more example bug fixes
This commit is contained in:
Steve Plimpton
@ -21,9 +21,9 @@ a driver and couple to an engine that is either a stand-alone code or
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a plugin. Examples for all these use cases are in this directory.
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The example commands below illustrate how to run all the variants.
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To use LAMMPS as a plugin engine, you must build it as a shared library.
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Something like this, which also builds the normal LAMMPS executable
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lmp_mpi:
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To use LAMMPS as a plugin engine, you must build it as a shared
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library. Something like this with make, which also builds the normal
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LAMMPS executable lmp_mpi:
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cd src
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make yes-mdi
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@ -33,189 +33,59 @@ To use the serial_driver.py example you will need Python 3 with Numpy
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and mpi4py available in your Python. Make sure LAMMPS and Python are
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using same the same version of MPI.
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5 use-case examples are explained below.
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See the Run.sh file for commands to run each of the examples
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in all the different modes.
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In the first 3 examples, results running with MDI should be identical
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to running without MDI (alone log files). Example #4 has no non-MDI
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run. Example #5 results should match the non-MDI run of example #1.
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-------------------------------------------------
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-------------------------------------------------
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* Example #1 = run ab inito MD (AIMD)
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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* Example #1 = run ab initio MD (AIMD)
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See the log aimd files.
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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LAMMPS is a surrogate for a quantum code.
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Note that the 2 input scripts in.aimd.alone and in.aimd.driver
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have an option for running in NVE vs NPT mode. Comment in/out
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the appropriate line to change modes. Nothing needs to be
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changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
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---
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-------------------------------------------------
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-------------------------------------------------
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
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% lmp_mpi -log log.aimd.alone < in.aimd.alone
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See the log snapshot and dump snapshot files.
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With MDI, the thermo output of the driver should match the thermo
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output of the in.aimd.alone script.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
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% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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LAMMPS is a surrogate for a quantum code
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-------------------------------------------------
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-------------------------------------------------
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* Example #1b = run LAMMPS, compute QM forces on snapshots from a long run
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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* Example #3 = run LAMMPS, compute QM forces on series of independent systems
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---
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files See the log series and dump series files.
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi -log log.snapshot.alone < in.snapshot.alone
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With MDI, the thermo output of the driver should match the thermo
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output of the in.snapshot.alone script. Likewise the dump file written
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by the driver should match dump.snapshot.alone.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
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% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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LAMMPS is a surrogate for a quantum code
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-------------------------------------------------
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-------------------------------------------------
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* Example #1c = run LAMMPS, compute QM forces on series of independent systems
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
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---
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See the log sequence files.
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi -log log.series.alone < in.series.alone
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With MDI, the thermo output of the driver should match the thermo
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output of the in.series.alone script. Likewise the dump files written
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by the driver should match dump.series.alone files.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
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% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
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-------------------------------------------------
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-------------------------------------------------
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* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
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Each calculation can be a single-point evaluation, MD run, or minimization
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Each calculation can be a single-point evaluation, MD run, or
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minimization
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The sequence_driver.py code allows for optional switches in addition
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to -mdi (required) and the -plugin and -plugin_args switches which are
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@ -244,101 +114,21 @@ copied here:
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# -seed 12345
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# random number seed > 0, default = 12345
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---
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Run with TCP: 1 proc each
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% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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% lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
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---
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Run with TCP: 2 proc + 4 procs
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% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence.python
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---
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Run with MPI: 2 procs + 4 procs
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% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence -in in.sequence.python
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---
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Run in plugin mode: 1 proc
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% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
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-------------------------------------------------
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-------------------------------------------------
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* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
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First LAMMPS instance performs the MD timestepping
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Second LAMMPS instance is surrogate QM = computes forces
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* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
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See the log aimdpy files.
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First LAMMPS instance performs the MD timestepping. Second LAMMPS
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instance is surrogate QM to compute forces.
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The aimd_driver.py code allows for an optional switch in addition to
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-mdi (required) and the -plugin and -plugin_args swiches which are
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used to link to the 2 engines as a plugin libraries. The example run
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commands below use the default values of the optional switch. The
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switch is also explained the top of the file; the info is copied
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here:
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switch is also explained the top of the file; the info is copied here:
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# -nsteps 5
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# number of timesteps in dynamics runs, default = 5
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---
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi -log log.aimd.alone < in.aimd.alone
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With MDI, the driver prints the QM and Total energies. These should
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match the PotEng and TotEng output of the in.aimd.alone script.
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---
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Run with TCP: 1 proc each
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% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
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% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
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% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
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---
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Run with TCP: 2 procs + 2 procs + 3 procs
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% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
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% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
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% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
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---
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Run with MPI: 2 procs + 2 procs + 3 procs
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% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
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Reference in New Issue
Block a user