[gmx-users] Parallel installation core2 quad -mpi?
Peyman Yamin
p.yamin at fz-juelich.de
Wed May 13 09:21:55 CEST 2009
Hello everyone,
I'm coming back to Gromacs. Before installing gromacs on our new SC I want to
do it on my desktop running SuSe 11.1 on an Intel Core2 Quad Q6700 @2.66GHz
CPU-arch.
Gromacs version 4.0.3
gmxtests version 4.0.4
1. Are these compatible? I could find neither a testset for 4.0.3 nor a
version 4.0.4 of gromacs!
2. The parallel installation (with --enable-mpi) leads to failure in all
tests. Can I run MPI-parallel runs with lam on my cpu at all? lamboot is
scared to be run by root and tests get some permission denied message for
grompp when run otherwise. How is the whole OpenMP(I) story going on?
3. normal installation (without --enable-mpi) leads to failure in (complex
only) "field", "tip4p" and "water". concerning pdb2gmx:
Error not all 45 pdb2gmx tests have been done successfully
Only 44 energies in the log file
however, -np 2 or 4 leads to a faster finishing with everything t he same
other than "only 0 energies in the log file"!
I'm wondering how does it all go parallel with no mpi?
Thanks in advance,
Peyman
P.S. Here are checkpot.out and checkvir.out for tip4p (test with no -np).
Those of field and water are similar.
CHECKPOT.OUT
comparing energy file reference_d.edr and ener.edr
There are 32 terms in the energy files
There are 4 terms to compare in the energy files
Files read succesfully
CHECKVIR.OUT
comparing energy file reference_d.edr and ener.edr
There are 32 terms in the energy files
There are 17 terms to compare in the energy files
Vir-YX step 0: -88.6406, step 0: -86.8772
Vir-YZ step 0: 6.84064, step 0: 7.13434
Vir-ZX step 0: -54.0067, step 0: -52.9951
Vir-ZY step 0: 6.84064, step 0: 7.62177
Vir-XY step 1: -51.1246, step 1: -52.1106
Vir-XZ step 1: -46.6056, step 1: -46.1179
Vir-YX step 1: -51.1246, step 1: -50.5221
Vir-ZX step 1: -46.6056, step 1: -45.8405
Vir-YZ step 2: 62.6018, step 2: 61.8139
Vir-XZ step 3: -15.0763, step 3: -14.869
Vir-YX step 3: -9.43724, step 3: -8.38063
Vir-YZ step 3: 83.9097, step 3: 85.0938
Vir-ZX step 3: -15.0763, step 3: -13.9701
Vir-XY step 4: -13.916, step 4: -13.4319
Vir-XZ step 4: 9.84575, step 4: 10.1562
Vir-ZX step 4: 9.84575, step 4: 9.57457
Vir-ZY step 4: 93.54, step 4: 94.6497
Vir-XY step 5: -34.0429, step 5: -33.1563
Vir-XZ step 5: 37.7852, step 5: 38.673
Vir-YX step 5: -34.0429, step 5: -33.5621
Vir-YZ step 5: 87.6469, step 5: 88.7462
Vir-ZX step 5: 37.7852, step 5: 38.247
Vir-XZ step 6: 64.9231, step 6: 63.4369
Vir-YX step 6: -63.5388, step 6: -62.7892
Vir-ZX step 6: 64.9231, step 6: 65.691
Vir-ZY step 6: 66.1302, step 6: 64.6016
Vir-XY step 7: -93.5354, step 7: -92.5473
Vir-YZ step 7: 32.4225, step 7: 33.1803
Vir-ZX step 7: 87.7836, step 7: 88.6865
Vir-ZY step 7: 32.4225, step 7: 33.6332
Vir-YZ step 8: -8.59918, step 8: -8.42516
Vir-ZY step 8: -8.59918, step 8: -9.54873
Vir-ZX step 9: 111.664, step 9: 110.52
Vir-ZY step 9: -52.1883, step 9: -53.1597
Vir-YX step 10: -116.858, step 10: -115.312
Vir-YX step 12: -66.7999, step 12: -65.7083
Vir-XY step 13: -33.7437, step 13: -34.3992
Vir-YX step 13: -33.7437, step 13: -34.804
Vir-XY step 14: -0.682353, step 14: -0.966198
Vir-YX step 14: -0.682353, step 14: -0.299812
Vir-XY step 15: 30.6329, step 15: 31.6687
Vir-XY step 16: 59.1005, step 16: 60.6541
Vir-XY step 17: 83.184, step 17: 82.2528
Vir-YX step 17: 83.184, step 17: 82.3063
Vir-ZX step 18: 138.834, step 18: 140.581
Vir-XY step 25: 43.465, step 25: 44.0824
Vir-YX step 25: 43.465, step 25: 41.8879
Vir-XY step 26: 18.5651, step 26: 17.6458
Vir-YX step 26: 18.5651, step 26: 18.9277
Vir-XY step 27: -15.0441, step 27: -17.3579
Vir-YX step 27: -15.0441, step 27: -13.4185
Vir-ZY step 27: -168.308, step 27: -170.416
Vir-XY step 28: -57.8682, step 28: -59.8756
Vir-XY step 29: -106.719, step 29: -108.352
Vir-ZY step 29: -136.829, step 29: -138.344
Vir-YZ step 37: -114.576, step 37: -115.75
Vir-YZ step 38: -113.964, step 38: -112.243
Vir-YZ step 39: -111.904, step 39: -113.181
Vir-ZY step 42: -109.407, step 42: -107.894
Vir-XY step 44: -134.534, step 44: -136.946
Vir-XZ step 44: 86.1219, step 44: 87.2183
Vir-ZY step 44: -122.268, step 44: -124.306
Vir-ZX step 45: 95.6349, step 45: 94.2682
Vir-XY step 47: -87.3978, step 47: -88.4946
Vir-YX step 47: -87.3978, step 47: -86.378
Vir-XY step 48: -63.2827, step 48: -63.9522
Vir-YX step 48: -63.2827, step 48: -64.2959
Vir-YZ step 48: -68.0685, step 48: -66.718
Vir-YZ step 49: -47.5998, step 49: -48.7157
Vir-XY step 50: -8.52874, step 50: -8.00819
Vir-YX step 50: -8.52874, step 50: -9.54901
Vir-YZ step 50: -37.5503, step 50: -36.2929
Files read succesfully
--
Peyman Yamin
Institut fuer Strukturbiologie und Biophysik (ISB)
ISB-3: Strukturbiochemie
Forschungszentrum Juelich
D-52425 Juelich
Tel: (49)-2461-61-2875
Fax: (49)-2461-61-2023
mailto: p.yamin[at]fz-juelich.de
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