Table of Contents

Help and answers

For questions, please contact the support crew support@nhr.zib.de.

Login

Login authentication is possible via SSH keys only. Please visit our tutorial SSH Login.

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office $ ssh -i $HOME/.ssh/id_rsa_nhr nhr_username@blogin.nhr.zib.de
Enter passphrase for key '...':
blogin1 $

File systems

Each complex has the following file systems available. More information about Quota, usage, and best pratices are available here. Hints for data transfer are given here.

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Software and environment modules

The webpage Software gives you information about available software on the NHR systems.

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To avoid conflicts between different compilers and compiler versions, builds of most important libraries are provided for all compilers and major release numbers.

Program build

Here only a brief introduction to program building using the intel compiler is given. For more detailed instructions, including important compiler flags and special libraries, refer to our webpage Compilation Guide.

Examples for building a program on the Atos system

To build executables for the Atos system, call the standard compiler executables (icc, ifort, gcc, gfortran) directly.

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module load intel
icc -qopenmp -o hello.bin hello.c

MPI, Communication Libraries, OpenMP

We provide several communication libraries:

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OpenMP support is available with the compilers from Intel and GNU.

Using the batch system

To run your applications on the systems, you need to go through our batch system/scheduler: Slurm. The scheduler uses meta information about the job (requested node and core count, wall time, etc.) and then runs your program on the compute nodes, once the resources are available and your job is next in line. For a more in depth introduction, visit our Slurm documentation.

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• Interactive job execution
• Job script execution

Resource specification

To request resources, there are multiple flags to be used when submitting the job.

Interactive jobs

Anker
interactive_jobs interactive_jobs

For using compute resources interactively, e.g. to follow the execution of MPI programs, the following steps are required. Note that non-interactive batch jobs via job scripts (see below) are the primary way of using the compute resources.

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blogin1 ~ $ salloc -t 00:10:00 -p standard96:test -N2 --tasks-per-node 24
salloc: Granted job allocation [...]
salloc: Waiting for resource configuration
salloc: Nodes bcn[1001,1003] are ready for job
# To get a shell on one of the allocated nodes at the Berlin complex/Lise (not required for Göttingen/Emmy)
blogin1 ~ $ srun --pty --interactive --preserve-env ${SHELL}
bcn1001 ~ $ srun hostname | sort | uniq -c
     24 bcn1001
     24 bcn1003
bcn1001 ~ $ exit
# Exit a second time for Berlin/Lise 
blogin1:~ > exit
salloc: Relinquishing job allocation [...]

Job scripts

Please go to our webpage CPU partition "Lise" for more details about job scripts. For introduction, standard batch system jobs are executed applying the following steps:

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#!/bin/bash
#SBATCH -t 00:20:00
#SBATCH -N 1
#SBATCH --cpus-per-task=96
#SBATCH -p large96:test

# This binds each thread to one core
export OMP_PROC_BIND=TRUE
# Number of threads as given by -c / --cpus-per-task
export OMP_NUM_THREADS=$(($SLURM_CPUS_PER_TASK * 2))
export KMP_AFFINITY=verbose,scatter

hello_world > hello.output

Job Accounting

The webpage Accounting and NPL gives you more information about job accounting.

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