7.6.9 Software issue in Linux

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7.6.9 Software issue in Linux

Postby Ahnilated » Tue Apr 21, 2020 2:11 am

Hello everyone,

System: AMD 2950x (16 cores/32 threads), 128GB ram, Nvidia GTX 1080Ti, Ubuntu 5.3.0-46-generic kernel.

I seem to be running into a bug in the 7.6.9 software, output pasted below. I just keep getting this error over and over when it tries to start up the CPU thread now. I didn't get this error in the previous version, don't remember exactly what it was. Folding power set to full. Let me know if you need any other information.

10:33:30:WU00:FS00:0xa7:ERROR:Fatal error:
10:33:30:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 25 ranks that is compatible with the given box and a minimum cell size of 1.37225 nm
10:33:30:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
10:33:30:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
10:33:30:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
10:33:30:WU00:FS00:0xa7:ERROR:website at (removed to be able to post)
10:33:30:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
10:33:34:WU00:FS00:0xa7:WARNING:Unexpected exit() call
10:33:34:WU00:FS00:0xa7:WARNING:Unexpected exit from science code
10:33:34:WU00:FS00:0xa7:Saving result file ../logfile_01.txt
10:33:34:WU00:FS00:0xa7:Saving result file md.log
10:33:34:WU00:FS00:0xa7:Saving result file science.log
10:33:35:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
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Re: 7.6.9 Software issue in Linux

Postby ajm » Tue Apr 21, 2020 6:31 am

This is a problem with the number of threads allocated to FAH. It looks like you have allocated 25 threads, which is a bad choice for domain decomposition. The number should be divisible by 2 and/or 3. You can edit the CPU slot in Fahcontrol and enter there the number of threads you want to allocate. 30 for example. Or 24 and another slot at 6. Whatever, but always multiples of 2 or, and possibly and 3.
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Re: 7.6.9 Software issue in Linux

Postby PantherX » Tue Apr 21, 2020 9:12 am

Welcome to the F@H Forum Ahnilated,

Please look up the troubleshooting steps for "There is no domain decomposition" in this thread: viewtopic.php?f=19&t=16526 :)
ETA:
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Re: 7.6.9 Software issue in Linux

Postby Ahnilated » Tue Apr 21, 2020 12:40 pm

Hello AJM,

Thank you, I have not allocated anything. The CPU slot is set at the default -1. That is why I am saying, this is a bug in the program.

I have removed the bad packet, as per the instructions thanks PantherX, and it is back to crunching fine with the same settings. Until it got a new packet and got the exact same bad one back, PRCG 14576 (0,4259,74). I have deleted it once again and posted about it in the forums.
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