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parallel questions Date: 2006/05/01 06:02 Name: Jeason Dear Prof. Ozaki, I think I have succesfully compiled the code in parallel. The enviroument is: icc9.0, acml3.1, lam7.0.6, Opeteron2.0G But when doing test, I find two problems: 1. When it parallel running, I require the same or more memory /per node than series run. 2. When I running the auto-test run, I get result: 1)running in single cpu, series run: 1 input_example/Benzene.dat Elapsed time(s)= 29.09 diff Utot= 0.000000000000 diff Force= 0.000000000001 2 input_example/C60.dat Elapsed time(s)= 364.59 diff Utot= 0.000000000001 diff Force= 0.000000000001 3 input_example/Cdia.dat Elapsed time(s)= 24.06 diff Utot= 0.000000000001 diff Force= 0.000000002656 4 input_example/CO.dat Elapsed time(s)= 130.29 diff Utot= 0.000000000000 diff Force= 0.000000000033 5 input_example/Cr2.dat Elapsed time(s)= 51.81 diff Utot= 0.000000000000 diff Force= 0.000000000000 6 input_example/Crys-MnO.dat Elapsed time(s)= 523.67 diff Utot= 0.000000000032 diff Force= 0.000000000060 7 input_example/GaAs.dat Elapsed time(s)= 337.79 diff Utot= 0.000000000074 diff Force= 0.000000001227 8 input_example/Glycine.dat Elapsed time(s)= 50.35 diff Utot= 0.000000000001 diff Force= 0.000000000001 9 input_example/Graphite4.dat Elapsed time(s)= 22.74 diff Utot= 0.000000000064 diff Force= 0.000000000213 10 input_example/H2O.dat Elapsed time(s)= 24.65 diff Utot= 0.000000000000 diff Force= 0.000000000001 11 input_example/H2O-EF.dat Elapsed time(s)= 37.07 diff Utot= 0.000000000000 diff Force= 0.000000000197 12 input_example/HYb.dat Elapsed time(s)= 100.95 diff Utot= 0.000000000002 diff Force= 0.000000000000 13 input_example/Methane.dat Elapsed time(s)= 18.26 diff Utot= 0.000000000045 diff Force= 0.000000004540 1 input_example/Benzene.dat Elapsed time(s)= 68.58 diff Utot= 0.000000000000 diff Force= 0.000000000001 2 input_example/C60.dat Elapsed time(s)= 381.21 diff Utot= 0.000000000010 diff Force= 0.000000000005 3 input_example/Cdia.dat Elapsed time(s)= 19.10 diff Utot= 0.000000000000 diff Force= 0.000000002025 4 input_example/CO.dat Elapsed time(s)= 113.78 diff Utot= 0.000000000000 diff Force= 0.000000000035 5 input_example/Cr2.dat Elapsed time(s)= 41.63 diff Utot= 0.000000000001 diff Force= 0.000000000000 6 input_example/Crys-MnO.dat Elapsed time(s)= 268.52 diff Utot= 0.000000000007 diff Force= 0.000000000219 7 input_example/GaAs.dat Elapsed time(s)= 404.82 diff Utot= 0.000000000123 diff Force= 0.000000000756 8 input_example/Glycine.dat Elapsed time(s)= 81.26 diff Utot= 0.000000000001 diff Force= 0.000000000001 9 input_example/Graphite4.dat Elapsed time(s)= 18.24 diff Utot= 0.000000000012 diff Force= 0.000000001777 10 input_example/H2O.dat Elapsed time(s)= 19.13 diff Utot= 0.000000000000 diff Force= 0.000000000001 11 input_example/H2O-EF.dat Elapsed time(s)= 26.73 diff Utot= 0.000000000002 diff Force= 0.000000000140 12 input_example/HYb.dat Elapsed time(s)= 121.02 diff Utot= 0.000000000001 diff Force= 0.000000000001 13 input_example/Methane.dat Elapsed time(s)= 23.37 diff Utot= 0.000000000001 diff Force= 0.000000000095 14 input_example/Mol_MnO.dat Elapsed time(s)= 169.46 diff Utot= 0.000000000013 diff Force= 0.000000000009 Which almost the same effiency. I want to know why Could you help me? Thanks 14 input_example/Mol_MnO.dat Elapsed time(s)= 161.71 diff Utot= 0.000000000026 diff Force= 0.000000000046 2) in 6 cpus, parallel run:

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Re: parallel questions ( No.1 ) Date: 2006/05/12 10:44 Name: T.Ozaki Hi, > 1. When it parallel running, I require the same or > more memory /per node than series run. For smaller systems consisting of less than 100 atoms with conventional diagonalization, the memory size required is not reduced significantly, since each spatially decomposed region has buffer spatial region so that matrix elements in the node can be constructed with a minium MPI communication. But, for O(N) methods or larger systems consisting more than 100 atoms, you can confirm that the memory size required can be largely reduced. > 2. When I running the auto-test run, I get result: I shall show you my runtest results using 1 and 6 cpus of an Opteron cluster. The result by 6 cpus is faster than that by 1 cpu in all the cases. And much acceleration is found especially for C60.dat with the DC method. I would wonder if your parallel environment is well optimized. Regards, TO ********** 1 CPU ************** 1 input_example/Benzene.dat Elapsed time(s)= 38.12 diff Utot= 0.000000000000 diff Force= 0.000000000002 2 input_example/C60.dat Elapsed time(s)= 456.74 diff Utot= 0.000000000001 diff Force= 0.000000000001 3 input_example/Cdia.dat Elapsed time(s)= 27.91 diff Utot= 0.000000000000 diff Force= 0.000000000764 4 input_example/CO.dat Elapsed time(s)= 299.52 diff Utot= 0.000000000000 diff Force= 0.000000000264 5 input_example/Cr2.dat Elapsed time(s)= 70.40 diff Utot= 0.000000000000 diff Force= 0.000000000000 6 input_example/Crys-MnO.dat Elapsed time(s)= 480.24 diff Utot= 0.000000000246 diff Force= 0.000000000193 7 input_example/GaAs.dat Elapsed time(s)= 452.82 diff Utot= 0.000000000234 diff Force= 0.000000000500 8 input_example/Glycine.dat Elapsed time(s)= 95.19 diff Utot= 0.000000000001 diff Force= 0.000000000000 9 input_example/Graphite4.dat Elapsed time(s)= 33.74 diff Utot= 0.000000000032 diff Force= 0.000000001536 10 input_example/H2O.dat Elapsed time(s)= 41.02 diff Utot= 0.000000000000 diff Force= 0.000000000001 11 input_example/H2O-EF.dat Elapsed time(s)= 99.10 diff Utot= 0.000000000005 diff Force= 0.000000000213 12 input_example/HYb.dat Elapsed time(s)= 169.89 diff Utot= 0.000000000001 diff Force= 0.000000000000 13 input_example/Methane.dat Elapsed time(s)= 30.41 diff Utot= 0.000000000006 diff Force= 0.000000001846 14 input_example/Mol_MnO.dat Elapsed time(s)= 444.23 diff Utot= 0.000000000023 diff Force= 0.000000000032 Total elapased time (s) 2739.32800 ********** 6 CPU ************** 1 input_example/Benzene.dat Elapsed time(s)= 18.26 diff Utot= 0.000000000000 diff Force= 0.000000000000 2 input_example/C60.dat Elapsed time(s)= 91.06 diff Utot= 0.000000000009 diff Force= 0.000000000004 3 input_example/Cdia.dat Elapsed time(s)= 18.96 diff Utot= 0.000000000000 diff Force= 0.000000004416 4 input_example/CO.dat Elapsed time(s)= 176.96 diff Utot= 0.000000000000 diff Force= 0.000000000038 5 input_example/Cr2.dat Elapsed time(s)= 56.44 diff Utot= 0.000000000001 diff Force= 0.000000000001 6 input_example/Crys-MnO.dat Elapsed time(s)= 138.47 diff Utot= 0.000000015518 diff Force= 0.000000008365 7 input_example/GaAs.dat Elapsed time(s)= 214.62 diff Utot= 0.000000000653 diff Force= 0.000000001369 8 input_example/Glycine.dat Elapsed time(s)= 37.54 diff Utot= 0.000000000001 diff Force= 0.000000000000 9 input_example/Graphite4.dat Elapsed time(s)= 17.76 diff Utot= 0.000000000006 diff Force= 0.000000000071 10 input_example/H2O.dat Elapsed time(s)= 22.84 diff Utot= 0.000000000000 diff Force= 0.000000000001 11 input_example/H2O-EF.dat Elapsed time(s)= 34.30 diff Utot= 0.000000000001 diff Force= 0.000000000003 12 input_example/HYb.dat Elapsed time(s)= 135.32 diff Utot= 0.000000000002 diff Force= 0.000000000000 13 input_example/Methane.dat Elapsed time(s)= 15.36 diff Utot= 0.000000000000 diff Force= 0.000000000000 14 input_example/Mol_MnO.dat Elapsed time(s)= 267.92 diff Utot= 0.000000000065 diff Force= 0.000000000080 Total elapased time (s) 1245.79800

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