Galileo23 Master-class 1 - GPU HPC in Julia

Solid Earth and Geohazards in the Exascale Era | BARCELONA | SPAIN | 23–26 MAY 2023

Master class on GPU HPC for the exascale era in geosciences

by Ludovic Räss and Ivan Utkin (ETH Zurich)

👀 ATTENTION: The content was just updated, make sure to git pull before getting started!

Program

Slot	Program
Slot 1	Introduction about GPU HPC - Student short presentation (5 min each) - Getting started with GPU node access on `octopus` - Brief intro about Julia for HPC
Slot 2	Hands-on I - GPU computing and HPC - Julia GPU and MPI stack - Model design and implementation: Stokes flow in a channel
Slot 3	Hands-on II - Multi-GPU computing - Performance limiters - Performance measure $T_\mathrm{eff}$
Slot 4	OPTION 1 - Towards scalable inverse modelling - AD (GPU) tools in Julia - Jacbian-vector product (JVP) computation in a multi-GPU model - Advanced 1: towards sensitivity kernels and adjoint solutions - Advanced 2: the accelerated pseudo-transient method Wrap-up discussion

Slot 1

Getting started

This section provides directions on getting your GPU HPC dev environment ready on the octopus supercomputer at the University of Lausanne, Switzerland. During this Master-class, we will use SSH to login to a remote multi-GPU compute node on octopus. Each of the participant should get access to 4 Nvidia Titan Xm 12GB.

⚠️ It is warmly recommended trying to perform the Getting started steps before the beginning of the workshop.

CLICK HERE for the getting started steps 🚀

In the following, we will give directions on how to use VSCode and the Remote-SSH extension to access the compute resources. However, feel free to access the resources using your preferred SSH setup.

Download VSCode and Julia on your laptop.
Install the Remote-SSH and Julia extensions by clicking the Extensions button on the left side of VSCode.
Retrieve your confidential login credentials from the email you received titled "MC1 login credentials", namely your username <username> (in the format courseXX) and dedicated compute node ID <nodeID> (in the format nodeXX).
Setup a password-less SSH config to access octopus (see e.g. here on "how-to"). Ideally, use ed25519 encryption.

Edit the SSH config file to add the infos about octopus login (replacing <username> with the username you got assigned - note the node ID should always be a 2 digit number):

Host octo-login
  HostName achsrv0.unil.ch
  User <username>
  IdentityFile ~/.ssh/id_ed25519

Host node<nodeID>
  HostName node<nodeID>.octopoda
  User <username>
  ProxyJump octo-login

Connect to your assigned node, check you are in your home folder (using pwd) and clone this repo into your home:
```
git clone https://github.com/PTsolvers/Galileo23-MC1-GPU.git
```
Move to the directory:
```
$cd Galileo23-MC1-GPU
```
Launch Julia using the Command Palette of VSCode >Julia: Start REPL. Note that the following modules got loaded automatically:
```
module load julia cuda/11.4 openmpi/gcc83-314-c112
```
In Julia, type ] to enter the "package-mode". There, activate the current project and resolve the packages we will need typing:
```
(@v1.9) pkg> activate .

(@Galileo23-MC1-GPU) pkg> instantiate
```

To make sure you are all set, check your CUDA and MPI install:

julia> using CUDA, MPI

julia> CUDA.versioninfo()
CUDA runtime 11.2, local installation
CUDA driver 12.1
NVIDIA driver 530.30.2

# [skipped lines]

4 devices:
  0: NVIDIA GeForce GTX TITAN X (sm_52, 11.918 GiB / 12.000 GiB available)
  1: NVIDIA GeForce GTX TITAN X (sm_52, 11.918 GiB / 12.000 GiB available)
  2: NVIDIA GeForce GTX TITAN X (sm_52, 11.918 GiB / 12.000 GiB available)
  3: NVIDIA GeForce GTX TITAN X (sm_52, 11.918 GiB / 12.000 GiB available)

julia> MPI.MPI_LIBRARY_VERSION_STRING
"Open MPI v3.1.4, package: Open MPI root@node01.octopoda Distribution, ident: 3.1.4, repo rev: v3.1.4, Apr 15, 2019\0"

Let's try now to run some basic plotting scripts within Julia and get the output inlined to VSCode. For this, you need to install the Julia extension on the node (as you did already on your laptop) and start Julia using the Command Palette of VSCode (>Julia: Start REPL). Change to the correct directory using the "shell mode" of Julia (by typing ; in the REPL):
```
shell> cd Galileo23-MC1-GPU/scripts_start/
/home/courseN/Galileo23-MC1-GPU/scripts_start
```
In the scripts_start folder, run the scripts_start/visu_2D.jl script as:
```
julia> include("visu_2D.jl")
```
which should produce a heatmap of a Gaussian distribution in 2D.
Finally, you should at this stage be able to run the following scripts to make sure MPI-based GPU selection and GPU-aware MPI is running as expected in Julia. Exit Julia and go to the scripts_start folder:
```
cd scripts_start
```
Run the scripts_start/hello_mpi_gpu.jl script to make sure GPU selection works as expected:
```
mpirun -np 4 -mca btl_openib_warn_default_gid_prefix 0 julia --project hello_mpi_gpu.jl
```
Run the scripts_start/alltoall_mpi_gpu.jl script to verify GPU-aware MPI is working:
```
mpirun -np 4 -mca btl_openib_warn_default_gid_prefix 0 julia --project alltoall_mpi_gpu.jl
```

If you made it here you should be all set 🚀

The small print

Note that the following config is already set in your .bashrc to prepare the correct environment:

# User specific aliases and functions
# load modules
module load julia cuda/11.4 openmpi/gcc83-314-c112
# Julia setup
alias juliap='julia --project'
# new Preferences.jl based config
export JULIA_LOAD_PATH="$JULIA_LOAD_PATH:/soft/julia/julia_prefs/"
export JULIA_CUDA_MEMORY_POOL=none

Useful resources

The Julia language: https://julialang.org
PDE on GPUs ETH Zurich course: https://pde-on-gpu.vaw.ethz.ch
Julia Discourse (Julia Q&A): https://discourse.julialang.org
Julia Slack (Julia dev chat): https://julialang.org/slack/

Julia and HPC

Some words on the Julia at scale effort, the Julia HPC packages, and the overall Julia for HPC motivation (two language barrier)

The (yet invisible) cool stuff

Today, we will develop code that:

Runs on graphics cards using the Julia language
Uses a fully local and iterative approach (scalability)
Retrieves automatically the Jacobian Vector Product (JVP) using automatic differentiation (AD)
(All scripts feature less than 400 lines of code)

Too good to be true? Hold on 🙂 ...

Why to still bother with GPU computing in 2023

It's around for more than a decade
It shows massive performance gain compared to serial CPU computing
First exascale supercomputer, Frontier, is full of GPUs

Performance that matters

Taking a look at a recent GPU and CPU:

Nvidia Tesla A100 GPU
Nvidia Titan Xm GPU
AMD EPYC "Rome" 7282 (16 cores) CPU

Device	TFLOP/s (FP64)	Memory BW TB/s	Imbalance (FP64)
Tesla A100	9.7	1.55	9.7 / 1.55 × 8 = 50
AMD EPYC 7282	0.7	0.085	0.7 / 0.085 × 8 = 66

Meaning: we can do about 50 floating point operations per number accessed from main memory. Floating point operations are "for free" when we work in memory-bounded regimes.

👉 Requires to re-think the numerical implementation and solution strategies

Unfortunately, the cost of evaluating a first derivative $∂A / ∂x$ using finite-differences:

q[ix] = -D * (A[ix+1] - A[ix]) / dx

consists of:

1 reads + 1 write => $2 × 8$ = 16 Bytes transferred
1 (fused) addition and division => 1 floating point operations

👉 assuming $D$, $∂x$ are scalars, $q$ and $A$ are arrays of Float64 (read from main memory)

Performance that matters - an example

Not yet convinced? Let's have a look at an example.

Let's assess how close from memory copy (1355 GB/s) we can get solving a 2D diffusion problem on an Nvidia Tesla A100 GPU.

$$ ∇⋅(D ∇ C) = \frac{∂C}{∂t} $$

👉 Let's test the performance using a simple scripts_s1/perftest.jl script.

Why to still bother with GPU computing in 2022

Because it is still challenging

Why?

Very few software uses it efficiently
It requires to rethink the solving strategy as non-local operations will kill the fun

Slot 2

Hands-on I

Now it's time to get started. In the coming 2 hours, we will program a 2D transientdiffusion equation in a vectorised fashion in Julia. Then, we will turn it into a multi-threaded loop version, and finally into a GPU code. The last part will consist of modifying the diffusion code to solve the channel flow in 2D with free-surface and variable viscosity.

Solving transient 2D diffusion on the CPU I

Starting from the scripts_start/visu_2D.jl script, create a new script diffusion_2D.jl where we will add diffusion physics:

$$ \frac{∂C}{∂t} = -∇⋅q~, $$

$$ q = -D~∇C ~, $$

where $D$ is the diffusion coefficient.

Let's use a simple explicit forward Euler time-stepping scheme and keep the same Gaussian distribution as initial condition.

The diffusion coefficient $D = d_0$ should be defined in all gird points such that it could be spatially variable in a later stage:

D = d0 .* ones(...)

💡 If you struggle getting started, check-out the scripts_s2/diffusion_2D.jl script and try replacing the ?? by some more valid content.

The solution script can be found at scripts_solutions/diffusion_2D_sol.jl

Solving transient 2D diffusion on the CPU II

We will perform one additional step in order to make our code closer to be ready for kernel programming on GPUs.

We will here isolate the lines that perform the actual computations, i.e., solve the PDE, and move those operations into functions. To avoid race conditions and keep correct synchronisation, we need to define 2 different compute functions, one for assigning the fluxes (update_q!) and one for updating the values of $C$ (update_C!).

💡 Note the exclamation mark ! in the function name. This is a Julia convention if the function modifies the arguments passed to it.

Create a new script, diffusion_2D_fun.jl, where you will use the following template for the compute functions:

function update_q!()
    Threads.@threads for iz = 1:size(C, 2)
        for iy = 1:size(C, 1)
            if (iy <= ?? && iz <= ??) qy[iy, iz] = ?? end
            if (iy <= ?? && iz <= ??) qz[iy, iz] = ?? end
        end
    end
    return
end

The Threads.@threads in front of the outer loop allows for shared memory parallelisation on the CPU (aka multi-threading) if Julia is launched with more than one thread.

Perform the similar tasks for update_C! function.

Also, replace the averaging helper functions my macros, and use macros as well to define helper functions for performing the derivative operations.

💡 If you run out of ideas, check-out the scripts_s2/diffusion_2D_fun.jl script and try replacing the ?? by some more valid content.

The solution script can be found at scripts_solutions/diffusion_2D_fun_sol.jl

Solving transient 2D diffusion on GPU

Let's now move to GPU computing. Starting from the diffusion_2D_fun.jl script you just finalised, we'll make it ready for GPU execution.

In a new script diffusion_2D_cuda.jl, we first need to modify the compute functions (or kernels hereafter) to replace the spatial loops by 2D vectorised indices that will parallelise the execution over many GPU threads:

function update_q!()
    iy = (blockIdx().x - 1) * blockDim().x + threadIdx().x
    iz = (blockIdx().y - 1) * blockDim().y + threadIdx().y
    ??
    return
end

Then, in the # numerics section, we need to define some kernel launch parameters to specify the number of parallel workers to launch on the GPU:

nthreads = (16, 16)
nblocks  = cld.((ny, nz), nthreads)

You'll find more details about GPU kernel programming in the CUDA.jl documentation or on this course website.

In the # init section, we will have now to specify that the arrays should be "uploaded" to the GPU. The C init can be wrapped by CuArray(). The fluxes and D array can be initialised on the GPU by adding CUDA. before ones or zeros. Also, one needs to specify the arithmetic precision as we want to perform double precision Float64 computations, e.g., CUDA.zeros(Float64, nx, ny).

The kernel launch configuration and synchronisation need to be passed to the kernel launch call as following:

CUDA.@sync @cuda threads=nthreads blocks=nblocks update_q!()

Finally, one needs to gather back on the host the C array for plotting, resulting in calling Array(C).

💡 If you run out of ideas, check-out the scripts_s2/diffusion_2D_cuda.jl script and try replacing the ?? by some more valid content.

The solution script can be found at scripts_solutions/diffusion_2D_cuda_sol.jl

Channel flow in 2D

The final step is to now turn the diffusion script into a channel flow script with non-linear viscosity and a free-surface.

We consider the shear-driven Stokes flow with power-law rheology in a quasi-2D setup:

$$ \frac{\partial \tau_{xy}}{\partial y} + \frac{\partial\tau_{xz}}{\partial z} + \rho g\sin\alpha = 0 $$

$$ \tau_{ij} = 2\eta \varepsilon_{ij}, \quad \varepsilon_{ij} = \frac{1}{2}\left(\frac{\partial v_i}{\partial x_j} + \frac{\partial v_j}{\partial x_i} \right) $$

$$ \eta = k \varepsilon_\mathrm{II}^{n-1} $$

Modify the diffusion script to turn it into a free-surface channel flow. To this end, following changes are necessary:

the flux become the viscous stresses $τ_{ij}$
the quantity $C$ becomes the out-of-plane velocity $v_x$
$\rho g\sin\alpha$ needs to be added as source term to the flux balance equation
the diffusion coefficient $D$ turns now into the nonlinear viscosity $η$
the force-balance equation can be used to retrieve $v_x$ iteratively.

For the iterative process can be designed as augmenting the force balance equation with a pseudo-time step $\partial τ$ one can then use to reach a steady state:

$$ \frac{\partial \tau_{xy}}{\partial y} + \frac{\partial\tau_{xz}}{\partial z} + \rho g\sin\alpha = \frac{\partial v_x}{\partial τ} ~.$$

We now have a rule to update $v_x$ as function of the residual of the balance equation $\mathrm{R}v_x$:

$$ \mathrm{R}v_x = \frac{\partial \tau_{xy}}{\partial y} + \frac{\partial\tau_{xz}}{\partial z} + \rho g\sin\alpha~,$$

$$ \frac{\partial v_x}{\partial τ} = \mathrm{R}v_x~,$$

such that:

$$ \partial v_x = \partial v_x + \partial τ * \mathrm{R}v_x~.$$

This simple iterations results in a Picrad-like scheme; simple but not ideal in terms of number of iterations to converge to a given tolerance.

👀 This simple "pseudo-transient" scheme can be accelerated by using a second order scheme. This is on-going research. Check out this lecture and related publication (Räss et al., 2022) if curious about it.

To proceed, start from the diffusion_2D_fun.jl script from this previous step and make sure the new physics is correctly implemented. In a second step, we will then port it to GPU kernel programming.

Start a new script titled channel_flow_2D.jl or start from the provided scripts_s2/channel_flow_2D.jl script. There, we introduce some new physics parameters:

# physics
# non-dimensional
npow    = 1.0 / 3.0
sinα    = sin(π / 12)
# dimensionally independent
ly, lz  = 1.0, 1.0 # [m]
k0      = 1.0      # [Pa*s^npow]
ρg      = 1.0      # [Pa/m]
# scales
psc     = ρg * lz
ηsc     = psc * (k0 / psc)^(1.0 / npow)
# dimensionally dependent
ηreg    = 1e4 * ηsc

namely, power-law exponent npow, slope angle sinα, consistency factor k0, gravity acceleration ρg and some scaling relations.

Then we need some additional numerics parameters:

# numerics
ϵtol    = 1e-6
ηrel    = 5e-1
maxiter = 20000max(ny, nz)
ncheck  = 500max(ny, nz)

namely, the nonlinear tolerance ϵtol, some relaxation for the viscosity continuation ηrel, and a modification of the iteration parameter definition.

In the # init section, rename C as vx, D as ηeff, qy as τxy and qz as τxz. Also, no longer need to initialise C now vx with a Gaussian; simply use zeros.

From the equations, we see that the nonlinear viscosity $\eta$ is function of the second strain-rate invariant $ɛ_\mathrm{II}$ at a given power. You can implement eII as a macro in the code:

macro eII() esc(:(sqrt.((avz(diff(vx, dims=1) ./ dy)) .^ 2 .+ (avy(diff(vx, dims=2) ./ dz)) .^ 2))) end

Also, we now have to include the err >= ϵtol condition in our while loop, such that:

while err >= ϵtol && iter <= maxiter
    # iteration loop
end

For the boundary condition, enforce no-slip condition at the bottom and open-box at the top. This can be achieved as following:

vx[:, end] .= vx[:, end-1]
vx[1, :]   .= vx[2, :]

Make finally sure to update the error checking and plotting as well:

if iter % ncheck == 0
    err = maximum(abs.(diff(τxy, dims=1) ./ dy .+ diff(τxz, dims=2) ./ dz .+ ρg * sinα)) * lz / psc
    push!(iters_evo, iter / nz); push!(errs_evo, err)
    p1 = heatmap(yc, zc, vx'; aspect_ratio=1, xlabel="y", ylabel="z", title="Vx", xlims=(-ly / 2, ly / 2), ylims=(0, lz), c=:turbo, right_margin=10mm)
    p2 = heatmap(yv, zv, ηeff'; aspect_ratio=1, xlabel="y", ylabel="z", title="ηeff", xlims=(-ly / 2, ly / 2), ylims=(0, lz), c=:turbo, colorbar_scale=:log10)
    p3 = plot(iters_evo, errs_evo; xlabel="niter/nx", ylabel="err", yscale=:log10, framestyle=:box, legend=false, markershape=:circle)
    display(plot(p1, p2, p3; size=(1200, 400), layout=(1, 3), bottom_margin=10mm, left_margin=10mm))
    @printf("  #iter/nz=%.1f, err=%1.3e\n", iter / nz, err)
end

Running the code should produce a figure similar to:

💡 If you run out of ideas, check-out the scripts_s2/channel_flow_2D.jl script and try replacing the ?? by some more valid content.

The solution script can be found at scripts_solutions/channel_flow_2D_sol.jl

In a second step, create now a GPU code titled channel_flow_2D_cuda.jl out of the channel flow script using kernel programming. Apply the same workflow as done for the diffusion codes.

On the GPU, we now need 4 kernels to avoid sync issues and ensure correct execution:

update_ηeff!()
update_τ!()
update_v!()
apply_bc!()

💡 If you run out of ideas, check-out the scripts_s2/channel_flow_2D_cuda.jl script and try replacing the ?? by some more valid content.

The solution script can be found at scripts_solutions/channel_flow_2D_cuda_sol.jl

Slot 3

Hands-on II

We will now port the single process codes we developed in the previous step to use distributed memory parallelisation using MPI.

Multi-CPU diffusion solver

In a first step, we will port the CPU-based diffusion solver to MPI. To exemplify the approach, let's have a look at the scripts_s3/diffusion_2D_mpi.jl script, which implements non-blocking task-based asynchronous MPI halo exchange.

We provide the following functions cooperative_wait, cooperative_mpi_wait, exchange_halo! and gather! but won't spend much time on what's going in there. In the code, we in addition need initialise MPI and prepare the Cartesian topology to use:

MPI.Init()
# create MPI communicator
comm = MPI.Cart_create(MPI.COMM_WORLD, dims)
me = MPI.Comm_rank(comm)
neighbors = ntuple(Val(length(dims))) do idim
    MPI.Cart_shift(comm, idim - 1, 1)
end
coords = Tuple(MPI.Cart_coords(comm))

Then, we have to define the global number of grid points which takes into account 2 cells of overlap:

ny_g, nz_g = (ny - 2) * dims[1] + 2, (nz - 2) * dims[2] + 2

The initial condition needs also to be handled with care in order to define a Gaussian that would spread over different MPI processes:

# init
y0, z0  = coords[1] * (ny - 2) * dy, coords[2] * (nz - 2) * dz
yc      = [y0 + iy * dy + dy / 2 - ly / 2 for iy = 1:ny]
zc      = [z0 + iz * dz + dz / 2          for iz = 1:nz]

Note that one now needs to correctly account for some shift in y0, z0 as function of coords.

Nextm MPI send and receive buffers need to be initialised:

# MPI buffers
send_bufs = [[zeros(nz) for side in 1:2], [zeros(ny) for side in 1:2]]
recv_bufs = deepcopy(send_bufs)

In the time-loop, we need to call the exchange halo function right after the two comptue kernels to update the internal boundary conditions:

exchange_halo!(C, neighbors, send_bufs, recv_bufs, comm)

For visualisation, we can use the provided gather! function in order to collect all sub-arrays into a single global array the process 0 me == 0 can save to disk.

C_g = me == 0 ? zeros(dims[1] * (ny - 2), dims[2] * (nz - 2)) : nothing

MPI.Barrier(comm)
gather!(C_g, C[2:end-1, 2:end-1], comm)

As last, one needs to finalise MPI calling MPI.Finalize().

To debug, you can run the MPI script from within the Julia REPL; for this you need to comment MPI.Init() and MPI.Finalize() from the code as you are only allowed to call them once per Julia session. If you then want to run the diffusion MPI script on multiple processors, you can do so as following:

mpirun -np 4 -mca btl_openib_warn_default_gid_prefix 0 julia --project diffusion_2D_mpi.jl

If this runs, you have now a Julia code the runs on distributed memory parallelisation!

💡 Additional resources and exercises to familiarise with MPI halo exchange concepts for staggered grids can be found in this course material.

Multi-GPU diffusion solver

The cool thing with Julia is that porting the previous CPU-based code to GPU is fairly straight-forward. The only thing to do is to make arrays and send/receive buffers GPU arrays/vectors.

You can either start from the previous CPU-MPI code and add the GPU specific bits, or start from the GPU diffusion code and add the MPI bits.

💡 Note that if you are running out of ideas, you can always look up the solution code scripts_solutions/diffusion_2D_mpi_cuda_sol.jl

Multi-GPU channel flow

Now that you made it for the Julia GPU MPI implementation for the diffusion equation in 2D, you could implement the channel flow with MPI by analogy.

Slot 4

OPTION 1

AD tools in Julia

Automatic differentiation (AD) allows evaluating the gradients of functions specified by code. Using AD, the partial derivatives are evaluated by repeatedly applying the chain rule of differentiation to the sequence of elementary arithmetic operations constituting a computer program.

💡 Many constructs in computer programs aren't differentiable, for example, I/O calls or system calls. AD tools must handle such cases.

Automatic differentiation is a key ingredient of differentiable programming, a programming paradigm enabling gradient-based optimisation of the parameters of an arbitrary computer program.

Julia has a rich support for differential programming. With the power of tools like Enzyme.jl it is possible to automatically compute the derivatives of arbitrary Julia code, including the code targeting GPUs.

VJP calculations

One of the main building blocks in many optimization algorithms involves computing the vector-jacobian product (JVP). AD tools simplify evaluating JVPs by generating the code automatically given the target function.

Let's familiarise with Enzyme.jl, the Julia package for performing AD.

💡 There are many other Julia packages for performing AD, e.g., Zygote.jl. In this tutorial, we use Enzyme as it supports some features currently missing in other packages, e.g., differentiating mutating functions and GPU kernels.

Let's start with a simple example:

julia> using Enzyme

julia> f(ω,x) = sin(ω*x)
f (generic function with 1 method)

julia> ∇f(ω,x) = Enzyme.autodiff(Reverse,f,Active,Const(ω),Active(x))[1][2]
∇f (generic function with 1 method)

julia> @assert ∇f(π,1.0) ≈ π*cos(π)

In this line: ∇f(x) = Enzyme.autodiff(Reverse,f,Active,Active(x))[1][1], we call Enzyme.autodiff function, which computes the partial derivatives. We pass Reverse as a first argument, which means that we use the reverse mode of accumulation (see below). We mark the arguments as either Const or Active to specify which partial derivatives are computed.

Let's make more advanced example, differentiating the vector-valued function. We'll use the 1D residual function for the steady-state diffusion:

function residual!(R,C,dc,dx)
    for ix in 2:length(R)-1
        R[ix] = dc*(C[ix-1] - 2.0 * C[ix] + C[ix+1])/dx^2
    end
end

This function mutates it's argument R, storing the result of computing the residual in-place. Also, this function is vector-valued, and returns a vector as well. Information about partial derivatives of such functions is described by its Jacobian matrix.

In reverse mode of derivative accumulation, also known as backpropagation, one call to Enzyme computes the product of transposed Jacobian matrix and a vector, known as VJP (vector-Jacobian product).

To propagate the gradient information, extra storage is needed to store the vector, and the computed derivatives.

function grad_residual!(R̄,C̄,R,C,dc,dx)
    Enzyme.autodiff(Reverse,residual!,Duplicated(R,R̄),Duplicated(C,C̄),Const(dc),Const(dx))
    return
end

Here, we introduced the new parameter activity type, Duplicated. The first element of Duplicated argument takes the value of a variable, and the second the adjoint.

Often the residual computation is split in several functions, or kernels. In that case, the simplest solution is to manually apply the chain rule (better alternative involves defining custom rules, which is out of scope for this tutorial):

$$ \left[\frac{\partial R(q(C))}{\partial C}\right]^\mathrm{T} = \left[\frac{\partial R(q)}{\partial q} \frac{\partial q(C)}{\partial C}\right]^\mathrm{T} = \left[\frac{\partial q(C)}{\partial C}\right]^\mathrm{T} \left[\frac{\partial R(q)}{\partial q}\right]^\mathrm{T} $$

Starting from the scripts_s4/diffusion_1D_enzyme.jl, implement the multiple-kernels version of residual evaluation, by replacing the ?? symbols with some meaningful content.

If the residual function is a GPU kernel, the syntax is a little bit different:

function grad_residual!(R̄,C̄,R,C,dc,dx)
    Enzyme.autodiff_deferred(Reverse,residual!,Duplicated(R,R̄),Duplicated(C,C̄),Const(dc),Const(dx))
    return
end

💡 Note that we call autodiff_deferred instead of autodiff.

Try to port the 1D diffusion code with Enzyme to GPU. Use the scripts_s4/diffusion_1D_enzyme_cuda.jl as a starting point.

Apply the knowledge to differentiate the residual of the 2D channel flow problem. Use the scripts_s4/channel_flow_2D_enzyme_cuda.jl as a starting point.

Advanced

Towards sensitivity kernels and adjoint solutions

Now, as we know how to compute VJPs using Enzyme, it's time to use the knowledge to compute the sensitivity of the solution, i.e., the velocity, to the steady channel flow problem with respect to changes in effective viscosity.

To quantify the sensitivity, we need to define some metric. We will use the sensitivity kernel definition from Reuber 2021, which defines the sensitivity kernel as the derivative of the following function with respect to the parameter of interest:

$$ J(v) = \int v $$

To evaluate the derivative, we can use the chain rule:

$$ \frac{\mathrm{d}J\left(v(η)\right)}{\mathrm{d}η} = \frac{\partial J\left(v(η)\right)}{\partial v} \frac{\mathrm{d}v}{\mathrm{d}\eta} $$

The tricky term to evaluate is the derivative of the solution to the problem w.r.t. the solution, $\frac{\mathrm{d}v}{\mathrm{d}\eta}$. To compute this derivative, we use the fact that at the steady state the residual of the right-hand side of the system of the equations reaches it's minimum. Taking the derivative of the residual with respect to the viscosity $\eta$ and using the chain rule again, we obtain:

$$ \frac{\mathrm{d}R}{\mathrm{d}\eta} = \frac{\partial R}{\partial v} \frac{\mathrm{d}v}{\mathrm{d}\eta} + \frac{\partial R}{\partial\eta} = 0 $$

Solving for $\frac{\mathrm{d}v}{\mathrm{d}\eta}$ and plugging into the sensitivity kernel, we obtain:

$$ \frac{\mathrm{d}J\left(v(η)\right)}{\mathrm{d}η} = -\frac{\partial J\left(v(η)\right)}{\partial v} \left(\frac{\partial R}{\partial v}\right)^{-1} \frac{\partial R}{\partial\eta} $$

Directly inverting the matrix $\frac{\partial R}{\partial v}$ is prohibitibvely expensive, but instead we can use the temporary variable, called the adjoint state:

$$ \left(\frac{\partial R}{\partial v}\right)^\mathrm{T}\Psi = \frac{\partial J}{\partial v} $$

$$ \frac{\mathrm{d}J}{\mathrm{d}\eta} = -\Psi^\mathrm{T}\frac{\partial R}{\partial\eta} $$

In this way, we can compute the point-wise sensitivity in only one additional linear solve. To solve the system of equations $\left(\frac{\partial R}{\partial v}\right)^\mathrm{T}\Psi = \frac{\partial J}{\partial v}$, we can use the same pseudo-transient method that we employed for the forward problem:

$$ \frac{\partial\Psi}{\partial\tau} + \left(\frac{\partial R}{\partial v}\right)^\mathrm{T}\Psi = \frac{\partial J}{\partial v} $$

To integrate this system in pseudo-time, we need to iteratively apply the transposed jacobian to the adjoint state variable vector. And this is exactly what is computed using the AD!

Extend the 2D channel flow example with the VJP calculation with an iterative loop to update the adjoint variable v̄ using the same approach as the original problem.

💡 Note that in this particular case, $\frac{\partial J}{\partial v}$ = 1

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Galileo23 Master-class 1 - GPU HPC in Julia

Master class on GPU HPC for the exascale era in geosciences

Program

Content

Slot 1

Getting started

The small print

Useful resources

Julia and HPC

The (yet invisible) cool stuff

Why to still bother with GPU computing in 2023

Performance that matters

Performance that matters - an example

Why to still bother with GPU computing in 2022

Slot 2

Solving transient 2D diffusion on the CPU I

Solving transient 2D diffusion on the CPU II

Solving transient 2D diffusion on GPU

Channel flow in 2D

Slot 3

Multi-CPU diffusion solver

Multi-GPU diffusion solver

Multi-GPU channel flow

Slot 4

AD tools in Julia

VJP calculations

Advanced

Towards sensitivity kernels and adjoint solutions

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Name		Name	Last commit message	Last commit date
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docs		docs
scripts_s1		scripts_s1
scripts_s2		scripts_s2
scripts_s3		scripts_s3
scripts_s4		scripts_s4
scripts_solutions		scripts_solutions
scripts_start		scripts_start
.gitignore		.gitignore
LICENSE		LICENSE
Project.toml		Project.toml
README.md		README.md

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Galileo23 Master-class 1 - GPU HPC in Julia

Master class on GPU HPC for the exascale era in geosciences

Program

Content

Slot 1

Getting started

The small print

Useful resources

Julia and HPC

The (yet invisible) cool stuff

Why to still bother with GPU computing in 2023

Performance that matters

Performance that matters - an example

Why to still bother with GPU computing in 2022

Slot 2

Solving transient 2D diffusion on the CPU I

Solving transient 2D diffusion on the CPU II

Solving transient 2D diffusion on GPU

Channel flow in 2D

Slot 3

Multi-CPU diffusion solver

Multi-GPU diffusion solver

Multi-GPU channel flow

Slot 4

AD tools in Julia

VJP calculations

Advanced

Towards sensitivity kernels and adjoint solutions

About

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Contributors 3

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