Hello everyone,
I am a beginner with lammps,
I have compiled the python package of Lammps with the cmake interface on windows 10.
then to check that python and lammps are embedded, I made some examples in the python subfolder of the example folder. I took the example in.python.lmp whose script invokes the function funcs.py, and so far I have an error that I do not understand.
can someone help me please?
Glenn
This part of the LAMMPS code has not been ported to Windows yet.
Your best shot at getting this functionality to work on Windows is currently to install the Windows subsystem for Linux (WSL) and then compile with Linux tools and libraries inside the bash shell.
After some checking with a Linux to Windows cross compiler and running the resulting executable with a wine docker container on a Linux machine with singularity (I don’t think there is a more indirect way of testing this…), it looks like I was able to identify the changes that are necessary to compile a working Python support on Windows. It basically boils down to the fact that a long int on Linux and macOS is a 64-bit integer, while on Windows it is (still) 32-bit and you need to use a long long int to store a 64-bit integer. The actual change is in this commit.
and will be released with the next LAMMPS patch release (aka pre-release).
$ singularity exec --bind /usr/x86_64-w64-mingw32 ~/compile/lammps/wine.sif env WINEPATH="D:\\bin;..\\..\\" env PYTHONPATH=..\\python wine lammps-shell.exe
LAMMPS Shell version 1.1 OS: Windows 6.1 (7601) on x86_64
GNU C++ 10.3.1 20210422 (Fedora MinGW 10.3.1-1.fc34) with OpenMP 4.5
LAMMPS (14 May 2021)
using 4 OpenMP thread(s) per MPI task
LAMMPS Shell> source in.python
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
1 by 1 by 1 MPI processor grid
Created 4000 atoms
create_atoms CPU = 0.001 seconds
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
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
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.366 | 6.366 | 6.366 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.0600009 on 4 procs for 10 steps with 4000 atoms
Performance: 71998.924 tau/day, 166.664 timesteps/s
83.3% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044 | 0.044 | 0.044 | 0.0 | 73.33
Neigh | 0.011001 | 0.011001 | 0.011001 | 0.0 | 18.33
Comm | 0.0019999 | 0.0019999 | 0.0019999 | 0.0 | 3.33
Output | 0.0019999 | 0.0019999 | 0.0019999 | 0.0 | 3.33
Modify | 0.0010002 | 0.0010002 | 0.0010002 | 0.0 | 1.67
Other | | 0 | | | 0.00
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5841.00 ave 5841 max 5841 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155984.0 ave 155984 max 155984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155984
Ave neighs/atom = 38.996000
Neighbor list builds = 1
Dangerous builds = 0
Inside simple function
Factorial of 10 = 3628800
Factorial of 20 = -2102132736
LOOP ARGS 10 1.0 -4.0 <capsule object NULL at 0x0000000007c25030>
Setting up Verlet run ...
Unit style : lj
Current step : 10
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.00900102 on 4 procs for 10 steps with 4000 atoms
Performance: 479945.787 tau/day, 1110.986 timesteps/s
111.1% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 44.44
Neigh | 0.003 | 0.003 | 0.003 | 0.0 | 33.33
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0.002001 | 0.002001 | 0.002001 | 0.0 | 22.23
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0 | | | 0.00
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2083.00 ave 2083 max 2083 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 17727.0 ave 17727 max 17727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17727
Ave neighs/atom = 4.4317500
Neighbor list builds = 1
Dangerous builds = 0
PE 0.39300382487856356 -4.0
Setting up Verlet run ...
Unit style : lj
Current step : 20
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.0140009 on 4 procs for 10 steps with 4000 atoms
Performance: 308551.755 tau/day, 714.240 timesteps/s
71.4% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.003 | 0.003 | 0.003 | 0.0 | 21.43
Neigh | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 28.57
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0.003 | 0.003 | 0.003 | 0.0 | 21.43
Modify | 0.0019999 | 0.0019999 | 0.0019999 | 0.0 | 14.28
Other | | 0.002001 | | | 14.29
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2087.00 ave 2087 max 2087 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21036.0 ave 21036 max 21036 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21036
Ave neighs/atom = 5.2590000
Neighbor list builds = 1
Dangerous builds = 0
PE -0.8316621917281097 -4.0
Setting up Verlet run ...
Unit style : lj
Current step : 30
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.0150001 on 4 procs for 10 steps with 4000 atoms
Performance: 287997.986 tau/day, 666.662 timesteps/s
66.7% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.006 | 0.006 | 0.006 | 0.0 | 40.00
Neigh | 0.0040002 | 0.0040002 | 0.0040002 | 0.0 | 26.67
Comm | 0.00099993 | 0.00099993 | 0.00099993 | 0.0 | 6.67
Output | 0.003 | 0.003 | 0.003 | 0.0 | 20.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0009999 | | | 6.67
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2250.00 ave 2250 max 2250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 24095.0 ave 24095 max 24095 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24095
Ave neighs/atom = 6.0237500
Neighbor list builds = 1
Dangerous builds = 0
PE -2.186832445057782 -4.0
Setting up Verlet run ...
Unit style : lj
Current step : 40
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.0190001 on 4 procs for 10 steps with 4000 atoms
Performance: 227367.782 tau/day, 526.314 timesteps/s
52.6% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01 | 0.01 | 0.01 | 0.0 | 52.63
Neigh | 0.0050001 | 0.0050001 | 0.0050001 | 0.0 | 26.32
Comm | 0.00099993 | 0.00099993 | 0.00099993 | 0.0 | 5.26
Output | 0.0020001 | 0.0020001 | 0.0020001 | 0.0 | 10.53
Modify | 0.00099993 | 0.00099993 | 0.00099993 | 0.0 | 5.26
Other | | 0 | | | 0.00
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2572.00 ave 2572 max 2572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27137.0 ave 27137 max 27137 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 27137
Ave neighs/atom = 6.7842500
Neighbor list builds = 1
Dangerous builds = 0
PE -3.1173703652218787 -4.0
Setting up Verlet run ...
Unit style : lj
Current step : 50
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.022001 on 4 procs for 10 steps with 4000 atoms
Performance: 196354.461 tau/day, 454.524 timesteps/s
90.9% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.014001 | 0.014001 | 0.014001 | 0.0 | 63.64
Neigh | 0.0049999 | 0.0049999 | 0.0049999 | 0.0 | 22.73
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0.0020001 | 0.0020001 | 0.0020001 | 0.0 | 9.09
Modify | 0.00099993 | 0.00099993 | 0.00099993 | 0.0 | 4.54
Other | | 0 | | | 0.00
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3013.00 ave 3013 max 3013 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 30887.0 ave 30887 max 30887 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30887
Ave neighs/atom = 7.7217500
Neighbor list builds = 1
Dangerous builds = 0
PE -3.6616013599521033 -4.0
Setting up Verlet run ...
Unit style : lj
Current step : 60
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.02 on 4 procs for 10 steps with 4000 atoms
Performance: 216000.206 tau/day, 500.000 timesteps/s
100.0% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.011 | 0.011 | 0.011 | 0.0 | 55.00
Neigh | 0.006 | 0.006 | 0.006 | 0.0 | 30.00
Comm | 0.00099993 | 0.00099993 | 0.00099993 | 0.0 | 5.00
Output | 0.0019999 | 0.0019999 | 0.0019999 | 0.0 | 10.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0 | | | 0.00
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3388.00 ave 3388 max 3388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35959.0 ave 35959 max 35959 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35959
Ave neighs/atom = 8.9897500
Neighbor list builds = 1
Dangerous builds = 0
PE -3.9657094549806113 -4.0
Setting up Verlet run ...
Unit style : lj
Current step : 70
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes
Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.0310011 on 4 procs for 10 steps with 4000 atoms
Performance: 139349.934 tau/day, 322.569 timesteps/s
96.8% CPU use with 1 MPI tasks x 4 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.019001 | 0.019001 | 0.019001 | 0.0 | 61.29
Neigh | 0.007 | 0.007 | 0.007 | 0.0 | 22.58
Comm | 0.0020001 | 0.0020001 | 0.0020001 | 0.0 | 6.45
Output | 0.0020001 | 0.0020001 | 0.0020001 | 0.0 | 6.45
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0009999 | | | 3.23
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3612.00 ave 3612 max 3612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 43239.0 ave 43239 max 43239 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43239
Ave neighs/atom = 10.809750
Neighbor list builds = 1
Dangerous builds = 0
PE -4.183135662582033 -4.0
LAMMPS Shell> exit
Total wall time: 0:01:08
Thank you so much Axel,
it works
Best regards
Glenn