materials to work with mathworks on slurm

README.md

-# mathworks-shared
 
-Shared repo to work with Mathworks on slurm, etc
\ No newline at end of file
+Command line just with singularity:
+
+module load singularity
+singularity run /ptmp/containers/<PICK A SINGULARITY CONTAINER> -nodesktop -nojvm -r "run('/ptmp/bfitch/workflow-slurm-matlab/cpu_bench.m'); exit;"

cpu_bench.m

+
+maxNumCompThreads(64)
+
+%for N=[10, 100, 1000, 2500, 5000, 7500, 10000, 100000]
+for N=[1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048] %, 4096, 8192, 16384, 32768]
+
+    N_mult = 32768 / N;
+
+    fprintf('N = %d: ', N);
+
+    rng(1);
+    A = rand(N);
+    B = rand(N);
+    A_pd = A*A';
+
+    tic;
+    svd(A);
+    t_svd = toc;
+    fprintf('SVD ');
+
+    tic;
+    chol(A_pd);
+    t_chol = toc;
+    fprintf('Chol ');
+
+    tic;
+    qr(A);
+    t_qr = toc;
+    fprintf('QR ');
+
+    tic;
+    for k=1:N_mult
+        A*B;
+    end
+    t_mult = toc;
+    fprintf('%d mult ', N_mult);
+
+    tic;
+    inv(A);
+    t_inv = toc;
+    fprintf('Inv ');
+
+    tic;
+    pinv(A);
+    t_pinv = toc;
+    fprintf('Pinv\n\n');
+
+    fprintf('TIME IN SECONDS (SIZE: %d):\n', N);
+    fprintf('maxNumCompThreads %d\n', maxNumCompThreads );
+    fprintf('SVD: %f\n', t_svd);
+    fprintf('Cholesky: %f\n', t_chol);
+    fprintf('QR: %f\n', t_qr);
+    fprintf('%d matrix products: %f\n', N_mult, t_mult);
+    fprintf('Inverse: %f\n', t_inv);
+    fprintf('Pseudo-inverse: %f\n\n', t_pinv);
+end

nyx-sing-slurm.job.sh

+#!/bin/bash -l
+# Standard output and error:
+#SBATCH -o ./tjob.out.%j
+#SBATCH -e ./tjob.err.%j
+# Initial working directory:
+#SBATCH -D ./
+# Job Name:
+#SBATCH -J ml_bench
+#
+#
+# Queue (Partition):
+#SBATCH --partition=compute  # nyx partitions: compute, highmem, gpu
+#
+# Number of nodes and MPI tasks per node:
+#SBATCH --nodes=1
+#SBATCH --tasks=1
+#SBATCH --cpus-per-task=64
+#SBATCH --exclusive
+#
+#SBATCH --mail-type=END,FAIL
+#SBATCH --mail-user=blake.fitch@tuebingen.mpg.de
+#
+# Wall clock limit:
+#SBATCH --time=01:00:00
+
+module purge
+module load singularity
+
+export SINGULARITY_BIND="/ptmp,/scratch"
+export SINGULARITYENV_MATLABPATH=$PWD
+export MATLAB_CONTAINER_PATH=/ptmp/containers/matlab_r2021a-2021-05-10.sif
+
+echo "Here we go..."
+time ${MATLAB_CONTAINER_PATH} -nodesktop -nojvm -r "run('/home/bfitch/workflow-slurm-matlab/cpu_bench.m'); exit;"
+echo " ... done."
+
+