Linux SMP error

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Linux SMP error

Postposted on Fri Apr 25, 2008 3:54 pm

Code: Select all
--- Opening Log file [April 25 20:45:40]


# Linux Console Edition #######################################################
###############################################################################

                       Folding@Home Client Version 6.02beta

                          http://folding.stanford.edu

###############################################################################
###############################################################################

Launch directory: /home/robert/folding/FAH
Executable: ./fah6


[20:45:40] - Ask before connecting: No
[20:45:40] - User name: crimsonjax (Team 2630)
[20:45:40] - User ID: 758DFE8C35CBD554
[20:45:40] - Machine ID: 1
[20:45:40]
[20:45:41] Loaded queue successfully.
[20:45:41]
[20:45:41] + Processing work unit
[20:45:41] Core required: FahCore_a1.exe
[20:45:41] Core found.
[20:45:41] Working on Unit 01 [April 25 20:45:41]
[20:45:41] + Working ...
[20:45:41]
[20:45:41] *------------------------------*
[20:45:41] Folding@Home Gromacs SMP Core
[20:45:41] Version 1.74 (November 27, 2006)
[20:45:41]
[20:45:41] Preparing to commence simulation
[20:45:41] - Looking at optimizations...
[20:45:41] - Created dyn
[20:45:41] - Files status OK
[20:45:42] - Expanded 2443303 -> 12907669 (decompressed 528.2 percent)
[20:45:42] - Starting from initial work packet
[20:45:42]
[20:45:42] Project: 2605 (Run 12, Clone 77, Gen 44)
[20:45:42]
[20:45:42] Assembly optimizations on if available.
[20:45:42] Entering M.D.
NNODES=1, MYRANK=0, HOSTNAME=ubuntu
      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out http://www.gromacs.org for more information.

        This inclusion of Gromacs code in the Folding@Home Core is under
        a special license (see http://folding.stanford.edu/gromacs.html)
         specially granted to Stanford by the copyright holders. If you
          are interested in using Gromacs, visit www.gromacs.org where
                you can download a free version of Gromacs under
         the terms of the GNU General Public License (GPL) as published
       by the Free Software Foundation; either version 2 of the License,
                     or (at your option) any later version.

[20:45:48] Rejecting checkpoint
run input file work/wudata_01.xyz was made for 4 nodes,
             while Core_A1.exe expected it to be for 1 nodes.: Address family not supported by protocol
[20:45:49]
[20:45:49] Folding@home Core Shutdown: UNKNOWN_ERROR
[20:45:50] CoreStatus = 61 (97)
[20:45:50] + Client running with incorrect SMP settings for work unit.  Please check settings and restart




I followed the easy SMP installation thread and got everything running smooth until I tried to start the program for the first time. When I first started the SMP program in the terminal, it hang up on the ¨Ëntering M.D." step. So I tried to close it down and restart the program. When I restarted the SMP, this is the error I get now. I there a way to clear the checkpoint?
crimsonjax
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 4:03 pm

You need to use the -smp flag when you start the linux folding client to fold SMP WUs.

Open a command window and type: ./fah6 -smp

and then hit return to start the client. You can also use the -forceasm, -advmethods & vebosity 9 flags if you like. They're all fun. :D
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jeffry55
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 4:11 pm

kk, thanks. That got me past the error. How long does it take before it starts working?

Code: Select all
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.

2 cores detected


--- Opening Log file [April 25 21:06:55]


# SMP Client ##################################################################
###############################################################################

                       Folding@Home Client Version 6.02beta

                          http://folding.stanford.edu

###############################################################################
###############################################################################

Launch directory: /home/robert/folding/FAH
Executable: ./fah6
Arguments: -smp

[21:06:55] - Ask before connecting: No
[21:06:55] - User name: crimsonjax (Team 2630)
[21:06:55] - User ID: 758DFE8C35CBD554
[21:06:55] - Machine ID: 1
[21:06:55]
[21:06:55] Loaded queue successfully.
[21:06:55]
[21:06:55] + Processing work unit
[21:06:55] Core required: FahCore_a1.exe
[21:06:55] Core found.
[21:06:55] Working on Unit 01 [April 25 21:06:55]
[21:06:55] + Working ...
[21:06:55]
[21:06:55] *------------------------------*
[21:06:55] Folding@Home Gromacs SMP Core
[21:06:55] Version 1.74 (November 27, 2006)
[21:06:55]
[21:06:55] Preparing to commence simulation
[21:06:55] - Ensuring status. Please wait.
[21:06:56] - Starting from initial work packet
[21:06:56]
[21:06:56] Project: 2605 (Run 12, Clone 77, Gen 44)
[21:06:56]
[21:06:57] Assembly optimizations on if available.
[21:06:57] Entering M.D.
[21:07:14]  percent)
[21:07:14] - Starting from initial work packet
[21:07:14]
[21:07:14] Project: 2605 (Run 12, Clone 77, Gen 44)
[21:07:14]
[21:07:14] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=ubuntu
NNODES=4, MYRANK=1, HOSTNAME=ubuntu
NNODES=4, MYRANK=3, HOSTNAME=ubuntu
NNODES=4, MYRANK=2, HOSTNAME=ubuntu
NODEID=2 argc=15
NODEID=0 argc=15
NODEID=3 argc=15
NODEID=1 argc=15
      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2004, The GROMACS development team,
            check out http://www.gromacs.org for more information.

        This inclusion of Gromacs code in the Folding@Home Core is under
        a special license (see http://folding.stanford.edu/gromacs.html)
         specially granted to Stanford by the copyright holders. If you
          are interested in using Gromacs, visit www.gromacs.org where
                you can download a free version of Gromacs under
         the terms of the GNU General Public License (GPL) as published
       by the Free Software Foundation; either version 2 of the License,
                     or (at your option) any later version.

[21:07:22] g local files
[21:07:22] in in POPC
[21:07:22] Writing local files
starting mdrun 'Protein in POPC'
500000 steps,   1000.0 ps.

[21:07:23] Extra SSE boost OK.


This is where itś stuck..
crimsonjax
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 4:14 pm

Strange, you should at least get the current percentage while it is working.
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Flying Fox
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 4:19 pm

Task manager shows it using 86-94% of the CPU... maybe a bad SMP client??
crimsonjax
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 8:11 pm

Maybe it is a complex simulation. I have never seen a 2605 WU before.
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jeffry55
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 8:19 pm

jeffry55 wrote:Maybe it is a complex simulation. I have never seen a 2605 WU before.

Most of my WUs have been 2605s. They seem to come up when you have dual cores.
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 8:19 pm

2605 takes a couple days to process on my E6300.
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 10:25 pm

bthylafh wrote:2605 takes a couple days to process on my E6300.

That may be why. How long does each step usually take? I would just like to know if the client is working correctly. :o
crimsonjax
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Re: Linux SMP error

Postposted on Fri Apr 25, 2008 10:32 pm

The 2605 I'm folding right now takes about 20-25 minutes per percent.
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Re: Linux SMP error

Postposted on Sat Apr 26, 2008 3:03 pm

bth, those numbers are exactly what I'm getting, 20-25 minutes a percentage point. Thanks. This must be a beast of a WU! :)
crimsonjax
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Re: Linux SMP error

Postposted on Sat Apr 26, 2008 4:33 pm

crimsonjax wrote:bth, those numbers are exactly what I'm getting, 20-25 minutes a percentage point. Thanks. This must be a beast of a WU! :)

Let's say 20min/%. This means it takes 33.3333 hours or slightly over a day to finish the WU. Project 2605 is worth 1760 points, so
1760/(33.33333/24) = 1267ppd. Compared to your previously "puny" 150ppd this is night and day. Now you see why SMP is all the rage these days? ;)
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Re: Linux SMP error

Postposted on Sat Apr 26, 2008 8:45 pm

:lol:

Yep, now I need to get a farm together... :P
crimsonjax
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Re: Linux SMP error

Postposted on Sat Apr 26, 2008 9:10 pm

crimsonjax wrote::lol:

Yep, now I need to get a farm together... :P


AQnd change your username to UnitedGerbilNation! :D
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