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eth-vaw-glaciology · Oct 15, 2024 · 92d58c8 · 92d58c8
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diff --git a/slide-notebooks/deploy_notebooks.jl b/slide-notebooks/deploy_notebooks.jl
@@ -1,6 +1,6 @@
 using Literate
 ## include Literate scripts starting with following 3 letters in the deploy
-incl = "l4_"
+incl = "l5_"
 ## Set `sol=true` to produce output with solutions contained and hints stripts. Otherwise the other way around.
 sol = true
 ##

diff --git a/slide-notebooks/notebooks/l5_1-cpu-parallel.ipynb b/slide-notebooks/notebooks/l5_1-cpu-parallel.ipynb
@@ -465,10 +465,10 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "t_toc = ...\n",
-    "A_eff = ...          # Effective main memory access per iteration [GB]\n",
-    "t_it  = ...          # Execution time per iteration [s]\n",
-    "T_eff = A_eff/t_it   # Effective memory throughput [GB/s]"
+    "t_toc = Base.time() - t_tic\n",
+    "A_eff = (3*2)/1e9*nx*ny*sizeof(Float64)  # Effective main memory access per iteration [GB]\n",
+    "t_it  = t_toc/niter                      # Execution time per iteration [s]\n",
+    "T_eff = A_eff/t_it                       # Effective memory throughput [GB/s]"
    ],
    "metadata": {},
    "execution_count": null
@@ -480,7 +480,7 @@
     "- Round `T_eff` to the 3rd significant digit.\n",
     "\n",
     "```julia\n",
-    "@printf(\"Time = %1.3f sec, ... \\n\", t_toc, ...)\n",
+    "@printf(\"Time = %1.3f sec, T_eff = %1.2f GB/s (niter = %d)\\n\", t_toc, round(T_eff, sigdigits=3), niter)\n",
     "```"
    ],
    "metadata": {
@@ -508,8 +508,10 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "function Pf_diffusion_2D(;??)\n",
+    "function Pf_diffusion_2D(;do_check=false)\n",
+    "    if do_check && (iter%ncheck == 0)\n",
     "    ...\n",
+    "    end\n",
     "    return\n",
     "end"
    ],
@@ -672,19 +674,19 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "for iy=??\n",
-    "    for ix=??\n",
-    "        qDx[??] -= (qDx[??] + k_ηf_dx* ?? )*_1_θ_dτ\n",
+    "for iy=1:ny\n",
+    "    for ix=1:nx-1\n",
+    "        qDx[ix+1,iy] -= (qDx[ix+1,iy] + k_ηf_dx*(Pf[ix+1,iy]-Pf[ix,iy]))*_1_θ_dτ\n",
     "    end\n",
     "end\n",
-    "for iy=??\n",
-    "    for ix=??\n",
-    "        qDy[??] -= (qDy[??] + k_ηf_dy* ?? )*_1_θ_dτ\n",
+    "for iy=1:ny-1\n",
+    "    for ix=1:nx\n",
+    "        qDy[ix,iy+1] -= (qDy[ix,iy+1] + k_ηf_dy*(Pf[ix,iy+1]-Pf[ix,iy]))*_1_θ_dτ\n",
     "    end\n",
     "end\n",
-    "for iy=??\n",
-    "    for ix=??\n",
-    "        Pf[??]  -= ??\n",
+    "for iy=1:ny\n",
+    "    for ix=1:nx\n",
+    "        Pf[ix,iy]  -= ((qDx[ix+1,iy]-qDx[ix,iy])*_dx + (qDy[ix,iy+1]-qDy[ix,iy])*_dy)*_β_dτ\n",
     "    end\n",
     "end"
    ],
@@ -709,8 +711,8 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "macro d_xa(A)  esc(:( $A[??]-$A[??] )) end\n",
-    "macro d_ya(A)  esc(:( $A[??]-$A[??] )) end"
+    "macro d_xa(A)  esc(:( $A[ix+1,iy]-$A[ix,iy] )) end\n",
+    "macro d_ya(A)  esc(:( $A[ix,iy+1]-$A[ix,iy] )) end"
    ],
    "metadata": {},
    "execution_count": null
@@ -726,19 +728,19 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "for iy=??\n",
-    "    for ix=??\n",
-    "        qDx[??] -= (qDx[??] + k_ηf_dx* ?? )*_1_θ_dτ\n",
+    "for iy=1:ny\n",
+    "    for ix=1:nx-1\n",
+    "        qDx[ix+1,iy] -= (qDx[ix+1,iy] + k_ηf_dx*@d_xa(Pf))*_1_θ_dτ\n",
     "    end\n",
     "end\n",
-    "for iy=??\n",
-    "    for ix=??\n",
-    "        qDy[??] -= (qDy[??] + k_ηf_dy* ?? )*_1_θ_dτ\n",
+    "for iy=1:ny-1\n",
+    "    for ix=1:nx\n",
+    "        qDy[ix,iy+1] -= (qDy[ix,iy+1] + k_ηf_dy*@d_ya(Pf))*_1_θ_dτ\n",
     "    end\n",
     "end\n",
-    "for iy=??\n",
-    "    for ix=??\n",
-    "        Pf[??]  -= ??\n",
+    "for iy=1:ny\n",
+    "    for ix=1:nx\n",
+    "        Pf[ix,iy]  -= (@d_xa(qDx)*_dx + @d_ya(qDy)*_dy)*_β_dτ\n",
     "    end\n",
     "end"
    ],
@@ -803,15 +805,28 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "function compute_flux!(...)\n",
+    "function compute_flux!(qDx,qDy,Pf,k_ηf_dx,k_ηf_dy,_1_θ_dτ)\n",
     "    nx,ny=size(Pf)\n",
-    "    ...\n",
+    "    for iy=1:ny,\n",
+    "        for ix=1:nx-1\n",
+    "            qDx[ix+1,iy] -= (qDx[ix+1,iy] + k_ηf_dx*@d_xa(Pf))*_1_θ_dτ\n",
+    "        end\n",
+    "    end\n",
+    "    for iy=1:ny-1\n",
+    "        for ix=1:nx\n",
+    "            qDy[ix,iy+1] -= (qDy[ix,iy+1] + k_ηf_dy*@d_ya(Pf))*_1_θ_dτ\n",
+    "        end\n",
+    "    end\n",
     "    return nothing\n",
     "end\n",
     "\n",
-    "function update_Pf!(Pf,...)\n",
+    "function update_Pf!(Pf,qDx,qDy,_dx,_dy,_β_dτ)\n",
     "    nx,ny=size(Pf)\n",
-    "    ...\n",
+    "    for iy=1:ny\n",
+    "        for ix=1:nx\n",
+    "            Pf[ix,iy]  -= (@d_xa(qDx)*_dx + @d_ya(qDy)*_dy)*_β_dτ\n",
+    "        end\n",
+    "    end\n",
     "    return nothing\n",
     "end"
    ],
@@ -891,9 +906,9 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "function compute!(Pf,qDx,qDy, ???)\n",
-    "    compute_flux!(...)\n",
-    "    update_Pf!(...)\n",
+    "function compute!(Pf,qDx,qDy,k_ηf_dx,k_ηf_dy,_1_θ_dτ,_dx,_dy,_β_dτ)\n",
+    "    compute_flux!(qDx,qDy,Pf,k_ηf_dx,k_ηf_dy,_1_θ_dτ)\n",
+    "    update_Pf!(Pf,qDx,qDy,_dx,_dy,_β_dτ)\n",
     "    return nothing\n",
     "end"
    ],
@@ -911,8 +926,8 @@
    "outputs": [],
    "cell_type": "code",
    "source": [
-    "t_toc = @belapsed compute!($Pf,$qDx,$qDy,???)\n",
-    "niter = ???"
+    "t_toc = @belapsed compute!($Pf,$qDx,$qDy,$k_ηf_dx,$k_ηf_dy,$_1_θ_dτ,$_dx,$_dy,$_β_dτ)\n",
+    "niter = 1"
    ],
    "metadata": {},
    "execution_count": null
@@ -1024,11 +1039,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.5"
+   "version": "1.11.0"
   },
   "kernelspec": {
-   "name": "julia-1.10",
-   "display_name": "Julia 1.10.5",
+   "name": "julia-1.11",
+   "display_name": "Julia 1.11.0",
    "language": "julia"
   }
  },

diff --git a/slide-notebooks/notebooks/l5_2-unit-test.ipynb b/slide-notebooks/notebooks/l5_2-unit-test.ipynb
@@ -314,11 +314,11 @@
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.10.5"
+   "version": "1.11.0"
   },
   "kernelspec": {
-   "name": "julia-1.10",
-   "display_name": "Julia 1.10.5",
+   "name": "julia-1.11",
+   "display_name": "Julia 1.11.0",
    "language": "julia"
   }
  },

diff --git a/website/_literate/l5_1-cpu-parallel_web.jl b/website/_literate/l5_1-cpu-parallel_web.jl
@@ -262,10 +262,10 @@ md"""
 - Compute the elapsed time `t_toc` at the end of the time loop and report:
 """
 
-t_toc = ...
-A_eff = ...          # Effective main memory access per iteration [GB]
-t_it  = ...          # Execution time per iteration [s]
-T_eff = A_eff/t_it   # Effective memory throughput [GB/s]
+t_toc = Base.time() - t_tic
+A_eff = (3*2)/1e9*nx*ny*sizeof(Float64)  # Effective main memory access per iteration [GB]
+t_it  = t_toc/niter                      # Execution time per iteration [s]
+T_eff = A_eff/t_it                       # Effective memory throughput [GB/s]
 
 #src #########################################################################
 #nb # %% A slide [markdown] {"slideshow": {"slide_type": "slide"}}
@@ -274,7 +274,7 @@ md"""
 - Round `T_eff` to the 3rd significant digit.
 
 ```julia
-@printf("Time = %1.3f sec, ... \n", t_toc, ...)
+@printf("Time = %1.3f sec, T_eff = %1.2f GB/s (niter = %d)\n", t_toc, round(T_eff, sigdigits=3), niter)
 ```
 """
 
@@ -286,8 +286,10 @@ md"""
 - Define a `do_check` flag set to `false`
 """
 
-function Pf_diffusion_2D(;??)
+function Pf_diffusion_2D(;do_check=false)
+    if do_check && (iter%ncheck == 0)
     ...
+    end
     return
 end
 
@@ -363,19 +365,19 @@ md"""
 Implement a nested loop, taking car of bounds and staggering.
 """
 
-for iy=??
-    for ix=??
-        qDx[??] -= (qDx[??] + k_ηf_dx* ?? )*_1_θ_dτ
+for iy=1:ny
+    for ix=1:nx-1
+        qDx[ix+1,iy] -= (qDx[ix+1,iy] + k_ηf_dx*(Pf[ix+1,iy]-Pf[ix,iy]))*_1_θ_dτ
     end
 end
-for iy=??
-    for ix=??
-        qDy[??] -= (qDy[??] + k_ηf_dy* ?? )*_1_θ_dτ
+for iy=1:ny-1
+    for ix=1:nx
+        qDy[ix,iy+1] -= (qDy[ix,iy+1] + k_ηf_dy*(Pf[ix,iy+1]-Pf[ix,iy]))*_1_θ_dτ
     end
 end
-for iy=??
-    for ix=??
-        Pf[??]  -= ??
+for iy=1:ny
+    for ix=1:nx
+        Pf[ix,iy]  -= ((qDx[ix+1,iy]-qDx[ix,iy])*_dx + (qDy[ix,iy+1]-qDy[ix,iy])*_dy)*_β_dτ
     end
 end
 
@@ -387,25 +389,25 @@ We could now use macros to make the code nicer and clearer. Macro expression wil
 Let's use macros to replace the derivative implementations
 """
 
-macro d_xa(A)  esc(:( $A[??]-$A[??] )) end
-macro d_ya(A)  esc(:( $A[??]-$A[??] )) end
+macro d_xa(A)  esc(:( $A[ix+1,iy]-$A[ix,iy] )) end
+macro d_ya(A)  esc(:( $A[ix,iy+1]-$A[ix,iy] )) end
 
 md"""
 And update the code within the iteration loop:
 """
-for iy=??
-    for ix=??
-        qDx[??] -= (qDx[??] + k_ηf_dx* ?? )*_1_θ_dτ
+for iy=1:ny
+    for ix=1:nx-1
+        qDx[ix+1,iy] -= (qDx[ix+1,iy] + k_ηf_dx*@d_xa(Pf))*_1_θ_dτ
     end
 end
-for iy=??
-    for ix=??
-        qDy[??] -= (qDy[??] + k_ηf_dy* ?? )*_1_θ_dτ
+for iy=1:ny-1
+    for ix=1:nx
+        qDy[ix,iy+1] -= (qDy[ix,iy+1] + k_ηf_dy*@d_ya(Pf))*_1_θ_dτ
     end
 end
-for iy=??
-    for ix=??
-        Pf[??]  -= ??
+for iy=1:ny
+    for ix=1:nx
+        Pf[ix,iy]  -= (@d_xa(qDx)*_dx + @d_ya(qDy)*_dy)*_β_dτ
     end
 end
 
@@ -438,15 +440,28 @@ md"""
 Create a `compute_flux!()` and `compute_Pf!()` functions that take input and output arrays and needed scalars as argument and return nothing.
 """
 
-function compute_flux!(...)
+function compute_flux!(qDx,qDy,Pf,k_ηf_dx,k_ηf_dy,_1_θ_dτ)
     nx,ny=size(Pf)
-    ...
+    for iy=1:ny,
+        for ix=1:nx-1
+            qDx[ix+1,iy] -= (qDx[ix+1,iy] + k_ηf_dx*@d_xa(Pf))*_1_θ_dτ
+        end
+    end
+    for iy=1:ny-1
+        for ix=1:nx
+            qDy[ix,iy+1] -= (qDy[ix,iy+1] + k_ηf_dy*@d_ya(Pf))*_1_θ_dτ
+        end
+    end
     return nothing
 end
 
-function update_Pf!(Pf,...)
+function update_Pf!(Pf,qDx,qDy,_dx,_dy,_β_dτ)
     nx,ny=size(Pf)
-    ...
+    for iy=1:ny
+        for ix=1:nx
+            Pf[ix,iy]  -= (@d_xa(qDx)*_dx + @d_ya(qDy)*_dy)*_β_dτ
+        end
+    end
     return nothing
 end
 
@@ -483,18 +498,18 @@ md"""
 The `compute!()` function:
 """
 
-function compute!(Pf,qDx,qDy, ???)
-    compute_flux!(...)
-    update_Pf!(...)
+function compute!(Pf,qDx,qDy,k_ηf_dx,k_ηf_dy,_1_θ_dτ,_dx,_dy,_β_dτ)
+    compute_flux!(qDx,qDy,Pf,k_ηf_dx,k_ηf_dy,_1_θ_dτ)
+    update_Pf!(Pf,qDx,qDy,_dx,_dy,_β_dτ)
     return nothing
 end
 
 md"""
 can then be called using `@belapsed` to return elapsed time for a single iteration, letting `BenchmarkTools` taking car about sampling
 """
 
-t_toc = @belapsed compute!($Pf,$qDx,$qDy,???)
-niter = ???
+t_toc = @belapsed compute!($Pf,$qDx,$qDy,$k_ηf_dx,$k_ηf_dy,$_1_θ_dτ,$_dx,$_dy,$_β_dτ)
+niter = 1
 
 #nb # > 💡 note: Variables need to be interpolated into the function call, thus taking a `$` in front.
 #md # \note{Note that variables need to be interpolated into the function call, thus taking a `$` in front.}

diff --git a/website/homework.md b/website/homework.md
@@ -11,8 +11,8 @@ hascode = false
 | Lect. 2      | 02.10.2024 - 23h59 CET | [Moodle (notebooks)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=1115224), [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=1103813) | For the notebooks submission, submit a folder containing all exercise notebooks from [JupyterHub](https://jhub-let-04-23586.ethz.ch/hub/home). For the commit hash + PR submission, copy the git commit hash (SHA) of the final push on the branch `homework-2` and open a pull request on the `main` branch. Paste both the commit hash and the PR link on Moodle (check [Logistics](/logistics/#submission) for more details on how to set up the GitHub repository).|
 | Lect. 3      | 11.10.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=1103821) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-3` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
 | Lect. 4      | 18.10.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=1103827) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-4` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
-<!-- | Lect. 5      | 25.10.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=966854) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-5` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
-| Lect. 6      | 01.11.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=969655) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-6` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
+| Lect. 5      | 25.10.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=1103833) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-5` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
+<!-- | Lect. 6      | 01.11.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=969655) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-6` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
 | Lect. 7      | 08.11.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=972195) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-7` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
 | Lect. 8      | 15.11.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=976353) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-8` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. |
 | Lect. 9 (first project hand in) | 01.12.2024 - 23h59 CET | [Moodle (commit hash + PR)](https://moodle-app2.let.ethz.ch/mod/assign/view.php?id=981745) | For the submission, copy the git commit hash (SHA) of the final push on the branch `homework-9` and open a pull request on the `main` branch. Paste both the SHA and the PR link on Moodle. Make sure that the project is contained inside the `PorousConvection` folder. |