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bit	Xplor-NIH	VMD-XPLOR

pyXplor.txt

usage: pyXplor [option] [file]

where option is one of:

-c <command>     - invoke the Python interpreter, running
                   the specified command.
-m module...     - invoke the Python interpreter, running
                   the specified module.
-help            - print this message.
-version         - print version info
-features        - print version info, and a list of features

If no file is specified on the command-line, commands will be read from stdin.

Common options:

-debug <cmd> - run xplor under debugger given by cmd
-notrace         - turn command echoing off (set echo=off)
-quiet           - turn off verbose output (set messages=NONE)
-nice <#>        - specify a nice (see man nice) increment
-omp <#>         - specify the number of OpenMP threads to use.
                   This overrides the value of the environment
                   variable OMP_NUM_THREADS.
                   The default value is 1.
-fpe             - enable detection of floating point exceptions.
                   If an overflow, divide by zero occurs, the
                   program will halt and core dumped

Options for VMD-XPLOR:

-host        - specify host on which VMD is running
-port        - specify port for connection to VMD

Options for parallel jobs:

-parallel    - spawn multiple jobs on remote hosts
-machines <spec> - The spec argument is a space-separated
                   list of machines on which to run, or the
                   name of a file with one machine name per
                   line (lines beginning with the # character
                   are ignored as comments). The name
                   localhost'' is special in that it causes
                   a new processes to be forked on the local
                   machine. Each instance of a machine name
                   causes one process to be run, and if the
                   names are specified consecutively, one rsh
                   connection is made, and a process forked for
                   the number of times the machine is
                   specified. This option overrides the
                   MACHINES environment variable.
-crash_on_startup - specify this flag if you wish a parallel
                    calculation to fail at startup if any
                    process fails to startup. The default
                    behavior is to continue the full calculation
                    using only those processes which start.
-startup_delay <#> - specify a delay factor for processes
                     connecting to the server (process 0).
                     The delay time is the factor multiplied by
                     the process number.
-pport <port #>  - port for parallel communication. This
                   overrides the environment variable
                   XPLOR_PPORT. By default this value is
                   9021 + PID mod 1000, where
                   PID is the process id.
-rsh <cmd>       - command to connect to remote machine.
                   This overrides env var XPLOR_RSH
                   [default value: ssh -n -x]
-slurm           - used when called by slurmXplor. Specifies
                   that srun is used to launch each process
                   individually instead of forking N local
                   processes on each node.
-scyld <#>       - on a Scyld cluster, specify the number of
                   structures to run in parallel. This option
                   overrides the environment variable
                   SCYLD_PROCESSES.
-smp <#>         - on a multiprocessor node, specify the number of
                   structures to run in parallel. This option
                   overrides the environment variable
                   SMP_PROCESSES.
-o <file>        - specify prefix for log file.
                 name will be file.XPLOR_PROCESS

Options for parallelization of ensemble calculations:

-num_threads <#> - number of processors to use in
                   ensemble calculations. This option
                   overrides the environment variable
                   NUM_THREADS
-thread_filename <prefix> - prefix for thread output (used to
                            debug for ensemble calculations).
                            Each non-zero ensemble member will
                            have an output file named
                            prefix-schwitrs-UID-i, where i is the
                            ensemble member index.