...
During run time only few files are involved in NAMD's I/O activities. As long as standard MD runs are carried out, this is unlikely to impose stress on the Lustre file system ($WORK). For the case of replica-exchange runs (REMD), however, the situation can be different. Here we already observed cases where the high frequency of file metadata operations (file create, open, close, rename) has overloaded our Lustre metadata servers (MDS) resulting in a severe slowdown of the entire Lustre file system. Candidates for heavy metadata file I/O are the individual "*colvars.state*" files located in every replica's subdirectory when they get renamed, created, opened, and closed by every replica in too short intervals. Users are advised to set corresponding NAMD input parameters such that each replica performs metadata I/O on these files in intervals of at least one second, or, when affordable, that these files are written only at the end of the run.
...