Article ID: 737 - Last Modified: May 1, 2012
When using Glide, I got this message:
Disk quota exceeded
FATAL: Unable to copy input file "glide-grid_prot3.tmp10902.inp" to jobdb
Error: jlaunch failed.
What do I do?
It looks like either your home file system filled up, or the user quota was exceeded.
There are three storage areas to consider:
1) The launch directory. This is where the command-line job is run, or the current working directory for the Maestro session. Some input files are located here, and the output files are copied here at the completion of the job. If space on the home file system is limited, we suggest running jobs or Maestro from a file system with more space.
2) The job directory. When the docking job runs, by default input files are copied to a temporary job directory on the compute machine, and any output files are copied back to the launch directory. This job directory is a temporary directory on the machine where the job is running (not necessarily the machine from which the job was launched). This directory is specified as the "tmpdir" setting in the hosts file (schrodinger.hosts). It should be a local filesystem with sufficient space (e.g., /scr). To change the job directory, you can
i) change the "tmpdir" setting in the hosts file (recommended),
ii) use the SCHRODINGER_TMPDIR environment variable to indicate a different tmpdir, or
iii) use the '-TMPDIR' command-line option.
3) The job database directory ($HOME/.schrodinger/.jobdb2, by default, .jobdb prior to Suite 2011). Job records and various job-related files (e.g., batch scripts for queue submission) are placed here. The job database is periodically cleaned up, but if it is too large for this space-limited filesystem, you can
i) shorten the cleanup interval via the SCHRODINGER_JOBDB_CLEANUP environment variable,
ii) set a smaller maximum size via the SCHRODINGER_JOBDB_MAXSIZE env var, or
iii) move the job database to a larger filesystem (SCHRODINGER_JOBDB).
These environment variables are described in more detail in Chapter 3 and Appendix B of the Job Control Guide.
Keywords: working directory, lauch directory, job directory, jobs database directory, storage areas
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