sean-smith

👾 Slurm CUDA MPS Prolog

The following Slurm Prolog starts the CUDA MPS server on each compute node before the job is started.

cat << EOF > /opt/slurm/etc/prolog.sh
#!/bin/sh

# start mps
nvidia-cuda-mps-control -d

biochem-fan

RELION interoperabiity with Warp and M

This document examines how to use RELION 4.0 (beta2 as of writing) with Warp 1.09 and M 1.09 for single particle analysis.

Special thanks to Alister Burt, Pranav Shah and Dimitry Tegunov for discussion on this Twitter thread.

Download the movies

We use the RELION tutorial dataset (beta-galactosidase collected on JEOL CRYO ARM 200, a subset of EMPIAR-10204).

sean-smith

AWS ParallelCluster + AWS Batch

Today I'm going to demonstrate running High Performance Conjucate Grandients (HPCG) in a containerized workload. This takes advantage of AWS ParallelCluster, AWS Batch, and OpenMPI.

First install aws-parallelcluster:

$ pip install aws-parallelcluster

dmennis

---
AWSTemplateFormatVersion: '2010-09-09'

Description: Mobile App CICD Demo

Parameters:

  DeviceFarmProjectName:
    Type: String
    Default: demo-app-devicefarm

eshelman

Latency Comparison Numbers
--------------------------
L1 cache reference/hit                       1.5 ns                      4 cycles
Floating-point add/mult/FMA operation        1.5 ns                      4 cycles
L2 cache reference/hit                       5   ns                      12 ~ 17 cycles
Branch mispredict                            6   ns                      15 ~ 20 cycles
L3 cache hit (unshared cache line)          16   ns                      42 cycles
L3 cache hit (shared line in another core)  25   ns                      65 cycles
Mutex lock/unlock                           25   ns
L3 cache hit (modified in another core)     29   ns                      75 cycles

mirakui

source :gemcutter
gem 'pit'
gem 'sauberia-aws-s3'