Rename MPI to MPIProcesses to Fix #189 and #185

Author: alexandrebouchard

docs/src/mpi.md

@@ -86,12 +86,12 @@ mpi_run = pigeons(
     target = toy_mvn_target(1000000), 
     n_chains = 1000,
     checkpoint = true,
-    on = MPI(
+    on = MPIProcesses(
         n_mpi_processes = 1000,
         n_threads = 1))
 ```
 
-This will start a distributed PT algorithm with 1000 chains on 1000 MPI processes, each using one thread, targeting a one million 
+This will start a distributed PT algorithm with 1000 chains on 1000 MPIProcesses processes, each using one thread, targeting a one million 
 dimensional target distribution. On the UBC Sockeye cluster, the last 
 round of this run (i.e. the last 1024 iterations) takes 10 seconds to complete, versus more than 
 2 hours if run serially, i.e. a >700x speed-up. 
@@ -126,11 +126,11 @@ are built-in inside the Pigeons module.
 However in typical use cases,
 some user-provided code needs to be provided to 
 [`ChildProcess`](@ref) 
-and [`MPI`](@ref) so that the other participating Julia 
+and [`MPIProcesses`](@ref) so that the other participating Julia 
 processes have access to it. 
 This is done with the argument `dependencies` (of type `Vector`;  present in 
 both [`ChildProcess`](@ref) 
-and [`MPI`](@ref)). 
+and [`MPIProcesses`](@ref)). 
 Two types of elements can be used in the vector of dependencies, and they can be mixed:
 
 - elements of type `Module`: for each of those, an `using` statement will be generated in the script used by the child process;

docs/src/output-mpi-postprocessing.md

@@ -17,7 +17,7 @@ Option (1) is more convenient than (2) but it uses more RAM.
 
 Many of Pigeons' post-processing tools take as input a [`PT`](@ref) struct.
 When running locally, [`pigeons()`](@ref) returns a [`PT`](@ref) struct, 
-however, when running a job via [`MPI`](@ref) or [`ChildProcess`](@ref), 
+however, when running a job via [`MPIProcesses`](@ref) or [`ChildProcess`](@ref), 
 [`pigeons()`](@ref) returns a [`Result`](@ref) struct (which only holds the  
 directory where samples are stored). 
 

src/Pigeons.jl

@@ -63,7 +63,7 @@ include("includes.jl")
 
 export pigeons, Inputs, PT,
     # for running jobs:
-    ChildProcess, MPI,
+    ChildProcess, MPIProcesses,
     # references:
     DistributionLogPotential,
     # targets:

src/includes.jl

@@ -34,7 +34,7 @@ include("tempering/NonReversiblePT.jl")
 include("tempering/StabilizedPT.jl")
 include("tempering/tempering.jl")
 include("swap/swap_graph.jl")
-include("submission/MPI.jl")
+include("submission/MPIProcesses.jl")
 include("targets/BlangTarget.jl")
 include("submission/MPISettings.jl")
 include("submission/ChildProcess.jl")

src/pt/checks.jl

@@ -56,7 +56,7 @@ function check_against_serial(pt)
     # run a serial copy
     dependencies =
         if isfile("$(pt.exec_folder)/.dependencies.jls")
-            # this process was itself spawn using ChildProcess/MPI
+            # this process was itself spawn using ChildProcess/MPIProcesses
             # so use the same dependencies as this process
             deserialize("$(pt.exec_folder)/.dependencies.jls")
         else

src/submission/MPI.jl renamed to src/submission/MPIProcesses.jl

@@ -14,7 +14,7 @@ Fields:
 
 $FIELDS
 """
-@kwdef struct MPI <: Submission
+@kwdef struct MPIProcesses <: Submission
     """
     The number of threads per MPI process, 1 by default.
     """
@@ -51,7 +51,7 @@ end
 """
 $SIGNATURES
 """
-function pigeons(pt_arguments, mpi_submission::MPI)
+function pigeons(pt_arguments, mpi_submission::MPIProcesses)
     if !is_mpi_setup()
         error("call setup_mpi(..) first")
     end
@@ -77,13 +77,13 @@ function pigeons(pt_arguments, mpi_submission::MPI)
 end
 
 # todo: abstract out to other submission systems
-function mpi_submission_cmd(exec_folder, mpi_submission::MPI, julia_cmd) 
+function mpi_submission_cmd(exec_folder, mpi_submission::MPIProcesses, julia_cmd) 
     r = rosetta()
     submission_script = mpi_submission_script(exec_folder, mpi_submission, julia_cmd)
     return `$(r.submit) $submission_script`
 end
 
-function mpi_submission_script(exec_folder, mpi_submission::MPI, julia_cmd)
+function mpi_submission_script(exec_folder, mpi_submission::MPIProcesses, julia_cmd)
     # TODO: generalize to other submission systems
     # TODO: move some more things over from mpi-run
     info_folder = "$exec_folder/info"
@@ -133,23 +133,23 @@ const _rosetta = (;
 
 supported_submission_systems() = filter(x -> x != :queue_concept && x != :custom, keys(_rosetta))
 
-resource_string(m::MPI, symbol) = resource_string(m, Val(symbol))
+resource_string(m::MPIProcesses, symbol) = resource_string(m, Val(symbol))
 
-resource_string(m::MPI, ::Val{:pbs}) =
+resource_string(m::MPIProcesses, ::Val{:pbs}) =
                                     #                             +-- each chunks should request as many cpus as threads,
                                     # +-- number of "chunks"...   |                   +-- NB: if mpiprocs were set to more than 1 this would give a number of mpi processes equal to select*mpiprocs
                                     # v                           v                   v               
     "#PBS -l walltime=$(m.walltime),select=$(m.n_mpi_processes):ncpus=$(m.n_threads):mpiprocs=1:mem=$(m.memory)"
 
-resource_string(m::MPI, ::Val{:slurm}) =
+resource_string(m::MPIProcesses, ::Val{:slurm}) =
     """
     #SBATCH -t $(m.walltime)
     #SBATCH --ntasks=$(m.n_mpi_processes)
     #SBATCH --cpus-per-task=$(m.n_threads)
     #SBATCH --mem-per-cpu=$(m.memory) 
     """
 
-function resource_string(m::MPI, ::Val{:lsf})
+function resource_string(m::MPIProcesses, ::Val{:lsf})
     @assert m.n_threads == 1 "TODO: find how to specify number of threads per node with LSF"
     """
     #BSUB -W $(m.walltime)

src/submission/submission_utils.jl

@@ -114,7 +114,7 @@ function find_rank_file(folder, machine::Int)
     return nothing
 end
 
-# construct launch cmd and script for MPI and ChildProcess
+# construct launch cmd and script for MPIProcesses and ChildProcess
 
 function launch_cmd(pt_arguments, exec_folder, dependencies, n_threads::Int, on_mpi::Bool)
     script_path  = launch_script(pt_arguments, exec_folder, dependencies, on_mpi)
@@ -200,7 +200,7 @@ function launch_code(
             Pigeons.deserialize_immutables!(raw"$path_to_serialized_immutables")
             deserialize(raw"$path_to_serialized_pt_arguments")
         catch e
-            println("Hint: probably missing dependencies, use the dependencies argument in MPI() or ChildProcess()")
+            println("Hint: probably missing dependencies, use the dependencies argument in MPIProcesses() or ChildProcess()")
             rethrow(e)
         end
 

test/activate_test_env.jl

@@ -4,7 +4,7 @@
 # If we do not do this, we will end up testing the 
 # latest released version instead of the one checked out.
 
-# We have to do this because ChildProcess/MPI depend on  
+# We have to do this because ChildProcess/MPIProcesses depend on  
 # a single toml file to know how to load Pigeons and other 
 # dependencies.