HPC/Applications/lammps: Difference between revisions

From CNM Wiki
Jump to navigation Jump to search
m (migrate GPU/USER-CUDA/OMP to sub-pages)
 
(24 intermediate revisions by the same user not shown)
Line 1: Line 1:
== Binaries ==
== Binaries ==
As of module version lammps/2012-10-10-3 (which currently is the default) several LAMMPS binaries are provided within one module.
Several LAMMPS binaries are provided by the LAMMPS module, giving you options to run with MPI and/or a couple of GPU packages.
Earlier modules only contained one MPI binary.
Binaries compiled with GPU support will not run on nodes without a GPU
Binaries compiled with GPU support will not run on nodes without a GPU
(CUDA libraries are deliberately only installed on GPU nodes.)
(CUDA libraries are deliberately only installed on GPU nodes.)
Line 19: Line 20:
|}
|}
To use the *-gpu and *=user-cuda binaries, load the [[../#cuda|<code>cuda</code>]] module in addition to lammps.
To use the *-gpu and *=user-cuda binaries, load the [[../#cuda|<code>cuda</code>]] module in addition to lammps.
  module load cuda lammps
  module load '''cuda'''
module load lammps
To use any one of the binaries, simply name the appropriate one in the job file; full paths are neither necessary nor recommended.
To use any one of the binaries, simply name the appropriate one in the job file; full paths are neither necessary nor recommended.


=== GPU support ===
== Library linking ==
* Consult the [http://lammps.sandia.gov/doc/Section_howto.html#library-interface-to-lammps LAMMPS documentation]
* Carbon-specifics: To point your compiler and linker to the installed LAMMPS module, always use the environment variable <code>$LAMMPS_HOME</code>, never full path names. Edit the makefile of your application and add settings similar to the following:
<source lang="make">
CPPFLAGS += -I${LAMMPS_HOME}/include
FPPFLAGS += -I${LAMMPS_HOME}/include
LDFLAGS += -L$(FFTW3_HOME) -L${LAMMPS_HOME}/lib -llammps -lfftw3 -limf
</source>
: These settings refer to variables customarily used in makefiles for GNU Make. Your package might use different variables. Adapt as needed.
* The library created with the <code>-llammps</code> link option provides the same LAMMPS package set as the main binary, and supports MPI and OpenMP. It is actually equivalent to using:
-llammps_mpi-main
: This variant is available for both ''static'' (*.a) and ''dynamic'' (*.so) linkage but supports no GPUs.
* To use GPU nodes, link with one of the following instead:
-llammps_mpi-gpu
-llammps_mpi-user-cuda
: These variants are only available for ''static'' linkage.
 
Inspect a sample code that uses LAMMPS as a library at:
<source lang="bash">
cd ${LAMMPS_HOME}/src/examples/COUPLE/simple
less README Makefile
</source>
 
== GPU support ==
LAMMPS offers ''two different'' packages for using GPUs, one official, the other user-contributed.
LAMMPS offers ''two different'' packages for using GPUs, one official, the other user-contributed.
Only one of these packges can be used for a run.
Only one of these packges can be used for a run.
The packages are fully documented in the following sections of the [http://lammps.sandia.gov/doc/Manual.html LAMMPS manual]:
The packages are fully documented in the following sections of the [http://lammps.sandia.gov/doc/Manual.html LAMMPS manual]:
* [http://lammps.sandia.gov/doc/Section_accelerate.html 5. Accelerating LAMMPS performance]
* [http://lammps.sandia.gov/doc/Section_accelerate.html 5. Accelerating LAMMPS performance]
<!-- ** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_5 5.5 USER-OMP package] -->
** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_6 5.6 GPU package]
** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_6 5.6 GPU package]
** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_7 5.7 USER-CUDA package]
** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_7 5.7 USER-CUDA package]
** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_8 5.8 Comparison of GPU and USER-CUDA packages]
** [http://lammps.sandia.gov/doc/Section_accelerate.html#acc_8 5.8 Comparison of GPU and USER-CUDA packages]
To use LAMMPS with GPUs on Carbon you must read and understand these sections. A summary and Carbon-specific details are given in the following two sections.


; General note on GPU jobs:
To use LAMMPS with GPUs on Carbon you must read and understand these sections. A summary and Carbon-specific details are given in the next section.
* To request your job to run on a GPU node use in the job file:
#PBS -l nodes=…:gpus=1
At the moment this is synonymous with but preferable to:
#PBS -l nodes=…:gen3
* Each GPU node has 12 cores; if you submit jobs with <code>:ppn &lt; 12</code> and <code>:gpus=1</code> the node may be shared with purely CPU jobs. It is to be tested if and how much interference this causes for either job. See [[HPC/Submitting and Managing Jobs/Advanced node selection|Advanced node selection]] to reserve entire nodes while controlling <code>ppn</code> for MPI or OpenMP.


== Package-specific hints ==
=== Using GPU packages ===
[[../lammps/Package GPU]]
* [[../lammps/Package GPU]]
[[../lammps/Package USER-CUDA]]
* [[../lammps/Package USER-CUDA]]
[[../lammps/Package OMP]]
* [[../lammps/Package OMP]] – if you really want to.


=== Jobs on Carbon ===
For sample PBS scripts, consult these files:
For sample PBS scripts, consult these files:
  $LAMMPS_HOME/sample.job
  $LAMMPS_HOME/sample.job
  $LAMMPS_HOME/sample-hybrid.job
  $LAMMPS_HOME/sample-hybrid.job
* See also [[ HPC/Submitting and Managing Jobs/Example Job Script#GPU nodes]]


== Benchmark (pre-GPU version) ==
== Benchmark (pre-GPU version) ==

Latest revision as of 21:58, August 11, 2015

Binaries

Several LAMMPS binaries are provided by the LAMMPS module, giving you options to run with MPI and/or a couple of GPU packages. Earlier modules only contained one MPI binary. Binaries compiled with GPU support will not run on nodes without a GPU (CUDA libraries are deliberately only installed on GPU nodes.) Moreover, a binary built with the USER-CUDA package will attempt to access the GPU by default [1].

Binary name Description
lmp_openmpi-main The baseline binary, containing the packages shown by module help lammps.
lmp_openmpi The distribution's default name; synonym for lmp_openmpi-main;
lmp_openmpi-gpu The package "gpu" and all packages from main.
lmp_openmpi-user-cuda The package "user-cuda" and all packages from main.
lmp_openmpi-jr A custom build for user J.R.

To use the *-gpu and *=user-cuda binaries, load the cuda module in addition to lammps. 

module load cuda
module load lammps

To use any one of the binaries, simply name the appropriate one in the job file; full paths are neither necessary nor recommended.

Library linking

  • Consult the LAMMPS documentation
  • Carbon-specifics: To point your compiler and linker to the installed LAMMPS module, always use the environment variable $LAMMPS_HOME, never full path names. Edit the makefile of your application and add settings similar to the following:
CPPFLAGS += -I${LAMMPS_HOME}/include
FPPFLAGS += -I${LAMMPS_HOME}/include
LDFLAGS += -L$(FFTW3_HOME) -L${LAMMPS_HOME}/lib -llammps -lfftw3 -limf
These settings refer to variables customarily used in makefiles for GNU Make. Your package might use different variables. Adapt as needed.
  • The library created with the -llammps link option provides the same LAMMPS package set as the main binary, and supports MPI and OpenMP. It is actually equivalent to using:
-llammps_mpi-main
This variant is available for both static (*.a) and dynamic (*.so) linkage but supports no GPUs.
  • To use GPU nodes, link with one of the following instead:
-llammps_mpi-gpu
-llammps_mpi-user-cuda
These variants are only available for static linkage.

Inspect a sample code that uses LAMMPS as a library at: 

cd ${LAMMPS_HOME}/src/examples/COUPLE/simple
less README Makefile

GPU support

LAMMPS offers two different packages for using GPUs, one official, the other user-contributed. Only one of these packges can be used for a run. The packages are fully documented in the following sections of the LAMMPS manual:

To use LAMMPS with GPUs on Carbon you must read and understand these sections. A summary and Carbon-specific details are given in the next section.

Using GPU packages

Jobs on Carbon

For sample PBS scripts, consult these files: 

$LAMMPS_HOME/sample.job
$LAMMPS_HOME/sample-hybrid.job

Benchmark (pre-GPU version)

Using a sample workload from Sanket ("run9"), I tested various OpenMPI options on node types gen1 and gen2.

LAMMPS performs best on gen2 nodes without extra options, and pretty well on gen1 nodes over ethernet(!).

Job tag Node type Interconnect Additional OpenMPI options Relative speed
(1000 steps/3 hours)		 Notes
gen1 gen1 IB (none) 36
gen1srqpin gen1 IB -mca btl_openib_use_srq 1
-mca mpi_paffinity_alone 1		 39
gen1eth gen1 Ethernet -mca btl self,tcp 44 fastest for gen1
gen2eth gen2 Ethernet -mca btl self,tcp 49
gen2srq gen2 IB -mca btl_openib_use_srq 1 59
gen2 gen2 IB (none) 59 fastest for gen2

Diagnostic for hybrid parallel runs

  • LAMMPS echoes it parallelization scheme first thing in the output:
LAMMPS (10 Feb 2012)
  using 4 OpenMP thread(s) per MPI task
...
  1 by 2 by 2 MPI processor grid
  104 atoms
...

and near the end: 

Loop time of 124.809 on 16 procs (4 MPI x 4 OpenMP) for 30000 steps with 104 atoms
  • To see if OpenMP is really active, log into a compute node while a job is running and run top or psuser – The %CPU field should be about OMP_NUM_THREADS × 100%
 PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                                             
8047 stern     25   0 4017m  33m 7540 R 401.8  0.1   1:41.60 lmp_openmpi                                                                                         
8044 stern     25   0 4017m  33m 7540 R 399.9  0.1   1:43.50 lmp_openmpi                                                                                         
4822 root      34  19     0    0    0 S  2.0  0.0 115:34.98 kipmi0

References

Retrieved from "https://wiki.anl.gov/wiki_cnm/index.php?title=HPC/Applications/lammps&oldid=5252"