miroi
commented
5 years ago Well, on the main node the application is running (there we have g++ 6.3 due to installed devtoolset ):
milias@login.grid.umb.sk:~/Work/open-collection/theoretical_chemistry/software_runs/lammps/runs/melt/.mpirun -np 4 /home/milias/Work/qch/software/lam
mps/lammps_stable/src/lmp_mpi -in in.melt
LAMMPS (7 Aug 2019)
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
Created 4000 atoms
create_atoms CPU = 0.000918659 secs
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 2.706 | 2.706 | 2.706 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.34736 on 4 procs for 250 steps with 4000 atoms
Performance: 310916.549 tau/day, 719.714 timesteps/s
92.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22404 | 0.23568 | 0.25712 | 2.6 | 67.85
Neigh | 0.027579 | 0.028371 | 0.029572 | 0.5 | 8.17
Comm | 0.04958 | 0.072869 | 0.084434 | 5.1 | 20.98
Output | 0.0003319 | 0.00036758 | 0.00042612 | 0.0 | 0.11
Modify | 0.0057379 | 0.0059653 | 0.006437 | 0.4 | 1.72
Other | | 0.004107 | | | 1.18
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00
milias@login.grid.umb.sk:~/Work/open-collection/theoretical_chemistry/software_runs/lammps/runs/melt/.mpirun --version
mpirun (Open MPI) 4.0.1
Report bugs to http://www.open-mpi.org/community/help/
milias@login.grid.umb.sk:~/Work/open-collection/theoretical_chemistry/software_runs/lammps/runs/melt/.mpiCC --version
g++ (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
rhc54
Hello,
my OpenMPI applications are crashing on our cluster, we do not know if this is due to an old linux kernel. Here is the info:
OpenMPI installed as
Error by running application:
and on comp04 node the g++ version is lower: