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 Table of Contents

How to install split IMAS  

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You can use a different version of Python.

Configuring easybuild 

[config]
prefix=/pfs/work/g2pbloch/imasenv_eb
modules-tool=EnvironmentModulesC
module-syntax=Tcl
[override]
insecure-download=True

Change the prefix to the path where do you want your installation.

Create a secret.txt  file in $HOME/.config/easybuild/ and paste the HTTPS ACCESS TOKEN  into ITER  repo.

Authorization: Bearer <token>

Downloading files

The configuration is located in the file $HOME/.config/easybuild/config.cfg. Set the prefix path to the directory where the installation should be performed. Clone the repository https://gitlab.eufus.psnc.pl/g2pbloch/easybuild-files and  https://gitlab.eufus.psnc.pl/g2pbloch/easybuild-imas-files and  specify the paths to them in the --robot  option.  

installation of DD

start the IMAS installation ( in `easybuild-imas-files`):

eb Data-Dictionary/Data-Dictionary-3.40.1-GCCcore-10.2.0.eb --allow-modules-tool-mismatch --robot=/pfs/work/g2pbloch/test_instruction/easybuild-imas-files:/pfs/work/g2pbloch/test_instruction/eb_files_repo  --http-header-fields-urlpat="^https://git.iter.org::$HOME/.config/easybuild/secret.txt"

Configuring path in IMAS files

After DD installation change path in this line in HLI easyconfigs to your  `{prefix}/software/Data-Dictionary/3.40.1-GCCcore-10.2.0/dd_3.40.1/`:

 preconfigopts = 'export IMAS_VERSION="0.0.0" &&  export IMAS_PREFIX="/pfs/work/g2pbloch/test_instruction/software/Data-Dictionary/3.40.1-GCCcore-10.2.0/dd_3.40.1/" &&' 

In python configuration files IMAS-AL-Python, IMAS-AL-Python-Bindings  you have to change path  to python to $prefix/software/Python/3.8.6-GCCcore-10.2.0/ 

Introduction

EasyBuild is a framework for building and managing software on HPC systems. It automates compiling, installing, and configuring scientific applications while handling dependencies, toolchains, and environment modules.

A key concept is easyconfig files — text-based receipts that define build parameters, dependencies, versions, and toolchains. By using these receipts, EasyBuild installs software along with all its dependencies, ensuring a consistent, reproducible, and optimized HPC software environment.

How it works? The dependency resolution mechanism constructs a full dependency graph for the software package(s) being installed, after which a list of dependencies is composed for which no module is available yet. Each of the retained dependencies will then be built and installed, in the required order as indicated by the dependency graph.

This page shows how to install IMAS ecosystem using EasyBuild. The installation will be performed on the Gateway cluster but it can be done anywhere.

Prerequisites

Before you start, make sure that:

• Easybuild is installed and publicly available via module system

• Easybuild configuration file exists and is properly configured

• IMAS related receipts are downloaded 

• All modules are purged and EasyBuild module is the only module loaded:

  Code Block
  module purge module load EasyBuild

• $EASYCONFIG_PATHS system variable is set to point to all directories with easyconfig files 

• 
  

Downloading easyconfigs

To allow the users to seamlessly switch between EUROfusion and ITER clusters, the environment that is built on the Gateway mimics (to some extent) the one of the ITER SDCC machines. 

To achieve this a receipts from the ITER cluster are utilised to install software on the GW.

Downloading configuration (EB) files

Source SDCC: /work/imas/opt/EasyBuild/ebfiles_repo/ 

rsync -av --delete -e "ssh -J <user>@sdcc-login.iter.org"  <user>@sdcc-login02.iter.org:/work/imas/opt/EasyBuild/ebfiles_repo/ ./iter-receipts/

System variable EASYCONFIGS_PATH

Set system variable EASYCONFIGS_PATH  that points to the directory with receipts

export EASYCONFIGS_PATH=`pwd`/iter-receipts

Installation of software components

Searching for receipts

EasyBuild needs a receipt to install any software component. The following command can be used to look for receipts:

eb --search <software_name> --robot-paths=$EASYCONFIG_PATHS

A <software_name>  could be only part of the name being searched. Additionally EasyBuild search is case insensitive. E.g. "dox"  string can be provided while looking for "Doxygen" 

shell> eb --search dox --robot=$EASYCONFIG_PATHS

== found valid index for /gw/swimas/easybuild/opt/software/EasyBuild/5.0.0/easybuild/easyconfigs, so using it...
 * /afs/eufus.eu/user/g/g2bpalak/work/easybuild/all_iter/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb
 * /afs/eufus.eu/user/g/g2bpalak/work/easybuild/all_iter/Doxygen/Doxygen-1.13.2-GCCcore-13.2.0.eb
...
 * /gw/swimas/easybuild/opt/software/EasyBuild/5.0.0/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb
 * /gw/swimas/easybuild/opt/software/EasyBuild/5.0.0/easybuild/easyconfigs/d/Doxygen/Doxygen-1.11.0-GCCcore-13.3.0.eb  

Usually receipt name uses following syntax:

<software name>-<software version>-<toolchain>-<toolchain version>

e.g.:
Doxygen-1.9.8-GCCcore-13.2.0.eb

Installation

...

Code Block
language bash title IMAS
eb IMAS-AL-Cpp/IMAS-AL-Cpp-5.2.0dev-foss-2020b-DD-3.40.1.eb --allow-modules-tool-mismatch --robot=/pfs/work/g2pbloch/test_instruction/easybuild-imas-files:/pfs/work/g2pbloch/test_instruction/eb_files_repo --http-header-fields-urlpat="^https://git.iter.org::$HOME/.config/easybuild/secret.txt" eb IMAS-AL-Fortran/IMAS-AL-Fortran-5.2.0dev-foss-2020b-DD-3.40.1.eb --allow-modules-tool-mismatch --robot=/pfs/work/g2pbloch/test_instruction/easybuild-imas-files:/pfs/work/g2pbloch/test_instruction/eb_files_repo --http-header-fields-urlpat="^https://git.iter.org::$HOME/.config/easybuild/secret.txt" eb IMAS-AL-Java/IMAS-AL-Java-5.2.0dev-foss-2020b-Java-11-DD-3.40.1.eb --allow-modules-tool-mismatch --robot=/pfs/work/g2pbloch/test_instruction/easybuild-imas-files:/pfs/work/g2pbloch/test_instruction/eb_files_repo --http-header-fields-urlpat="^https://git.iter.org::$HOME/.config/easybuild/secret.txt" eb IMAS-AL-Python/IMAS-AL-Python-5.2.0dev-foss-2020b-DD-3.40.1.eb --allow-modules-tool-mismatch --robot=/pfs/work/g2pbloch/test_instruction/easybuild-imas-files:/pfs/work/g2pbloch/test_instruction/eb_files_repo --http-header-fields-urlpat="^https://git.iter.org::$HOME/.config/easybuild/secret.txt"

How to use IMAS

<receipt name>.eb --robot --robot-paths=$EASYCONFIG_PATHS

e.g.:
eb Doxygen-1.9.8-GCCcore-13.2.0.eb --robot --robot-paths=$EASYCONFIGS_PATHS 

Installation of the 'production' software

To install the 'production' version of the software belonging to IMAS ecosystem, a few extra options have to be added to point out EB to the dedicated public directory /gw/swimas/easybuild  

--prefix='/gw/swimas/easybuild/opt' 
--installpath-modules='/gw/swimas/easybuild/etc'
--ignore-checksums (optional)


# TO BE DISCUSSED: Accessing sources while debugging. Should 'source' directory be public, as well? 

Installation of the IMAS bundle

The IMAS bundle is (usually) provided by ITER and loads all IMAS High Level Interfaces and related modules:

Content of IMAS bundle

IMAS bundle consist of:

• IMAS High Level Interfaces
  
  • IMAS-AL-Cpp 
  • IMAS-AL-Fortran 
  • IMAS-AL-Java 
  • IMAS-AL-Matlab 
  • IMAS-AL-Python 
• Related modules:
  • IDStools 

IMAS bundle receipts

The IMAS bundle receipts name usually contains the 'IMAS' string, Data Dictionary version, date of release and toolchain version, e.g.: IMAS-3.42.0-2024.09-foss-2023b.eb  or IMAS-4.0.0-2024.12-foss-2023b.eb  

Before installation search for a proper IMAS bundle version

shell> eb --search IMAS-3 --robot-paths=$EASYCONFIG_PATHS

== found valid index for /gw/swimas/easybuild/opt/software/EasyBuild/5.0.0/easybuild/easyconfigs, so using it...
...
 * /gss_efgw_work/work/g2bpalak/easybuild/iter-receipts/IMAS/IMAS-3.42.0-2024.08-foss-2023b.eb
 * /gss_efgw_work/work/g2bpalak/easybuild/iter-receipts/IMAS/IMAS-3.42.0-2024.08-intel-2023b.eb
...
 * /gss_efgw_work/work/g2bpalak/easybuild/iter-receipts/IMAS/IMAS-3.42.0-2024.09-foss-2023b.eb
 * /gss_efgw_work/work/g2bpalak/easybuild/iter-receipts/IMAS/IMAS-3.42.0-2024.09-intel-2023b.eb
...
 

Installation

Once the receipt with a proper version of Data Dictionary and toolchain is found, the IMAS bundle can be installed as any other software:

eb <IMAS bundle receipt>.eb --robot --robot-paths=$EASYCONFIG_PATHS 

e.g.:
eb IMAS-3.42.0-2024.08.1-intel-2023b.eb --robot --robot-paths=$EASYCONFIG_PATHS

How to use IMAS

After installation After installtion you can load IMAS  modules i.e:

module use {prefix}/modules/all
module load DataIMAS-AL-Dictionary/Cpp/5.2.0dev-foss-2020b-DD-3.40.1-GCCcore-10.2.0
module load IMAS-AL-Fortran/5.2.0dev-foss-2020b-DD-3.40.1
module load IMAS-AL-PythonJava/5.2.0dev-foss-2020b-Java-11-DD-3.40.1

How it works:

...

module load IMAS-AL-

...

Python/5.2.0dev-foss-2020b-DD-3.40.1

imasenv module

Adding software components to existing installation

• Set  MODULEPATH system variable 

  Code Block
  export MODULEPATH=/gw/swimas/easybuild/etc/all

Useful tips

Installing dependencies as hidden modules

The key feature of the EasyBuild is the ability to install a software component with all its dependencies. Unfortunatlely EasyBuild installs module not only for the requested software but for every dependency as well.

It results with the number of available modules growing with every installation, becoming less and less hard to navigate for the users. 

There are few options to hide modules, unfortunately every of them has its disadvantages, 

• eb - path to EasyBuild configuration file

• --allow-modules-tool-mismatch - flag
• --robot - paths to configuration files
• --http-header-fields-urlpat - secret to downloading files from ITER repo

...

• --hide-deps=<moduleName1>,<moduleName2>,..., <moduleNameN>   option of eb requires for all modules to be explicitly listed

• eb --hide-all-dependencies -  implemented in working branch but PR#3217 has been not merged since 2020
• module-hide <module-name> - Lmod module system command (see documentation). . Modules have to be hide one by one.

Change the default tmp directory

Anchor
tmp_dir_change tmp_dir_change

Easybuild produces a lot of temporary content (logs, intermediate build files, etc)

The default /tmp  dir on the GW offers quite small capacity. Once tmp is full, system cannot work properly.

It is strongly recommended to change the default /tmp  to a directory in $ITMWORK 

tmpdir=$ITMWORK/tmp

export TMP=${tmpdir}
export TEMP=${tmpdir}
export TMPDIR=${tmpdir}

Run a massive builds on the worker nodes

# Run 'interactive' batch job using SLURM 'srun' command
# -p gw                  : 'gw' queue offering the longer walltime than the default 'gwdebug'
# --ntasks-per-node=48   : number of cores requested (1 node provides up to 48 cores)
# --time=48:0:0          : walltime (documentation says that the default walltime in 'gw' queue is 48h but not explicitly specified is set to 1h - To Be Checked)
# --x11                  : X11 forwarding (optional)
# --pty /bin/bash        : pseudoterminal

bash> srun -p gw --ntasks-per-node=48 --time=48:0:0 --pty /bin/bash

Once resources are allocated, a new shell opens on the working node usually reporting file system error:

bash: /afs/eufus.eu/user/g/g2<user>/.bashrc: Permission denied

It means that the Kerberos token should be set/renewed, to allow access to the filesystem:

bash> kinit; aklog

Now .bash_profile  could be 'sourced' to enable user's startup settings:

bash> source .bash_profile

Now EasyBuild can be used to build a software.

Increasing the length of error/warning message

Easybuild shows only the first 300 characters of error/warning message and cuts (usually the most interesting) remaining part of the message.

The message length value is hardcoded and can be change only by 'hacking' the EB codes:

1. Open <easybuild virtual env>/lib/python3.10/site-packages/easybuild/framework/easyblock.py 
2. Look for value "300" (line 4295 in EB version 4.9.4) 

   Code Block
   title easyblock.py
   except EasyBuildError as err:         first_n = 300 # <=== HERE is the limit hardcoded         errormsg = "build failed (first %d chars): %s" % (first_n, err.msg[:first_n])         _log.warning(errormsg)         result = False

3. Increase the limit to bigger value (e.g. 3000) or remove the message cutting err.msg[:first_n])  ==> err.msg 
4. Save the file    

Other

• If you have compilation problems try adding the --parallel=1  option
• If you have problem with Perl : 

  Code Block

  make[1]: Entering directory `/afs/gw/swimas/easybuild/opt/build/Perl/5.38.0/GCCcore-13.2.0/perl-5.38.0/utils' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/afs/gw/swimas/easybuild/opt/build/Perl/5.38.0/GCCcore-13.2.0/perl-5.38.0/utils' Everything is up to date. Type 'make test' to run test suite. ./perl -Ilib -I. installperl --destdir= mkdir /afs/.gw: Read-only file system at ./install_lib.pl line 146. make: *** [install-all] Error 30 (at easybuild/tools/run.py:682 in parse_cmd_output)

  The reason may be the installation path starting with /afs . Try changing it.
• If you have problem with cairo  and old ttx you can link old ttx  to /usr/bin/true .
• Problem with IMAS modules → change easyblock to Bundle