Alankar Dutta dutta-alankar

Building CUDA-aware OpenMPI 5.0 + parallel HDF5 2.0.0 on Freya (MPCDF) GPU nodes

Reproducible recipe for a hand-built, CUDA-aware OpenMPI 5.0.10 and a parallel HDF5 2.0.0 linked against it, using the gcc/15 + cuda/13.0 toolchain. This mirrors the site module openmpi_gpu/cuda_11.6-11.6.2-gcc_11-11.2.0/4.1.6 and the older hdf5-2.0.0-openmpi_gpu-4.1 stack, modernised for OpenMPI 5.x.

Built / verified: 2026-07-14 on Freya (SLE 15, SLURM 24.11).

What lands where

Internet Browsing on the MPCDF Cluster (Firefox Fix)

Problem

Firefox opens but all pages fail to load. The browser shows connection errors for every URL, even though the cluster node has full internet connectivity (e.g. curl https://www.google.com returns HTTP 200).

	import numpy as np
	import vtk
	from vtk.util import numpy_support as ns
	# Output Data Set Type = vtkPolyData

	# ---------------- user settings ----------------
	AXIS = 2 # 0=x, 1=y, 2=z : integrate along this axis
	FIELDS = None # ["nMgII_PIE_Z1.0_z0.0"] # or None for every cell array
	SUFFIX = "_proj"
	KPC = 3.0856775814913673e21 # cm

	#!/usr/bin/env python3
	"""Fetch a halo from the IllustrisTNG API (https://www.tng-project.org/api).

	Fetches the metadata of a halo (FoF group) as JSON and, by default, downloads
	its full HDF5 cutout: all particle types (gas, dm, stars, bhs) with all fields.
	The cutout can optionally be restricted to a subset of particle types/fields.

	Usage:
	python fetch_halo.py HALO_ID --api-key KEY [options]

	#!/bin/bash
	#SBATCH --job-name="ion_box"
	#SBATCH --output="tjob.out.%j.%N.out"
	#SBATCH --partition=ghx4
	#SBATCH --mem=0
	#SBATCH --nodes=2
	#SBATCH --ntasks-per-node=4 # could be 1 for py-torch
	#SBATCH --cpus-per-task=8 #6 # spread out to use 1 core per numa, set to 64 if tasks is 1
	#SBATCH --gpus-per-node=4
	#SBATCH --account=bdiz-dtai-gh

	# -- coding: utf-8 --
	"""
	Created on Mon May 04 11:06:28 2026

	@author: alankar

	MPI + multi-GPU absorption spectrum calculator.

	This script reads per-cell ion density (nIon) and hydro fields, then computes
	line-of-sight absorption spectra in parallel:

	#!/usr/bin/env python3
	# -- coding: utf-8 --
	"""
	Created on Tue Mar 29 00:07:48 2026

	@author: alankar

	Compute Slurm submit-to-start waiting time statistics for a partition.

	Default behavior (source=auto):

	# -- coding: utf-8 --
	"""
	Created on Fri Nov 17 12:22:19 2023

	@author: alankar

	Absorption-line utilities for synthetic spectra along a sightline.

	This module provides helper functions to build an absorption profile from
	cell-wise gas properties (temperature, LOS velocity, ion density, and path

	#!/bin/python3
	# -- coding: utf-8 --
	"""
	Created on Mon Mar 28 11:27:48 2026

	@author: alankar.

	ParaView programmable source helper to load an entire snapshot with one particle type.

	This script:

	#!/bin/python3
	# -- coding: utf-8 --
	"""
	Created on Mon Mar 28 10:49:48 2026

	@author: alankar.

	ParaView programmable source helper to load one halo and one particle type.

	This script:

Alankar Dutta dutta-alankar

Building CUDA-aware OpenMPI 5.0 + parallel HDF5 2.0.0 on Freya (MPCDF) GPU nodes

What lands where

Internet Browsing on the MPCDF Cluster (Firefox Fix)

Problem

Root Cause