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Frequently Asked Questions (FAQ) (Last updated January 2, 2007 ) Other
FAQs FAQs on new hardware
What is protein folding? Please see our scientific background section for more details. Who "owns" the results? What will happen to them? Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a nonprofit institution dedicated to science research and education. We will not sell the data or make any money off of it. Moreover, we will make the data available for others to use. In particular, the results from Folding@home will be made available on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication, and these journal articles will be posted on the web page after publication. Next, after publication of these scientific articles which analyze the data, the raw data of the folding runs will be available for everyone, including other researchers, here on this web site. How can I see how many other people are participating? What has been "folded" so far? And how much have I folded so far? We keep many types of statistics of users and work accomplished on our web page. You can check out your Individual stats, Team stats, and overall project stats. Also, please check out the Results, Press, and Papers sections. Why don't you post the source code? Most of the critical parts of FAH are publicly available. The Tinker and Gromacs source codes can be downloaded and run. Unlike many computer projects, the paramount concern is not functionality, but the scientific integrity, and posting the source code in a way that would allow people to reverse engineer the code to produce bogus scientific results would make the whole project pointless. What has the project completed so far? We have been able to fold several proteins in the 5-10 microsecond time range with experimental validation of our folding kinetics. This is a fundamental advance over previous work. Scientific papers detailing our results can be found at papers.html. We are now moving to other important proteins used in structural biology studies of folding as well as proteins involved in disease. There are many peer-reviewed and published in top journals (Science, Nature, Nature Structural Biology, PNAS, JMB, etc) which have resulted from FAH. Current, more than all of the other major distributed computing projects combined! Why not just use a supercomputer? Modern supercomputers are essentially clusters of hundreds of processors linked by fast networking. The speed of these processors is comparable to (and often slower than) those found in PCs! Thus, if an algorithm (like ours) does not need the fast networking, it will run just as fast on a supercluster as a supercomputer. However, our application needs not the hundreds of processors found in modern supercomputers, but hundreds of thousands of processors. Hence, the calculations performed on Folding@Home would not be possible by any other means! Moreover, even if we were given exclusive access to all of the supercomputers in the world, we would still have fewer cycles than we do with the Folding@Home cluster! This is possible since PC processors are now very fast and there are hundreds of millions of PCs sitting idle in the world. Can I run Folding@Home on a machine I don't own? Please only run Folding@Home on machines you either own or on which you have the permission of the owner to run our software. Any other use of Folding@Home violates our license agreement (and just isn't a good idea in general). What are the minimum system requirements?
All computers can contribute to Folding@Home. However, if the computer is too slow (eg wasn't bought in the last 3-4 years or so), the computer might not be fast enough to make the deadlines of typical work units. In this case, one should run with deadlineless work units. My client got assigned to the IP address 0.0.0.0. What's up? From time to time, we may not have work that matches the requirement of every platform. When that is true, we will not supply you with duplicated work that really isn't needed. We'd rather have some clients idle and repeatedly rechecking for new work than busy for long periods working on something that doesn't need to be completed. Even though your computer may see occasional idle periods, we still value your donations. If this continues for an extended period of time, be sure to ask for help because that's not normal. I have a modem, can I use Folding@home? Yes. It can be configured to dial up automatically, or wait until you connect. There may be some problems with modems and the screen saver version. If you are experiencing any, please use the console version of Folding@Home. I'm behind a firewall, can I use Folding@home? Yes. Please configure your Firewall or Proxy server in the config panel. You can reach the config panel by right clicking in the graphical display or by clicking on the task bar icon. Folding@home Windows installer doesn't do anything. If you are attempting to install the Windows graphical client or screen saver, and see "Setup is starting ..." pop up, but then nothing else happen (no error message even), the problem is likely due to the presence of files named "setup.exe" in some directory present in your path (likely culprits are the directory in which the F@h installer is, your Desktop, and your temp directory). Remember that you may have multiple temp directories, depending on your operating system. Delete or move the setup.exe files and all should work fine. Folding@home looks strange (windows) or segfaults (Linux). Folding@home requires at least 32 MB of RAM. Weird things happen under windows with less memory and the console client simply segfaults under Linux under low memory conditions. My screen saver just looks like a black screen with little dots floating around. What gives? We think we have diagnosed this problem. It appears to be caused by a monitor or graphics card that does not support 8-bit color. Also, we have found problems with old graphics drivers. If you are having problems, please make sure that you have the most recent graphics and OpenGL drivers. Windows asks for some DLL. Where can I find it? Microsoft has these DLLs on their site. In particular, you need DLLs for winsock2 and OpenGL. These are built into most copies of windows NT, 98, and 2000. However, many copies of windows 95 do not have these.
I get an error like "Format:MyForm not found" when I try to download. This appears to be an error with Stanford's server, not our computers, and we are trying to identify the exact cause of the problem. It is fairly rare, however, and for now we suggest trying again at a later time. I get an error like "Network Recv Timeout" or in the console version (or in the file scrlog.txt). If you get something like:
then don't worry. It is having problems connecting to the server, and is waiting to try again. We have a few server problems right now, and many users are having this same problem. Just wait for a while, and it will connect. If it fails to connect for a day or so, it might be best to start it over again or reinstall. For the console version, hit Cntl-C to exit gracefully (note: this feature was recently added in, so it may not work for your version, and you may have to kill it instead), and start it again. I get an error like "Running self tests.......test failed, error -1" in the console version (or in the file scrlog.txt), but it seems to be running OK after that. Don't worry, if it seems to be working fine, it is. This error message is part of the Cosm distributed computing library upon which Folding@home is based, and as far as we have been able to tell, does not affect normal functioning of the Folding@home programs. I get an error like "Running self tests.......test failed, error -1" in the console version (or in the file scrlog.txt), and it dies. Uninstall, make sure the foldingathome folder in the "Program Files" folder has been removed, and reinstall. Most of the time, this should work. When I'm running the screen saver, it crashes, and says something about a page fault. If you get something like this:
followed by a bazillion dialog boxes you have to click away, there is not enough memory for the screen saver to start. Suggestions for solving this are closing other applications when the screen saver is running, and setting the wait time higher (perhaps 5 or 10 minutes), so that the screen saver won't come on while you are working.
Open GL games don't work or get minimized when running the FAH graphical client. OpenGL games don't work or get minimized when running the FAH graphical client. There is an known issue that can occur when running F@H and any other application that uses OpenGL, which are mainly games. This issue is not due to F@H itself, but rather that OpenGL, which is used in the F@H graphical client, does not allow itself to be used by two programs simultaneously. The workaround for this issue is to uninstall the F@H graphical client and install the console client. Thanks to [Spectre] and ellroy80 for contributing this FAQ entry .
What is the Genome@Home project and how does it related to the Folding@Home project? Genome@Home was another distributed computing project also from the Pande Lab. As of April 15, 2004, the project has concluded. You can find more details at http://genomeathome.stanford.edu Genome@Home's goal is protein design and its applications. One central application of ours for protein design is the creation of large libraries of designed protein sequences, in a sense "redesigning" or "reverse-engineering" an existing Genome (hence the name "Genome@Home"). Another application of protein design is to understand why proteins fold and why they misfold and aggregate. This is a central question of Folding@Home and directly relates to our study of protein folding and misfolding, as it is related to misfolding-related diseases, such as Alzheimer's, ALS, etc. What does the 'gah' selection do now? We have developed certain WUs which don't lead to new ones and hence don't need deadlines. These so-called "timeless" WUs are on a server and you can request one with the gah selection in the client. These WUs are best for slower machines or machines which can't be on the internet. The client will cache these WUs as well. For clients version 5.00 and later, deadlineless WUs are listed explicitly. For earlier clients, use the Genome@Home setting.
I just finished a WU and now I got another for the same protein. Is there something wrong? No, most likely everything is fine. We're studying the dynamics of a few proteins, so you're likely to get the same protein to work on multiple times. Each WU gives us additional information about the dynamics of that protein, so it is important to us. Indeed, if we did only 1 WU per protein, we would not learn very much. Does Folding@home run on dual processor or multi-core machines? Yes, you
can in two ways. For linux or OSX/Intel, one can run our SMP client. Is there anything special I should do to run on a cluster? The main aspect to consider is to make sure that the CPUID for each machine is unique. To help fight from having duplicate IDs, the windows versions (v. 3 and later) keep their IDs in the registry and the Linux version (v. 3.11 and later) keep it in a special file MachineDependent.dat. Ways to avoid duplicating IDs:
Why should I update my Folding@home software to the current version? We are constantly and rapidly improving the Folding@home software. We release new versions to fix bugs reported by the users to help make the project run as smoothly as possible. How do I run the screen saver when nobody is logged on (for screen saver client version 4 and earlier)? We encourage having the screen saver running when nobody is logged in in order to get the most useful running time possible. In order to do this you must edit the Windows registry. You can do this by using the program regedit (or also regedt32 in Windows 2000), usually located in the C:\WINDOWS folder. If it is not there, you can find it by using the "Find" utility in the Start menu. It might be necessary to have administrator privileges to do this. If you don't have administrator privileges, try to convince somebody that does to do this :) Once you start regedit, expand the HKEY_USERS folder by pressing the plus sign next to it. Then expand the .DEFAULT folder, then the Control Panel folder, then the Desktop folder. Select the Desktop folder, and you should see a list of names and data in the right hand window. Select the ScreenSaveActive name, right click, and select modify. The value should be set to one. This guarantees that the screen saver comes on when nobody is logged in. Next select SCRNSAVE.EXE, and change it to winfah.scr. (It might be necessary to set it to the absolute location, something like C:\windows\winfah.scr - wherever it's located). This selects the Folding@home screen saver as the default screen saver, when nobody is logged in. Finally, select ScreenSaveTimeOut and change it to 60. This makes sure that the screen saver comes on promptly (60 seconds, as a matter of fact) after somebody logs out. So, to summarize, to run a screen saver when nobody is logged on, update the registry keys:
How do the results get back to you? Your computer will automatically upload the results to our server each time it finishes a work unit, and download a new job at that time. At this time, there may be problems if your computer is only connected to the Internet sporadically. We are working on better support for these cases. Only the console version currently works at all over a modem connection, and there still may occasionally be a few bugs with that. Can I download more than one unit at a time? The algorithm we use works best if everybody downloads one work unit at a time, and checks back after each unit is completed, so therefore there is no option to download multiple units. If you have multiple processors in your computer, it is possible to have each processor work on a different unit; see what to do here. Don't try to run two copies on different machines that use the same directory on the same filesystem, either-- they NEED to run in different directories. How long does it take to finish a work unit? How do you measure a work unit? This varies, of course, on the speed of the computer and the size of the protein under study. Depending on the protein and the property studied, different size work units may be used. The project summary page has information on particular proteins' sizes and the deadline allotted each for completion. Can I run both the screen saver and console version at the same time? What happens if I run two console versions at the same time? ONLY if you install in different directories. Also, DO NOT just copy the files from one directory to each other. This will cause our server to get confused, and 1) you won't get credit for the work you do, and 2) it will be no use for science. Instead, run the install program twice into each directory. If you have already copied the program into multiple directories and are trying to run it, find the client.cfg file and delete the "userid=xxxxxxxx" line. Next time it connects to F@H, it should reset the client.cfg file, and all should be well. How can I make sure my results are being sent back and used? How can I tell how much work I've processed? To find out data that has been reported back you can check Individual stats, Team stats, and overall project stats. If your computer is returning data, you should see your username there along with the number of work units completed. If your name isn't there, and your screen saver or console version seems to be working fine, then either it hasn't finished a unit yet (this can take a few days, or even longer with an older computer to finish a WU), the list hasn't been updated yet. Check back in a day or two, and it should be there . . . as long as you remember correctly what you typed in for your donor name :) Why does adjusting the core process priority via the task manager not affect its performance? How do I manually adjust the priority of the Folding@home core? Currently when users try to change the priority of the core via the Windows NT/2000/XP task manager this does not affect how much CPU the core gets. The reason for this is that the work is done by the core thread, which is fixed to run at idle priority and is not affected by the task manager priority for the process (which displays as 'normal' by default). In order to change the priority manually users must use a program that allows thread-level priority adjustments. Can I run Folding@home when SETI@home is running? Yes, Seti@Home and other distributed applications can be run alongside Folding@Home, provided you have enough system memory. Some programs, including Seti@Home run at a higher priority than Folding@Home, which prevents Folding@Home from progressing if it is run at the same time. If you notice that Folding@Home is not progressing, you can fix this by enabling the "Slightly Higher Priority" Option in Folding@Home. This can be done through the advanced options page for the Windows client, or by running "FAH2Console -config" for the console versions. Are there any limits to how long my machine can take to finish a work unit (WU)? Yes. Depending on the work unit, unfinished work units for most projects "expire" and are reassigned to new machines. Since new WUs are generated by finishing old ones, we must keep things moving along by expiring units. As we move to longer WUs we will extend this time as needed. Expirations vary on the order of a week to a few weeks, depending on the nature of the WU. You will get stats credit for all units that you complete, even if they have expired, but they will not be as useful scientifically. Can I run the Linux version on FreeBSD? Yes. Please do the following: Install emulators/Linux_base from FreeBSD CD. Edit /compat/Linux/etc/yp.conf and put the correct server in there. Download the Linux folding console (FAHxConsole, where x is the version number) and cd to the directory. % brandelf -t Linux FAHxConsole As of Version 3.24, all you have to do from here is specify the "-freeBSD" flag when you run the client, % ./FAHxConsole -freeBSD and it will automatically brand the scientific cores it downloads. For clients prior 3.24, the -freeBSD flag is not supported and you have to do the following:after starting the client, wait till it download the core than kill the fold job. % brandelf -t Linux FahCore_65.exe % ./FAHxConsole and you're done! (Thanks to "gotti" for the suggestion).
What about OpenBSD? It works almost as easily as FreeBSD. Just follow these steps: 1. Install /usr/ports/emulators/redhat/base from ports on 3.4 or later.
If you're on an earlier version, or just prefer packages, install redhat_base-8.0p2. #!/bin/sh In either case, make sure the brandelf script is executable and in the
path of the user running FAH. Thanks to Alex Kirk for the OpenBSD info.
What is simulation instability? The simulation of molecular motion involves a great deal of computation. Each run consists of a number of time steps (each very small). At each time step, the position of the various atoms is calculated and updated, based on a number of factors. Sometimes, the simulation enters into a state that is not legal (i.e. atoms are too close, bonds are in impossible angles, etc.). At times like this, the Core exits, and information is uploaded to the server. The client will then get another assignment. If your computer is stable, then you haven't done anything wrong. On unstable computers, it is possible that the simulation instability was brought on by a fault of the system rather than something intrinsic to the work unit. Because of this, a work unit may be sent out again at some time if it is returned as having run into instability. In a given project, we expect a small percentage of units to encounter legitimate instability. What if I turn off my computer? Does the client save its work (i.e. checkpoint)? Periodically, the core writes data to your hard disk so that if you stop the client, it can resume processing that WU from some point other than the very beginning. With Tinker, that happens at the end of every frame. With GAH it happens at the end of each sequence. As proteins become more complex and run longer, it is better to have more frames in a WU so that you don't loose so much progress if you have to restart - - hence WUs that have 400 frames instead of 100. That still doesn't take the speed of the machine into account. A fast machine completes a frame in a few minutes while a slow one may take hours, and the donor with the slow machine still doesn't want to lose 99% of those "hours" yet the fast machine doesn't really want the overhead of writing the checkpoints every "few minutes" - - and neither of them wants the upload time associated with results containing many frames. With Gromacs, these checkpoints can happen almost anywhere and they are not tied to the data recorded in the results. Initially, this was set to every 1% of a WU (like 100 frames in Tinker) and then a timed checkpoint was added every 15 minutes, so that on a slow machine, you never loose more that 15 minutes work. In the 4.x version of the client, you can set the 15 minute default to another value. Thanks to Bruce Borden for this FAQ entry. How can I change my username (donor name)? The simplest way to change your username is go to the configuration panel (right click in the graphical display or click on the sys tray icon). You can change your username at any time. However, old work units will remain credited to the old username. How can I join/create a team? To create a team, please fill out this form. To join a team, just put the team's number in the configuration panel (on graphical clients) or enter the team number at the first time you run the client (for text console versions). I'm running multiple machines behind a firewall. Can they all have the same username? Yes. They can all have the same name. Note that in the past, one needed to append #1, #2, etc to the usernames. THIS IS NO LONGER NEEDED! Thanks. Are there any characters I should avoid in a username? We strongly recommend to stick to just letters, numbers and underscore. Right now, we reserve the characters # ^ ~ |. # is used for firewall differentiation (see above). We want to save ^ | and ~ for other problems which might come up. Also, don't put spaces in your username; please use some character like "_" instead. Finally, please note that usernames are case sensitive, so "Dave" and "dave" and "dAVE" are all different usernames. How do you decide how much credit a work unit
is worth? How do you
determine how many points a work unit is worth? Before putting
out any new work unit, we benchmark it on
a dedicated 2.8GHz Pentium 4 machine with SSE2 disabled
(more specifically, as reported by /proc/cpuinfo on linux: vendor_id
: GenuineIntel, cpu family : 15, model : 2, model name : Intel(R)
Pentium(R) 4 CPU 2.80GHz, stepping : 9, cpu MHz : 2806.438, cache
size : 512 KB). This machine runs linux, so all WUs are benchmarked
with the linux core.
How do you set the deadlines for the work units? Each work unit is benchmarked on a dedicated 2.8 GHz Pentium 4 machine with SSE2 disabled. For most work units (although there may be exceptions, described in the next paragraph), we apply this equation
where daysPerWU
is the number of days it took to complete the unit. The "+2" days
is there to give an additional buffer for fast WUs (to allow
for servers down, etc). If 30*daysPerWU is less than 10 days,
we set the deadline to 10 days, as a minimum time for all projects.
The timeout is the time at which the WU is resent to another
client and the deadline is the last time which we will give stats
credit for the WU. How can I get a copy of all of the current stats? Please feel free to download http://fah-web.stanford.edu/daily_user_summary.txt or http://fah-web.stanford.edu/daily_team_summary.txt . These files are updated every 6 hours. Please DO NOT run a crawler on our cgi pages. Such actions will result in your IP being permanently banned. Screen saver (Windows: version 4 and earlier; OSX: all versions):
Should I run the screen saver or console version? The graphical console version shows the same info as the screen saver, just in a window. You should run it if you
You should run the "screen saver only" version if you
If you're still not sure, try them both!
What's the screen saver showing? There are currently two visualization modes: Space-filling and ball-and-stick. In ball-and-stick mode, each small ball represents an atom, and the sticks represent bonds between atoms. In the space-filling model, each filled sphere represents the approximate volume that the electrons occupy around each atom. In both modes, carbon atoms are drawn in dark gray, hydrogen atoms are drawn in light gray (although some hydrogen atoms are not drawn at all), oxygen atoms are drawn in red, nitrogen atoms are drawn in blue, and sulfur atoms are drawn in yellow. The pie charts denotes the completed fraction of the current run and the fraction of the frame completed, respectively. My monitor is set to turn off after a while. Can I still run the screen saver? Energy saving features which turn the monitor off after a specified period of time do no affect the screen saver. As long as the computer is running, the screen saver will continue to run and accumulate useful data, even if the monitor is off. Does the screen saver use a lot of CPU time? The screen saver is designed to use very little CPU time. Even without any OpenGL hardware, the screen saver only uses about 5% of the CPU time for graphics. If you have some sort of OpenGL support on your graphics card, the CPU time becomes virtually zero. Since the spacefilling ("orb") drawing of the atoms can be seen in the process of drawing, it may look like it is taking a lot of processor space, but that delay is set by a timer, and does not occur because it takes a long time to draw. Will extra 3D hardware help make the screen saver go faster? 3D acceleration cards will make some difference for complex proteins. How do I shut down the screen saver? The screen saver is designed so that it shuts down on mouse click or key press. It will NOT shut down by simply moving the mouse. This is to prevent users from inadvertently closing down Folding@home, since it takes a short while to start processing every time it starts up.
Where did the logo come from? Our logo is an abstract representation of our goal: to go from the protein sequence encoded in the genome to the protein's structure. The double helix on the left of the logo denotes the genome (DNA is a double helical molecule) and the arrows on the right are representations of protein structure (beta sheet structure is often drawn as ribbons with arrows). Do you have web buttons that I can download to use with links to your site? How about this (thanks to RPH IV)
How much power/money is used by keeping a F@H
running 24/7 on a computer? Roughly, a CPU uses
about as much power as a watt light bulb. Here's a report
on computer
power management from Lawrence Berkeley government
labs, and there are other references on the web you can find.
Although
power
supplies on most computers are rated at 400 watts, average usage
is lower. On average, a Pentium-type computer uses about 100 watts
(if the monitor is off). So, the daily difference
between off and running F@H is about 24x100 = 2.4
kWh. At $0.15 per kWh ( from PG&E here in California), this
works out to about $0.36 per day. In
general, lighting and climate control use a much larger share
of household power than computers do. So the best bet for cutting
costs and conserving energy would be to turn off lights, turn off
your computer monitors (which use more power than a CPU), and
turn
down the heat. What about security issues? We have worked very hard to maintain the best security possible with modern computer science methodology. Our software will upload and download data only from our data server here at Stanford. The Cores are also digitally signed (see below) to make sure that you're getting the true Stanford cores and nothing else. How is this possible? We take extensive measures to check all of the data entering your computer and the results we send back to Stanford with 2048 bit digital signatures. If the signatures don't match (on either the input or the output) the client will throw away the data and start again. This ensures, using the best software security measures developed to date (digital signatures and PKI in version 3.0), that we are keeping the tightest possible security. Finally, the client/screen saver are available for download only from this web site, so that we can guarantee the integrity of the software. We do not support Folding@home software obtained elsewhere and prohibit others to distribute the software.
What are you going to add in later versions of the software? A good place to hear about new versions, beta versions, etc is the folding community forum ( http://forum.folding-community.org). |
