question about log.lammps

[zhaoxiao9302]

Normally, the last lines of log.lammps should be like Total # of neighbors = 3289152 Ave neighs/atom = 272.281 Ave special neighs/atom = 1.99338 Neighbor list builds = 26346 Dangerous builds = 0 Total wall time: 5:00:32

But when using fix ordern and comput rdf/ext, the last line of Total wall time is not there.

Besides, if I use the loop structure inside lammps to run it for 3 times, for example, variable i loop 0 2 ... fix 3 all ordern diffusivity ${Nevery_ordern} ${th} c_0 file diffself-${i}.log diffonsager-${i}.log run 100000 clear next i jump SELF it will only generate the result for i=0 and shows the error and stops. No result for i=1,2.

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 2124 RUNNING AT q16copt057.crc.nd.edu = EXIT CODE: 11 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions

What is wrong here? I am using LAMMPS (7 Aug 2019). Thank you.

[zhaoxiao9302]

I tested it with one core and everything seems fine. There was the Total wall time line and loop structure worked well. How should we fix it so that it can be run normally on multiple cores as one core? Thank you.

[AlperTung]

Normally, the last lines of log.lammps should be like Total # of neighbors = 3289152 Ave neighs/atom = 272.281 Ave special neighs/atom = 1.99338 Neighbor list builds = 26346 Dangerous builds = 0 Total wall time: 5:00:32

But when using fix ordern and comput rdf/ext, the last line of Total wall time is not there.

Besides, if I use the loop structure inside lammps to run it for 3 times, for example, variable i loop 0 2 ... fix 3 all ordern diffusivity ${Nevery_ordern} ${th} c_0 file diffself-${i}.log diffonsager-${i}.log run 100000 clear next i jump SELF it will only generate the result for i=0 and shows the error and stops. No result for i=1,2.

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 2124 RUNNING AT q16copt057.crc.nd.edu = EXIT CODE: 11 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions

What is wrong here? I am using LAMMPS (7 Aug 2019). Thank you.

The total wall time should appear in the output file when the simulation is completed.

Your error seems about compiling OCTP for multiple processor. Please see supporting info of our paper (Page S8) "Installation of the OCTP Plugin in LAMMPS"

I just made a quick test if the loop works in OCTP, The loop commands (variable-loop, label, run, next, jump) seem working. The way how the output is written on the files is up to the user. So the user must handle the necessary lammps-related commanding itself, please see https://lammps.sandia.gov/doc/jump.html.

Hope these works

[zhaoxiao9302]

Here is my test file. water_test.zip

I compiled OCTP exactly as in you paper.

I first tested it with lmp_mpi -in water.in. It run well. Then I run it with mpirun -np 8 lmp_mpi -in water.in. It stoped after the first loop. And the error again is

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 32215 RUNNING AT scm = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions

Could you please test it for me? I just cannot find where the problem is. Thank you.

[zhaoxiao9302]

I even got the same problem with you example (simulation.in) in your package when using loop structure.