Bug#670547: lammps: Most examples crash with standard compilation
lammps
emmanuel.quemener at ens-lyon.fr
Thu Apr 26 15:43:37 UTC 2012
Package: lammps
Version: 0~20120305.git5d7feb1-1
Severity: important
Tags: d-i
Dear Maintainer,
*** Please consider answering these questions, where appropriate ***
* What led up to the situation?
When I want to check the launches of examples provided in lammps-doc, I discover that most of the
examples crashed on launch.
Only following examples work: in.crack in.flow.pois in.flow.couette in.friction in.indent
in.indent.min in.kim.lj.lmp in.melt in.min in.min.box in.nemd in.obstacle in.rigid
* What exactly did you do (or not do) that was effective (or
ineffective)?
- copy examples /tmp
- cd to each example folder
- launch : mpirun -np 4 lammps < in.example
- examine launch result
* What was the outcome of this action?
LAMMPS (5 Mar 2012)
Lattice spacing in x,y,z = 10 10 10
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
Created 900 atoms
Setting atom values ...
861 settings made for type/fraction
Setting atom values ...
39 settings made for mass
Setting atom values ...
861 settings made for mass
ERROR: Invalid pair style (force.cpp:168)
* What outcome did you expect instead?
LAMMPS (20 Apr 2012)
Lattice spacing in x,y,z = 10 10 10
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
Created 900 atoms
Setting atom values ...
861 settings made for type/fraction
Setting atom values ...
39 settings made for mass
Setting atom values ...
861 settings made for mass
Setting up run ...
Memory usage per processor = 2.87079 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
6000 2.1073955 0.0076740311 2.112728 0.097657373 21544.21
7000 2.0843684 -0.001996932 2.0800555 0.11036967 17791.247
8000 2.0640518 0.0014998478 2.0632583 0.1290879 15498.836
9000 2.0466103 0.010705612 2.0550419 0.15352798 13893.115
10000 2.0318438 0.028356092 2.0579423 0.18270658 12603.157
11000 2.0482958 0.011332233 2.0573522 0.18794244 11521.406
12000 2.0293441 0.028678366 2.0557677 0.22972445 10593.809
13000 2.0420839 0.01483778 2.0546527 0.22626616 9831.1583
14000 2.0338765 0.023745084 2.0553618 0.24529893 9189.3544
15000 2.0340888 0.022597365 2.0544261 0.26912559 8660.1104
16000 2.0411572 0.016823213 2.0557124 0.2760664 8188.6833
17000 2.0430659 0.015914639 2.0567105 0.32031354 7754.6692
18000 2.0224619 0.034246299 2.054461 0.34823296 7363.4419
19000 2.0371616 0.020151129 2.0550492 0.36689711 7021.8023
20000 2.0012442 0.053534782 2.0525553 0.42286829 6747.0668
21000 2.0083023 0.043623646 2.0496945 0.45023495 6566.0902
22000 2.0192977 0.034152125 2.0512062 0.41736924 6355.2922
23000 2.0273904 0.029918658 2.0550564 0.41517637 6128.6153
24000 2.0319943 0.028045787 2.0577824 0.44666963 5918.5309
25000 2.019247 0.036332528 2.0533359 0.55128018 5772.6787
26000 2.0158834 0.046764159 2.0604077 0.57716691 5619.2113
27000 2.0135076 0.051582114 2.0628525 0.52574126 5453.3723
28000 2.0350823 0.028946582 2.0617677 0.51729456 5315.585
29000 2.0176307 0.045285243 2.0606741 0.53512692 5196.9665
30000 2.0205338 0.045244338 2.0635331 0.54623793 5064.8937
31000 2.0158642 0.051548399 2.0651727 0.61937877 4958.8369
32000 2.0044378 0.067401781 2.0696124 0.68527774 4839.1972
33000 2.0363851 0.034934931 2.0690573 0.59809076 4739.2817
34000 2.0097689 0.062020161 2.069556 0.73015447 4636.3026
35000 2.0134645 0.056040653 2.0672679 0.71619168 4564.4498
36000 2.0156115 0.058054367 2.0714262 0.72849082 4513.168
37000 1.9987392 0.078404935 2.0749233 0.72044263 4447.7092
38000 2.0415363 0.041662858 2.0809308 0.71039981 4349.3632
39000 1.9977115 0.079015616 2.0745074 0.79655246 4287.1736
40000 2.0120545 0.062164481 2.0719834 0.85157727 4245.1717
41000 2.0134976 0.070334303 2.0815947 0.78270295 4191.0843
42000 2.043454 0.041834722 2.0830182 0.73907133 4128.4218
43000 1.9882601 0.10049196 2.0865428 0.84271687 4044.7081
44000 2.0162608 0.068660865 2.0826814 0.91094454 3983.637
45000 1.9845299 0.098358952 2.0806838 1.0071356 3938.8775
46000 1.9907544 0.10281874 2.0913612 0.99642452 3894.9687
47000 1.9983608 0.088786976 2.0849274 0.94749158 3884.577
48000 2.0037673 0.085759123 2.0873 0.95989914 3839.7023
49000 1.9851308 0.10772525 2.0906504 1.1113189 3796.4636
50000 2.0266464 0.071578787 2.0959733 0.9022645 3764.5149
Loop time of 8.00124 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 2.02808 (25.3471)
Neigh time (%) = 0.442457 (5.52985)
Comm time (%) = 2.84339 (35.5369)
Outpt time (%) = 0.00272191 (0.0340186)
Other time (%) = 2.68458 (33.5521)
Nlocal: 225 ave 242 max 201 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 316.5 ave 322 max 310 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 1487.5 ave 1648 max 1337 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 5950
Ave neighs/atom = 6.61111
Neighbor list builds = 3115
Dangerous builds = 0
In my opinion, lammps is not compiled with optional libraries. I provide some information to compile it
completely in http://www.cbp.ens-lyon.fr/emmanuel.quemener/dokuwiki/doku.php?id=lammps4debian
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Kernel: Linux 3.2.0-2-amd64 (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages lammps depends on:
ii libc6 2.13-30
ii libfftw3-3 3.3-1
ii libgcc1 1:4.7.0-3
ii libjpeg8 8d-1
ii libopenmpi1.3 1.4.3-2.1
ii libstdc++6 4.7.0-3
Versions of packages lammps recommends:
ii lammps-doc 0~20120305.git5d7feb1-1
ii mpi-default-bin 1.0.1
lammps suggests no packages.
-- no debconf information
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