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Only members of the namd user group have access to NAMD executables provided by HLRN. To have their user ID included in this group, users can send a message to their consultant or our to HLRN support.
Modules
The environment modules shown in the table below are available to include NAMD executables in the directory search path. To see what is installed and what is the current default version of NAMD at HLRN, a corresponding overview can be obtained by saying module avail namd.
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| NAMD Version | NAMD Modulefile | MPI Requirement |
|---|---|---|
| 2.13 | namd/2.13 | impi/* (any version) |
File I/O
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Considerations
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, 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 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 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.
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