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Added 'timeout <value>' option to the adios reader, so that a rerun can concurrently run with the first simulation

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Podhorszki Norbert
2020-01-20 15:52:21 -05:00
parent 95d3b9e708
commit 44a814ec1d
6 changed files with 55 additions and 12 deletions
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10
doc/src/read_dump.rst
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@ -43,7 +43,9 @@ Syntax
*format* values = format of dump file, must be last keyword if used
*native* = native LAMMPS dump file
*xyz* = XYZ file
*adios* = dump file written by the :doc:`dump adios <dump_adios>` command
*adios* [*timeout* value] = dump file written by the :doc:`dump adios <dump_adios>` command
*timeout* = specify waiting time for the arrival of the timestep when running concurrently.
The value is a float number and is interpreted in seconds.
*molfile* style path = VMD molfile plugin interface
style = *dcd* or *xyz* or others supported by molfile plugins
path = optional path for location of molfile plugins
@ -67,6 +69,7 @@ Examples
read_dump dump.dcd 0 x y z format molfile dcd
read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.bp 5000 x y z vx vy vz format adios
read_dump dump.bp 5000 x y z vx vy vz format adios timeout 60.0
Description
"""""""""""
@ -144,7 +147,10 @@ entire dump is read in parallel across all the processes, dividing
the atoms evenly amongs the processes. The number of writers that
has written the dump file does not matter. Using the adios style for
dump and read_dump is a convenient way to dump all atoms from *N*
writers and read it back by *M* readers.
writers and read it back by *M* readers. If one is running two
LAMMPS instances concurrently where one dumps data and the other is
reading it with the rerun command, the timeout option can be specified
to wait on the reader side for the arrival of the requested step.
Support for other dump format readers may be added in the future.

2
doc/src/rerun.rst
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@ -44,6 +44,8 @@ Examples
rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj
rerun dump.dcd dump x y z box no format molfile dcd
rerun ../run7/dump.file.gz skip 2 dump x y z box yes
rerun dump.bp dump x y z box no format adios
rerun dump.bp dump x y z vx vy vz format adios timeout 10.0
Description
"""""""""""