Recently, I filled a 4 foot rolling rack with equipment.  A 4 core IBM eSeries server with 2 TB of SCSI storage running ESXi is one of the main components.  I always like to keep the server online for various sundry items, but it usually sits largely idle, even with two Red Hat Linux instances running on it while I am studying.  This is somewhat of a waste in my opinion because the server is sitting idle with spinning fans while not doing much of anything.  A wonderful solution to this is have ESXi run a guest, specifically for the folding application.  If set up correctly, you can even have ESXi dedicate as much of the machine’s resources for CPU and memory as possible during downtime, and have it throttle it back when other applications are working on mission critical things.  I’m looking at you, small business and enterprise owners.

Most people download and install Ubuntu, or Windows as their OS choice for Folding@Home.  Since these OS’s are geared more toward the Desktop user, they have a little too much overhead for my liking when picking something for one process (yes, I just said that).   My OS of choice for this process was CentOS 5.5, but that’s just personal preference.  I aimed to install a minimally loaded, no frills OS with bare minimum internet connectivity and libraries required to make Folding@Home run, but it can happily share any Linux box you’ve got.  My base installation, along with a few programming libraries and a webserver, took about 2.5 gigs (keep in mind that a lot of this was the swap file I allocated during install, you may choose an amount that is drastrically lower).  If you aren’t familiar with the Linux command line, you’re going to want to install the GUI, but I’m right at home there, so I opted to save space.

It’s then a simple matter of downloading and installing their client onto your machine, here’s the blow by blow:

(Note: Be sure to find the correct version by checking http://folding.stanford.edu/English/Download)

Once you’ve determined your version, find a suitable install target, download and install by unarchiving…

Make the directory. Go to it.
ewolf@folding$ mkdir folding; cd folding/

This command downloads the package from Stanford, substitute the link to your install here.
ewolf@folding$ wget http://www.stanford.edu/group/pandegroup/folding/release/FAH6.29-Linux.tgz

Uncompress and unarchive the install.

ewolf@folding$ tar -xzvf FAH6.29-Linux.tgz

This will leave you with 2 files.

ewolf@folding$ ls
fah6     mpiexec

Give the binary execute permissions.

ewolf@folding$ chmod u+x fah6

Now, we have to configure the client settings by running the following command:

ewolf@folding$ ./fah6 -configonly

Follow the onscreen setup instructions.  These are the same as the configuration pane on Windows, just in text form.

Next, make it easy on yourself.  Build a start script for the startup command, give execute permissions:

ewolf@folding$ echo “./fah6 -verbosity 9 $*” > fah; chmod u+x fah

If this is a dedicated VM or machine, and you want this process to use all of your allocated processor power, this is the last step required for configuration.  To run this script on demand, simply execute it:

ewolf@folding$ ./fah

This will bring up a super neato (Not) screen with status information on your fold workload.

(click for full size)

Now for the tweaks.  There are two you may want to do right off the bat: CPU throttling and Automatic startup.  Here’s what my VM performance looks like when running this with minimal configuration:

(Click for full size)

This may be a problem if you aren’t fond of running your CPU’s at full utilization, due to electricity costs, wear and tear/etc….  If that is the case for you, there is a 3rd party utility available (freeware) to get the cpu utilization throttled back called “fahlimit” (click here for website in new window).  Run it as a part of your start/stop script I am going to cover shortly if this is a consideration.

<rant> Just as an aside, there’s a lot of talk on the Folding@Home website about how you should be able to run your processors at 100% all the time, without consequence (other than power consumed).  I’m here to tell you that this is just NOT TRUE.  Any amount of added heat, especially from processing wear and tear, will always cause your electronics to fail sooner than they would have if they had an average load on them.  Heat is the absolute enemy of electronics.  100% CPU utilization all of the time causes LOTS of heat.  The fact that the heat is dissipated with adequate heat sinking and fan cooling is immaterial.  These measures only will prevent your CPU from absolute failure from overheating. </rant>

Here’s what I did to install fahlimit:

First, get into the install directory (substitute $FAH with your install directory path)

ewolf@folding$ cd $FAH/

Download fahlimit.

ewolf@folding$ wget http://calxalot.net/downloads/versions/fahlimit/0.6/fahlimit-0.6-linux.tgz

Unarchive and uncompress fahlmit.

ewolf@folding$ tar -xzvf fahlimit-0.6-linux.tgz

Now run the extracted tool, also called fahlimit, with your desired utilization with this command:

ewolf@folding$ ./fahlimit -daemon -percent 50

As you can see, I’m using 50 percent here, and it’s brought my CPU utilization down accordingly:

(Click for full size)

Now that we’ve configured everything for optimum use within the OS, I will show you how to put it all together and autostart your folding when your VM comes up.  Instead of explaining everything in the start/stop script, and pasting it here, I am offering it in a .txt file, viewable here.

I installed a copy in my installation directory, and soft linked it to /etc/init.d, but it will of course work just as well if you have a copy in both spots.  Pay close attention and edit the script as necessary to suit your own installation needs.  And also, don’t forget to give the start script execute permission:

chmod u+x folding

To get it to start with the server, we just register it with chkconfig (You will probably have to be root to move the file into /etc/init.d as well as register with chkconfig):

root@folding# chkconfig –add folding

And that’s all it takes.  To verify it’s going to start, just query chkconfig to tell you which runlevels it will start with:

root@folding# chkconfig –list folding

You should see the word “on” after runlevels 3, 4, and 5.  If this is not the case, please consult the man page for chkconfig for further assistance.

Next, continue on to part 3, where I will briefly show you how to set up ESXi to utilize this lovely purpose-driven VM during off hours and non-peak processing times……but first, I need some sleep.  More to come in the next few days!

]]> http://www.n5ebw.com/2010-05/the-foldinghome-project-with-a-little-vmware-part-2/feed/ http://www.n5ebw.com/2010-05/the-foldinghome-project-with-a-little-vmware-part-1/ http://www.n5ebw.com/2010-05/the-foldinghome-project-with-a-little-vmware-part-1/#comments Sat, 22 May 2010 08:45:28 +0000 n5ebw http://www.n5ebw.com/?p=326 Around this time last year, I made a post about helping the environment through a service called “Earth911″ (See that post here).  This post isn’t about the environment, nor is it about woodworking, electronics, weather, or any of the other weird stuff you’ve come to expect from my writings.  This is about helping the thing we all hold most dear in this life: ourselves.  Readers in my audience who are on the techie side of things will likely have already known about this for years, but I also know I have others in my audience who are not.

Normal, healthy proteins take on a shape called a “fold” during their natural course of action in a healthy environment.  Protein mis-folding causes diseases such as Mad Cow, Cystic Fibrosis, Alzheimer’s, and some cancers, just to name a few.

Here’s where it gets personal.  My father-in-law (from whom I inherited all of the tools I restored), passed away at the age of 55 from complications of early onset Alzheimer’s due to a stroke.  Two of my grandmother’s are breast cancer survivors, but 1 also has Alzheimer’s, and my grandfather has an ongoing battle with Lung Cancer.  I am doing this to not only contribute to the research of these horrible diseases for their health and well being, but at the risk of sounding slightly vain and selfish, I’m doing it for myself, as well as my siblings, and immediate family.  We’ve determined the risks for these diseases are abundantly heightened in our family.  I’m quite sure I’m not the only one, otherwise Folding@Home would not exist.

Now that you have way too much background on the “why”, I’ll go into the “what” and “how”.

The “Folding @ Home” project (http://folding.stanford.edu/) harnesses the distributed computing power of idle computers on the internet to study protein folding.  Stanford’s protein folding researchers have developed a desktop application that runs in the background of your computer and does “simulated protein folding” to glean the output of different scenarios they can’t observe in the real world in abundance. It would take 10,000 CPU days to simulate folding, one CPU alone doing it would take 30 years (folds happen in a matter of 10,000 nanoseconds).  That’s unacceptable.  With the computer power harnessed from idle CPU power, the workload is distributed and results are produced much faster in their simulated folding time line environment.  I’m participating in the folding project by dedicating one of my idle CPU cores (I’m running a dual core) and as much available RAM as I can spare (I have 8 gigs total) to the cause while I do low CPU tasks like browsing the internet, listening to music, even as I write this article.  You can participate, too.  Go to the Folding@Home website, download the install program, which is very small, AND cross platform for all of you Linux and Mac users out there, install it, and turn it on.  (There’s even a app for your Playstation 3!) I promise that you won’t even notice it’s there, other than the icon on your taskbar, which usually brings a smile to my face.  Without sounding too cliche, “The life that you save may be your own”.

I’m taking it one step further, though.  Most of you will agree that if there were a kingdom where all of the subjects over-engineered and over-thought every little thing, I’d be a Prince.  Probably not the purple velvet wearing, pancake making one, though.  Now, I’m going to discuss how to get this running with spare CPU and memory on a VMWare server, so discontinue if this isn’t your brand of tech.

(Continue to Part 2 by Clicking Here)

Refurbishing Old Hand Planes Part 1: Flattening the Sole
Refurbishing Old Hand Planes Part 2: Truing the Frog
Refurbishing Old Hand Planes Part 3: Modifying the throat and chip breaker
Refurbishing Old Hand Planes Part 4: Sharpening the iron

• A Honing Guide (I got mine at Amazon for less than $8.00 USD)
• Our float glass with 120 grit paper from previous articles
• A jig for measuring the distance between the edge of the honing guide and the edge of the iron.
• 1000 grit/6000 grit combo Japanese waterstones (Which I also got from Amazon)

The reason we use the honing guide, is because like most of you visiting this article, I CANNOT judge angles by eye for sharpening, and, honestly, people that claim they can are, in my opinion, cheating themselves out of sharpening accuracy. Do what you want with your tools, but mine will be using the guide :-).

Anyway, if you take a look at the side of the honing guide, there is a legend that tells you the space in between the end of the guide tool and the tip of the tool that it takes to achieve a desired angle (feel free to do the necessary trigonometry if you don’t wish to use the legend).

(Note: I know this isn’t the best picture. It was hard to get a contrasting picture of the back bevel with the trashy fluorescent lighting in the shop, so I apologize)

(I know this isn’t a great picture either, but since I couldn’t get a good contrasting shot, look at how the light shimmers off of the edge in comparison)

We’ve got our sole flattened and our frog is true, and now it’s a good time to address tweaking a few of the components that deal with chip removal: the plane throat, and the chip breaker.

First, for some, I may have to justify what I am about to do. A lot of people skip this step because they are more concerned with the blade being sharp and removing thin layers of material that look like a piece of lace in my grandmothers china hutch. The simple fact of the matter is, planes don’t JUST remove really thin layers of material, but thicker ones as well (in woodworking, we refer to this as a more aggressively tuned plane). These, above others, have a tendency to bind in the throat of the plane because they are more rigid and stronger than their thin counterparts. Any good plane should be set up to plane thick shavings as well as thin ones.

Let’s imagine, through the magic of bitmap graphics, a side cutaway view of what our planer looks like with an unmodified chip breaker and shavings being removed from a piece of wood stock (Ok so my animation skills are terrible and this isn’t EXACTLY like it might look, but you get the idea):

If your shavings don’t perfectly roll up inside of the plane (and let’s face it, they rarely do), then they need somewhere to go. Notice on the circled areas of the cutaway view where our major binding points are: the throat opening, and where the chip breaker mates with the plane iron.

Again, using a little imagination, here’s a modified cutaway of what we’re going for:

I see my faithful readers getting irritated with my long-winded explanations, so on with the modification!

First, I chuck the Planer sole into a vise, using some scraps (in this case, some offcuts from a new cedar fence I just finished) to protect the metal:

Here’s a before and after picture so you can get a feel for how much material was removed:

The next thing we’re going to want to do is modify our chipbreaker so the tip of it is not elevated from the top of the plane iron. Apparently, my father in law, or whoever owned the plane beforehand, did this step for me, so I really don’t have a lot to demonstrate except for what it’s supposed to look like and a quick pictorial of how it is done. In order to achieve a result similar to the above, you must re-establish the bevel of the chip breaker so that the tip contacts the plane iron rather than the heel (In other words, we’re gonna make the angle steeper). This can be accomplished by going back over to our piece of float glass where we’ve pretty much done all of the milling work to our plane:

Not quite perfect, but certainly better than sawdust! Next time, we’ll put the finishing touches on our plane restoration by completely re-establishing the bevel on our worn plane iron and demonstrating proper sharping technique. See you then!

Related Posts:
Refurbishing Old Hand Planes Part 1: Flattening the Sole.
Refurbishing Old Hand Planes Part 2: Truing the Frog
Refurbishing Old Hand Planes Part 4: Sharpening the iron

So now the sole of the plane is flat.  I would have to say that 80 percent of your grunt work here is done…..but there are a few other crucial things left to accomplish.  If the bottom of our plane is flat, we need to ensure that the rest of that translates all the way up to the plane iron, because what have we really accomplished if we stop here?  Flattening and truing the Frog isn’t JUST to make it parallel to the sole, it also ensures we have a mating surface for the blade to rest on the whole time the plane is in operation.  When this surface is not flat, we get that ever so annoying movement named “chatter”.  As the plane iron skims across the wood substrate, it will unseat itself and bounce around on the surface of the frog, causing an inconsistent cut.

With all of that in mind, let’s look at the Frog of our test subject, the Stanley #4:

To disassemble our frog from the sole, there are two screws that hold it to the sole which need to be taken out.  From there, removal of the frog is easy.  We also need to push the pin out that anchors the blade fine adjustment screw lever to the frog (see circled item in above photo).  I used a thin punch, and it easily came apart.  One thing we ARE NOT removing here is the blade pivot lever that is used to pivot the blade left or right for cut adjustment.  It is riveted to the body of the frog.  Extra care will be used to avoid this part in the next step.

First, we need to address the tooling marks left on the top where the frog meets the blade:

Using the same method we used in part 1, we will again use the float glass and 220 grit sandpaper to GENTLY remove the tooling marks.  First, we’ll put some guidelines on the frog:

Again, being very cautious, it only takes a few minutes against our flat surface to produce a surface with most of the tooling marks removed:

Note that there’s a slight bit of tooling on the surface to the left (near the blade guide lever).  It’s not perfect.  On the frog, there’s very little material to work with on the mating surface for the blade, and we want to be careful not to remove too much.  This should be leaps and bounds above what was there before though, and the ultimate goal is to increase the surface area where the frog meets the blade, which we have done in large quantities.

The bottom of the frog also needs to be addressed for flatness.  Luckily, there wasn’t really anything out of square here, and basically, I just took a little time to remove the surface rust off of the mating surfaces with a flat file:

Your mileage may vary here, but unfortunately, there wasn’t anything to show with my plane.

The last step we are going to address related to the frog is where it mates to the sole.  There were a few tooling marks left over at the bottom at the four mating points.  I marked the surface with a Sharpie on all four, and used a flat file to knock down the back surfaces.  Use caution to make sure you aren’t beveling the surface, but flattening it out, or it will defeat the purpose of removing the tooling marks!  For the front two mating surfaces, I used some emory cloth and a 1/2″ piece of dowel rod and just twisted the cloth back and forth until the tooling marks and Sharpie markup lines were gone.  Here’s the before and after result:

Well, that’s all for truing up the frog.  We now have a parallel surface between our blade and material.  Next time, we will talk about how to modify our plane’s throat and chipbreaker for optimal removal of shavings so they don’t get jammed in the opening.  See you then!

Related:

Refurbishing Old Hand Planes Part 1: Flattening the Sole

Refurbishing Old Hand Planes Part 3: Modifying the throat and chip breaker.

Refurbishing Old Hand Planes Part 4: Sharpening the iron

Join me in this journey in the next couple of articles.

<rant>To tell you the truth, if these weren’t family heirlooms, I probably would have sold them and bought brand new Lie-Nielsen’s or something that was ready out of the box.  When taking my time into account, it would have been hard to justify doing this to every plane I come across that needs work.  The learning curve on the needed process wasn’t too bad, but this was incredibly time consuming. </rant>

Enough of that.  On to the project!  From doing some research, I made the following assumptions:

1. The sole had to be flat (duh, right?)
2. To reduce chatter, the area that the blade iron contacted needed to be as flat as possible. This part of the plane is an area known as “the frog”.
3. The areas where the frog meets the plane have to be parallel and flat.

Having a membership over at Finewoodworking.com, I was able to find an article suggested by Matt Vanderlist, from Matt’s Basement Workshop titled “Handplane Tune-Up“.  It pretty much confirmed the above, but also added the following:

1. The chip breaker must rest flat against the blade iron to reduce binding.
2. A relief cut should be milled into the throat of the sole to allow optimum chip clearing.  This does not mean WIDEN the throat, but instead of the opening being 90 degrees to the bottom of the sole, the front edge would get a 15 degree angle filed into it, leaving more room for the chips to clear the throat.

Note: Feel free to click on any of the smaller pictures to enlarge them (they’re thumbnails to conserve bandwidth)

The first step in restoring the #4 was to flatten the sole. Here’s a picture of what it looked like next to the flat sole of the block plane. As you can see, there’s a good bit of surface rust on the sole.  I’ve often heard a horse analogy that can be applied here: “Ridden hard and put away wet”.  A coat of paste wax every now and again couldn’t have hurt. In this situation, there are a few options: Either take the plane to a machine shop and have them flatten the bottom using a milling machine, or sand it down against a dead flat surface, such as a piece of granite, or float glass.  I, obviously, chose the latter of the two.

The first thing I did was to disassemble the plane down to the sole, leaving only the handles.  I knocked the surface rust off of the bottom and sides using some 80 grit that was attached to an old, thick piece of copier glass (thanks to my friend Dan for hooking me up with this, another repurposed thing out of the landfill!) with a small homogeneous amount of 3M spray on adhesive.

After knocking the surface rust off, I scribed lines diagonally across the bottom of the sole with a Sharpie marker to give a good indication of how true and flat it was.

Working on it for about an hour, and 2 sheets of 80 grit, I was still quite a ways from flat.

After about an hour longer with the 80 grit, I was left with a “true on 3 sides” plane.  As you can see, 80 grit leaves real deep grooved scratches in the metal (again, duh).  From here on out, we’ll step the grit down to sand out the scratches.  In between grits, I just pulled the piece of paper off of the glass (the adhesive was still tacky but not hard), shot another thin layer of the spray on down, and secured my paper.

Next up is the 220 grit. Notice immediately that the metal is starting to develop a luster!

Now the 400 grit………

I had some 600 grit laying around. Why not?!

And since we’re going this far, might as well wet sand it too…..

And finally, to protect all of that freshly sanded metal, a good coat of paste wax.

A lot of people seem to go overboard (that’s not to say that I didn’t take it a little too far as well, but I had the paper laying around) and use 1000 grit and 8000 grit wet stones to finish out the job.  Why bother?  It seems that it’s more of an asthetics issue than accuracy at that point (hope you like how your wood substrate puts those scratches right back into the metal, too).  And if you want to argue accuracy, here’s proof positive we’re flat, as well as square to the sides using my shiney new “Guaranteed Accurate” (maximum deviation from nominal of less than 0.001″ at any point along the full length of the blade) Incra square:

I seriously doubt that any accuracy can be gained by polishing out any further (within my skill set anyway), and if you’re willing to whip out your electron microscope to prove me wrong, well, woodworking probably shouldn’t be a hobby of yours, stay away from me!

Keep in touch.  Next time, we’ll discuss truing up the frog using somewhat of a similar method.

Related:

Refurbishing Old Hand Planes Part 2: Truing the Frog

Refurbishing Old Hand Planes Part 3: Modifying the throat and chip breaker.

Refurbishing Old Hand Planes Part 4: Sharpening the iron

FOR IMMEDIATE RELEASE

May 19, 2009

iPhone App Makes Local Recycling Easy and Convenient

When it comes to recycling and properly disposing of your trash, knowing is half the battle. The other half is actually getting your stuff to where it needs to go – whether it’s in a curbside collection program, a retail drop-off point or a hazardous waste event. With iRecycle, a new iPhone app from Earth911.com, you’re equipped for all stages of reducing your waste: knowing what you can recycle and where you can take it in your neighborhood.

Compatible with both iPhone and iTouch, iRecycle brings you Earth911.com’s national, comprehensive database of over 100,000 recycling and proper disposal locations for over 200 products at the touch of a button. Whether you need to recycle motor oil and CFLs in San Francisco or rechargeable batteries and paint in Washington, DC, iRecycle can connect you with real, local options.

Simply start typing what you’ve got, select your location and get instant access to the nearest recycling and proper disposal spots near you:

• Auto-complete makes searches quick and effective
• Get directions to the nearest site from your current location
• Find additional information like hours of operation, other materials accepted (maybe you can recycle all those plastic bags from under your kitchen sink), their Web site, etc.
• Check your search history to replay old search results –also functions on iTouch when an Internet connection is not available
• Call locations directly from search results if you need more information

Wherever you are, iRecycle keeps you connected to your green efforts. Even when you’re travelling or in a new city, you’ll never be without the knowledge of where to take your electronics, water bottles, car batteries, tires, eyeglasses… well, you get the point.

At Earth911.com, we’ve spent a lot of time thinking about how to make recycling easy. With iRecycle, you can use your powers for good – not waste. 

Anyway, Earth911 is a search engine you can use to find locations for hazardous materials disposal.  As a woodworker, you could use this to dispose of old, or dirty varnish, or any other material so it doesn’t end up in the landfill.  If you are a DiY tinkerer like I am, the search engine is of GREAT use.  One thing that comes to mind is circuit board disposal (Or any E-Waste) where they can recycle the silver and gold, but also reclaim the lead.  If you don’t know my stance on this issue, you should read this article from last year.

The absolute first thing that I used this site for was car battery disposal.  I have been accumulating these in the garage for some reason…mainly because I didn’t know of a safe way to dispose of them.  Lo and behold, the search engine turned up an unexpected result: Wal Mart.  I was a little skeptical, so I called to verify, and sure enough, they do take car batteries to recycle!

I’m gonna use this website a LOT, and I invite you to do the same.