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Changes after the lecture on Friday September 15th 2023

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Francesc Verdugo committed 2023-09-15 16:39:05 +02:00
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notebooks/julia_distributed.ipynb
+27 -6
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@@ -614,6 +614,27 @@
"take!(chnl)"
]
},
{
"cell_type": "markdown",
"id": "ff0da45d",
"metadata": {},
"source": [
"### This will not work!\n",
"\n",
"You really need remote channels to communicate different processes. Standard Channels would not work. For instance, the following code would block at the `take!`. Worker 4 will receive a different copy of the channel and will put values in it. The channel defined in the main process will remain empty and this will make the take! to block. \n",
"\n",
"```julia\n",
"chnl = Channel{Int}()\n",
"@spawnat 4 begin\n",
" for i in 1:5\n",
" put!(chnl,i)\n",
" end\n",
" close(chnl)\n",
"end\n",
"take!(chnl)\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "1b3f8dcc",
@@ -769,7 +790,7 @@
"source": [
"\n",
"<div class=\"alert alert-block alert-success\">\n",
"<b>Question (Q1):</b> How many integers are transferred between master and worker? Including both directions. \n",
"<b>Question (NB3-Q1):</b> How many integers are transferred between master and worker? Including both directions. \n",
"</div>\n",
"\n",
"\n",
@@ -803,7 +824,7 @@
"metadata": {},
"source": [
"<div class=\"alert alert-block alert-success\">\n",
"<b>Question (Q2):</b> How many integers are transferred between master and worker? Including both directions. \n",
"<b>Question (NB3-Q2):</b> How many integers are transferred between master and worker? Including both directions. \n",
"</div>\n",
"\n",
"\n",
@@ -838,7 +859,7 @@
"source": [
"\n",
"<div class=\"alert alert-block alert-success\">\n",
"<b>Question (Q3):</b> Which value will be the value of `x` ? \n",
"<b>Question (NB3-Q3):</b> Which value will be the value of `x` ? \n",
"</div>\n"
]
},
@@ -862,7 +883,7 @@
"metadata": {},
"source": [
"<div class=\"alert alert-block alert-success\">\n",
"<b>Question (Q4):</b> Which value will be the value of `x` ? \n",
"<b>Question (NB3-Q4):</b> Which value will be the value of `x` ? \n",
"</div>\n",
"\n",
"Which value will be the value of `x` ?"
@@ -1309,7 +1330,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Julia 1.9.3",
"display_name": "Julia 1.9.0",
"language": "julia",
"name": "julia-1.9"
},
@@ -1317,7 +1338,7 @@
"file_extension": ".jl",
"mimetype": "application/julia",
"name": "julia",
"version": "1.9.3"
"version": "1.9.0"
}
},
"nbformat": 4,
notebooks/mpi_tutorial.ipynb
+448 -50
View File
@@ -51,6 +51,36 @@
"- There are Julia bindings via the package MPI.jl https://github.com/JuliaParallel/MPI.jl"
]
},
{
"cell_type": "markdown",
"id": "99c6febb",
"metadata": {},
"source": [
"### What is MPI.jl ?\n",
"\n",
"- It is not a Julia implementation of the MPI standard\n",
"- It is a wrapper to the C interface of MPI\n",
"- You need a C MPI installation in your system\n",
"\n",
"\n",
"MPI.jl provides a convenient Julia API to access MPI. For instance, this is how you get the id (rank) of the current process.\n",
"\n",
"```julia\n",
"comm = MPI.COMM_WORLD\n",
"rank = MPI.Comm_rank(comm)\n",
"```\n",
"\n",
"Internally, MPI.jl uses `ccall` which is a mechanism that allows you to call C functions from Julia. In this, example we are calling the C function `MPI_Comm_rank` from the underlying MPI installation.\n",
"\n",
"```julia\n",
"comm = MPI.COMM_WORLD \n",
"rank_ref = Ref{Cint}()\n",
"ccall((:MPI_Comm_rank, MPI.API.libmpi), Cint, (MPI.API.MPI_Comm, Ptr{Cint}), comm, rank_ref)\n",
"rank = Int(rank_ref[])\n",
"```\n",
"\n"
]
},
{
"cell_type": "markdown",
"id": "82e6e98f",
@@ -81,6 +111,66 @@
"</div>"
]
},
{
"cell_type": "markdown",
"id": "a534e3a2",
"metadata": {},
"source": [
"### Basic information about MPI processes\n",
"\n",
"The following cells give information about MPI processes, such as the rank id, the total number of processes and the name of the host running the code respectively. Before calling this functions one needs to initialize MPI."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "96f7c14e",
"metadata": {},
"outputs": [],
"source": [
"using MPI\n",
"MPI.Init()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "bd8232f5",
"metadata": {},
"outputs": [],
"source": [
"comm = MPI.COMM_WORLD\n",
"rank = MPI.Comm_rank(comm)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0befa408",
"metadata": {},
"outputs": [],
"source": [
"nranks = MPI.Comm_size(comm)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ff01adcf",
"metadata": {},
"outputs": [],
"source": [
"MPI.Get_processor_name()"
]
},
{
"cell_type": "markdown",
"id": "f1a502a3",
"metadata": {},
"source": [
"Note that this note notebook is not running with different MPI processes (yet). So using MPI will only make sense later when we add more processes."
]
},
{
"cell_type": "markdown",
"id": "133327e2",
@@ -104,6 +194,32 @@
"println(\"Hello, I am process $rank of $nranks processes!\")"
]
},
{
"cell_type": "markdown",
"id": "baddbba1",
"metadata": {},
"source": [
"### Hello world in C\n",
"\n",
"```C\n",
"#include <mpi.h>\n",
"#include <stdio.h>\n",
"int main(int argc, char** argv) {\n",
" MPI_Init(NULL, NULL);\n",
" int world_size;\n",
" MPI_Comm_size(MPI_COMM_WORLD, &world_size);\n",
" int world_rank;\n",
" MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);\n",
" char processor_name[MPI_MAX_PROCESSOR_NAME];\n",
" int name_len;\n",
" MPI_Get_processor_name(processor_name, &name_len);\n",
" printf(\"Hello from %s, I am rank %d of %d ranks!\\n\",\n",
" processor_name, world_rank, world_size);\n",
" MPI_Finalize();\n",
"}\n",
"```"
]
},
{
"cell_type": "markdown",
"id": "e3901c57",
@@ -311,63 +427,14 @@
"\n",
"MPI provides collective communication functions for communication involving multiple processes. Some usual collective directives are:\n",
"\n",
"- `MPI.Scatter`: Distributes data from one process to all processes.\n",
"- `MPI.Gather`: Gathers data from all processes to a single process.\n",
"- `MPI.Scatter`: Distributes data from one process to all processes.\n",
"- `MPI.Bcast`: Broadcasts data from one process to all processes.\n",
"- `MPI.Barrier`: Synchronizes all processes.\n",
"\n",
"See more collective directives available from Julia here: https://juliaparallel.org/MPI.jl/stable/reference/collective/\n"
]
},
{
"cell_type": "markdown",
"id": "8b4254d1",
"metadata": {},
"source": [
"### Scatter\n",
"\n",
"The \"root\" rank contains a buffer (e.g., a vector) of values (one value for each rank in a communicator). Scatter sends one value to each rank (the root rank also receives a value). The root rank can be any process in a communicator."
]
},
{
"attachments": {
"g13389.png": {
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truncated
}
},
"cell_type": "markdown",
"id": "74d5b606",
"metadata": {},
"source": [
"<div>\n",
"<img src=\"attachment:g13389.png\" align=\"left\" width=\"350\"/>\n",
"</div>"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5ea413fd",
"metadata": {},
"outputs": [],
"source": [
"@everywhere workers() begin\n",
" comm = MPI.Comm_dup(MPI.COMM_WORLD)\n",
" nranks = MPI.Comm_size(comm)\n",
" rank = MPI.Comm_rank(comm)\n",
" root = 0\n",
" rcv = Ref(0) \n",
" if rank == root\n",
" snd = [10*(i+1) for i in 1:nranks]\n",
" println(\"I am sending: $snd\")\n",
" else\n",
" snd = nothing\n",
" end \n",
" MPI.Scatter!(snd,rcv,comm;root)\n",
" println(\"I have received: $(rcv[])\")\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "97dc2886",
@@ -414,6 +481,125 @@
"end"
]
},
{
"cell_type": "markdown",
"id": "8b4254d1",
"metadata": {},
"source": [
"### Scatter\n",
"\n",
"The root rank contains a buffer (e.g., a vector) of values (one value for each rank in a communicator). Scatter sends one value to each rank (the root rank also receives a value). The root rank can be any process in a communicator."
]
},
{
"attachments": {
"g13389.png": {
"image/png": 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truncated
}
},
"cell_type": "markdown",
"id": "74d5b606",
"metadata": {},
"source": [
"<div>\n",
"<img src=\"attachment:g13389.png\" align=\"left\" width=\"350\"/>\n",
"</div>"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5ea413fd",
"metadata": {},
"outputs": [],
"source": [
"@everywhere workers() begin\n",
" comm = MPI.Comm_dup(MPI.COMM_WORLD)\n",
" nranks = MPI.Comm_size(comm)\n",
" rank = MPI.Comm_rank(comm)\n",
" root = 0\n",
" rcv = Ref(0) \n",
" if rank == root\n",
" snd = [10*(i+1) for i in 1:nranks]\n",
" println(\"I am sending: $snd\")\n",
" else\n",
" snd = nothing\n",
" end \n",
" MPI.Scatter!(snd,rcv,comm;root)\n",
" println(\"I have received: $(rcv[])\")\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "ed8da7f9",
"metadata": {},
"source": [
"### Bcast (broadcast)\n",
"\n",
"Similar to scatter, but we send the same message to all processes."
]
},
{
"attachments": {
"g1657.png": {
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}
},
"cell_type": "markdown",
"id": "26b56c81",
"metadata": {},
"source": [
"<div>\n",
"<img src=\"attachment:g1657.png\" align=\"left\" width=\"350\"/>\n",
"</div>"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4de15781",
"metadata": {},
"outputs": [],
"source": [
"@everywhere workers() begin\n",
" comm = MPI.Comm_dup(MPI.COMM_WORLD)\n",
" nranks = MPI.Comm_size(comm)\n",
" rank = MPI.Comm_rank(comm)\n",
" root = 0\n",
" buffer = Ref(0)\n",
" if rank == root\n",
" buffer[] = 20\n",
" println(\"I am sending: $(buffer[])\")\n",
" end \n",
" MPI.Bcast!(buffer,comm;root)\n",
" println(\"I have received: $(buffer[])\")\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "6de37cc9",
"metadata": {},
"source": [
"### Barrier"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ff61f64a",
"metadata": {},
"outputs": [],
"source": [
"@everywhere workers() begin\n",
" comm = MPI.Comm_dup(MPI.COMM_WORLD)\n",
" sleep(rand(1:3))\n",
" MPI.Barrier(comm)\n",
" println(\"Done!\")\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "ac9a5b52",
@@ -435,6 +621,218 @@
"\n"
]
},
{
"cell_type": "markdown",
"id": "26879a46",
"metadata": {},
"source": [
"### Blocking communication\n",
"\n",
"If we start a receive before a matching send, we will block in the call to `MPI.Recv!`. Run the next cell and note that the message is not printed since the process is blocked at `MPI.Recv!` waiting for a matching send."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "68aa9ada",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 4 begin\n",
" buffer = Ref(0)\n",
" comm = MPI.COMM_WORLD\n",
" MPI.Recv!(buffer,comm;source=2-2,tag=0)\n",
" println(\"I have received $(buffer[]).\")\n",
"end;"
]
},
{
"cell_type": "markdown",
"id": "ace9c787",
"metadata": {},
"source": [
"If you run the next cell containing the corresponding send, the communication will take place."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e18347cd",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 2 begin\n",
" buffer = Ref(2)\n",
" comm = MPI.COMM_WORLD\n",
" MPI.Send(buffer,comm;dest=4-2,tag=0)\n",
" println(\"I have send $(buffer[]). It is now safe to overwite the buffer.\")\n",
"end;"
]
},
{
"cell_type": "markdown",
"id": "0a038200",
"metadata": {},
"source": [
"### MPI does not integrate well with Julia Tasks\n",
"\n",
"MPI blocks without yielding (we cannot switch to other Julia tasks). Run next cell:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d7da7d27",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 4 begin\n",
" buffer = Ref(0)\n",
" comm = MPI.COMM_WORLD\n",
" MPI.Recv!(buffer,comm;source=2-2,tag=0)\n",
" println(\"I have received $(buffer[]).\")\n",
"end;"
]
},
{
"cell_type": "markdown",
"id": "530b673b",
"metadata": {},
"source": [
"Now try to spawn other tasks on process 4 by running next cell. This task will not be served yet."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ae1165ac",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 4 println(\"Hello!\");"
]
},
{
"cell_type": "markdown",
"id": "c722d71e",
"metadata": {},
"source": [
"We first need to unlock the receive with a matching send. Then the task printing \"Hello!\" will be finally served."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9da6f76e",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 2 begin\n",
" buffer = Ref(2)\n",
" comm = MPI.COMM_WORLD\n",
" MPI.Send(buffer,comm;dest=4-2,tag=0)\n",
" println(\"I have send $(buffer[]). It is now safe to overwite the buffer.\")\n",
"end;"
]
},
{
"cell_type": "markdown",
"id": "6f4fa1cd",
"metadata": {},
"source": [
"### Non-blocking communication"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d6e2fbbf",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 4 begin\n",
" buffer = Ref(0)\n",
" comm = MPI.COMM_WORLD\n",
" req = MPI.Irecv!(buffer,comm;source=2-2,tag=0)\n",
" println(\"Not yet safe to read the buffer\")\n",
" MPI.Wait(req)\n",
" println(\"I have received $(buffer[]).\")\n",
"end;"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4aa426ff",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 2 begin\n",
" buffer = Ref(2)\n",
" comm = MPI.COMM_WORLD\n",
" req = MPI.Isend(buffer,comm;dest=4-2,tag=0)\n",
" println(\"Not yet safe to write the buffer\")\n",
" MPI.Wait(req)\n",
" println(\"I have send $(buffer[]). It is now safe to overwite the buffer.\")\n",
"end;"
]
},
{
"cell_type": "markdown",
"id": "30d9a970",
"metadata": {},
"source": [
"### Combining Julia Tasks and non-blocking communication\n",
"\n",
"We can implement our own blocking mechanism that combines well with the Julia task scheduler. This can be done by testing on the request in a while loop. The `yield` in the loop provides the opportunity of other tasks to run.\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "768b2439",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 4 begin\n",
" buffer = Ref(0)\n",
" comm = MPI.COMM_WORLD\n",
" req = MPI.Irecv!(buffer,comm;source=2-2,tag=0)\n",
" while MPI.Test(req) == false\n",
" yield()\n",
" end\n",
" println(\"I have received $(buffer[]).\")\n",
"end;"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "073d138c",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 4 println(\"Hello!\");"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "97bc403f",
"metadata": {},
"outputs": [],
"source": [
"@spawnat 2 begin\n",
" buffer = Ref(2)\n",
" comm = MPI.COMM_WORLD\n",
" req = MPI.Isend(buffer,comm;dest=4-2,tag=0)\n",
" while MPI.Test(req) == false\n",
" yield()\n",
" end\n",
" println(\"I have send $(buffer[]). It is now safe to overwite the buffer.\")\n",
"end;"
]
},
{
"cell_type": "markdown",
"id": "750fdacb",