bmin Command Help
Command: $SCHRODINGER/bmin
Usage: bmin <jobname> [OtherOptions] [JobOptions] [DiagnosticOptions]
<jobname> The name of the .com file leaving out the ".com".
Not needed or used if -TEST or -HELP are specified.
Other Options:
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-h, -help, -HELP Print this message and exit.
-DEBUGGER <debugger_name>
Run bmin in the foreground with specified debugger.
-TEST Run the standard test suite (jobname not needed).
-DEV_TEST Run the developers version of the standard test suite
(jobname not needed). Turns on -TEST.
Job Options:
------------
-DEBUG Show details of operation of the toplevel scripts.
-HOST <hostname> or
-HOST <hostname:nproc> or
-HOST "hostname1:nproc1 hostname2:nproc2 ... hostnameN:nprocN"
Distribute the job over the specified hosts. The driver
job is run on the first host specified. If -SUBHOST is
used to specify the hosts for the subjobs, the -HOST
option only specifies the host for the driver.
-HOSTFILE <host_file_name>
The name of the host file to use for this run.
-LOCAL Do not use a temporary directory for job files.
Keep files in the launch directory.
-NICE Run the job at reduced priority.
-NOJOBID Do not use job control and print bmin messages to the
screen.
-PROJ <name> Assign job to a Maestro project <name>.
-TMPDIR <directory>
The name of the directory used to store files
temporarily during a job.
-USER <name> Launch job as user <name>.
-WAIT Do not return a prompt until the job completes.
-RESTART Restart the previously failed parent job.
This facility works only for local jobs.
-ARCH <pattern> The platform tag must match <pattern> (e.g. mips3).
-COMPAT <dir> Require compatiblity with executables in <exec_dir>.
-REL <vernum> The version number must match <vernum>
(e.g. 80 or 80015).
-VER <pattern> Exec directory pathname must match <pattern>.
** Distributed job options:
-SUBHOST <hostname> or
-SUBHOST <hostname:nproc> or
-SUBHOST "hostname1:nproc1 hostname2:nproc2 ... hostnameN:nprocN"
Run the subjobs on the specified hosts.
The driver is run on the host specified with -HOST.
-NJOBS <number> Number of subjobs to create.
If this option is omitted, -NJOBS will be set to the
number of cpus requested with -SUBHOST option.
-JOBCTS <number> Ensure that each subjob has no more than this many
structures to process. Defaults to 10000.
-STRICT_END Terminate if any of the subjobs dies.
-MAX_RETRIES Number of allowed retries per subjob.
-first First structure to process.
-last Last structure to process.
-OUTPUT_ORG <option>
Produce more than one output structure file.
If option is BY_SUBJOB produce one output file for each
subjob. Otherwise create a new directory called: option
and create separate output files for each input ligand
within this new directory.
-NC or -nc Do not clean up by removing intermediate files.
By default many intermediate job files are removed.
-nx Do not run jobs, but create specified subjob directories
and input structures.
-j <range_values> Only run specified subjobs.
For example of range values;
10 job number 10
1:15 job numbers 1 to 15
"1, 5, 10" job numbers 1, 5, and 10
"1:15, 18" job numbers 1 to 15 and 18
"1:5, 15:20" job numbers 1 to 15 and 15 to 20
Diagnostic Options: (Provide information but the program will not run).
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-ALL Ignore platform compatibility (list all platforms).
-ENTRY List the relevant host entry(s) from the hosts file.
-HOSTS List the hosts available for remote jobs.
-LIST List all the platform-compatible versions of product.
-WHICH Report the product exec directory and MMSHARE_EXEC.
-WHY Show details of how the selected exec dir was chosen.