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My simulation seems to be running, but shouldn't there be any output? |
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Friday, 09 September 2005 |
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Your simulation might simply be (very) slow, and since output is buffered, it can take quite some time for output to appear in the respective files. If you are trying to fix some problems and you want to get output as fast as possible, you can set the environment variable LOG_BUFS to 0 by using setenv LOG_BUFS 0, this disables output buffering. Use unsetenv LOG_BUFS to turn buffering on again.
Something might be going wrong in your simulation, causing e.g. not-a-numbers (NAN) to be generated (these are the result of e.g. division by zero). Subsequent calculations with NAN's will generate floating point exceptions which slow everything down by orders of magnitude. On a SGI system this will usually result in a large percentage of CPU time being devoted to 'system' (check it with osview, or for a multi-processor machine with top and osview).
You might have all nst* parameters (see your .mdp file) set to 0, this will suppress most output.
Your disk might be full. Eventually this will lead to mdrun crashing, but since output is buffered, it might take a while for mdrun to realize it can't write.
You are runnning an executable compiled with MPI support (e.g. LAM) and did not start the LAM daemon (lamboot). See LAM documentation.
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