Linux Questions

[APOLLO]

I installed F@H in Linux for the first time and have a couple of questions. The program is working properly but there's no visible window to view its progress. It's as if it installed as a service, and I can't see where to stop and restart it. I installed the latest version of the Linux client.

Second, which flags should I include? I'm intending to work on SMP units. Third, anyone have a good recommendation for a file manager? The built-in file manager although decent for rudimentary tasks, is very limited and seems to lack advanced features. Its user interface also leaves a lot to be desired. I'm using Ubuntu 8.04. Nice distro. (thanks to Alan for the recommendation)

TIA.

 

[capreppy]

You can install as a service: run "./installService" to get it to start when the OS boots.

If you start via "./folding start", then it'll run in the background. If you start via the terminal screen using "./fah6" then you'll see it on the terminal screen (much like a Windows command window). You can check to see if it is running via Resource Manager. You can also periodically check the fahlog.txt.

I'm using "-smp -advmethods -verbosity 9 -forceasm" as my flags. The flags are similar to the Windows version. Only difference is the "-smp" flag. Without it, it will as single CPU client.

No recommendations for a file manager. Currently running via VM and it's set to just fold. I do like the Ubuntu 8.04 distro. Pretty straight forward.

 

[tkam]

I have mine setup the following way, I run ./fah6 -smp -advmethods to start the client and then i have fahmon installed to get the approx. ppd numbers. Fahmon is kind of a pain to install, but there are a few good guides around for doing it in Ubuntu.

 

[APOLLO]

You can install as a service: run "./installService" to get it to start when the OS boots.

I don't want it as a service and it's not currently installed that way.

If you start via "./folding start", then it'll run in the background. If you start via the terminal screen using "./fah6" then you'll see it on the terminal screen (much like a Windows command window).

I start the client through its executable (fah6) but it's not visible.

You can check to see if it is running via Resource Manager. You can also periodically check the fahlog.txt.

You mean System Manager? I don't see a Resource Manager, unless you're referring to the 'resources' tab of SM.

I'm using "-smp -advmethods -verbosity 9 -forceasm" as my flags. The flags are similar to the Windows version. Only difference is the "-smp" flag. Without it, it will as single CPU client.

Thanks.

I have mine setup the following way, I run ./fah6 -smp -advmethods to start the client and then i have fahmon installed to get the approx. ppd numbers. Fahmon is kind of a pain to install, but there are a few good guides around for doing it in Ubuntu.

I have everything up and going, I just need to make the client visible. Currently, I must bring up the log text every time I wish to view its progress, and stopping the client is impossible without terminating its process. I'm intending to get Samba working so I can have it monitored remotely from FahSpy, if that's at all possible.

 

[tkam]

You need to open up a terminal widow, browse to where you have f@h installed and then type: ./fah6 -smp

You'll then see the client running and can see it's progress via the terminal window.

 

[rmdashrrootsplat]

You could always tail the log file. As it's written to it'll update on the screen.

tail -f FAHlog.txt

 

[APOLLO]

Thanks for the suggestions guys, but I want this to be as efficient as possible and as straightforward as possible. I didn't install Linux to learn it, but fold on it. Why won't the terminal screen come up automatically upon executable startup? Is this a Linux idiosyncrasy?

 

[APOLLO]

You need to open up a terminal widow, browse to where you have f@h installed and then type: ./fah6 -smp

You'll then see the client running and can see it's progress via the terminal window.

The client won't execute in the terminal window for some reason. Anyone else have suggestions?

 

[SmokeRngs]

How exactly are you starting the client?

I don't use Ubuntu but openSUSE (w/ KDE) instead. For the clients I just created a shortcut on the desktop. In the options for the shortcut I can have it open in a terminal window or not. If I don't have it set to open in a terminal window it will run in the background. If I have it set to open in a terminal window I can watch the client like you would in Windows.

Also, so I don't have to start up the clients manually when the OS starts I have the KDE session saved to be loaded on startup.

As for the flags, I use -smp -forceasm -verbosity 9.

 

[APOLLO]

How exactly are you starting the client?

I don't use Ubuntu but openSUSE (w/ KDE) instead. For the clients I just created a shortcut on the desktop. In the options for the shortcut I can have it open in a terminal window or not. If I don't have it set to open in a terminal window it will run in the background. If I have it set to open in a terminal window I can watch the client like you would in Windows.

I don't see an option for a terminal window in the shortcut with my distro, unless I don't recognize it.

 

[SmokeRngs]

I don't see an option for a terminal window in the shortcut with my distro, unless I don't recognize it.

That's part of the problem, you're using Ubuntu which by default uses Gnome instead of KDE. There are a lot of differences between the two. Unfortunately, I haven't used Gnome in probably a year or more so I'm not sure where the options would be.

Well, just hooked up a monitor and mouse to one of my P3s which is running Ubuntu 7.04 and couldn't find an option for the shortcut to run in a window. I don't have F@H running on the machine but WCG instead so I never looked into it.

 

[APOLLO]

That's part of the problem, you're using Ubuntu which by default uses Gnome instead of KDE. There are a lot of differences between the two. Unfortunately, I haven't used Gnome in probably a year or more so I'm not sure where the options would be.

Well, just hooked up a monitor and mouse to one of my P3s which is running Ubuntu 7.04 and couldn't find an option for the shortcut to run in a window. I don't have F@H running on the machine but WCG instead so I never looked into it.

If worse comes to worst, I guess I could always install a KDE distro in another VM to try out. This OS was easier to install than virtually (no pun) any one I ever tried in my life. All I do now is double-click the F@H executable in the folder its located in. It doesn't start any other way. I can't even get it to start from a terminal window, which would have been sufficient for my needs.

Thanks for your help just the same.

 

[SmokeRngs]

If worse comes to worst, I guess I could always install a KDE distro in another VM to try out. This OS was easier to install than virtually (no pun) any one I ever tried in my life. All I do now is double-click the F@H executable in the folder its located in. It doesn't start any other way. I can't even get it to start from a terminal window, which would have been sufficient for my needs.

Thanks for your help just the same.

You don't actually need to install another copy in another VM. You can install KDE in the current install instead and at login or another way, select to use KDE instead of Gnome. I've done this before but anymore I don't install Gnome except for a few of the components like Gnome System Monitor.

Also, I don't see how you would have a problem starting it from a terminal window. All you would need to do is open the terminal, navigate to the directory where it's installed and then type ./fah6 -smp -forceasm -verbosity 9 . After that it should start up with no problems inside the terminal.

 

[rmdashrrootsplat]

If you want to try KDE in Ubuntu check this page out:

http://www.psychocats.net/ubuntu/kde

Alot of useful tips in there, including changing your default file manager.

 

[capreppy]

If you want to try KDE in Ubuntu check this page out:

http://www.psychocats.net/ubuntu/kde

Alot of useful tips in there, including changing your default file manager.

thanks for the link. very informative.

 

[alan2308]

I don't see an option for a terminal window in the shortcut with my distro, unless I don't recognize it.

Anytime that you can't find an option in the menu, you can also hit alt-f2 to bring up the run dialog box. In there you can enter the name of any app. The default terminal in Gnome is "gnome-terminal." Alt-f2 works in both Gnome and KDE.

I would also suggest not using -advmethods and memory=256, and you'll get 2605's at least 90% of the time with LinSMP. I get a 2653 once a week, a 2665 monthly or so, and 2605's the rest of the time.

 

[oraldlight]

Very un-scientific, but I notice Gnome feels faster/more responsive than KDE 3 or 4. Loads from cold boot in 1/3 the time it takes KDE to load as well (or longer depending upon how much 'fluff' you isntall alongside KDE).

KDE vs Gnome: Either one (or other GUI's) can be run form a single isntall. At login window there is a dropdown to select which GUI you want (or terminal). Looks like everyone else has covered the how-to/knowledge base so won't complicate with redundnat info.

I run Ubuntu 8.04+Gnome on one boxen. Installed FAH from Stanford web page, config'd, and click on the (I think) FAH6 icon, and away it goes. I could use one of the tools under prefs to auto load the app at boot, if I got off my lazy ass...

 

[APOLLO]

Anytime that you can't find an option in the menu, you can also hit alt-f2 to bring up the run dialog box. In there you can enter the name of any app. The default terminal in Gnome is "gnome-terminal." Alt-f2 works in both Gnome and KDE.

Alt F2 brings up the terminal window, but the client configured itself as a console not SMP client. I have the -smp flag in the executable and I assume that is in error, so where should the flag be to receive SMP units? Another thing I'd like is to place a F@H shortcut on the desktop, so whenever I click on the icon it will execute in a terminal window. What should be the simplest function doesn't seem very simple to do. I'd like to accomplish this without having to install anything else related to OS function.

 

[alan2308]

It should be on the executable. For example from a terminal

./fah6 -smp -verbosity 9 -forceasm

Also, I don't know if its been mentioned, but you do need the 32-bit libraries. From a terminal:

sudo apt-get install ia32-libs

To create a shortcut under KDE and I assume its the same/similar under gnome), right click on the desktop, create new... link to application. Put a name for the icon there, then under the tab for application, under command, put in

~/fah/fah6 -smp -verbosity 9 -forceasm

 

[APOLLO]

To create a shortcut under KDE and I assume its the same/similar under gnome), right click on the desktop, create new... link to application. Put a name for the icon there, then under the tab for application, under command, put in

~/fah/fah6 -smp -verbosity 9 -forceasm

The nomenclature is totally different in Gnome, but I got the gist of it. Seemed to have worked. The main issue I have now concerns file placement. Even though I have a separate F@H folder where the executable is located, once the terminal-modified shortcut is started, all the files are installed in the account folder instead. Strange. The problem with this arises when the client looks for mpiexec and can't find it with the rest of the files. I guess I could place it with all the other files to get the client working, but it would make for a messy installation.

 

[alan2308]

Another reason that it might not have run in a terminal windows is due to permissions. When you unpack the FAH6.02-Linux.tgz tarball, you have to "chmod 755 fah6."

Random thought here, but if learning Linux isn't your goal and you just want this up and running, have you looked at finstall? No fuss, the script does all the copying, installing, running, etc. for you. And if you're running this in a VM, you could always mount a NotFred .iso in the VM and boot from it.

 

[APOLLO]

Another reason that it might not have run in a terminal windows is due to permissions. When you unpack the FAH6.02-Linux.tgz tarball, you have to "chmod 755 fah6."

Even though I'm a geek at heart, that shot right past me as it probably would most first time installers. Maybe I'll try it for my second installation in the next day or two. Thanks for the tip.

In any event, I finally have my installation working with SMP WUs. All I did was move the mpiexec file to where all the other files wanted to install and the client worked immediately. Now, the only thing I have to decide is if it's worth running a second console client in the XP host OS since one client alone still leaves quite a bit of the available cores untapped.

Random thought here, but if learning Linux isn't your goal and you just want this up and running, have you looked at finstall? No fuss, the script does all the copying, installing, running, etc. for you.

I'd like to learn Linux and I was intending to migrate from MS to Linux many, many years ago, until I tried XP. Then I gradually lost interest. Now, my main concern is getting some of my systems back their lost production ever since Stanford started releasing slower WUs. I am actually learning quite a bit despite that not being my primary objective ATM.

And if you're running this in a VM, you could always mount a NotFred .iso in the VM and boot from it.

I first tried Notfred and then CentOS but both failed (probably did something wrong). Ubuntu was my third attempt and that went so effortlessly and quick, I was shocked. Thanks again for the recommendation and all the help, it's very much appreciated.

 

[alan2308]

Glad to hear you got it all sorted out. Now just don't go doing anything that I find myself doing, namely continuing to mess with things AFTER they're running properly.

 

[APOLLO]

I have a couple of additional rather pressing questions. It mostly concerns shares. I'm having difficulty getting my folders to be viewed and thus monitored across the network. Main problem that arises is the SMP client refusing to work after I enable sharing. It stops dead at the listing of the 'nnodes' 'myrank' and 'hostname.' The only thing I did was enabled the Samba sharing service and selected the folder to share. I disabled sharing to get the client working again but it still refuses to work. What can be the problem?

Another thing that's annoying is the fact that I can't seem to install the client in its own folder. It insists on moving everything to the root directory of the user account folder. If I move the files to their own custom folder, the client refuses to work properly. I have a gut feeling the two problems are somehow related but since I hardly know anything about Linux, any help would be greatly appreciated

 

[Xilikon]

You are correct, both is related and this is because you are logged as root. I suggest you log yourself as a user then work with sudo to get root permissions correctly and in the right place.

 

[APOLLO]

Thanks Xilikon for informing me on the cause of the problem, but before I get the time to properly resolve the issue, how do I get the client to fold again? It will not commence processing despite the fact I restored everything the way it was before.

 

[Xilikon]

I'm almost as noob as you with Linux but this method worked perfectly for me :

-Install Ubuntu 8.04.1 on the HDD (during setup, it will ask for a new username and password, take note of these infos).
-When you are done, login with the username and password you created during setup.
-Open the terminal window. You should be on your home folder (normally /home/[username]/).
-type (or copy/paste) the following commands :

sudo apt-get install curl ia32-libs

Enter the password, same as your user password.

curl -O http://ra.vendomar.ee/~ivo/finstall

This will download the script you need to install F@H

chmod +x finstall
./finstall smp

It should start the download and installation process. Say yes or no to the various questions (it should be self-explanatory).

When the process is completed, you need to go to the new foldingathome folder :

cd foldingathome

You should install this as a linux service so it start automatically when you reboot :

./installService

When you are ready, either reboot to start it or just type this :

./folding start

To stop the client, type :

./folding stop

To check the status, type :

./folding status

At this point, you can then use the file manager and setup a share on your home folder and you should be set to run.

 

[APOLLO]

The steps you outlined above requires that I reinstall everything. Although greatly appreciated, for now I only want to resume folding where I last left off. I don't have the time to go through another installation at the moment. I can't comprehend why it won't recommence folding.

 

[Tigerbiten]

I agree with Xilikon.
Use Finstall to install the SMP client as a service.
That how I set my VM's.

Edit.
Once you have the new setup installed just move the files from the old install into the new install to pick up where you left off.
The Work folder, queue.dat, client.cfg, machinedependent.dat are the inportant files to move.

Luck ............

 

[APOLLO]

Service installations aren't an option, unfortunately.

 

[APOLLO]

Maybe I should ask another question. If I create a second user account, can I transfer my uncompleted WU to the client of the new user?? Or, will I have the same problem of the client not initiating?

 

[alan2308]

Maybe I should ask another question. If I create a second user account, can I transfer my uncompleted WU to the client of the new user?? Or, will I have the same problem of the client not initiating?

Yes, you can transfer the WU to another user account. You just have to remember to change ownership of the files to the new user. Like any other WU transfer, you just have to move the work directory and the queue.dat file. Once the necessary files are copied over, cd into the directory where they live and

sudo chown -R username *
sudo chgrp -R username *

 

[SmokeRngs]

Something to keep in mind if you are running the client from a shortcut is to make sure that if the shortcut has a place to show the "working directory" to make sure the main F@H directory is shown there. Otherwise, it might try to run it from the /home directory instead. I ran into this before and it caused me some problems until I got the path for the F@H folder entered into the working directory area.

Here's a screenshot of what I'm talking about. This is from my openSUSE install using KDE so it's not going to match up but should give you a better idea of what I'm talking about by being able to see the Work Path area I'm talking about.

 

[APOLLO]

Something to keep in mind if you are running the client from a shortcut is to make sure that if the shortcut has a place to show the "working directory" to make sure the main F@H directory is shown there. Otherwise, it might try to run it from the /home directory instead. I ran into this before and it caused me some problems until I got the path for the F@H folder entered into the working directory area.

I have the client running from a shortcut and I do have that problem. I am not exactly sure what you mean by 'working directory.' I don't see a place to add this in the shortcut properties.

 

[APOLLO]

OK, I see what you mean, but Gnome apparently does not have the same features. My window only shows 'description,' 'command' and 'comment' in that order. I'm starting to wish I installed KD instead of Gnome.

 

[SmokeRngs]

OK, I see what you mean, but Gnome apparently does not have the same features. My window only shows 'description,' 'command' and 'comment' in that order. I'm starting to wish I installed KD instead of Gnome.

My experience with Gnome isn't bad but I have found it seems to be much easier working with KDE. In your case, it would be easiest to grab the Kubuntu CD instead and use that for any future installs. That way you have KDE as the default at install. Otherwise, it should be the exact same as Ubuntu.

 

[APOLLO]

I'll ask a dumb question, is there a way to switch desktops without affecting the current configuration and apps like F@H?

 

[SmokeRngs]

I'll ask a dumb question, is there a way to switch desktops without affecting the current configuration and apps like F@H?

It shouldn't affect too much, but using synaptic (I believe that's what you use in Ubuntu) you should be able to install KDE from that. Then, when you boot the OS up, you should have a choice to use KDE or Gnome. I don't know where it would be, but there should be an option somewhere in which you should be able to choose which one to start as default.

That said, any shortcuts you have made will no longer work and you will have to create new shortcuts since Gnome and KDE use different types of shortcuts which are made by the user. Most or all the things in the current menus should still be there although they may be in a different place. I have very little experience with (K)Ubuntu so I'm not sure how exactly it acts.

 

[alan2308]

I'll ask a dumb question, is there a way to switch desktops without affecting the current configuration and apps like F@H?

sudo apt-get install kde or do it from synaptics. The kde metapackage will grab and install all of the KDE desktop. But you'll have to log out/log in to fire up the new desktop, so if you're running from a desktop shortcut, you'll have to restart.

 

[alan2308]

It shouldn't affect too much, but using synaptic (I believe that's what you use in Ubuntu) you should be able to install KDE from that. Then, when you boot the OS up, you should have a choice to use KDE or Gnome. I don't know where it would be, but there should be an option somewhere in which you should be able to choose which one to start as default.

That said, any shortcuts you have made will no longer work and you will have to create new shortcuts since Gnome and KDE use different types of shortcuts which are made by the user. Most or all the things in the current menus should still be there although they may be in a different place. I have very little experience with (K)Ubuntu so I'm not sure how exactly it acts.

Gnome and KDE both use the .desktop format for shortcuts (amongst other things) and both locate them in ~/Desktop. They'll be there in both desktops.