New Protomol Projects 10009, 10012-17, 10019-20

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New Protomol Projects 10009, 10012-17, 10019-20

Postby izaguirr » Mon Apr 05, 2010 7:39 pm

Projects 10009, 10012, 10013, 10014, 10015, 10016, 10017, 10019, 10020 using the new ProtoMol core have just entered advanced methods.


WARNING
We're using core version 23. A known issue is that killing and restarting the client forces the simulation to restart. We're working to address this problem.


These are all WW domain mutants. We will eventually have about 30 mutants running as separate projects. The goal is to gain further insight into the effect these mutations have on folding. Hopefully the simulations will match the predictions in the referenced paper.

points: 126
timeout: 4.6 days
deadline: 34.5 days

Reference:
"An experimental survey of the transition between two-state and downhill protein folding scenarios"
Feng Liu, Deguo Du, Amelia A. Fuller, Jennifer E. Davoren, Peter Wipf, Jeffery W. Kelly, and Martin Gruebele
PNAS February 19, 2008 vol. 105 no. 7 2369-2374
Prof. Jesus A. Izaguirre, Ph.D.
Department of Computer Science and Engineering
Interdisciplinary Center for Network Science and Applications
University of Notre Dame, IN, USA
Member, Folding@Home Consortium, Stanford University, CA, USA
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New protomol projects 10009, 10012-17, 10019-20 - Failures

Postby pcowley » Thu Apr 08, 2010 10:55 am

After a long period of now work units, I received a new B4 core work unit 10014, however it fails at 28% with a core communication error, over and over, and over. Houston, I think there's a wee problem here ...
Code: Select all
[07:48:14] Completed 124900 out of 499375 steps (25%)
[08:09:44] Completed 129900 out of 499375 steps (26%)
[08:31:13] Completed 134900 out of 499375 steps (27%)
[08:52:41] Completed 139900 out of 499375 steps (28%)
[09:12:36] CoreStatus = 0 (0)
[09:12:36] Client-core communications error: ERROR 0x0
[09:12:36] Deleting current work unit & continuing...
[09:12:38] Trying to send all finished work units
[09:12:38] + No unsent completed units remaining.
[09:12:38] - Preparing to get new work unit...
[09:12:38] + Attempting to get work packet


This on a fairly oldish Linux (Centos derivative - 2.6.9-89.0.16.EL) box with 767k memory and a single processor (CPU: Intel(R) Pentium(R) 4 CPU 1.60GHz stepping 02 ), which has been chugging away for a year or so at least.

Cheers
Pete
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Re: New Protomol Projects 10009, 10012-17, 10019-20

Postby bruce » Thu Apr 08, 2010 4:29 pm

We need to know which WU is involved. Please post the segment of FAHlog.txt showing where it starts processing the WU. (The characteristics of your hardware are also shown there.)

This might be a problem with your distro, but it might also be a problem with the particular WU.
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Re: New Protomol Projects 10009, 10012-17, 10019-20

Postby pcowley » Thu Apr 08, 2010 10:11 pm

Hi Here is the info from the start of the WU processing:
Code: Select all
[09:12:52] + Processing work unit
[09:12:52] Core required: FahCore_b4.exe
[09:12:52] Core found.
[09:12:52] Working on Unit 02 [April 7 09:12:52]
[09:12:52] - Calling './FahCore_b4.exe -dir work/ -suffix 02 -checkpoint 15 -ver
bose -lifeline 9432 -version 602'

[09:12:52] *********************** Log Started 07/Apr/2010 09:12:52 ************
***********
[09:12:52] ************************** ProtoMol Folding@Home Core ***************
***********
[09:12:52]   Version: 23
[09:12:52]      Type: 180
[09:12:52]      Core: ProtoMol
[09:12:52]   Website: http://folding.stanford.edu/
[09:12:52] Copyright: (c) 2009 Stanford University
[09:12:52]    Author: Joseph Coffland <joseph@cauldrondevelopment.com>
[09:12:52]      Args: -dir work/ -suffix 02 -checkpoint 15 -verbose -lifeline 94
32 -version
[09:12:52]            602
[09:12:52] ************************************ Build **************************
***********
[09:12:52]      Date: Mar 21 2010
[09:12:52]      Time: 10:27:10
[09:12:52]  Revision: 1789
[09:12:52]  Compiler: Intel(R) C++ g++ 4.1 mode 1110
[09:12:52]   Options: -std=gnu++98 -mia32 -O3 -funroll-loops
[09:12:52]            -axSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -restrict
[09:12:52]   Defines: NDEBUG _REENTRANT HAVE_GEEKINFO HAVE_PTHREADS HAVE_PTHREAD
S
[09:12:52]            HAVE_EXPAT HAVE_OPENSSL HAVE_LIBFAH HAVE_LAPACK
[09:12:52]  Platform: Linux 2.4.27-3-386
[09:12:52]      Bits: 32
[09:12:52]      Mode: Release
[09:12:52] ************************************ System *************************
***********
[09:12:52]        OS: Linux 2.6.9-89.0.16.EL i686
[09:12:52]       CPU: Intel(R) Pentium(R) 4 CPU 1.60GHz
[09:12:52]    CPU ID: GenuineIntel Family 15 Model 1 Stepping 2
[09:12:52]      CPUs: 1 Logical, 1 Physical
[09:12:52]    Memory: 757 MB
[09:12:52]   Threads: Linux
[09:12:52] *********************************************************************
[09:12:52] *********************************************************************
***********
[09:12:52] Project: 10014 (Run 292, Clone 0, Gen 0)
[09:12:52] Reading tar file par_all27_prot_lipid.inp
[09:12:52] Reading tar file scpismQuartic.inp
[09:12:52] Reading tar file ww.pdb



It is currently on the 4th attempt at Project 10014 and it has redownloaded the b4 core twice so far!

Hope this helps

Cheers
Pete
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Re: New Protomol Projects 10009, 10012-17, 10019-20

Postby bruce » Fri Apr 09, 2010 1:20 am

I've reported Project: 10014 (Run 292, Clone 0, Gen 0) as a bad WU.
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Re: New Protomol Projects 10009, 10012-17, 10019-20

Postby slugbug » Tue May 11, 2010 9:49 pm

One of my quad core VM folders(configured for SMP2) got one of these last night and it crapped out completely, screwing up the VM in the process. Why would a VM configured to use 4 cores get one of these work units anyway?
No matter how many times I restarted the VM it just would not resume or even get a new work unit. I had to delete the VM and install a new copy to get it working again.
Image
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Re: New Protomol Projects 10009, 10012-17, 10019-20

Postby codysluder » Wed May 12, 2010 4:27 am

slugbug wrote:One of my quad core VM folders(configured for SMP2) got one of these last night and it crapped out completely, screwing up the VM in the process. Why would a VM configured to use 4 cores get one of these work units anyway?
No matter how many times I restarted the VM it just would not resume or even get a new work unit. I had to delete the VM and install a new copy to get it working again.


Did you happen to read any of the topics on the forum before you asked your questions? There are topics in almost every forum about problems with the Assignment Server plus a Pande Group Announcement dated last evening. Everybody reported getting improper assignments so the fact that your VM got an incorrect assignment doesn't surprise anybody.

Deleting the VM and reinstalling it was probably one way to fix it, but others had the same problem and fixed it by discarding /work and queue.dat.
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