Quick Start

Brief description

You can find documentation on our clusters at https://www.pdc.kth.se/hpc-services/computing-systems

How to log in

Use your current configuration of Kerberos and ssh, and log in to Dardel with

kinit -f <user name>@NADA.KTH.SE
ssh <user name>@dardel.pdc.kth.se

For more details on how to log in, see How to log in with SSH keys.

Storage

The user home directories, project directories, and scratch file area are stored on a Lustre file system which is mounted to the Dardel compute and login nodes.

The home directories have a quota of 25 GB.

The project directories are not backed up. You are advised to always move data, and keep additional copies of the most important input and output files.

The scratch area is intended for temporary large files that are used during calculations. The scratch area is automatically cleaned by removing files that has not been changed within a certain time. You are advised to always move data, and keep additional copies of the most important input and output files.

For more details on storage, see Klemming (on Dardel).

Transfer of files

Files and directories can be transferred to and from Dardel with the scp (secure copy) command.

# To transfer a file from local computer to Dardel
scp localfile <user name>@dardel.pdc.kth.se:<directory>/.
# To transfer a file from Dardel to local computer
scp <user name>@dardel.pdc.kth.se:<directory>/<file> .

For more details on how to transfer files, see Using scp/rsync.

The Lmod module system

Dardel is using the Lmod environment module system. Lmod allows for dynamic add/remove of installed software packages to the running environment. To access, list and search among the installed application programs, libraries, and tools, use the module command (or the shortcut ml)

ml
# lists the loaded software modules

ml avail <program name>
# lists the available versions of a given software

Many softwares are not directly available using the above command as they are built within different Cray programming environments. To find all software and all its dependencies.

ml spider <program name>
# lists the available versions of a given software and what dependent modules need to be loaded

When you have found the program you are looking for, use

ml <program>
# to load the program module

Many software modules become available after loading the latest PDC module.

ml PDC

For more details on how to use modules, see How to use module to load different softwares into your environment.

The Cray programming environment

The Cray Programming Environment (CPE) provides a consistent interface to multiple compilers and libraries. On Dardel you can load the cpe module to enable a specific version of the CPE. For example

ml cpe/21.11

In addition to the cpe module, there are also the PrgEnv- modules that provide compilers for different programming environment

  • PrgEnv-cray: loads the Cray compiling environment (CCE) that provides compilers for Cray systems.

  • PrgEnv-gnu: loads the GNU compiler suite.

  • PrgEnv-aocc: loads the AMD AOCC compilers.

By default the PrgEnv-cray is loaded upon login. You can switch to different compilers by loading another PrgEnv- module

ml PrgEnv-gnu
ml PrgEnv-aocc

After loading the cpe and the PrgEnv- modules, you can now build your parallel applications using compiler wrappers for C, C++ and Fortran

cc -o myexe.x mycode.c      # cc is the wrapper for C compiler
CC -o myexe.x mycode.cpp    # CC is the wrapper for C++ compiler
ftn -o myexe.x mycode.f90   # ftn is the wrapper for Fortran compiler

The compiler wrappers will choose the required compiler version, target architecture options, and will automatically link to the math and MPI libraries. There is no need to add any -I, -l or -L flags for the Cray-provided libraries.

  • Math libraries:

    There are the cray-libsci and cray-fftw modules that are designed to provide optimal performance from Cray systems. The cray-libsci module provides BLAS/LAPACK/ScaLAPACK and supports OpenMP. The number of threads can be controlled by the OMP_NUM_THREADS environment variable.

  • MPI library:

    There is the cray-mpich module, which is based on ANL MPICH and has been optimized for Cray programming environment.

All softwares at PDC are installed using a specific CPE and the softwares installed using the latest CPE can be accessed by

ml PDC

The PDC modules are directly related to the CPE version and a number of older software modules can also be viewed by looking at older PDC modules.

Build your first program

Example 1: Build an MPI parallelized Fortran code within the PrgEnv-cray environment

In this example we build and test run a Hello World code hello_world_mpi.f90.

program hello_world_mpi
include "mpif.h"
integer myrank,size,ierr
call MPI_Init(ierr)
call MPI_Comm_rank(MPI_COMM_WORLD,myrank,ierr)
call MPI_Comm_size(MPI_COMM_WORLD,size,ierr)
write(*,*) "Processor ",myrank," of ",size,": Hello World!"
call MPI_Finalize(ierr)
end program

The build is done within the PrgEnv-cray environment using the Cray Fortran compiler, and the testing is done on a Dardel CPU node reserved for interactive use.

# Check which compiler the compiler wrapper is pointing to
ftn --version
# returns Cray Fortran : Version 13.0.0

# Compile the code
ftn hello_world_mpi.f90 -o hello_world_mpi.x

# Test the code in interactive session.
# First queue to get one node reserved for 10 minutes
salloc -N 1 -t 0:10:00 -A <project name> -p main
# wait for the node. Then run the program using 128 MPI ranks with
srun -n 128 ./hello_world_mpi.x
# with program output to standard out
# ...
# Processor  123  of  128 : Hello World
# ...
# Processor  47  of  128 : Hello World
# ...

Having here used the ftn compiler wrapper, the linking to the cray-mpich library was done without the need to specify linking flags. As is expected for this code, in runtime each MPI rank is writing its Hello World to standard output without any synchronization with the other ranks.

Example 2: Build a C code with PrgEnv-gnu. The code requires linking to a Fourier transform library.

# Download a C program that illustrates use of the FFTW library
mkdir fftw_test
cd fftw_test
wget https://people.math.sc.edu/Burkardt/c_src/fftw/fftw_test.c

# Change from the PrgEnv-cray to the PrgEnv-gnu environment
ml PDC/21.11
ml cpeGNU/21.11
# Lmod is automatically replacing "cce/13.0.0" with "gcc/11.2.0".
# Lmod is automatically replacing "PrgEnv-cray/8.2.0" with "cpeGNU/21.11".
# Due to MODULEPATH changes, the following have been reloaded:
  1) cray-mpich/8.1.11

# Check which compiler the cc compiler wrapper is pointing to
cc --version
# gcc (GCC) 11.2.0 20210728 (Cray Inc.)

ml avail
# The listing reveals that cray-libsci/21.08.1.2 is already loaded.

# In addition, the program needs linking also to a Fourier transform library.
ml spider fftw
# gives a listing of available Fourier transform libraries.
# Load a recent version of the Cray-FFTW library with
module add cray-fftw/3.3.8.12

# Build the code with
cc fftw_test.c -o fftw_test.x

# Test the code in interactive session.
# First queue to get one reserved core for 10 minutes
salloc -n 1 -t 0:10:00 -A <project name> -p shared
# wait for the core. Then run the program with
srun -n 1 ./fftw_test.x

Having loaded the cray-fftw module, no additional linking flag(s) was needed for the cc compiler wrapper.

Example 3: Build a program with the EasyBuild cpeGNU/21.09 toolchain

# Load an EasyBuild-user module
ml PDC/21.11
ml EasyBuild-user/4.5.0

# Look for a recipe for the Libxc library
eb -S Libxc
# Returns a list of available EasyBuild easyconfig files.
# Choose an easyconfig file for the cpeGNU/21.11 toolchain.

# Make a dry-run
eb libxc-5.1.6-cpeGNU-21.11.eb --robot --dry-run

# Check if dry-run looks reasonable. Then proceed to build with
eb libxc-5.1.6-cpeGNU-21.11.eb --robot

# The program is now locally installed in the user's
# ~/.local/easybuild directory and can be loaded with
ml PDC/21.11
ml EasyBuild-user/4.5.0
ml libxc/5.1.6-cpeGNU-21.11

How to use EasyBuild

At PDC we have EasyBuild installed to simplify the installation of HPC software and several easyconfig software recipes are available via the command line. In order to use EasyBuild in your local folder

ml PDC/21.11
ml EasyBuild-user/4.5.0

EasyBuild installed software will build into ~/.local/easybuild folder and are automatically available as modules.

For more information regarding how to EasyBuild at PDC go to Installing software using EasyBuild

Submit a batch job to the queue

PDC uses the Slurm Workload Manager to schedule jobs.

You are advised to always submit jobs from a directory within the project and scratch partitions of the file system.

Keep additional copies of the most important input and output files in your home directory.

The Dardel CPU nodes have 128 cores. Please note that if you request a full node, your project allocation will be charged for use of 128 cores, even if your program uses a smaller number of cores. You are advised to submit jobs that will use fewer cores than 128 to the shared partion.

For more details on the partition, see Dardel partitions.

Example 1: Submit an batch job to run on 64 cores of a node that is shared with other jobs.

In this example we will run a batch job for the hello_world_mpi.f90 code. To this end, we prepare a jobscript.sh

#!/bin/bash -l
# The -l above is required to get the full environment with modules
# Set the allocation to be charged for this job
# not required if you have set a default allocation
#SBATCH -A <project name>
# The name of the script is myjob
#SBATCH -J myjob
# 10 minutes wall-clock time will be given to this job
#SBATCH -t 00:10:00
# The partition
#SBATCH -p shared
# The number of tasks requested
#SBATCH -n 64
# The number of cores per task
#SBATCH -c 1

echo "Script initiated at `date` on `hostname`"
srun -n 64 hello_world_mpi.x
echo "Script finished at `date` on `hostname`"

The batch job is submitted to the job queue with the sbatch command. After submission with

sbatch jobscript.sh

The status of the job (pending in queue, running, etc) can be monitored with the squeue command.

squeue -u $USER

The standard output of the program is written to a file slurm-<job number>.out. We inspect the output

Script initiated at thu oct 28 14:52:26 CEST 2021 on nid001064
..
Processor  25  of  64 : Hello World!
Processor  34  of  64 : Hello World!
..
Script finished at thu oct 28 14:52:28 CEST 2021 on nid001064

For more details on how to write batch scripts and submit batch jobs to queues, see How to Run Jobs and Queueing jobs.

Example 2: Submit a batch job to queue for a center installed software

In this example we will perform a calculation on two Dardel CPU compute nodes with the ABINIT package for modeling of condensed matter. The example calculation is a density functional theory (DFT) simulation of the properties of the material SrVO3. ABINIT is available as a PDC center installed software, as listed on the page Available Software.

For ABINIT can be found general information, use information and build information.

We activate the ABINIT software module with

ml PDC/21.11
ml ABINIT/9.6.2-cpeGNU-21.11

In order to learn more about what environment variables were set by the ml command

ml show ABINIT/9.6.2-cpeGNU-21.11
#which reveals that
# /pdc/software/21.11/eb/software/ABINIT/9.6.2-cpeGNU-21.11/bin
# was appended to the PATH

In order to set up the simulation for SrVO3 we need an abi input file and a set of pseudopotentials for the chemical elements. These are contained in the ABINIT 9.6.2 release

Download and extract the ABINIT 9.6.2 release

mkdir ABINIT
cd ABINIT
wget https://www.abinit.org/sites/default/files/packages/abinit-9.6.2.tar.gz
tar xf abinit-9.6.2.tar.gz
# where the files and directories needed for this example are
abinit-9.6.2/tests/tutoparal/Input/tdmft_1.abi
abinit-9.6.2/tests/Psps_for_tests/

In order to run the calculation as a batch job on two nodes, prepare a jobscriptabinit.sh where the your-project-account should be an active compute project, and Psps_for_tests should be the path to the pseudopotentials.

#!/bin/bash -l
# time allocation
#SBATCH -A <your-project-account>
# name of this job
#SBATCH -J abinit-job
# wall time for this job
#SBATCH -t 00:30:00
# number of nodes
#SBATCH --nodes=2
# The partition
#SBATCH -p main
# number of MPI processes per node
#SBATCH --ntasks-per-node=128

ml PDC/21.11
ml ABINIT/9.6.2-cpeGNU-21.11

export ABI_PSPDIR=<Psps_for_tests>

echo "Script initiated at `date` on `hostname`"
srun -n 256 abinit tdmft_1.abi > out.log
echo "Script finished at `date` on `hostname`"

The batch job is submitted to the job queue with the sbatch command

sbatch jobscriptabinit.sh

The status of the job (pending in queue, running, etc) can be monitored with the squeue command.

squeue -u $USER

The standard output of the program was directed to the file out.log. We inspect the last 20 lines of the output

tail -n 20 out.log
# which prints
--- !FinalSummary
program: abinit
version: 9.6.2
start_datetime: Fri Nov 26 11:32:57 2021
end_datetime: Fri Nov 26 11:33:07 2021
overall_cpu_time:        2489.9
overall_wall_time:        2632.7
exit_requested_by_user: no
timelimit: 0
pseudos:
    V   : e583d1cc132dd79ce204b31204bd83ed
    Sr  : 02b29cc3441fa9ed5e1433b119e79fbc
    O   : c8ba4c11dba269a1224b8b74498fed92
usepaw: 1
mpi_procs: 256
omp_threads: 1
num_warnings: 1
num_comments: 0
...

Exercise The final summary states one warning. Search in out.log for warning messages. What do they indicate on the matching of hardware requested for the job, and the problem size?

More details on this particular example can be found in the ABINIT tutorial on DFT+DMFT.

References

Dardel HPE Cray EX supercomputer at PDC

PDC Available Software

PDC Support web pages

HPE Cray EX product line

The Cray programming environment (CPE)