux and MacOS, has an excellent
implementation for Windows.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
x27;t talking about vendors
supporting the Linux kernel. I was talking about independent
software projects. One such example is Eclipse. It once was
totally IBM and now it's independent. And there are the various
projects run by the Apache Foundation.
Could SGE find a home outside of Sun?
--
J
easy but that's another issue.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
___
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a clear OS direction. As we know, it only
got worse. To their credit, Sun has lasted longer than DEC, which
had an even more severe lack of OS direction.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
ld be to not pay too much attention to
the subjective reviews you'll see here, including mine. Instead,
I'd suggest finding and understanding a switch benchmark program
that gives a more objective evaluation.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
1
rding head never touches the disk media."
(from AnandTech's website).
I wonder if these drives will come out in both enterprise
and consumer versions. Note especially the mention
of vibration reduction.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hal
1U with a ton of fans the extra $25 is worth it.
If there are real differences between the drives then this would be an
easier decision. There doesn't appear to be a consensus, however, that
the differences in the field are significant.
Cordially,
--
Jon Forrest
Research Computing Support
C
Greg Lindahl wrote:
On Wed, Jan 21, 2009 at 05:21:25PM -0800, Jon Forrest wrote:
As a wise man once said, "Why pay more?".
A wise man once told me to not price weird stuff at newegg.
An even wiser man once told me that Seagate 1TB drives
aren't weird stuff. They're the
Greg Lindahl wrote:
On Wed, Jan 21, 2009 at 04:19:55PM -0800, Jon Forrest wrote:
The
last time I checked, the enterprise drives were ~25%
more expensive than the consumer drives. This difference
might have changed since then.
Last time I checked, it was +$10 on a $300 drive. I bought
the
is concerned, my life wouldn't have been
improved if I had spent the extra money for the enterprise drives.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
jlforr...@berkeley.edu
__
cables really mess things up. Plus, they're expensive.
For modern clusters with pretty reliable hardware, I just
use a crash cart or equivalent. I don't need to do this
very often so it works out OK.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
Uni
Greg Lindahl wrote:
On Tue, Sep 30, 2008 at 09:05:16AM -0700, Jon Forrest wrote:
Probably the most dangerous is modifying
shared libraries and executables.
Uh, this is the safest, if you do it correctly. How do you think
people can use rpm/apt/whatever to update their systems with nothing
with very little, but you can build what you want and add
it to the vnfs capsules.
Comparing and contrasting these approaches is a good topic
for another thread.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
Bogdan Costescu wrote:
On Sun, 28 Sep 2008, Jon Forrest wrote:
There are two philosophies on where a compute node's OS and basic
utilities should be located:
You forget a NFS-root setup, this doesn't require memory for the RAM
disk on which you later mount NFS dirs.
You're
are some of your favorite issues, positive or negative, with
each approach?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
ists spent more time worrying
about microsecond latency, parallel barriers,
or XML overhead but reality always gets in the way.
In the future I hope to sin less often but it's a
growing experience. Reading this, and other, email
lists sometimes helps.
Cordially,
--
Jon Forrest
Research Computin
it's
just a 2X improvement it will be easy to justify.
I'm expecting it to be a lot more because much
of what goes on around here has already been ported
and summarized on the CUDA web site with >=10X improvements.
Then, once I've hooked the faculty I'll get them to buy
a high
ain creators will only have to create one
tool chain.
Anyway, I wasn't really asking about all this.
I was only wondering which board provides the
most power for the least amount of money for
a near-term pilot project.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
17
A graphics boards?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
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To c
m find this
discussion via Google so that they can save themselves some time.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
___
Beo
Matt Lawrence wrote:
On Fri, 8 Aug 2008, Jon Forrest wrote:
What's weird about this is that the root file system starts
on cylinder 1, as confirmed by the fdisk command. This is
using a brand new SuperMicro X7SBE motherboard with the
newest BIOS.
I suggest you create a /boot partiti
Needless to say, I have
a message in to them.
Any ideas could cause this?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
___
B
7;m not sure the same architecture would
make sense now, even with fast networks.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
my department to use CUDA, but I'm waiting
for V2 of the SDK to come out.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
___
B
Joe Landman wrote:
Hi Jon
Jon Forrest wrote:
First of all, I like Microsoft, and I voluntarily use
Vista as my desktop of choice. I've built and run the
Windows environments for the top CS and Civil Engineering
departments in the US, and I was the first to port
Postgres to Windo
standard Linux
clusters before they get any mainstream interest? What technical
features could they add that couldn't be added to a Linux
cluster?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
nglish. The same thing
has happened recently with "e-mail", which didn't
used to exist in common usage in plural form.
Now you see "e-mails" used by all kinds of people.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of Cal
y in the scientific realm, such as
what many of us deal with regularly.
Does anybody know how this usage first came about?
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PRO
core.
The main thing I'd like to know is whether
hyper-threading can do any harm when cpu
bound jobs are run.
Cordially,
--
Jon Forrest
Research Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[
realtime and I saw that I wasn't
even close to sending enough data to tax the switch.
I still don't know the cause of the problem but
I'm pretty sure it's not cause by excessive
network traffic. I suggest you try iftop to
see what your program is really doing.
Cordially,
e MacWorld Expo
exhibit floor and see how much activity is iPod/iPhone related
and how much is Mac related. I'm looking forward to doing
just this in January.
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
n the Postgres group in the Computer Science Dept.
here at UC Berkeley. I managed to port Postgres from Unix to
the MIPS version of Windows NT, back in the mid 90s. It was
surprisingly easy. Most of the problems were due to Postgres,
not to Windows NT.
Cordially,
--
Jon Forrest
Unix Computing Support
Colle
gh overhead for most people
to notice.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
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noise in a character stream.
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
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To change your
ea.)
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
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To change your subscription
ay and HPC computations. Even if it would only
be used for HPC computations its resources will have to be scheduled
one day. Maybe it could be scheduled as a asymetric MP, which
certain tasks, e.g. the graphics and HPC tasks, having affinity to
the GPU.
--
Jon Forrest
Unix Computing Support
College of Che
ht to do
completely right.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
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To cha
ut it probably is slow...
The vast majority of the time, when something seems slow to me,
it's because either my fingers or my brain are slow, often both,
not my computer. Note that I'm not talking the HPC applications
themselves. I always run those on Linux.
Co
gh edges that remain. I should add that
I've been using Unix since 1975.
I am *not* proposing running Windows in a cluster.
There are technical and financial reasons why
this might not be such a smart idea.
Go ahead. Make my day...
--
Jon Forrest
Unix Computing Support
College of C
ter
nodes. It would be nice if your program could let the user
choose which of these methods to use.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
ut what's important and what's not important.
Note that I'm not saying that a modern processor should
be some kind of hybrid mutant with 32-bit text pointers
and 64-bit data pointers. That would be ridiculous.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Ta
size of *every* executable
program and library I found on my Fedora Core 6 system. I did
not do a very good job at weeding out the dups caused by
symbolic links and the like, but the sum total of *all* these
text segments would have easily fit in a 32-bit address space.
--
Jon Forrest
Unix Computi
vs 64-bits question, so I'd welcome additional
comments, especially dealing with situations where programs
*don't* need the additional address space of the 64-bit model.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkele
d handle the complexity
of creating a program with 2-3MB, or even 16MB, of text. But,
there's a wall up there somewhere that you, and everybody else, will
hit long before you get to 4GB of text.
Cordially,
Jon Forrest
Unix Computing Support
College of
rograms
in both environments to see what comes out.
But I stand firm on my claim that no human, or group
of humans, can write a program that requires more than
32-bits of text space.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkele
maybe they exist, and that's what I'm talking
about human written programs.
Cordially,
--
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
University of California Berkeley
Berkeley, CA
94720-1460
510-643-1032
[EMAIL PROTECTED]
luser, it was configured and purchased
before I got here, so I had nothing to do with choosing
its components but I have to admit that I'm not
sure what I would have done differently.
Cordially,
Jon Forrest
Unix Computing Support
College of Chemistry
173 Tan Hall
Un
itch be making
a mistake while under heavy load when computing
the FCS values?
I'd like to find the definitive cause of the problem
before I ask the vendor to replace massive amounts
of hardware. How would you isolate the cause
of this problem?
Cordially,
--
Jon Forrest
Unix Computing Support
C
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