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Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..."
Date: 2020/05/04 22:14
Name: Christopher

Hello,

We have recently recompiled openmx on our computational cluster. Our new 3.9 version seems to run 1.5x to 2x faster on most computations but we have some issues when the system either becomes very large or too cumbersome to calculate. Usually, when the calculation is almost finished the code gets stuck after "outputting data on grids to files..." (this line seems to only exist in OutData_Binary.c and OutData.c files). Do you have any suggestions as to if this is a bug or a compilation issue? In either case, is there some step that you can think of that commenting out a subroutine would actually allow the calculation to finish?


If need be I can share the input, output, or compilation.

Thanks
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Re: Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..." ( No.1 )
Date: 2020/05/04 23:17
Name: Naoya Yamaguchi

Hi,

Please refer to the following and try it:
http://www.openmx-square.org/openmx_man3.9/node218.html

Regards,
Naoya Yamaguchi
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Re: Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..." ( No.2 )
Date: 2020/05/04 23:58
Name: Christopher

Thanks for the response Naoya,

Flagging OutData.bin.flag did not seem to resolve the issue. Any other ideas? The only clue I can give is we edited the files in question and the calculation seems to hang when starting the subroutines (such as out_density() etc, before the MPI process splitting).
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Re: Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..." ( No.3 )
Date: 2020/05/05 00:52
Name: Naoya Yamaguchi

Dear Christopher,

Did the calculation stop actually (e.g. killed by some signal)?
If you check whether the installation of OpenMX was successful, you can do an automatic running test: http://www.openmx-square.org/openmx_man3.9/node17.html
I think that the test should fail at least if there are some problems of the compilation.

Regards,
Naoya Yamaguchi
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Re: Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..." ( No.4 )
Date: 2020/05/05 07:13
Name: Kirou Sankaran

Dear Naoya,

The tests are fine.

1 input_example/Benzene.dat Elapsed time(s)= 6.86 diff Utot= 0.000000000038 diff Force= 0.000000000005 2 input_example/C60.dat Elapsed time(s)= 22.65 diff Utot= 0.000000000001 diff Force= 0.000000000002 3 input_example/CO.dat Elapsed time(s)= 13.29 diff Utot= 0.000000000119 diff Force= 0.000000000947 4 input_example/Cr2.dat Elapsed time(s)= 12.16 diff Utot= 0.000000001339 diff Force= 0.000000000058 5 input_example/Crys-MnO.dat Elapsed time(s)= 79.86 diff Utot= 0.000000020500 diff Force= 0.000000097164 6 input_example/GaAs.dat Elapsed time(s)= 58.78 diff Utot= 0.000000002745 diff Force= 0.000000000014 7 input_example/Glycine.dat Elapsed time(s)= 6.96 diff Utot= 0.000000000001 diff Force= 0.000000000001 8 input_example/Graphite4.dat Elapsed time(s)= 12.37 diff Utot= 0.000000000022 diff Force= 0.000000000119 9 input_example/H2O-EF.dat Elapsed time(s)= 5.55 diff Utot= 0.000000000001 diff Force= 0.000000000001 10 input_example/H2O.dat Elapsed time(s)= 4.57 diff Utot= 0.000000000001 diff Force= 0.000000000509 11 input_example/HMn.dat Elapsed time(s)= 18.79 diff Utot= 0.000000000025 diff Force= 0.000000000002 12 input_example/Methane.dat Elapsed time(s)= 3.90 diff Utot= 0.000000000009 diff Force= 0.000000000001 13 input_example/Mol_MnO.dat Elapsed time(s)= 11.47 diff Utot= 0.000000000014 diff Force= 0.000000000034 14 input_example/Ndia2.dat Elapsed time(s)= 8.99 diff Utot= 0.000000000088 diff Force= 0.000000000069 Total elapsed time (s) 266.20

Any other ideas?

Best regards,
Kirou
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Re: Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..." ( No.5 )
Date: 2020/05/05 14:06
Name: Naoya Yamaguchi

Dear Kirou,

The test seems normal. I can't find what causes your problem from the information you provided. Please give additional information such as the input file. And, please show some evidence that you judged the calculation hung, if any.

Regards,
Naoya Yamaguchi
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Re: Openmx 3.9 compilation sometimes freezes after "outputting data on grids to files..." ( No.6 )
Date: 2020/05/14 15:23
Name: T. Ozaki

Hi,

Rather than OpenMX itself, this problem may happen due to the file system of computational
enviroment, which can be getting in trouble when many files are saved at a nearly same time.
The limitation of number of files which are saved at the same time must be determined by
both the hardware and software in the file system.

Regards,

TO
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