32: add various ways to calculate pi

serial, disbatch, mpi4py + sbatch examples

32_IntroToHPC/main.md

@@ -100,6 +100,25 @@ Activities where participants all actively work to foster an environment which e
 
 
 
+## Environment management
+
+
+## What you'll need
+
+- Remote access to the cluster via terminal
+  - on 'FI' wifi network: `ssh username@rusty`
+  - or... `ssh -p 61022 [email protected]`, `ssh rusty`
+  - or... `https://jupyter.flatironinstitute.org`
+- Way to edit files on cluster
+  - terminal `emacs/vi/nano/ed`
+  - or... remote edit via `vscode/emacs/vi/sshfs`
+  - or... `https://jupyter.flatironinstitute.org`
+
+
+##
+
+
+
 ## SciWare Survey [TODO]
 <!-- <center> -->
 <!-- <img width="50%" src="./qr.png"> -->

32_IntroToHPC/mc_pi/average_logs.py

@@ -0,0 +1,10 @@
+import os
+import numpy as np
+
+pivals = []
+for fname in os.listdir('logs'):
+    with open(os.path.join('logs', fname), 'r') as f:
+        pivals.append(float(f.read()))
+
+pi = np.array(pivals).mean()
+print(f'{pi:.16f}')

32_IntroToHPC/mc_pi/create_env.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+module -q reset
+module load python
+if [[ ! -d "venv" ]]; then
+    python -m venv venv --system-site-packages
+fi
+mkdir -p logs

32_IntroToHPC/mc_pi/disbatch_taskfile

@@ -0,0 +1,2 @@
+#DISBATCH PREFIX seed=$DISBATCH_REPEAT_INDEX ; ( cd ~/mc_pi ; source load_env.sh ; python pi.py 100000 $seed ) &> logs/pi_s${seed}.log
+#DISBATCH REPEAT 256

32_IntroToHPC/mc_pi/load_env.sh

@@ -0,0 +1,3 @@
+module -q reset
+module load openmpi python python-mpi
+source venv/bin/activate

32_IntroToHPC/mc_pi/mpi_pi.py

@@ -0,0 +1,17 @@
+import numpy as np
+from mpi4py import MPI
+import sys
+
+N = int(float(sys.argv[1]))
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+np.random.seed(rank)
+
+hits = 0
+for i in range(N):
+    hits += int(np.linalg.norm(np.random.uniform(low=-1.0, high=1.0, size=2)) <= 1.0)
+
+hits_arr = comm.gather(hits, root=0)
+if rank == 0:
+    pi = 4 * np.array(hits_arr).mean() / N
+    print(f'{pi:.16f}', np.abs(100 * (1 - pi/np.pi)))

32_IntroToHPC/mc_pi/mpi_pi.sbatch

@@ -0,0 +1,12 @@
+#!/bin/bash 
+#SBATCH -o mpi_pi.log
+#SBATCH -e mpi_pi.err
+#SBATCH -N 2
+#SBATCH -c 1
+#SBATCH -n 256
+#SBATCH -p scc
+#SBATCH -C rome
+#SBATCH -t 1:00
+
+source load_env.sh
+mpirun python mpi_pi.py 100000

32_IntroToHPC/mc_pi/pi.py

@@ -0,0 +1,13 @@
+import numpy as np
+import sys
+
+N = int(float(sys.argv[1]))
+seed = int(sys.argv[2])
+np.random.seed(seed)
+
+hits = 0
+for i in range(N):
+    hits += int(np.linalg.norm(np.random.uniform(low=-1, high=1.0, size=2)) <= 1.0)
+
+pi = 4 * hits / N
+print(f'{pi:.16f}')