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Old Jan 23, 2007, 04:35 PM   #1
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caveman-jim
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Linux How To: Install VMware Server, Ubuntu & FAH_SMP_Linux

This guide is intended to show how to install, configure and run the Stanford [email protected] linux SMP client beta on an Ubuntu 64bit installation, running in a Virtual Machine provided by VMware Server. For free! This guide assumes a little knowledge of the FAH console client, but steps through everything else.

Min Requirements:
VMware Server supports virtual machines with 64-bit guest operating systems only on host machines that have one of the following 64-bit processors:
- AMD Athlon 64, revision D or later
- AMD Opteron, revision E or later
- AMD Turion 64, revision E or later
- AMD Sempron, 64-bit-capable revision D or later (experimental support)
- Intel EM64T VT-capable processors (experimental support)
VMware provide a free tool to test your CPU and check if you can run a 64bit guest OS or not. Download it here for Windows.

The [email protected] Linux SMP beta is designed to run on 4 core boxes. However, the minimum requirement is 2 cores.
- Two or more cores - physical cores, e.g. a dual core processor or two sockets popluated with single core processors. (Hyperthreaded processors won't work as they don't support Intel VT. A Pentium4 3Ghz HT enabled system should be able to complete Windows SMP Work Units, however.)
- 1024Mb of RAM or more
- 7Gb hard drive space

Recommended Hardware:
To get the best performance, the faster and newer your hardware, the better. Vanderpool Technology/Pacifica enabled CPU's had hardware extensions to reduce the impact of running virtualization, and will give the best results. A list of current CPU's that support these technologies is:
AMD socket AM2 / Socket F
Intel most Pentium D 9x0, Xeon 3xxx/5xxx/7xxx, Core Duo and Core 2 Duo processors [excluding the mobility T5200 & T5500, and E4x00 Core 2 Duo range]. Use the Intel Processor Spec finder to be sure. Intel VT is required on Intel processors to run a 64-bit Virtual Machine, irrespective of 64-bit capability.
If you have a processor not on this list, you will likely still be able to run vmware server and the vm, but performance will not be as good as it could be with the newer technology. It's not a huge difference, either, so don't worry too much - just be aware.

2048Mb RAM (give 1Gb to your host, 1Gb to your VM['s])

Recommended: Dedicated partition on separate disk from Host OS for Virtual Machine storage

Install Procedure:

1 - Download & Install VMware Server
Get VMWare Server from http://www.vmware.com/download/server/ . Complete the Free Registration to receive a serial number. Download and install the VMware Server, no reboot should be required. Nice easy windows installer, accept the defaults. If you get an error message about IIS is not installed, don't worry about it (unless you plan on remotely administering your virtual machines at a web level).

Also note that disabling autorun won't take effect until you reboot. With autorun enabled, if your VM uses the host CD-ROM device any CD that is inserted is not only autorun by the host but by the guest as well. This can cause some odd hitches and slow read times from optical devices. Best practice is to turn it off, but you could simply just not auto connect your CD-ROM to your virtual machine - which we'll get into later.

2 - Download Ubuntu
Now you need to download the 'guest' OS, for which we are going to use Ubuntu 8.04 64bit Desktop or Server. Go to ubuntu.com and find a download that suits you - there are worldwide local mirrors and torrents available. Begin the download, and while we wait let's get the Virtual Machine ready. This is a ~700+Mb download, so it's going to be a while.

3 - Create a Virtual Machine
Open VMware server. First we need to configure the host, so click on the 'Configure the Host' button. Under the 'General' tab we can pick the default location for storing the virtual machine (virtual hard drive and other files). I would recommend a separate partition on a different physical disk than your host OS install. Next move to the 'Memory' tab. Here you can specify how much memory ALL your VM's can use of your physical resources. I would suggest you limit this option, unless you are not going to use the host at all, other than for running virtual server. I set my memory reservation to 1/2 my total RAM, at 1024mb. VMware Server can also swap VM ram to disk if you have VM's running using more RAM than is available. This will reduce performance dramatically, so don't do it unless you have no choice. I select 'Fit All VM Memory into reserved host RAM' so that there is no chance a VM will need disk access to write to RAM. We're not going to change the other options, so click OK to save your changes. If you plan on gaming on this box, the best option might be to allow some or most ram to be swapped. This will give RAM back to other applications, but slow down your VM.

Now create a new virtual machine, use the New Virtual machine button to start the wizard. Use 'typical' configuration, and Select "Linux" option and select "Ubuntu 64bit" from the drop down. Set the VM name to whatever you want, this is the name that will display in VMware server and will be used as the file name also. I called mine 'FAH_SMP_Linux'. For network connection, some have been selecting "NAT" option, as it saves messing about with network settings, and just bridges your windows internet connection, but if you are doing this at home and have a DHCP server/NAT [e.g. a router], then use bridged networking. If you are on a work connection and don't have permission to add machines to the network, or request IP addresses (either static or dhcp), then use NAT. You may want to let your IT Networking staff know what you're doing. For disk capacity, 5Gb should be plenty. I pre-allocate all disk space and split the disk into 2Gb files - makes backups, moves and defrags (host and guest) easier. Additionally, you should do a defrag on the disk you will create the virtual hd before you create your VM. Once the VM has been created (which will take a couple of minutes), highlight it in the left pane and then click on 'Edit Settings' in the right pane. Click on Processors and set number of proc's to 2, and click OK.

4 - Install ubuntu
Other guides will have you burn a CD to install from. This is not necessary, as the VMware server software is clever enough to mount an ISO as a virtual CD-ROM for your Virtual Machine to boot from, directly from your drive - meaning faster load times. To do this, edit your VM's CD-ROM options [click Edit Settings, highlight CD-ROM] and select 'Use ISO Image' instead of 'Host device'. Browse to the downloaded ubuntu 8.04 64bit image you found earlier, and click ok.

Start the virtual machine and it will boot from the CD and in a couple of minutes you will be at the 'Live Desktop'. From here double click on the install icon on the desktop, follow the prompts and off you go! Best practice is to name the machine the same as you did when you created the VM. When you get to the end of the install, select reboot and watch for the 'ubuntu' logo to disappear. When it looks like its rebooting [the screen shrinks down and goes black] right click on the VM name and click 'settings' to edit the VM settings. Uncheck the box for 'connected' for the CD-ROM. Now when your VM boots, it won't see the cd image in the cdrom drive - kinda like leaving the drive tray open.

4a - Configure Networking & Updating ubuntu
Now you may need to setup your networking ('System menu - Administration - Networking Tools : configure your IP, host name etc.) so you can get connected to intarweb. Once you have net capability, run the Update Manager [System menu - Administration - Update Manager] (it may be already nagging you) and install the updates avaialble. Once it gets done, download the 32bit install libraries by opening terminal [Applications - Accessories - Terminal] and typing:
Code:
sudo apt-get install autoconf autobuild binutils gcc make ia32-libs
You will be asked to enter your password - this is required for sudo ('SuperUser DO'). Say yes if prompted for hard drive space.
We also need to install some other pre-requisites, the build-essential libraries and headers needed for compiling vmware tools, and samba for filesharing. Note that the results of the 'uname -r' command are used in the headers command - replace these manually. It'll likely be 2.6.26-16-x, where X is distro type (desktop or server). We'll also make sure we're updated.
Code:
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install build-essential
sudo apt-get install linux-headers-$(uname -r)
sudo apt-get install samba
Close the terminal session when completed [hit X or type exit].

4b - Install VMware Tools
Now we need to install VMware tools. This lets VMware server gracefully auto-start/stop the VM when the host OS start/stops, and allows host-guest time synchronization. Due to the nature of Virtualization, VM's can loose time very quickly, which can screw up ppd calculations and deadline processing. VMware tools also improve performance for graphics rendering and input processing.
From the VMware server console, click the VM menu and then select 'Install VMwareTools'. Inside your ubuntu VM, this will automount and open a new CD image. open a terminal session and perform the following:
Code:
cd /tmp
tar zxpf /media/cdrom/VMwareTools-x.x.x-xxxxx.tar.gz
cd vmware-tools-distrib
sudo ./vmware-install.pl
What we did here was change to the tmp folder then extract the tgz from the CD and run the installer. Note if you get an error message then double check the name of the tar package - for example under ESX server 3.0.1 the tar will be VMwareTools-3.0.1-32039.tar.gz. Accept the defaults and go through the install. when prompted say yes to compile code for your distro, and don't worry about the missing lib error message.
After it gets done run the tool:
Code:
/usr/bin/vmware-toolbox
and in the dialogue that opens select 'synchronise time with host'

If your VM didn't detect the CD change, then the following commands will mount the CD for you (remember to substitute the correct release version and build numbers into the Vmware-Tools filename -TIP: use tab to autocomplete):
Code:
sudo mount /dev/cdrom /mnt/
tar zxpf /mnt/VMwareTools-x.x.x-xxxxx.tar.gz
cd vmware-tools-distrib
sudo ./vmware-install.pl
and to unmount it after you're finished:
Code:
sudo umount /mnt
Close the application and the terminal session.

5 = Download & Configure SMP Folding @ Home for Linux
Now we need to download and configure the linux SMP client.
Open a new terminal session. Now we need to create the working directory, download the client and configure it with your username and team number (64!!!!). Type:
Code:
mkdir -p ~/FAH
cd ~/FAH
wgethttp://www.stanford.edu/group/pandegroup/folding/release/FAH6.02-Linux.tgz
tar xzf FAH6.02-Linux.tgz
./fah6 -configonly
note the ~/ is a shortcut for /home/userid. [thanks MDC!]

5a = Configure [email protected] autostart with ubuntu
Now all that remains is to get this sucker up and folding! It would be nice to start it automatically when the OS starts, so now in terminal we do the following:
Code:
sudo nano /etc/rc.local
This opens the rc.local file for editing. Above the line that reads 'exit 0' (last line), add the following entry:
Code:
sudo sh -c "cd /home/user/FAH; ./fah6 -smp -local -verbosity 9"
note:
- change 'user/FAH'to your profile name and folding install directory - use the pwd command to find your full path.
- the example above uses the -local and verbosity 9 flags. remove them if you don't want to run them, but they're a good idea.
- the '-smp' flag is required for running SMP work units.
- the example also uses the -forceasm flag - the beta client is having problems inappropriately disabling SSE. use this to force it on for full performance.
Press Ctrl-O and hit enter to save your changes, then Ctrl-X to exit.
Close terminal.
Reboot and everything should come up automagically! Login and to monitor your event log, with autorefresh every60 seconds, open terminal and type:
Code:
cd ~/FAH
tail -s 60 -f FAHlog.txt
6 - Configure Virtual Machine to start/stop with Windows
Last but not least, make sure that in VMware server the VM is set to auto start/shutdown with the host (your windows install) by editing the VM settings, select the 'Options' tab, and click on 'Startup/Shutdown'. Set the VM to use the Local System account. change the 'on host startup' setting to 'power on virtual machine' and the 'on host shutdown' to 'shutdown guest OS'. Click OK to save.

Calculate PPD:
Look in the fahinfo log to see the WU type and make a note of one time period between step completions. Open EMiii calc, select the WU and enter the time, and ping! PPD!

Some of these beta WU's don't have entries in the EM3 protein list yet, so you won't be able to use the EMIII calc app. To manually calculate the PPD, use this formula:
Code:
(WU points)*[(1440 minutes in a day)/(time for 1% in minutes * 100)]
where you can find the WU points from the project protein database at stanford. The time for 1% should be that same time from completed step to completed step.
Example: from a log file like this:
Code:
[01:32:31] Completed 120000 out of 125000 steps  (96)
[01:37:18] Writing local files
[01:37:18] Completed 121250 out of 125000 steps  (97)
[01:42:04] Writing local files
[01:42:04] Completed 122500 out of 125000 steps  (98)
[01:46:49] Writing local files
[01:46:50] Completed 123750 out of 125000 steps  (99)
[01:51:36] Writing local files
[01:51:36] Completed 125000 out of 125000 steps  (100)
the 1% time is 5 mins, give or take a few seconds.
So for project 2606, which is 364points, the ppd is 364 *[1440 / (5 * 100)]; which gives 1048ppd.

Any questions or comments, spell checks or grammar corrections, please give your feedback!

Last edited by caveman-jim : Apr 13, 2009 at 01:41 PM. Reason: Updated for Client full release changes.
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Old Feb 1, 2007, 09:50 AM   #2
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I'm just wondering what running [email protected] on a guest OS does to the performance of the host OS. Is anyone actually doing this on their primary gaming machine?
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Old Feb 1, 2007, 11:51 AM   #3
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I don't game much, but it hasnt affected performance that I can see. I have restricted the amount of RAM my VM's can use, and windows task scheduling lets other apps have horsepower as its needed.

My host performance is actually better because the linux smp client uses less cpu and ram for more results, than running two windows clients natively.
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Old Feb 1, 2007, 08:10 PM   #4
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Thanks again Captain Caveman! I got to reinstall Ubuntu on my X2-4800+ box twice today. Once because I was trying to vmware tools and it wouldn't boot up anymore after switching from other 64bit to ubuntu 64 bit. The second time because I screwed up the vmware tools install. Anyway, it worked great after I cleared up the operator errors.

I've created a launcher for the tail command. Just copy the command and use "application in terminal" as the type.
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Old Feb 1, 2007, 08:16 PM   #5
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you're welcome... i think???
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Old Feb 3, 2007, 05:29 PM   #6
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Quote:
Originally Posted by caveman-jim View Post
you're welcome... i think???
Another of my boxes had a problem yesterday and these instructions were a great help! This time it wasn't a VM, but a straight linux install that was having hard disk issues. I had it up and folding on another disk in 30 minutes.
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Old Feb 8, 2007, 01:53 AM   #7
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Awesome guide Jimbodiah.
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Old Feb 9, 2007, 03:05 PM   #8
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OK, I've loaded Ubuntu on a partition on my backup pc, and I'm trying to get the smp client running. I have followed these instructions.
Quote:
mkdir -p ~/FAH
cd ~/FAH
wget http://folding.stanford.edu/release/FAH_SMP_Linux.tgz
tar xzf FAH_SMP_Linux.tgz
./fah5 -configonly
and when I try to launch the fah5 executable, it tells me there is no such file or directory.
[email protected]:~/fah$ ./fah5.exe
bash: ./fah5.exe: No such file or directory
[email protected]:~/fah$
I've checked the folder, and the file is in there. I've redownloaded it, and it still tells me its not there. WTF am I doing wrong?
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Old Feb 9, 2007, 03:13 PM   #9
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Quote:
Originally Posted by hazindu View Post
OK, I've loaded Ubuntu on a partition on my backup pc, and I'm trying to get the smp client running. I have followed these instructions. and when I try to launch the fah5 executable, it tells me there is no such file or directory.
[email protected]:~/fah$ ./fah5.exe
bash: ./fah5.exe: No such file or directory
[email protected]:~/fah$
I've checked the folder, and the file is in there. I've redownloaded it, and it still tells me its not there. WTF am I doing wrong?
I got the same results when I missed the ia32-libs step:

Quote:
Originally Posted by caveman-jim View Post
4a - Configure Networking & Updating ubuntu
Now you may need to setup your networking ('System menu - Administration - Networking Tools : configure your IP, host name etc.) so you can get connected to intarweb. Once you have net capability, run the Update Manager [System menu - Administration - Update Manager] (it may be already nagging you) and install the 97+ updates avaialble. Once it gets done, download the 32bit install libraries by opening terminal [Applications - Accessories - Terminal] and typing:
Code:
sudo apt-get install ia32-libs
You will be asked to enter your password - this is required for sudo ('SuperUser DO'). Say yes if prompted for hard drive space.
Close the terminal session when completed [hit X or type exit].
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Old Feb 9, 2007, 03:32 PM   #10
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Quote:
Originally Posted by Lupine View Post
I got the same results when I missed the ia32-libs step:
Oh thanks, I though I could put the updates off until later. It'll be awhile before I can try again.
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Old Feb 9, 2007, 04:30 PM   #11
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Quote:
Originally Posted by hazindu View Post
Oh thanks, I though I could put the updates off until later. It'll be awhile before I can try again.
Those libraries aren't available via the updates - you have to manually do it per Caveman's instructions.
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Old Feb 9, 2007, 04:53 PM   #12
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EDIT - The IA32 libs are needed to run the client, despite it being designed for 64bit operation...

Remember also that CASE is important in commands and filenames in linux.

Last edited by caveman-jim : Feb 9, 2007 at 05:00 PM.
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Old Feb 9, 2007, 11:38 PM   #13
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The SMP client.cfg options do NOT include the standard "stop if on battery" option. Is there a way to implement this for our laptop SMP folders?
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Old Feb 10, 2007, 12:51 PM   #14
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Last night I made some progress, but it wasn't folding anything
Quote:
[16:24:23]
[16:24:23] Project: 3027 (Run 8, Clone 76, Gen 13)
[16:24:23]
[16:24:23] Entering M.D.
[16:24:24] one 76, Gen 13)
[16:24:24]
[16:24:24] Entering M.D.
NNODES=4, MYRANK=3, HOSTNAME=ubuntu
NNODES=4, MYRANK=0, HOSTNAME=ubuntu
NNODES=4, MYRANK=1, HOSTNAME=ubuntu
NNODES=4, MYRANK=2, HOSTNAME=ubuntu
It stayed like that for about 30minutes, then I left for the hockey game, and when I got home it had apparently crashed. My monitor had no signal and there was no way to wake it up although the computer was still running. This morning I remade the directories and reinstalled [email protected], and I'm getting the same thing. No crash yet though.

Also, I checked the resource usage, and the processor usage was low.
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Old Feb 10, 2007, 05:18 PM   #15
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This error points to a network problem, either your VM network settings aren't working right or you've changed the host name and not updated the HOSTS file.
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Old Feb 11, 2007, 02:03 PM   #16
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Edited the guide to include adding the '-forceasm' flag.

Apparently the beta client has issues with sometimes disabling SSE inappropriately; use this flag to force SSE boost on for maximum performance.

To use it, change your /etc/rc.local file to

Code:
sudo sh -c "cd /home/user/FAH' ./fah5 -local -forceasm -verbosity 9"
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Old Feb 12, 2007, 08:05 AM   #17
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Quote:
Originally Posted by caveman-jim View Post
This error points to a network problem, either your VM network settings aren't working right or you've changed the host name and not updated the HOSTS file.
Thanks for the support Caveman-jim, and you too Lupine. Unfortunately I'm going to have to put this project on hold for a week or two or however long it takes to RMA a motherboard. Everything you told me to do worked, I just need working hardware so it doesn't shut off every few hours.

Edit: Replacement has been stable for 13hrs and counting....
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Last edited by hazindu : Feb 21, 2007 at 09:05 AM.
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Old Feb 12, 2007, 09:01 AM   #18
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man, that sucks. hope you get it back soon!
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Old Feb 12, 2007, 03:13 PM   #19
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Quote:
Originally Posted by hazindu View Post
Thanks for the support Caveman-jim, and you too Lupine. Unfortunately I'm going to have to put this project on hold for a week or two or however long it takes to RMA a motherboard. Everything you told me to do worked, I just need working hardware so it doesn't shut off every few hours.
You're very welcome. Fun working through this stuff with you guys.

Sorry to hear about the mobo issues. I'm going through a similar experience w/ my main computer's DFI Ultra-D. Looks like the regulator is dying.
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Old Mar 1, 2007, 04:56 PM   #20
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Instructions work for Kubuntu as well. I blew up a VM today while working on a server problem, so why not. Only bad thing is that I lost an incomplete WU (won't say how complete it was since it would make me cry).
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Old Mar 1, 2007, 11:11 PM   #21
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I didn't mention that a new VMware server is available. 1.0.2 was released yesterday. It may be just me, but it seems to boot the VM much faster.

http://www.vmware.com/download/server/
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Old Mar 1, 2007, 11:29 PM   #22
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Cool, good heads up. Thanks!

Reading the release notes, this is mostly bugfixes and not a major release.

Microsoft and VMware are about to get into a monoply litigation I think, as vmware is accusing them of anti-competitive practices and licensing. But that's not for this thread
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Old Mar 2, 2007, 02:32 AM   #23
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So I take it you have to uninstall the existing version first? Any catches to watch out for?
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Old Mar 2, 2007, 09:15 AM   #24
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Quote:
Originally Posted by Lupine View Post
So I take it you have to uninstall the existing version first? Any catches to watch out for?
It uninstalls the old version when you run the 1.0.2 installer as part of the process. It does prompt you about whether you want to keep your registry entries, and I most definitely said yes. When I finished the process, my VM was back up and running on it's own.
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Old Mar 2, 2007, 09:24 AM   #25
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I was wondering if I'd install this VMWare stuff would I be able to port my FAH work into it from an existing (native) Linux install?
Or even better make it automatically work on the existing FAH folder? (so that I could switch from Ubuntu native to WinXP+VMWare and continue work and then switch back like it was running all the time)
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Old Mar 2, 2007, 03:43 PM   #26
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XS,
You might look into the virtualization software from vmware.com and see if you can dual boot and run it as a VM when not running native. I just don't know the answer.
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Old Mar 2, 2007, 04:11 PM   #27
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Think of it like two networked computers, both would need a common storage location for the files to be read from where it wouldn't matter if one or the other is running or not.
Create an extra efs partition on your drive where you store your folding files, and run the client from there in both your native and virtualized ubuntu installs. You can attach a physical drive as a drive to a VM. Add a new drive, but select physical disk, and select the drive and partition you want to use.
I would suggest a new partition, unformatted. Add it to the VM and then format it, install and configure your folding client but don't download any WU's. Then reboot into your native distro and access the disk and copy the wu data over and repoint the config to run from there.
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Old Mar 3, 2007, 05:04 AM   #28
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Thanks. I'll give it a try when I finish this WU.
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Old Mar 3, 2007, 08:52 PM   #29
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owkay this is just weird, I can see the partition in partition manager in the vmware ubuntu version but I can't mount it. It says it doesn't know vfat

By the way do I need to reinstall graphics drivers for it, cause it runs irritatingly slow in vmware.
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Old Mar 3, 2007, 11:38 PM   #30
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create a new partition, and format it from inside the vm. other than that, we're pushing my knowledge of ubuntu - might be a topic to raise in the linux forums.

as for graphics, have you installed vmware tools? if you don't have that installed and running, then the responsiveness to input is much slower.
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