I wanted to pass along a potential problem I’ve come across in doing output via the dump command. When running simulations my dump files sometimes stop being filled (i.e. the files are created but are totally empty), then after many thousands of timesteps the dump files return to normal. The problem is relatively rare so it is not a critical bug.
Despite running through a series of test runs I have not been able to figure out the source of this problem. In talking through the problem with the system manager for the computing cluster I am using he thought it might be a problem with the way the LAMMPS C++ code interacts with the network filesystems (NFS).
The ‘NFS’ filesharing protocol that is used to share disk space across the cluster (at least the one I’m using) has a few apparent quirks…
File attributes (including size) are cached locally and will not always
be up-to-date with the version on disk.
Attribute updates can be delayed until the machine writing the file
explicitly asks. This happens on close.
- Linux only pretends to write directly to files. The data is really held
in memory until there is enough to flush to disk or 30 seconds has
That being said this is only one potential idea of what might be causing the problem I’m seeing so if anyone else has had this type of difficulty with LAMMPS and was able to solve/identify it please let me know.