[easybuild] live stream (YouTube) for EasyBuild User Meeting (23-25 April 2024)

[Kenneth Hoste]

Dear EasyBuilders,

If you didn't register for the EasyBuild User Meeting this week, you can 
still (virtually) attend the talks you are interested in via the live 
stream in the EasyBuild YouTube channel.


A playlist with all scheduled talks is available at 
https://www.youtube.com/playlist?list=PLhnGtSmEGEQild9FmlP8Qmz9Csc_gOJKF


Full agenda of EUM'24 is available at https://easybuild.io/eum24/#program

If you have any questions for the speakers, you can raise them via the 
#eum channel in the EasyBuild Slack (join via 
https://easybuild.io/join-slack).




regards,

Kenneth

Re: [easybuild] 7th EasyBuild User Survey (please participate, help us reach at least 100 participants)

[Kenneth Hoste]

Dear EasyBuilders,

Since we haven't reached 100 participants yet, I would like to do one 
more (final) call.


Help us get a good view on the EasyBuild community by participating in 
the annual EasyBuild User Survey:


https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74


Please consider asking friends & colleagues to also participate!

The survey results will be discussed during my "EasyBuild: State of the 
Union" talk at the upcoming EasyBuild User Survey.



regards,

Kenneth


On 02/04/2024 10:47, Kenneth Hoste wrote:

Dear EasyBuilders,

This is another (hopefully last) reminder to participate in the 7th 
EasyBuild User Survey:


 https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74>> 

Please take ~15min to fill out the survey and provide valuable insights 
into how you are using EasyBuild.


With your participation, we can once again break the magic threshold of 
100 participants!


We will close the survey at the end of this week, so please participate 
ASAP!



regards,

Kenneth


On 18/03/2024 09:55, Kenneth Hoste wrote:

Dear EasyBuilders,

This is a friendly reminder to participate in the 7th EasyBuild User 
Survey.


 => 
https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74 <=


The survey results give us valuable insight in how EasyBuild is used 
throughout the community, and it shouldn't take you more time than it 
does to drink a cup of coffee or tea...


The survey will close on 31 March 2024.

In recent previous surveys we had over 100 participants, it would be 
nice to achieve that again (currently we have 50 participants).



regards,

Kenneth

On 04/03/2024 11:18, Kenneth Hoste wrote:

Dear EasyBuilders,

By annual tradition, we are doing a survey to get a better view on 
the EasyBuild community.


This is the 7th time we are doing the EasyBuild User Survey, and it 
would be great if you are willing to participate (again)!



Please take ~15 min of your time to fill it out:

 https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74 In addition, 
please consider sharing the survey link with friends or colleagues who you know 
are using EasyBuild but may not be subscribed to this mailing list.
It would be great if we could (again) have more responses than last 
time (118 for 6th EasyBuild User Survey that was held in March 2023)...


This survey will be closed on Sun 31 March 2024.

Results will be made public shortly after it is closed, and will also 
be discussed during my "EasyBuild" State of the Union" talk at the 
next EasyBuild User Meeting 
(https://easybuild.io/eum The results of previous surveys are available via https://docs.easybuild.io/user-survey .



regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.9.1

[Kenneth Hoste]

Dear EasyBuilders,

We're pleased to announce the release of EasyBuild v4.9.1 [1].

We had to bump the version for this one, because it's the best EasyBuild 
release so far!


EasyBuild v4.9.1 is primarily a bugfix & update release, but it also 
includes various enhancements.



The executive summary for this release:

  - Support for --from-commit and --include-easyblocks-from-commit;

  - 1 new sofware-specific easyblocks for DualSPHysics;

  - Support for installing 101 (!) new software applications, tools, 
and libraries;


  - Easyconfigs for various recent software versions, including CuPy 
13.0.0, Gurobi 11.0.0, OCaml 4.14.0, OpenFOAM v2312, ParaView-5.12.0, R 
4.3.3, R-bundle-Bioconductor 3.18, WIEN2k 23.2, and many more;


  - Fixes/changes to easyblocks/easyconfigs that require 
reinstallation, including for GCC, OpenMPI, and Python (more info below);



Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.9.1)



## Highlighted enhancements & updates

[enhancements or updates that (may) warrant updating existing 
installations are marked with (***)]


- new software-specific easyblock for DualSPHysics;

- enhancement to generic easyblocks: Conda, GoPackage, PerlModule, 
PythonPackage;


- updated & enhancements to custom easyblocks for Clang-AOMP, GCC, 
Gurobi, LAMMPS, MCR, OCaml, OpenSSL wrapper, PyTorch, VEP, WIEN2k;


- (***) significant improvements to QuantumESPRESSO easyblock, incl. 
running the test suite;


- enhancements to GCC easyblock and additional patch for recent GCC 
versions to support installation on RISC-V systems;


- (***) add extensions to R-bundle-CRAN v2023.12 (use '--rebuild --skip' 
[3]);


- (***) add support for Vulkan software rendering in Mesa v23.1.9 by 
adding Wayland dependency;


- (***) add MODIStsp extension (+ required dependencies) to R 4.2.2 (use 
'--rebuild --skip' [3]);



## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant re-installing easyconfigs are 
marked with (***)]


- bug fixes for generic easyblocks: Cargo, CMakeMake,

- bug fixes in custom easyblocks for BerkeleyGW, Clang, LAMMPS, LibInt, 
NVHPC, OpenFOAM, OpenMPI, PETSc, Python, PyTorch, QuantumESPRESSO, R, 
SLEPc, torchvision;


- (***) fix link order in PETSc easyblock for SCOTCH >= 7.x;

- (***) do not rename GCC's include-fixed directory by default + add 
script to regenerate it;
  Re-installing GCC 13.2.0 is required to ensure compatibility with 
CUDA 12.4.0, see easyblocks PR #3254 for more info.


- (***) add patch for adding a write memory barrier to all OpenMPI 4.1.x 
easyconfigs, to bug in smcuda component;

  We recommend re-installing OpenMPI 4.1.x to pick up this fix.

- (***) add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 
13.2.0 for ARM architectures with SVE support;


- (***) add patch for GCCcore 13.2.0 to fix unguarded use of 
is_convertible builtin;


- add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 
13.x easyconfigs;


- (***) move setuptools_scm extension from hatchling to Python easyconfig;
  We strongly recommend to install the missing extensions for 
Python/3.11.3-GCCcore-12.3.0 and Python/3.11.3-GCCcore-12.3.0 using "eb 
--rebuid --skip" (or the reinstall these modules) [3].


- add patches for PyTorch v2.1.2 to fix test failures;

- add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+;

- (***) add missing zlib + OpenSSL deps to Ruby easyconfigs + promote 
binutils to runtime dependency;



## Supported software

Support for installing 101 (!) new software packages has been added, 
including (but not limited to):


  AMICA
  Circlator
  Clarabel.rs
  DeepLoc
  devbio-napari
  EpiSCORE
  ExtremeLy
  GenomeComb
  GRASP-suite
  IDG
  IonQuant
  libspectre
  MLflow
  MSFragger
  noise
  PAGAN2
  phyluce
  python-casacore
  QuPath
  RHEIA
  SemiBin
  Sentence-Transformers
  SQLAlchemy
  Vamb
  zUMIs

  => This brings the total number of supported software packages to 
3,470 (excluding extensions)!

 An up-to-date list of supported software is available at [4].


Various software updates have been added, including (but not limited to):

  anvio 8
  arrow-R 14.0.0.2
  BerkeleyGW 3.1.0 + 4.0
  Cartopy 0.22.0
  Clang-Python-bindings 16.0.6
  CUDA 12.3.2 + 12.4.0
  CuPy 13.0.0
  CVXPY 1.4.2
  DeepLabCut 2.3.6
  EggLib 3.3.0
  ESMF 8.4.2
  FDS 6.8.0
  Flask 3.0.0
  FLINT 3.1.1
  GATK 4.5.0.0
  GLFW 3.4
  GROMACS 2024.1
  Gurobi 11.0.0
  HeFFTe 2.4.0
  LAMMPS 2Aug2023_update2
  likwid 5.3.0
  matplotlib 3.8.2
  medaka 1.11.3
  MOABB 1.0.0
  MONAI 1.3.0
  NCCL 2.20.5
  NGSpeciesID 0.3.0
  NLTK 3.8.1
  NVHPC 24.1
  OCaml 4.14.0
  ONNX 1.15.0
  OpenFOAM v2306 + v2312
  OpenSSL/3 (wrapper)
  PAPI 7.1.0
  ParaView 5.12.0
  PETSc 3.20.3
  plotly.py 5.18.0
  PyQt5 5.15.10
  

Re: [easybuild] 7th EasyBuild User Survey (please participate, closes soon!)

[Kenneth Hoste]

Dear EasyBuilders,

This is another (hopefully last) reminder to participate in the 7th 
EasyBuild User Survey:


https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74


Please take ~15min to fill out the survey and provide valuable insights 
into how you are using EasyBuild.


With your participation, we can once again break the magic threshold of 
100 participants!


We will close the survey at the end of this week, so please participate 
ASAP!



regards,

Kenneth


On 18/03/2024 09:55, Kenneth Hoste wrote:

Dear EasyBuilders,

This is a friendly reminder to participate in the 7th EasyBuild User 
Survey.


 =>  
https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74 <=


The survey results give us valuable insight in how EasyBuild is used 
throughout the community, and it shouldn't take you more time than it 
does to drink a cup of coffee or tea...


The survey will close on 31 March 2024.

In recent previous surveys we had over 100 participants, it would be 
nice to achieve that again (currently we have 50 participants).



regards,

Kenneth

On 04/03/2024 11:18, Kenneth Hoste wrote:

Dear EasyBuilders,

By annual tradition, we are doing a survey to get a better view on the 
EasyBuild community.


This is the 7th time we are doing the EasyBuild User Survey, and it 
would be great if you are willing to participate (again)!



Please take ~15 min of your time to fill it out:

 https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74>>> In addition, please consider sharing the survey link with friends or 
colleagues who you know are using EasyBuild but may not be subscribed 
to this mailing list.
It would be great if we could (again) have more responses than last 
time (118 for 6th EasyBuild User Survey that was held in March 2023)...


This survey will be closed on Sun 31 March 2024.

Results will be made public shortly after it is closed, and will also 
be discussed during my "EasyBuild" State of the Union" talk at the 
next EasyBuild User Meeting 
(https://easybuild.io/eum The results of previous surveys are available via https://docs.easybuild.io/user-survey .



regards,

Kenneth

[easybuild] Re: [eum] 9th EasyBuild User Meeting (EUM'24) - Tue-Thu 23-25 April 2024 in Umeå (Sweden)

[Kenneth Hoste]

Dear EasyBuilders,

The agenda for EUM'24 is now complete, see 
https://easybuild.io/eum24/#program .


The registration deadline has been extended to Wed 10 April 2024.

If you plan to attend EUM'24, do make sure you are registered ASAP!

https://event.ugent.be/registration/eum24


regards,

Kenneth

On 29/02/2024 10:40, Kenneth Hoste wrote:

Dear EasyBuilders,

The preliminary (incomplete) program for EUM'24 is now available at 
https://easybuild.io/eum24/#program .


Do not forget to register your attendance, in particular if you are 
planning to join in-person in Umeå.


We still have several open slots (~30min each) for people who would like 
to present how they are using EasyBuild (or EESSI) at their site, or for 
talks on topics loosely related to EasyBuild/EESSI or scientific 
software in general.


Suggestions for speakers/talks/topics are still welcome!

For questions, please reply to this message, or contact the organisers 
via e...@lists.ugent.be .



regards,

Kenneth

On 15/01/2024 17:40, Kenneth Hoste wrote:

Dear EasyBuilders,

We're pleased to announce that the registration for the 9th annual 
EasyBuild User Meeting (EUM'24) is now open.


** Event page **

https://easybuild.io/eum24>>> ** Venue & dates **

Umeå University, Sweden
Tue 23 - Thu 25 April 2024


** Organization **


Åke Sandgren (Umeå University, Sweden)
Lars Viklund (Umeå University, Sweden)
Lara Peeters (HPC-UGent, Belgium)
Kenneth Hoste (HPC-UGent, Belgium)


** Registration **

Attendance is free, but registration is required for practical purposes.

 https://event.ugent.be/registration/eum24

Registration closes on Sun 31 March 2024.


** Agenda **

The agenda is currently still fairly empty, but is actively being 
worked out. We will gradually extend it in the coming days and weeks.


We intend to focus on the various aspects of the EESSI project 
(https://eessi.io/ on Thu 25 April.


If you have a suggestion for a talk, presenter, or topic (e.g. a 
tutorial on a particular topic), please contact the EUM'24 organisers 
via e...@lists.ugent.be, or via the EasyBuild or EESSI Slack.


Likewise, if you would like to give a talk yourself about your 
experiences with EasyBuild or EESSI, or about other tools or topics 
somewhat related to these projects, please contact the EUM'24 organisers.


For more information, please consult 
https://easybuild.io/eum24 .



** Question & suggestions **

For questions or suggestions related to the EasyBuild User Meeting, 
please email e...@lists.ugent.be, or contact one of the organisers in 
the EasyBuild or EESSI Slack.



regards,

Åke, Lars, Lara, Kenneth
EUM'24 organisers

[easybuild] next EasyBuild conf call: Wed 27 Mar 2024 (*today*) at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for today Wed 27 Mar 2024 at
09:00 UTC (16:00 CET), and will be hosted by Alex.

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] 7th EasyBuild User Survey (please participate!)

[Kenneth Hoste]

Dear EasyBuilders,

This is a friendly reminder to participate in the 7th EasyBuild User Survey.

=>  https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74  <=

The survey results give us valuable insight in how EasyBuild is used 
throughout the community, and it shouldn't take you more time than it 
does to drink a cup of coffee or tea...


The survey will close on 31 March 2024.

In recent previous surveys we had over 100 participants, it would be 
nice to achieve that again (currently we have 50 participants).



regards,

Kenneth

On 04/03/2024 11:18, Kenneth Hoste wrote:

Dear EasyBuilders,

By annual tradition, we are doing a survey to get a better view on the 
EasyBuild community.


This is the 7th time we are doing the EasyBuild User Survey, and it 
would be great if you are willing to participate (again)!



Please take ~15 min of your time to fill it out:

 https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74>> 

In addition, please consider sharing the survey link with friends or 
colleagues who you know are using EasyBuild but may not be subscribed to 
this mailing list.
It would be great if we could (again) have more responses than last time 
(118 for 6th EasyBuild User Survey that was held in March 2023)...


This survey will be closed on Sun 31 March 2024.

Results will be made public shortly after it is closed, and will also be 
discussed during my "EasyBuild" State of the Union" talk at the next 
EasyBuild User Meeting 
(https://easybuild.io/eum>> 
The results of previous surveys are available via 
https://docs.easybuild.io/user-survey .



regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 13 Mar 2024 (*today*) at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for today Wed 13 Mar 2024 at
16:00 UTC (17:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] 7th EasyBuild User Survey (please participate!)

[Kenneth Hoste]

Dear EasyBuilders,

By annual tradition, we are doing a survey to get a better view on the 
EasyBuild community.


This is the 7th time we are doing the EasyBuild User Survey, and it 
would be great if you are willing to participate (again)!



Please take ~15 min of your time to fill it out:

https://ugent.qualtrics.com/jfe/form/SV_2gHTeURk1MKBG74


In addition, please consider sharing the survey link with friends or 
colleagues who you know are using EasyBuild but may not be subscribed to 
this mailing list.
It would be great if we could (again) have more responses than last time 
(118 for 6th EasyBuild User Survey that was held in March 2023)...


This survey will be closed on Sun 31 March 2024.

Results will be made public shortly after it is closed, and will also be 
discussed during my "EasyBuild" State of the Union" talk at the next 
EasyBuild User Meeting (https://easybuild.io/eum).


The results of previous surveys are available via 
https://docs.easybuild.io/user-survey .



regards,

Kenneth

[easybuild] Re: [eum] 9th EasyBuild User Meeting (EUM'24) - Tue-Thu 23-25 April 2024 in Umeå (Sweden)

[Kenneth Hoste]

Dear EasyBuilders,

The preliminary (incomplete) program for EUM'24 is now available at 
https://easybuild.io/eum24/#program .


Do not forget to register your attendance, in particular if you are 
planning to join in-person in Umeå.


We still have several open slots (~30min each) for people who would like 
to present how they are using EasyBuild (or EESSI) at their site, or for 
talks on topics loosely related to EasyBuild/EESSI or scientific 
software in general.


Suggestions for speakers/talks/topics are still welcome!

For questions, please reply to this message, or contact the organisers 
via e...@lists.ugent.be .



regards,

Kenneth

On 15/01/2024 17:40, Kenneth Hoste wrote:

Dear EasyBuilders,

We're pleased to announce that the registration for the 9th annual 
EasyBuild User Meeting (EUM'24) is now open.


** Event page **

https://easybuild.io/eum24>> 


** Venue & dates **

Umeå University, Sweden
Tue 23 - Thu 25 April 2024


** Organization **


Åke Sandgren (Umeå University, Sweden)
Lars Viklund (Umeå University, Sweden)
Lara Peeters (HPC-UGent, Belgium)
Kenneth Hoste (HPC-UGent, Belgium)


** Registration **

Attendance is free, but registration is required for practical purposes.

 https://event.ugent.be/registration/eum24

Registration closes on Sun 31 March 2024.


** Agenda **

The agenda is currently still fairly empty, but is actively being worked 
out. We will gradually extend it in the coming days and weeks.


We intend to focus on the various aspects of the EESSI project 
(https://eessi.io/ on Thu 25 April.


If you have a suggestion for a talk, presenter, or topic (e.g. a 
tutorial on a particular topic), please contact the EUM'24 organisers 
via e...@lists.ugent.be, or via the EasyBuild or EESSI Slack.


Likewise, if you would like to give a talk yourself about your 
experiences with EasyBuild or EESSI, or about other tools or topics 
somewhat related to these projects, please contact the EUM'24 organisers.


For more information, please consult 
https://easybuild.io/eum24 .



** Question & suggestions **

For questions or suggestions related to the EasyBuild User Meeting, 
please email e...@lists.ugent.be, or contact one of the organisers in the 
EasyBuild or EESSI Slack.



regards,

Åke, Lars, Lara, Kenneth
EUM'24 organisers

Re: [easybuild] next EasyBuild conf call: Wed 28 Feb 2024 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Notes for today's call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20240228


Next call is scheduled for Wed 13 Mar 2024 at 16:00 UTC (17:00 CET), see 
also https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 27/02/2024 21:35, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 28 Feb 2024 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 28 Feb 2024 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 28 Feb 2024 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] EasyBuild conf call was today Wed 14 Feb 2024 at 16:00 UTC

[Kenneth Hoste]

Dear EasyBuilders,

I somehow forgot to send a timely reminder to this mailing list about 
today's EasyBuild conf call, my apologies for that.


Maybe I was distracted by all the Valentine's shenanigans...
(a man has to find an excuse, no?)

Notes for today's call are now available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20240214 
.



The next EasyBuild conf call is planned for Wed 28 Feb 2024 at
09:00 UTC (10:00 CET).

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 31 Jan 2024 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20240131 
.


Next call is scheduled for Wed 14 Feb 2024 at 16:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 30/01/2024 21:22, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 31 Jan 2024 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 31 Jan 2024 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 31 Jan 2024 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] Qt5-5.15.5-GCCcore-11.3.0.eb failure: File name too long

[Kenneth Hoste]

Dear Loris,

We've seen this problem before, but it seems like it was caused by a 
long path for the build directory (not the install directory), so it's 
easy to work around, see the discussion at 
https://github.com/easybuilders/easybuild-easyconfigs/pull/11386#issuecomment-700511479



regards,

Kenneth

On 26/01/2024 08:48, Loris Bennett wrote:

Hi,

There is a known problem with Qt5 which can occur when file names
created during the build process become too long:

   https://bugreports.qt.io/browse/QTBUG-59769?focusedCommentId=672710>> 
This seems to be biting me when I try to build


   Qt5-5.15.5-GCCcore-11.3.0.EasyBuild

as I get the following error:

   ninja: error: 
WriteFile(__third_party_blink_renderer_modules_mediacapturefromelement_mediacapturefromelement__jumbo_merge__trinity_shared_easybuild_arch_x86_64_intel_skylake_avx512_build_Qt5_5.15.5_GCCcore-11.3.0_qt-everywhere-src-5.15.5_qtwebengine_src_toolchain_target__rule.rsp):
 Unable to create file. File name too long

I am in the process of setting up architecture-dependent builds, which
will replace the path

   /trinity/shared/easybuild/arch/x86/64/intel/skylake_avx512

with

   /sw/sc/easybuild

which should be sufficient since the longer path above is 256 characters
long, which I suspect is tripping a problem which occurs when the file
name is 255 characters long.

Has any one else had this issue?  Is there another solution other than
simply shortening the path, as I will probably do via
architecture-dependent soft links?

Cheers,

Loris

Re: [easybuild] next EasyBuild conf call: Wed 17 Jan 2024 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders

The notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20240117


Next call is scheduled for Wed 31 Jan 2024 at 09:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 17/01/2024 09:16, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for today, Wed 17 Jan 2024 at
16:00 UTC (17:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Clang-based toolchains;

* supporting OSs with OpenSSL 3.x (like RHEL9);

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 17 Jan 2024 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for today, Wed 17 Jan 2024 at
16:00 UTC (17:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Clang-based toolchains;

* supporting OSs with OpenSSL 3.x (like RHEL9);

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] 9th EasyBuild User Meeting (EUM'24) - Tue-Thu 23-25 April 2024 in Umeå (Sweden)

[Kenneth Hoste]

Dear EasyBuilders,

We're pleased to announce that the registration for the 9th annual 
EasyBuild User Meeting (EUM'24) is now open.


** Event page **

https://easybuild.io/eum24


** Venue & dates **

Umeå University, Sweden
Tue 23 - Thu 25 April 2024


** Organization **


Åke Sandgren (Umeå University, Sweden)
Lars Viklund (Umeå University, Sweden)
Lara Peeters (HPC-UGent, Belgium)
Kenneth Hoste (HPC-UGent, Belgium)


** Registration **

Attendance is free, but registration is required for practical purposes.

https://event.ugent.be/registration/eum24

Registration closes on Sun 31 March 2024.


** Agenda **

The agenda is currently still fairly empty, but is actively being worked 
out. We will gradually extend it in the coming days and weeks.


We intend to focus on the various aspects of the EESSI project 
(https://eessi.io) on Thu 25 April.


If you have a suggestion for a talk, presenter, or topic (e.g. a 
tutorial on a particular topic), please contact the EUM'24 organisers 
via e...@lists.ugent.be, or via the EasyBuild or EESSI Slack.


Likewise, if you would like to give a talk yourself about your 
experiences with EasyBuild or EESSI, or about other tools or topics 
somewhat related to these projects, please contact the EUM'24 organisers.


For more information, please consult https://easybuild.io/eum24 .


** Question & suggestions **

For questions or suggestions related to the EasyBuild User Meeting, 
please email e...@lists.ugent.be, or contact one of the organisers in the 
EasyBuild or EESSI Slack.



regards,

Åke, Lars, Lara, Kenneth
EUM'24 organisers

Re: [easybuild] dorado 0.5.0

[Kenneth Hoste]

Hi all,

I was looking into an update of dorado too, and managed to finally 
puzzle together a working easyconfig for dorado 0.5.1, see 
https://github.com/easybuilders/easybuild-easyconfigs/pull/19489



regards,

Kenneth

On 03/01/2024 13:34, Loris Bennett wrote:

Hi Borut,

Borut Rozman  writes:


Hi everyone,

Has anyone had a chance on building dorado 0.5.0 with foss 2022a and
cuda 11.7? I made it work with binary - cpu only at the moment but
guidance on building it with cuda support would be nice.


Did you (or anyone else) make any progress with this?

Cheers,

Loris

Re: [easybuild] next EasyBuild conf call: Wed 3 Jan 2024 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20240103 
.


Next call is scheduled for Wed 17 Jan 2024 at 16:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 02/01/2024 22:08, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 3 Jan 2024 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 3 Jan 2024 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 3 Jan 2024 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.9.0

[Kenneth Hoste]

Dear EasyBuilders,

We're happy to announce the release of EasyBuild v4.9.0 [1].

This is a the best EasyBuild release to date...
It's a bit late for Christmas, but still in time to serve as a gift for 
New Year!


EasyBuild v4.9.0 is primarily a feature release, mainly because it 
includes the 2023b version of the common toolchains (foss + intel), but 
it also includes various bug fixes, and much more.


The executive summary for this release:

  - improved support for using recent version of Environment Modules as 
modules tool;


  - new generic CargoPythonBundle easyblock;

  - 3 new custom easyblocks: for flook, HPCC, and PALM;

  - easyconfigs for foss/2023b and intel/2023b;

  - Easyconfigs for various recent software versions, including GROMACS 
2023.3, NWChem 7.2.2, Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 
4.3.2, SciPy-bundle 2023.11, Spark 3.5.0, VTK 9.3.0, ...;


  - Support for installing 77 new software applications and libraries;


Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.9.0)



## Highlighted enhancements & updates

[enhancements or updates that (may) warrant updating existing 
installations are marked with (***)]


- add generic CargoPythonBundle easyblock;

- 3 new software-specific easyblocks for flook, HPCC, PALM;

- update easyblocks for intel-compilers, impi, imkl to support latest 
versions;


- update numpy easyblock for v1.26+;

- updates and enhancements to custom easyblocks for Ferret, SuiteSparse;

- add easyconfigs for foss/2023b and intel/2023b (see also [7]);


## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant re-installing easyconfigs are 
marked with (***)]


- fix support for Environment Modules as modules tool to pass unit tests 
with v4.2+;


- adapt module function check for Environment Modules v4+;

- disable LLVM build downloads from CI in Rust;

- update SuiteSparse easyblock to only install SuiteSparse libraries 
with make install;


- fix specifying path to SuiteSparse header files and libraries in 
numpy, Trilinos, PETSc easyblocks;


- add support for allowing version mismatch + consider versionsuffix 
when creating .modulerc in ModuleRC easyblock;


- fix det_pylibdir provided by PythonPackage easyblock for Python 3.12+;

- bug fixes for custom easyblocks for Clang, CUDA, numpy, NWChem, PETSc, 
PyTorch, Rust, SuiteSparse, TensorFlow, Trilinos


- add patch to fix regression in GCC 12.x on AVX512 systems (***);

- add patch for GCC 12.x to fix miscompiling C++ code causing 
double-free in case of exceptions (***);


- add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 
through 0.3.23;


- fix OpenBLAS 0.3.20+ on newer Intel CPUs;

- add patch to fix [cz]asums in OpenBLAS 0.3.24 (***);

- add patch to work around potential crash in PyTorch 1.13.1 caused by 
GCC 12 compiler bug (***);


- change toolchain in json-fortran easyconfigs to GCC, since it includes 
Fortran modules (***);


- use GCC toolchain in kim-api, since it includes Fortran modules (***);

- allow ITK legacy code and Python wrappers in ITK v5.2.1 (***);


## Supported software

Support for installing 77 new software packages has been added, 
including (but not limited to):


  BRiAl
  CellBender
  DIA-NN
  EUKulele
  FACE
  GFF3-toolkit
  HPCC
  iperf
  LoopTools
  MitoHiFi
  PFFT
  PySINDy
  R-bundle-CRAN
  scikit-lego
  SEACells
  solo
  Triton
  waLBerla

  => This brings the total number of supported software packages to 
3,369 (excluding extensions)!

 An up-to-date list of supported software is available at [4].


Various software updates have been added, including (but not limited to):

  Arrow 14.0.1
  Boost 1.83.0
  CellRanger 7.2.0
  CUDA 12.3.0
  f90wrap 0.2.11
  FPM 1.15.1
  GPyTorch 1.10
  GROMACS 2023.3
  ITK 5.3.0,
  LinBox 1.7.0
  magma 2.7.2,
  Molden 7.3
  NWChem 7.2.2
  phonopy 2.20.0
  PostgreSQL 16.1,
  Python-bundle-PyPI 2023.10
  PyTorch 2.1.2
  R 4.3.2
  SciPy-bundle 2023.11
  Seurat 4.4.0
  Spark 3.5.0
  SuiteSparse 7.1.0
  UCX-CUDA 1.15.0
  VTK 9.3.0
  XGBoost 2.0.2


These changes result from various contributions, made by 34 different 
contributors:


* 21 merged pull requests for EasyBuild framework
* 26 merged pull requests for easyblocks
* 276 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.9.0, there are several options [5].
Two particularly easy options include:

     * eb --install-latest-eb-release

     * eb --from-pr 19464  # use easyconfig from PR #19464 [6]


Enjoy!


regards,

Kenneth & Sebastian


[1] https://pypi.org/project/easybuild/4.9.0
[2] https://docs.easybuild.io/release-notes/#release_notes_eb490
[3] 

Re: [easybuild] next EasyBuild conf call: Wed 20 Dec 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20231220 
.


This was the last conf call for 2023, enjoy the Christmas holiday 
season, and see you in 2024!


Next call is scheduled for Wed 3 Jan 2024 at 09:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls .



regards,

Kenneth

On 20/12/2023 16:08, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for *today* Wed 20 Dec 2023 at
16:00 UTC (17:00 CET).

My apologies for the (very) late reminder...

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 20 Dec 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for *today* Wed 20 Dec 2023 at
16:00 UTC (17:00 CET).

My apologies for the (very) late reminder...

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 6 Dec 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20231206


Last conf call for this year is scheduled at Wed 20 Ded 2023 at 16:00 
UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 06/12/2023 08:01, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 8 Nov 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 6 Dec 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 8 Nov 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] "Streaming Optimised Scientific Software: an Introduction to EESSI" on Tue 5 Dec 2023 (14:30-16:30 CET, online)

[Kenneth Hoste]

Dear EasyBuilders,

Registration for this talk covering the EESSI project (https://eessi.io) 
in detail on Tue 5 Dec'23 is still open


https://event.ugent.be/registration/eurohpcncceessi202312


This event is organised in the context of the MultiXscale EuroHPC 
Centre-of-Excellence (https://www.multixscale.eu).



regards,

Kenneth

On 21/11/2023 09:33, Kenneth Hoste wrote:

Dear EasyBuilders,

On Tuesday 5 December 2023 (14:30-16:00 CET) there will be an online 
presentation on EESSI 
(https://eessi.io/ entitled "Streaming Optimised Scientific Software: an Introduction to EESSI", which is being organised in the context of the MultiXscale EuroHPC Centre-of-Excellence (https://www.multixscale.eu/ but open to anyone who's interested.



If you would like to attend this session, please register via:

     https://event.ugent.be/registration/eurohpcncceessi202312

(note: this is a different event from the "Best Practices for CernVM-FS 
in HPC" tutorial on Mon 4 Dec'23, see 
https://event.ugent.be/registration/cvmfshpc202312)



Have you ever wished that all the scientific software you use was 
available on all the resources you had access to, without having to go 
through the pain of getting them installed the way you want/need?


The European Environment for Scientific Software Installations (EESSI, 
pronounced "easy") is a common stack of scientific software 
installations for HPC systems and beyond, including laptops, personal 
workstations and cloud infrastructure. In many ways it works like a 
streaming service for scientific software, instantly giving you the 
software you need, when you need it, and compiled to work efficiently 
for the architecture you have access to.


In this talk, we'll explain what EESSI is, how it is being designed, how 
to get access to it, and how to use it.
We'll give a number of demonstrations and also give access to a resource 
where you can try EESSI out for yourself.



Please help us promote this event, by sharing it with colleagues and 
friends, and/or posting this event announcement on appropriate channels.



regards,

Kenneth

Re: [easybuild] "Best Practices for CernVM-FS in HPC" online tutorial on Mon 4 Dec 2023 (13:30-17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

It’s not too late to register for the online introductory tutorial on 
CernVM-FS (https://cernvm.cern.ch/fs) on Mon 4 Dec'23, but you better do 
it soon...


Over 150 people have registered so far!

  https://event.ugent.be/registration/cvmfshpc202312


This events is organised in the context of the MultiXscale EuroHPC 
Centre-of-Excellence (https://www.multixscale.eu).



regards,

Kenneth

On 13/11/2023 16:53, Kenneth Hoste wrote:

Dear EasyBuilders,

All 50 seats that were available initially for this event were filled in 
a couple of hours, we have added way more seats now, so if you tried to 
register earlier today but couldn’t, you can now try again!


regards,

Kenneth

On 13/11/2023 09:04, Kenneth Hoste wrote:

Dear EasyBuilders,

On Monday 4 December 2023 (13:30-17:00 CET) we are organising a 
half-day online introductory tutorial on CernVM-FS 
(https://cernvm.cern.ch/fs via Zoom, in collaboration with the CernVM-FS development team.


CernVM-FS, the CernVM File System (also known as CVMFS), is a file 
distribution service that is particularly well suited to distribute 
software installations across a large number of systems world-wide in 
an efficient way.


The focus of this tutorial is on explaining what CernVM-FS is, how to 
access existing CernVM-FS repositories (like EESSI, see 
https://eessi.io/docs and covering some aspects specific to using CernVM-FS on HPC systems.
It is intended for people with a background in HPC (system 
administrators, support team members, end users, etc.) who are new to 
CernVM-FS: no specific prior knowledge or experience with it is required.


High-level preliminary agenda (subject to minor changes):

- What is CernVM-FS?
- European Environment for Scientific Software Installations (EESSI)
- Accessing a CernVM-FS repository
- Configuring CernVM-FS on HPC infrastructure
- Troubleshooting and debugging CernVM-FS
- Performance aspects of CernVM-FS
- Different storage backends for CernVM-FS
- Containers and CernVM-FS
- Getting started with CernVM-FS (from scratch)

If you would like to attend this tutorial, please register via:

 https://event.ugent.be/registration/cvmfshpc202312


Please help us promote this event, by sharing it with colleagues and 
friends, and/or posting this event announcement on appropriate channels.



regards,

Kenneth
on behalf of the tutorial organisers

Re: [easybuild] next EasyBuild conf call: Wed 22 Nov 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20231122 
.


Next conf call is planned for Wed 6 Dec 2023 at 09:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 21/11/2023 22:34, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 22 Nov 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 22 Nov 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 22 Nov 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] "Best Practices for CernVM-FS in HPC" online tutorial on Mon 4 Dec 2023 (13:30-17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

All 50 seats that were available initially for this event were filled in 
a couple of hours, we have added way more seats now, so if you tried to 
register earlier today but couldn’t, you can now try again!


regards,

Kenneth

On 13/11/2023 09:04, Kenneth Hoste wrote:

Dear EasyBuilders,

On Monday 4 December 2023 (13:30-17:00 CET) we are organising a half-day 
online introductory tutorial on CernVM-FS 
(https://cernvm.cern.ch/fs via Zoom, in collaboration with the CernVM-FS development team.


CernVM-FS, the CernVM File System (also known as CVMFS), is a file 
distribution service that is particularly well suited to distribute 
software installations across a large number of systems world-wide in an 
efficient way.


The focus of this tutorial is on explaining what CernVM-FS is, how to 
access existing CernVM-FS repositories (like EESSI, see 
https://eessi.io/docs and covering some aspects specific to using CernVM-FS on HPC systems.
It is intended for people with a background in HPC (system 
administrators, support team members, end users, etc.) who are new to 
CernVM-FS: no specific prior knowledge or experience with it is required.


High-level preliminary agenda (subject to minor changes):

- What is CernVM-FS?
- European Environment for Scientific Software Installations (EESSI)
- Accessing a CernVM-FS repository
- Configuring CernVM-FS on HPC infrastructure
- Troubleshooting and debugging CernVM-FS
- Performance aspects of CernVM-FS
- Different storage backends for CernVM-FS
- Containers and CernVM-FS
- Getting started with CernVM-FS (from scratch)

If you would like to attend this tutorial, please register via:

 https://event.ugent.be/registration/cvmfshpc202312


Please help us promote this event, by sharing it with colleagues and 
friends, and/or posting this event announcement on appropriate channels.



regards,

Kenneth
on behalf of the tutorial organisers

[easybuild] "Best Practices for CernVM-FS in HPC" online tutorial on Mon 4 Dec 2023 (13:30-17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

On Monday 4 December 2023 (13:30-17:00 CET) we are organising a half-day 
online introductory tutorial on CernVM-FS (https://cernvm.cern.ch/fs), 
via Zoom, in collaboration with the CernVM-FS development team.


CernVM-FS, the CernVM File System (also known as CVMFS), is a file 
distribution service that is particularly well suited to distribute 
software installations across a large number of systems world-wide in an 
efficient way.


The focus of this tutorial is on explaining what CernVM-FS is, how to 
access existing CernVM-FS repositories (like EESSI, see 
https://eessi.io/docs), and covering some aspects specific to using 
CernVM-FS on HPC systems.
It is intended for people with a background in HPC (system 
administrators, support team members, end users, etc.) who are new to 
CernVM-FS: no specific prior knowledge or experience with it is required.


High-level preliminary agenda (subject to minor changes):

- What is CernVM-FS?
- European Environment for Scientific Software Installations (EESSI)
- Accessing a CernVM-FS repository
- Configuring CernVM-FS on HPC infrastructure
- Troubleshooting and debugging CernVM-FS
- Performance aspects of CernVM-FS
- Different storage backends for CernVM-FS
- Containers and CernVM-FS
- Getting started with CernVM-FS (from scratch)

If you would like to attend this tutorial, please register via:

https://event.ugent.be/registration/cvmfshpc202312


Please help us promote this event, by sharing it with colleagues and 
friends, and/or posting this event announcement on appropriate channels.



regards,

Kenneth
on behalf of the tutorial organisers

[easybuild] HPC, Big Data, and Data Science Devroom at FOSDEM'24

[Kenneth Hoste]

HPC, Big Data, and Data Science Devroom at FOSDEM'24


https://hpc-bigdata-fosdem24.github.io - https://fosdem.org/2024

** Call for Participation **

Submission deadline: Friday 1 Dec 2023
Devroom date: Sat 3 Feb 2024


We are proud to announce the 9th edition of the HPC, Big Data and Data 
Science devroom at FOSDEM 2024 in Brussels (Belgium).


It is organised by representatives of the HPC, Big Data, and Data 
Science communities, who are joining forces to bring them together.


The devroom will take place during the FOSDEM'24 weekend, on Saturday 3 
February 2024, and is open for everybody to join (no registration required).


Join us to enjoy a variety of talks, demos and interesting discussions 
on open-source HPC, Big Data, and Data Science.



Sounds interesting? Submit your talk proposal, and see you at FOSDEM'24!

Submissions are light weight: basically talk title + short description, 
plain text.



Please visit the website for more information, and consider sharing this 
call for participation with friends and colleagues.


Contact us via email at hpc-bigdata-devr...@lists.fosdem.org with 
questions or concerns, or via @fosdem_hpc on Twitter/X.


--

Kenneth Hoste - HPC team at Ghent University, Belgium
Adam Huffman - Big Data Institute, University of Oxford, UK

Re: [easybuild] next EasyBuild conf call: Wed 8 Nov 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20231108 



Next conf call is planned for Wed 22 Nov at 16:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 07/11/2023 21:37, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 8 Nov 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 8 Nov 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 8 Nov 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.8.2

[Kenneth Hoste]

Dear EasyBuilders,

It's our pleasure to announce the release of EasyBuild v4.8.2 [1].

After extensive discussions at PackagingCon'23 in Berlin last week, we 
can now safely state that this is the best EasyBuild release to date, 
since it has been verified by a panel of experts in the matter.



EasyBuild v4.8.2 is primarily a bugfix and update release, but it also 
includes various enhancements.


The executive summary for this release:

  - Various small enhancements and bug fixes in EasyBuild framework, 
easyblocks, and easyconfigs;


  - Easyconfigs for various recent software versions, including Cantera 
3.0.0, mold 2.3.1, Perl-bundle-CPAN 5.38.0, PyTorch 2.0.1, ...;


  - Support for installing 48 new software applications and libraries, 
incl. PyTensor, Qt6, SNAP-ESA;



Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.8.2)



## Highlighted enhancements & updates

[enhancements or updates that (may) warrant updating existing 
installations are marked with (***)]


- add dependency_names method to EasyConfig class to get set of names of 
(direct) dependencies;


- use more test programs in sanity check step of OpenMPI easyblock;

- updates and enhancements to various generic easyblocks, including 
CMake, Conda, ConfigureMake;


- updates and enhancements to custom easyblocks for imkl, numpy, Perl, 
PyTorch, WRF, wxPython;


- add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7;

- (***) don't disable building of third and fourth derivates in libxc 6.1.0;

- (***) also build Python bindings for ITK 5.2.1 with foss/2022a;

- (***) add extensions to recent versions of R and 
R-bundle-Bioconductor, use "eb --skip --rebuild" to install the missing 
extensions [3];



## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant re-installing easyconfigs are 
marked with (***)]


- reset tempfile.tempdir to None to avoid that tmpdir path gets 
progressively deeper with each easystack item;


- only use -DCMAKE_SKIP_RPATH=ON for CMake < 3.5.0;

- fix --sanity-check-only and --module-only for UCX plugins;

- enhance TensorFlow easyblock to avoid use of -mcpu=native for XNNPACK 
component when building on aarch64;


- fix the blas/lapack name passed to meson when building recent scipy 
versions (>= 1.9.0) on top of Intel MKL;


- (***) add patch to improve CUDA 11 compatibility of GCCcore/12.2.0 and 
GCCcore/12.3.0;


- (***) add missing required extensions + fix wrong version of 
extensions in recent Perl easyconfigs;


- rename ACT to Artemis;

- rename CVS to ConcurrentVersionsSystem, to avoid problems with recent 
setuptools versions;


- add patch for recent OpenBLAS versions (0.3.23, 0.3.24) to fix flaky 
and hanging tests;


- (***) add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3;

- (***) fix invalid pointer access in UCX 1.11-1.14;

- (***) statically link Boost 1.75 in Cufflinks v20190706 installed with 
GCC/11.2.0, so Boost can be changed to build dependency;


- add patch to fix issue with automatic detection of NeoverseV1 CPU 
architecture in OpenBLAS v0.3.20;


- (***) add missing dependencies for MONAI to support extras required by 
MONAI-Label;


- (***) disable threadedmpi in recent SCOTCH easyconfigs using gompi 
toolchain;




## Supported software

Support for installing 48 new software packages has been added, 
including (but not limited to):


  ALL
  bases2fastq
  biobakery-workflows
  CLEAR
  EveryBeam
  imutils
  Jmol
  MACS3
  MUSCLE3
  ProBiS
  PyPy
  PyTensor
  Qt6
  ResistanceGA
  scCODA
  SNAP-ESA
  starparser
  XBeach

  => This brings the total number of supported software packages to 
3,292 (excluding extensions)!

 An up-to-date list of supported software is available at [4].


Various software updates have been added, including (but not limited to):

  Amber 22.4
  BLAST+ 2.14.1
  Cantera 3.0.0
  CapnProto 1.0.1
  CGAL 5.6
  CUDA-Samples 12.1.1
  CuPy 12.1.0
  FastANI 1.34
  GDAL 3.7.1
  GMP 6.3.0
  GPAW 23.9.1
  HMMER 3.4
  IsoSeq 4.0.0
  libpng 1.6.40
  libxc 6.2.2
  MEGAN 6.25.3
  Mesa 23.1.9
  mold 2.3.1
  OpenBLAS 0.3.24
  OpenCV 4.8.1
  OpenMPI 4.1.6
  OrthoFinder 2.5.5
  ParaView 5.11.2
  Perl-bundle-CPAN 5.38.0
  pyEGA3 5.0.2
  Python 3.11.5
  PyTorch 2.0.1
  PyTorch-bundle 1.13.1
  RagTag 2.1.0
  RAxML-NG 1.2.0,
  RDFlib 7.0.0
  ReFrame 4.3.3
  Rust 1.73.0
  scikit-learn 1.3.1
  TensorRT 8.6.1
  UCX 1.15.0
  X11 20231019
  xtb 6.6.0


These changes result from various contributions, made by 23 different 
contributors:


* 15 merged pull requests for EasyBuild framework
* 20 merged pull requests for easyblocks
* 267 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.8.2, there are several options 

Re: [easybuild] next EasyBuild conf call: Wed 11 Oct 2023 (*today*) at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20231011 
.


The next EasyBuild conf call is scheduled for Wed 25 Oct 2023 at 15:00 
UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls.



regards,

Kenneth

On 11/10/2023 08:01, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 11 Oct 2023 (*today*) at
08:00 UTC (10:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] Building TensorFlow with CUDA support (2023a)

[Kenneth Hoste]

Hi Jakob,

On 11/10/2023 12:02, Strube, Alexandre wrote:

Hi Jakob,


I saw that there is a TensorFlow config for foss/2023a, but not with CUDA 
support.  Looking at earlier versions, it looked like the only difference 
between a non-CUDA and a CUDA version was adding the relevant dependencies, so 
I tried that.  However, if it were that easy somebody else would already have 
done it :-)



Tensorflow fails to compile.  When I google it, others have seen the same 
error, and it's because it only supports CUDA 11.8, not CUDA 12.1.1.  So I 
tried to change to that version, and make the few dependencies with that 
version too.  No luck: CUDA 11.8 does not support GCC 12.X.  Now I am clearly 
in too deep water...   And I assume there is no CUDA-supporting PyTorch for 
similar reasons.


Is it CUDA 11.8 that doesn't support GCC 12.x, or the other way around?

We merged a PR today that could maybe be relevant here (not entirely 
sure though): 
https://github.com/easybuilders/easybuild-easyconfigs/pull/18854



regards,

Kenneth



How do you handle stuff like that in EasyBuild? Is it just a matter of waiting 
till a new version of TensorFlow and PyTorch support CUDA 12.X?  Or are there 
some experts that hack stuff until it works?


So, you are right - and sometimes we patch things, and in other times, we wait. 
Numba is a case where they always have stuff way behind and we try to patch it 
here.

If tensorflow doesn’t support cuda 12 and cuda 12 doesn’t support gcc 12, 
you’re in bad luck - I would not recommend patching this monstrosity.

In fact, considering that Tensorflow is almost abandonware at this point, I 
would just use the previous toolchain for it.


Alex 

[easybuild] next EasyBuild conf call: Wed 11 Oct 2023 (*today*) at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 11 Oct 2023 (*today*) at
08:00 UTC (10:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* 2023b update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] EasyBuild Tech Talks VIII - AVX10 for HPC (Fri 13 Oct 2023 - 13:30 UTC)

[Kenneth Hoste]

Dear EasyBuilders,

A friendly (and final) reminder for the 8th EasyBuild Tech Talk "AVX10 
for HPC, A reasonable solution to the 7 levels of AVX-512 folly" by 
Felix LeClair which is taking place (online via Zoom + live-streamed via 
YouTube) this Friday 13 Oct at 13:30 UTC .


https://easybuild.io/tech-talks/008_avx10.html

If you want to join the Zoom session, please register via 
https://event.ugent.be/registration/ebtechtalk008avx10 (registration 
will close Wed 11 Oct).


We already have over 120 registrations for this talk, but there’s plenty 
more virtual seats available!



regards,

Kenneth

On 02/10/2023 10:44, Kenneth Hoste wrote:

Dear EasyBuilders,

This is a friendly reminder for the EasyBuild Tech Talk "AVX10 for HPC - 
A reasonable solution to the 7 levels of AVX-512 folly" by Felix LeClair 
on Fri 13 Oct 2023 at 13:30 UTC.


More information is available at 
https://easybuild.io/tech-talks/008_avx10.html .


If you would like to attend the Zoom session, please register via:

 https://event.ugent.be/registration/ebtechtalk008avx10


regards,

Alan, Kenneth, Simon

On 14/09/2023 15:41, Kenneth Hoste wrote:

Dear EasyBuilders,

I'm happy to announce the 8th EasyBuild Tech Talk: "AVX10 for HPC - A 
reasonable solution to the 7 levels of AVX-512 folly".


This talk is planned for **Friday 13 October 2023 at 13:30 UTC**, and 
will be presented by Felix LeClair.


More information including a detailed talk description and outline is 
available via 
https://easybuild.io/tech-talks/008_avx10.html .


Attending this talk is free, but please register if you plan to attend 
via:


 https://event.ugent.be/registration/ebtechtalk008avx10

Practical information on joining the live Zoom session will be sent to 
registered attendees a couple of hours before the start of the session.


The session will also be live streamed and recorded via the EasyBuild 
YouTube channel 
(https://www.youtube.com/c/EasyBuilders>>> The provided contact info when registering will only be used for 
informing you about specific details of this particular event, it will 
not be shared with others, nor be used for other purposes.



regards,

Alan, Kenneth, Simon
organizers of the EasyBuild Tech Talk sessions

Re: [easybuild] EasyBuild Tech Talks VIII - AVX10 for HPC (Fri 13 Oct 2023 - 13:30 UTC)

[Kenneth Hoste]

Dear EasyBuilders,

This is a friendly reminder for the EasyBuild Tech Talk "AVX10 for HPC - 
A reasonable solution to the 7 levels of AVX-512 folly" by Felix LeClair 
on Fri 13 Oct 2023 at 13:30 UTC.


More information is available at 
https://easybuild.io/tech-talks/008_avx10.html .


If you would like to attend the Zoom session, please register via:

https://event.ugent.be/registration/ebtechtalk008avx10


regards,

Alan, Kenneth, Simon

On 14/09/2023 15:41, Kenneth Hoste wrote:

Dear EasyBuilders,

I'm happy to announce the 8th EasyBuild Tech Talk: "AVX10 for HPC - A 
reasonable solution to the 7 levels of AVX-512 folly".


This talk is planned for **Friday 13 October 2023 at 13:30 UTC**, and 
will be presented by Felix LeClair.


More information including a detailed talk description and outline is 
available via 
https://easybuild.io/tech-talks/008_avx10.html .


Attending this talk is free, but please register if you plan to attend via:

 https://event.ugent.be/registration/ebtechtalk008avx10

Practical information on joining the live Zoom session will be sent to 
registered attendees a couple of hours before the start of the session.


The session will also be live streamed and recorded via the EasyBuild 
YouTube channel 
(https://www.youtube.com/c/EasyBuilders>> 

The provided contact info when registering will only be used for 
informing you about specific details of this particular event, it will 
not be shared with others, nor be used for other purposes.



regards,

Alan, Kenneth, Simon
organizers of the EasyBuild Tech Talk sessions

Re: [easybuild] Re: OpenBLAS-0.3.21-GCC-12.2.0.eb testing failed om AMD "Genoa" node

[Kenneth Hoste]

Hi Ole,

On 28/09/2023 10:45, Ole Holm Nielsen wrote:

Dear Kenneth,

On 9/28/23 09:42, Kenneth Hoste wrote:

I suspect the problem is more with OpenBLAS than GCC.

OpenBLAS 0.3.20 probably doesn't detect AMD Genoa (Zen4) correctly 
yet, and doesn't try to use AVX-512 instructions there.


OpenBLAS 0.3.21 detects Genoa, enbales AVX-512, but there's a bug in a 
kernel being used.


I would try and see whether you observe any problems with more recent 
OpenBLAS versions, like OpenBLAS-0.3.23-GCC-12.3.0.eb .


That version build correctly:

$ eb OpenBLAS-0.3.23-GCC-12.3.0.eb -r
(lines deleted)
== processing EasyBuild easyconfig 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb

== building and installing OpenBLAS/0.3.23-GCC-12.3.0...
== fetching files...
== ... (took 6 secs)
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== ... (took 57 secs)
== testing...
== ... (took 2 mins 34 secs)
== installing...
== ... (took 2 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 3 mins 42 secs)
== Results of the build can be found in the log file(s) 
/home/modules/software/OpenBLAS/0.3.23-GCC-12.3.0/easybuild/easybuild-OpenBLAS-0.3.23-20230928.103500.log

== Build succeeded for 22 out of 22

If not, we may be able to trace down the fix and patch OpenBLAS 0.3.21 
to fix the problem you're seeing...


So is there any hope that foss-2022b.eb with OpenBLAS/0.3.21-GCC-12.2.0 
can be made to work correctly on AMD Genoa nodes?



Not seeing the problem with OpenBLAS 0.3.23 is encouraging, that 
probably means a fix is hiding in either OpenBLAS 0.3.22 or 0.3.23 that 
we may be able to backport to 0.3.21.


I don't see anything obvious in the release notes though (see 
https://github.com/OpenMathLib/OpenBLAS/releases) at first glance.


Can you try and see if there's a problem with OpenBLAS 0.3.22, by using:

eb --try-software-version 0.3.22 OpenBLAS-0.3.23-GCC-12.3.0.eb

That would help narrow things down (a bit).


regards,

Kenneth



Thanks,
Ole


On 28/09/2023 09:26, Ole Holm Nielsen wrote:
It's interesting that while attempting to build the foss-2022a 
toolchain in stead of foss-2022b, the build of OpenBLAS with GCC 
11.3.0 succeeds without errors:


== processing EasyBuild easyconfig 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb

== building and installing OpenBLAS/0.3.20-GCC-11.3.0...
== fetching files...
== ... (took 4 secs)
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== ... (took 56 secs)
== testing...
== ... (took 2 mins 24 secs)
== installing...
== ... (took 1 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 3 mins 28 secs)

The only difference here appears to be GCC version 12.2.0 versus 11.3.0!

Any ideas about what's causing this error in the tests?

Perhaps GCC version 12.2.0 tries to use the new AVX-512 instructions 
in AMD Genoa and has a bug?


Thanks,
Ole


On 9/26/23 08:04, Ole Holm Nielsen wrote:
I'm starting EasyBuild up on our new AMD "Genoa" platform with 1 AMD 
EPYC 9124 16-Core Processor with 2 threads/core, 384 GB RAM, and 
AlmaLinux 8.8 OS.


Unfortunately, building the foss-2022b toolchain exits during the 
testing phase of OpenBLAS-0.3.21-GCC-12.2.0.eb as shown below.  Does 
anyone have ideas about what might be wrong?


$ eb foss-2022b.eb -r
(lines deleted)
== processing EasyBuild easyconfig 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb

== building and installing OpenBLAS/0.3.21-GCC-12.2.0...
== fetching files...
== ... (took 7 secs)
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== ... (took 53 secs)
== testing...
== ... (took 12 secs)
== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/OpenBLAS/0.3.21/GCC-12.2.0): build failed (first 300 
chars): cmd " make tests  BINARY='64'  CC='gcc'  FC='gfortran' 
MAKE_NB_JOBS='-1' USE_OPENMP='1'  USE_THREAD='1' " exited with exit 
code 2 and output:
/home/modules/software/binutils/2.39-GCCcore-12.2.0/bin/ld: warning: 
/tmp/eb-74m3kzgo/ccy1Gkzg.o: missing .note.GNU-stack section implies 
executable stack

/ (took 1 min 14 secs)
== Results of the build can be found in the log file(s) 
/tmp/eb-74m3kzgo/easybuild-OpenBLAS-0.3.21-20230925.161149.UfDUO.log
ERROR: Build of 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBL

Re: [easybuild] OpenMPI-4.1.4-GCC-12.2.0.eb Sanity check failed on AMD "Genoa" node

[Kenneth Hoste]

Dear Ole,

On 26/09/2023 08:24, Ole Holm Nielsen wrote:
I'm starting EasyBuild up on our new AMD "Genoa" platform with 1 AMD 
EPYC 9124 16-Core Processor with 2 threads/core, 384 GB RAM, Ethernet 
network only, and AlmaLinux 8.8 OS.


Unfortunately, building the foss-2022b toolchain exits during the 
testing phase of OpenMPI-4.1.4-GCC-12.2.0.eb as shown below.  Does 
anyone have ideas about what might be wrong?


$ eb foss-2022b.eb -r
(lines deleted)
== processing EasyBuild easyconfig 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb

== building and installing OpenMPI/4.1.4-GCC-12.2.0...
== fetching files...
== ... (took 1 secs)
== creating build dir, resetting environment...
== unpacking...
== ... (took 1 secs)
== patching...
== preparing...
== configuring...
== ... (took 2 mins 22 secs)
== building...
== ... (took 4 mins 24 secs)
== testing...
== ... (took 36 secs)
== installing...
== ... (took 1 min 15 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== ... (took 5 secs)
== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/OpenMPI/4.1.4/GCC-12.2.0): build failed (first 300 chars): 
Sanity check failed: sanity check command 
OMPI_MCA_rmaps_base_oversubscribe=1 mpirun -n 8 
/dev/shm/OpenMPI/4.1.4/GCC-12.2.0/mpi_test_hello_c exited with code 1 
(output: 
--
A requested component was not found, or was unable to be (took 8 mins 48 
secs)
== Results of the build can be found in the log file(s) 
/tmp/eb-watuyqhw/easybuild-OpenMPI-4.1.4-20230926.080727.GEZtD.log
ERROR: Build of 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb failed (err: 'build failed (first 300 chars): Sanity check failed: sanity check command OMPI_MCA_rmaps_base_oversubscribe=1 mpirun -n 8 /dev/shm/OpenMPI/4.1.4/GCC-12.2.0/mpi_test_hello_c exited with code 1 (output: --\nA requested component was not found, or was unable to be')



The log file shows messages about missing components:

(lines deleted)
--
[e000.nifl.fysik.dtu.dk:1849636] PML cm cannot be selected
[e000.nifl.fysik.dtu.dk:1849635] PML cm cannot be selected
[e000.nifl.fysik.dtu.dk:1849626] 2 more processes have sent help message 
help-mca-base.txt / find-available:not-valid
[e000.nifl.fysik.dtu.dk:1849626] Set MCA parameter 
"orte_base_help_aggregate" to 0 to see all help / error messages
[e000.nifl.fysik.dtu.dk:1849626] 1 more process has sent help message 
help-mca-base.txt / find-available:none found

)
sanity check command mpirun -n 1 
/dev/shm/OpenMPI/4.1.4/GCC-12.2.0/mpi_test_hello_usempi exited with code 
1 (output: 
--

A requested component was not found, or was unable to be opened.  This
means that this component is either not installed or is unable to be
used on your system (e.g., sometimes this means that shared libraries
that the component requires are unable to be found/loaded).  Note that
Open MPI stopped checking at the first component that it did not find.

Host:  e000.nifl.fysik.dtu.dk
Framework: mtl
Component: psm2
--
--
No components were able to be opened in the pml framework.

This typically means that either no components of this type were
installed, or none of the installed components can be loaded.
Sometimes this means that shared libraries required by these
components are unable to be found/loaded.

   Host:  e000
   Framework: pml
--
[e000.nifl.fysik.dtu.dk:1849661] PML cm cannot be selected
) (at easybuild/framework/easyblock.py:3655 in _sanity_check_step)
== 2023-09-26 08:16:16,111 build_log.py:267 INFO ... (took 5 secs)
== 2023-09-26 08:16:16,111 filetools.py:2012 INFO Removing lock 
/home/modules/software/.locks/_home_modules_software_OpenMPI_4.1.4-GCC-12.2.0.lock...
== 2023-09-26 08:16:16,112 filetools.py:383 INFO Path 
/home/modules/software/.locks/_home_modules_software_OpenMPI_4.1.4-GCC-12.2.0.lock successfully removed.
== 2023-09-26 08:16:16,112 filetools.py:2016 INFO Lock removed: 
/home/modules/software/.locks/_home_modules_software_OpenMPI_4.1.4-GCC-12.2.0.lock
== 2023-09-26 08:16:16,112 easyblock.py:4277 WARNING build failed (first 
300 chars): Sanity check failed: sanity check command 
OMPI_MCA_rmaps_base_oversubscribe=1 mpirun -n 8 
/dev/shm/OpenMPI/4.1.4/GCC-12.2.0/mpi_test_hello_c exited with code 1 
(output: 
--

A requested component was not found, or was unable to be
== 

Re: [easybuild] Re: OpenBLAS-0.3.21-GCC-12.2.0.eb testing failed om AMD "Genoa" node

[Kenneth Hoste]

Dear Ole,

I suspect the problem is more with OpenBLAS than GCC.

OpenBLAS 0.3.20 probably doesn't detect AMD Genoa (Zen4) correctly yet, 
and doesn't try to use AVX-512 instructions there.


OpenBLAS 0.3.21 detects Genoa, enbales AVX-512, but there's a bug in a 
kernel being used.


I would try and see whether you observe any problems with more recent 
OpenBLAS versions, like OpenBLAS-0.3.23-GCC-12.3.0.eb .


If not, we may be able to trace down the fix and patch OpenBLAS 0.3.21 
to fix the problem you're seeing...



regards,

Kenneth

On 28/09/2023 09:26, Ole Holm Nielsen wrote:
It's interesting that while attempting to build the foss-2022a toolchain 
in stead of foss-2022b, the build of OpenBLAS with GCC 11.3.0 succeeds 
without errors:


== processing EasyBuild easyconfig 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb

== building and installing OpenBLAS/0.3.20-GCC-11.3.0...
== fetching files...
== ... (took 4 secs)
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== ... (took 56 secs)
== testing...
== ... (took 2 mins 24 secs)
== installing...
== ... (took 1 secs)
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully (took 3 mins 28 secs)

The only difference here appears to be GCC version 12.2.0 versus 11.3.0!

Any ideas about what's causing this error in the tests?

Perhaps GCC version 12.2.0 tries to use the new AVX-512 instructions in 
AMD Genoa and has a bug?


Thanks,
Ole


On 9/26/23 08:04, Ole Holm Nielsen wrote:
I'm starting EasyBuild up on our new AMD "Genoa" platform with 1 AMD 
EPYC 9124 16-Core Processor with 2 threads/core, 384 GB RAM, and 
AlmaLinux 8.8 OS.


Unfortunately, building the foss-2022b toolchain exits during the 
testing phase of OpenBLAS-0.3.21-GCC-12.2.0.eb as shown below.  Does 
anyone have ideas about what might be wrong?


$ eb foss-2022b.eb -r
(lines deleted)
== processing EasyBuild easyconfig 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb

== building and installing OpenBLAS/0.3.21-GCC-12.2.0...
== fetching files...
== ... (took 7 secs)
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== ... (took 53 secs)
== testing...
== ... (took 12 secs)
== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/OpenBLAS/0.3.21/GCC-12.2.0): build failed (first 300 chars): 
cmd " make tests  BINARY='64'  CC='gcc'  FC='gfortran'  
MAKE_NB_JOBS='-1' USE_OPENMP='1'  USE_THREAD='1' " exited with exit 
code 2 and output:
/home/modules/software/binutils/2.39-GCCcore-12.2.0/bin/ld: warning: 
/tmp/eb-74m3kzgo/ccy1Gkzg.o: missing .note.GNU-stack section implies 
executable stack

/ (took 1 min 14 secs)
== Results of the build can be found in the log file(s) 
/tmp/eb-74m3kzgo/easybuild-OpenBLAS-0.3.21-20230925.161149.UfDUO.log
ERROR: Build of 
/home/modules/software/EasyBuild/4.8.1/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb failed (err: 'build failed (first 300 chars): cmd " make tests BINARY=\'64\'  CC=\'gcc\'  FC=\'gfortran\'  MAKE_NB_JOBS=\'-1\' USE_OPENMP=\'1\'  USE_THREAD=\'1\' " exited with exit code 2 and output:\n/home/modules/software/binutils/2.39-GCCcore-12.2.0/bin/ld: warning: /tmp/eb-74m3kzgo/ccy1Gkzg.o: missing .note.GNU-stack section implies executable stack\n/')



The log file shows some an error in test_kernel_regress.c:50:

(lines deleted)
./openblas_utest
TEST 1/37 max:smax_zero [OK]
TEST 2/37 max:dmax_positive [OK]
TEST 3/37 max:smax_negative [OK]
TEST 4/37 min:smin_zero [OK]
TEST 5/37 min:dmin_positive [OK]
TEST 6/37 min:smin_negative [OK]
TEST 7/37 amax:damax [OK]
TEST 8/37 amax:samax [OK]
TEST 9/37 ismax:negative_step_2 [OK]
TEST 10/37 ismax:positive_step_2 [OK]
TEST 11/37 ismin:negative_step_2 [OK]
TEST 12/37 ismin:positive_step_2 [OK]
TEST 13/37 drotmg:drotmg_D1_big_D2_big_flag_zero [OK]
TEST 14/37 drotmg:rotmg_D1eqD2_X1eqX2 [OK]
TEST 15/37 drotmg:rotmg_issue1452 [OK]
TEST 16/37 drotmg:rotmg [OK]
TEST 17/37 axpy:caxpy_inc_0 [OK]
TEST 18/37 axpy:saxpy_inc_0 [OK]
TEST 19/37 axpy:zaxpy_inc_0 [OK]
TEST 20/37 axpy:daxpy_inc_0 [OK]
TEST 21/37 zdotu:zdotu_offset_1 [OK]
TEST 22/37 zdotu:zdotu_n_1 [OK]
TEST 23/37 dsdot:dsdot_n_1 [OK]
TEST 24/37 swap:cswap_inc_0 [OK]
TEST 25/37 swap:sswap_inc_0 [OK]
TEST 26/37 swap:zswap_inc_0 [OK]
TEST 27/37 swap:dswap_inc_0 [OK]
TEST 28/37 rot:csrot_inc_0 [OK]
TEST 29/37 rot:srot_inc_0 [OK]
TEST 30/37 rot:zdrot_inc_0 [OK]
TEST 31/37 rot:drot_inc_0 [OK]
TEST 32/37 dnrm2:dnrm2_tiny [OK]
TEST 33/37 dnrm2:dnrm2_inf [OK]
TEST 34/37 potrf:smoketest_trivial [OK]
TEST 35/37 potrf:bug_695 [OK]
TEST 36/37 kernel_regress:skx_avx [FAIL]
   ERR: test_kernel_regress.c:50  expected 

Re: [easybuild] next EasyBuild conf call: Wed 27 Sept 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230927


Next call is scheduled for Wed 11 Oct at 08:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 26/09/2023 22:45, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 27 Sept 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 27 Sept 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 27 Sept 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] GCCcore-11.3.0.eb: system gcc too old

[Kenneth Hoste]

On top of what Åke mentioned (I have no idea how you managed to install 
GCC 2.20, that's beyond ancient...), you can always consider using an 
older GCC module as a build dependency when building GCCcore, via a hook 
for example (see https://docs.easybuild.io/hooks/)


But in this particular case, you should really figure out why you're not 
seeing GCC 4.8 as default GCC in CentOS 7...


regards,

Kenneth

On 22/09/2023 07:29, Åke Sandgren wrote:

On a CentOS7.9 system the system GCC should be 4.8.5 and that has no problem 
building GCC 11.3.0

GCC 2.2 was used back in the days of CentOS 4 or so


From: easybuild-requ...@lists.ugent.be  on behalf 
of Loris Bennett 
Sent: Thursday, September 21, 2023 16:09
To: easybuild
Subject: [easybuild] GCCcore-11.3.0.eb: system gcc too old

Hi,

Up until recently we had a homogenous cluster and built software for a
single microarchitecture.  We now have new nodes with different CPUs
need to rebuild a large number of packages.

However, rebuilding GCCcore-11.3.0.eb is failing with the following error:

   configure: error: *** A compiler with support for C++11 language features is 
required.

The system GCC is 2.20 (it is a CentOS 7.9 machine).

On the same machine it was apparently possible to build
GCCcore-11.3.0.eb in the past.  So do I now have to build an older
GCCcore, which EasyBuild can then subsequently use to build 11.3.0, or
how do I get around this issue?

Cheers,

Loris

--
Dr. Loris Bennett (Herr/Mr)
ZEDAT, Freie Universität Berlin

[easybuild] EasyBuild Tech Talks VIII - AVX10 for HPC (Fri 13 Oct 2023 - 13:30 UTC)

[Kenneth Hoste]

Dear EasyBuilders,

I'm happy to announce the 8th EasyBuild Tech Talk: "AVX10 for HPC - A 
reasonable solution to the 7 levels of AVX-512 folly".


This talk is planned for **Friday 13 October 2023 at 13:30 UTC**, and 
will be presented by Felix LeClair.


More information including a detailed talk description and outline is 
available via https://easybuild.io/tech-talks/008_avx10.html .


Attending this talk is free, but please register if you plan to attend via:

https://event.ugent.be/registration/ebtechtalk008avx10

Practical information on joining the live Zoom session will be sent to 
registered attendees a couple of hours before the start of the session.


The session will also be live streamed and recorded via the EasyBuild 
YouTube channel (https://www.youtube.com/c/EasyBuilders).



The provided contact info when registering will only be used for 
informing you about specific details of this particular event, it will 
not be shared with others, nor be used for other purposes.



regards,

Alan, Kenneth, Simon
organizers of the EasyBuild Tech Talk sessions

Re: [easybuild] next EasyBuild conf call: Wed 13 Sep 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230913 
.


Next call is planned for Wed 27 Sept'23 at 15:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 12/09/2023 20:08, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 13 Sep 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 13 Sep 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 13 Sep 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.8.1

[Kenneth Hoste]

Dear EasyBuilders,

We're pleased to announce the release of EasyBuild v4.8.1 [1].

Somehow several bugs were found in previous versions of EasyBuild, which 
were resolved in EasyBuild v4.8.1.

We are as flabbergasted as you are by this...
This does make this release the best release ever though (you know, 
because the bugs are fixed).


As usual, various attempts to distract you from this wonderful event 
have been made, including a Belgian youngster visiting Spain who is one 
day able to ride a bike like the wind, the next day pretending to have 
no idea how a bike works, only to then blow away the competition again 
the day after. Yeah, it's weird.



EasyBuild v4.8.1 is primarily a bugfix and update release, but it also 
includes various enhancements.


The executive summary for this release:

  - Support for various additional hooks that can be used to customize 
EasyBuild, including pre_run_shell_cmd_hook which allows tweaking shell 
commands right before they are run by EasyBuild;


  - 2 new custom easyblocks, for sympy and tensorflow-compression;

  - Easyconfigs for various recent software versions, including Clang 
16.0.6, CP2K 2023.1, FFmpeg 6.0, GCC 13.2.0, OpenFOAM 11, Pillow 10.0.0, 
TensorFlow 2.13.0, ...;


  - Support for installing 83 new software applications and libraries;


Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.8.1)



## Highlighted enhancements & updates

[enhancements or updates that (may) warrant updating existing 
installations are marked with (***)]


- support for additional hooks: pre_build_and_install_loop_hook + 
post_build_and_install_loop_hook, cancel_hook, fail_hook, 
pre_postiter_hook + post_postiter_hook, and pre_run_shell_cmd_hook + 
post_run_shell_cmd_hook; see https://docs.easybuild.io/hooks for more 
information;


- add --silence-hook-trigger configuration option to suppress printing 
of a debug message every time a hook is triggered;


- add support for using fine grained Github tokens;

- add support for submodule filtering and specifying extra Git 
configuration in git_config;


- new custom easyblocks for sympy and tensorflow-compression;

- add options to MesonNinja generic easyblock to customize build_cmd, 
install_cmd, build_dir;


- add support to PerlModule generic easyblock to customize prefix option 
used in installation command;


- updates and enhancements to custom easyblocks for Clang, CP2K, CUDA, 
FreeSurfer, LLVM, Mesa, MXNet, OpenCV, OpenFOAM, PETSc, PyTorch, scipy, 
Score-P, TensorFlow;


- add extensions to recent versions of R (tabletools, flextables) and 
R-bundle-Bioconductor (UCell, decoupleR, RnBeads), use "eb --skip 
--rebuild" to install the missing extensions [3] (***);



## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant re-installing easyconfigs are 
marked with (***)]


- improve error reporting w.r.t. missing checksums;

- only add extensions in module file if there are extensions (***);

- enhance PythonPackage easyblock to deal with posix_local installation 
scheme used by Python in recent Debian/Ubuntu versions;


- improve depot management in JuliaPackage easyblock (***);

- set $JULIA_DEPOT_PATH in Julia easyconfigs with default value (***);

- bug fixes for various custom easyblocks, incl. imkl-FFTW, Java, MATLAB 
(***), Mesa, OpenMPI, STAR-CCM+, TensorFlow;


- fix regression in GCC 12.1 + 12.2 with wrong warnings (***);

- fix installation of Python bindings for recent Arrow easyconfigs;

- various additional patches for recent PyTorch versions to fix bugs 
and/or failing tests (***);


- additional bug fixes in easyconfigs for Abseil, at-spi2-core, 
Automake, FreeSurfer, jupyter-server, JupyterHub, LIBSVM, MPFR, 
RapidJSON, ScaLAPACK, tRNAscan-SE (***);


- update Java/11 wrapper to Java/11.0.20 (***);

- use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7 
with GCCcore/12.2.0 (***);


- add patch for PMIx 4.x to use lchown so links are not followed (***);

- add hpctestlib to the $PYTHONPATH in ReFrame 4.2.0 easyconfig (***);

- add alternative checksum for Extrae v4.0.4;

- disable wx support in gnuplot 5.4.6 (***);

- set $MUJOCO_PY_FORCE_CPU to avoid that mujoco-py checks for nvidia-smi 
and aborts installation because /usr/lib/nvidia is not in $LD_LIBRARY_PATH;



## Supported software

Support for installing 83 new software packages has been added, 
including (but not limited to):


  Ax
  Boost.Python-NumPy
  CatBoost
  ChIPseeker
  cryptography
  GAPPadde
  GenerativeModels
  hatchling
  IsoQuant
  Jupyter-bundle
  JupyterNoteboo
  maturin
  Mikado
  NanoCaller
  Omnipose
  Optax
  pv
  Python-bundle-PyPI
  Sabre
  scib-metrics
  scikit-plot
  setuptools-rust
  tensorflow-compression
  torchvf
  TXR
  virtualenv

  => This 

Re: [easybuild] next EasyBuild conf call: Wed 30 Aug 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes of today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230830 
.


Next call is scheduled for Wed 13 Sept'23 at 08:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 29/08/2023 22:42, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 30 Aug 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 30 Aug 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 30 Aug 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb - tests stalled

[Kenneth Hoste]

Hi Loris,

On 29/08/2023 08:19, Loris Bennett wrote:

Hi,

When I try to install 'dorado' via

   dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb

the tests stall at some point.  The process tree is as follows:

   ├─ /bin/bash /var/spool/slurmd/job14269886/slurm_script
   │  └─ /usr/bin/python3.6 -m easybuild.main 
dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb --robot 
--cuda-compute-capabilities=6.1,7.5 --buildpath=/dev/shm --tmpdir=/scratch/eb-bu
   │ └─ /bin/bash -c export 
PYTHONPATH=/scratch/eb-build/eb-yoirmakd/tmpc14mrksg/lib/python3.10/site-packages:$PYTHONPATH 
&&  cd test && PYTHONUNBUFFERED=1 /trinity/shar
   │└─ /easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
run_test.py --continue-through-error --verbose -x 
distributed/elastic/utils/distrib
   │   ├─ /easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v --subprocess
   │   │  ├─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v TestRPCPickler.test_case
   │   │  │  ├─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v TestRPCPickler.test_case
   │   │  │  ...
   │   │  │  ├─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v TestRPCPickler.test_case
   │   │  │  ├─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python -s -c from 
multiprocessing.resource_tracker import main;main(30)
   │   │  │  ├─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v TestRPCPickler.test_case
   │   │  │  ├─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v TestRPCPickler.test_case
   │   │  │  └─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v TestRPCPickler.test_case
   │   │  └─ 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
distributed/rpc/test_share_memory.py -v --subprocess
   │   └─ /easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python 
run_test.py --continue-through-error --verbose -x distributed/elastic/utils/dist

The problem seems to be the that the following process hangs while
calling 'read':

   Trace of process 95404 - 
/easybuild/software/Python/3.10.4-GCCcore-11.3.0/bin/python -s -c from 
multiprocessing.resource_tracker import main;main(30)
   strace: Process 95404 attached
   read(30,

I have tried this twice and both times the installation has stopped like
this, so I assume it is not some temporary issue with the file system.

Does anyone have any ideas about what else I could look at?



Not sure at first sight, but maybe it's similar to a problem I ran into 
with scipy recently, which boiled down to pytext-xdist getting stuck 
when running in cgroups (for example when running from a Slurm job), see 
https://github.com/pytest-dev/pytest-xdist/issues/658 .


Doesn't look like it's exactly the same problem, but perhaps it gives 
you a push in the right direction...



regards,

Kenneth



Cheers,

Loris

Re: [easybuild] Install problems on Ubuntu 22.04

[Kenneth Hoste]

Hello,

You're hitting a known problem with installing Python packages with 
EasyBuild (like EasyBuild itself, which is also a (collection of) Python 
package(s)) when using the system Python that comes with Ubuntu 22.04, 
because they've tweaked the default behaviour of "pip install --prefix" 
to inject an extra /local/ subdirectory rather than directly installing 
in the specified prefix...


More details are available in 
https://github.com/easybuilders/easybuild-easyblocks/issues/2976 .


There is an open pull request that enhances the PythonPackage easyblock 
that should fix the problem you are seeing at 
https://github.com/easybuilders/easybuild-easyblocks/pull/2977, so 
please check if you can confirm that, and provide feedback in the issue 
or in the PR.


To test, try running:

eb --include-easyblocks-from-pr 2977 --install-latest-eb-release 
--prefix /tmp/easybuild



regards,

Kenneth

On 23/08/2023 17:44, Random Task wrote:
Please forgive me if this is a FAQ, but I searched for my answer in the 
docs, on github, and in this list's archive without finding any solution.


I'm trying to install easybuild Ubuntu 22.04. I've tried it on both a 
fully configured workstation as well as a minimal OS on a VM with the 
same results.


I'm following the instructions found at 

Re: [easybuild] c-ares-1.18.1-GCCcore-11.2.0.eb: source file name and checksum changed

[Kenneth Hoste]

Hi Loris,

It seems like you never got a reply to this...

I just checked, and I didn't see any download problems for c-ares 1.18.1 
at all ("eb --fetch" works fine).


Also, looking at 
https://github.com/c-ares/c-ares/releases/tag/cares-1_18_1, the tag that 
is used by that easyconfig is still there?



regards,

Kenneth

On 08/06/2023 13:51, Loris Bennett wrote:

Hi,

For

   c-ares-1.18.1-GCCcore-11.2.0.eb

both the name of the source file as well as the checksum have changed.  For
the 1.18.1 versions, the source file name is tweaked is the following way

   sources = ['%s-%s.tar.gz' % (name.replace('-', ''), version.replace('.', 
'_'))]

It seems like the developers may have misnamed this release and
then corrected it after the ECs were written.

What is the correct way of submitting a fix?  Do I just open a PR with
the corrected version of the file?

Cheers,

Loris

Re: [easybuild] next EasyBuild conf call: Wed 16 Aug 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230816 



Next call is scheduled for Wed 30 Aug'23 at 15:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 15/08/2023 21:22, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 16 Aug 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 16 Aug 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 16 Aug 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* quick status update on development for EasyBuild 5.0;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 2 Aug 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230802 
.


Next call is scheduled for Wed 16 Aug 2023 at 08:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 01/08/2023 22:40, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 2 Aug 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 2 Aug 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 2 Aug 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.8.0

[Kenneth Hoste]

Dear EasyBuilders,

We're happy to announce the release of EasyBuild v4.8.0 [1].

This must be the best EasyBuild release so far...
Wait, hold on. Checking...
Yes, yes it is.

Don't be distracted by a bunch of guys pretending that riding a bike all 
across a large European country in a couple of weeks, with an ugly shirt 
as the main prize for the winner, is a sensible thing to do.



EasyBuild v4.8.0 is primarily a feature release, but it also includes 
various minor bug fixes, enhancements, and updates.


The executive summary for this release:

  - Easyconfigs for the 2023a update of the foss + intel common toolchains;

  - 2 new easyblocks: a generic PerlBundle easyblock, and a custom 
easyblock for Rust;


  - Easyconfigs for various recent software versions, including elastix 
5.0.0, GROMACS 2023.1, PyTorch 1.13.1, VTK 9.2.6, ...;


  - Support for installing 76 new software applications and libraries;

Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.8.0)



## Highlighted enhancements & updates

[enhancements or updates that (may) warrant updating existing 
installations are marked with (***)]


- add PerlBundle generic easyblock for installing a bundle of Perl modules;

- add custom easyblock for Rust, which makes sure that all shared 
libraries use RPATH rather than RUNPATH if --rpath is used;


- add support for install_cmds in Binary easyblock;

- update OpenBLAS easyblock since make shared is necessary and 
sufficient with OpenBLAS 0.3.23 + recent parallel build fixes;


- (***) add extra packages to recent R easyconfigs;

- (***) add extra packages to recent R-bundle-Bioconductor easyconfigs;

- (***) enable building static libs and check for `libexslt.*` in libxslt;


## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are 
marked with (***)]


- fix regex for extracting glibc version from output of 'ldd --version' 
in Gentoo Linux;


- stop running tests with Python 2.7 since it is no longer supported in 
GitHub Actions;


- patch CMake's UnixPaths.cmake script if --sysroot is set;

- use upstream patch for symbol compatibility in XZ 5.2.5;

- (***) change base compiler for `intel/2023.03` to `GCCcore/12.3.0` 
(required to use it as intel/2023a);


- (***) use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2;

- (***) stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2;

- (***) fix exec permissions for all binaries & scripts of 
L_RNA_scaffolder 20190530;


- (***) update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add 
missing dependencies;


- (***) fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17);

- (***) fix toolchain for networkx-3.0 (`foss/2022b` -> `gfbf/2022b`);

- (***) bump OpenSSL 1.1 wrapper fallback to 1.1.1u;



## Supported software

Support for installing 76 new software packages has been added, 
including (but not limited to):


  alleleIntegrator
  BayesPrism
  Circuitscape
  DALI
  DaliLite
  ecFlow
  FragPipe
  GLIMPSE
  KerasTuner
  mannkendall
  MONAI-Label
  NanoStat
  pastml
  Perl-bundle-CPAN
  PyBioLib
  PyWBGT
  Sniffles
  Tapenade
  timm
  wrapt
  xclip

  => This brings the total number of supported software packages to 
3,161 (excluding extensions)!

 An up-to-date list of supported software is available at [4].


Various software updates have been added, including (but not limited to):

  alleleCount 4.2.1
  BayesTraits 3.0.2
  Bowtie2 2.5.1
  Cellpose 2.2.2
  CUDA 12.1.1 + 12.2.0
  CVXOPT 1.3.1
  deepTools 3.5.2
  DMTCP 3.0.0
  dorado 0.3.0 + 0.3.1
  duplex-tools 0.3.3
  fastp 0.23.4
  FreeSurfer 7.4.0
  GATK 4.4.0.0
  GCC 11.4.0
  Geant4 11.1.2
  GROMACS 2023.1
  Horovod 0.25.0
  Julia 1.9.0
  LibLZF 3.6
  MAGeCK 0.5.9.5
  MaxQuant 2.4.2.0
  MMseqs2 14-7e284
  MuJoCo 2.2.2
  ncbi-vdb 3.0.5
  ont-fast5-api 4.1.1
  openpyxl 3.1.2
  ParaView 5.11.1
  Perl 5.36.1
  PSI4 1.7
  Pysam 0.21.0
  Python 3.11.3
  PyTorch 1.13.1
  Rust 1.70.0
  seqtk 1.4
  SUNDIALS 6.5.1
  TransDecoder 5.5.0
  Transformers 4.29.2 + 4.30.2
  VTK 9.2.6
  xarray 2023.4.2
  zlib-ng 2.0.7

These changes result from various contributions, made by 25 different 
contributors:


* 9 merged pull requests for EasyBuild framework
* 13 merged pull requests for easyblocks
* 301 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.8.0, there are several options [5].
Two particularly easy options include:

     * eb --install-latest-eb-release

     * eb --from-pr 18282  # use easyconfig from PR #18282 [6]


Enjoy!


regards,

Kenneth & Miguel


[1] https://pypi.org/project/easybuild/4.8.0
[2] https://docs.easybuild.io/release-notes/#release_notes_eb480
[3] 

Re: [easybuild] next EasyBuild conf call: Wed 5 July 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes of today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230705 



Next call is scheduled for Wed 19 July 2023 at 08:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 04/07/2023 21:35, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 5 July 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* 2023a update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 5 July 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 5 July 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* 2023a update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 21 June 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 21 June 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* progress on 2023a update of common toolchains;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 7 June 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Hi all,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230607


Next call is scheduled for Wed 21 June 2023 at 08:00 UTC, more info via 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 06/06/2023 22:09, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 7 June 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* 2023a update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 7 June 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 7 June 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* 2023a update of common toolchains;

* Q

Suggestions for additional topics are always welcome!


More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.7.2

[Kenneth Hoste]

Dear EasyBuilders,

We're happy to announce the release of EasyBuild v4.7.2 [1].

There's no doubt that this is the best EasyBuild release so far.
Like, none at all.

Don't let the recent coronation of a new king, or silly events like 
meeting of a particular open source software community distract you from it!



The executive summary for this release:

  - Various small enhancements and bug fixes to EasyBuild framework, 
easyblocks, and easyconfigs;


  - Easyconfigs for various recent software versions, including 
AlphaFold 2.3.4, CP2K 2022.1, GCC 12.3.0 + 13.1.0, R-bundle-Bioconductor 
3.16, ...;


  - Support for installing 89 new software applications and libraries;


EasyBuild v4.7.2 is primarily a bugfix and update release, but it also 
includes various minor enhancements.


Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.7.2)



## Highlighted enhancements & updates

[enhancements or updates that (may) warrant updating existing 
installations are marked with (***)]


- extend (experimental) support for generating container images with 
Apptainer;


- 2 new generic easyblock for installing Rust crates with cargo: Cargo 
and CargoPythonPackage;


- (***) enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0;

- (***) add additional extensions to recent R and R-bundle-Bioconductor 
easyconfigs;


- (***) switch bamtofastq + Longshot to Cargo easyblock;

- (***) add egg file to OpenCV 4.6.0 python package for pip + pkgconfig 
file;


- (***) add missing FastTreeMP binary for FastTree;

- (***) bump versions in Java wrappers to latest builds that include 
ppc64le;



## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are 
marked with (***)]


- fix --check-github as gist url now includes username;

- (***) force building torchvision with CUDA support if CUDA is included 
as dependency by setting $FORCE_CUDA;


- (***) use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0;

- (***) add missing OpenJPEG dependency for recent GDAL versions;

- (***) upgrade traitlets, ipywidgets, and widgetsnbextension + 
downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known 
issues;


- (***) add missing dependencies and add patch for fix incorrect ids for 
BRAKER v2.1.6;


- (***) FLINT needs BLAS so move it up from GCC level;

- add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix 
broken test;


- exclude flaky test_optim + add patch to fix test_quantization for 
PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent;


- add make 4.3 as build dependency for recent OpenBLAS versions;

- add alternative checksum for MONAI 1.0.1;

- add historical repo paths to install command for old versions of texlive;



## Supported software

Support for installing 89 new software packages has been added, 
including (but not limited to):


  AGeNT
  Annocript
  BoltzTraP2
  Casanovo
  CellOracle
  ColabFold
  DiCE-ML
  ESPResSo
  FunGAP
  GLI
  HTSplotter
  IsoSeq
  LoRDEC
  OptaDOS
  PGPLOT
  pod5-file-format
  pytesseract
  Python-bundle
  PyTorch-bundle
  Raven
  Scalene
  SoPlex
  sysbench
  TOPAS
  turbinesFoam

  => This brings the total number of supported software packages to 
3,085 (excluding extensions)!

 An up-to-date list of supported software is available at [4].


Various software updates have been added, including (but not limited to):

  AlphaFold 2.3.4
  Arrow 11.0.0
  Clang 15.0.5
  CP2K 9.1 + 2022.1
  GCC 12.3.0 + 13.1.0
  intel/2023.03 (incl. intel-compilers 22023.1.0, impi 2021.9.0, imkl 
2023.1.0)

  OpenMM 8.0.0
  picard 3.0.0
  R-bundle-Bioconductor 3.16
  ReFrame 4.2.0
  UCC-CUDA 1.1.0

These changes result from various contributions, made by 27 different 
contributors:


* 14 merged pull requests for EasyBuild framework
* 15 merged pull requests for easyblocks
* 316 merged pull requests for easyconfigs


Thanks to everyone who contributed to this release in one way or another!


To upgrade to EasyBuild v4.7.2, there are several options [5].
Two particularly easy options include:

     * eb --install-latest-eb-release

     * eb --from-pr 17986  # use easyconfig from PR #17986 [6]


Enjoy!


regards,

Kenneth & Sebastian


[1] https://pypi.org/project/easybuild/4.7.2
[2] https://docs.easybuild.io/release-notes/#release_notes_eb472
[3] 
https://docs.easybuild.io/partial-installations/#partial_installation_skip

[4] https://docs.easybuild.io/version-specific/supported-software
[5] https://docs.easybuild.io/installation/#updating
[6] https://github.com/easybuilders/easybuild-easyconfigs/pull/17986

Re: [easybuild] EB file for building a recent version of Meep?

[Kenneth Hoste]

Hi Ole,

An easier approach would have been to look into recently merged 
easyconfigs, and using "eb --from-pr", see 
https://github.com/easybuilders/easybuild-easyconfigs/pull/17783 .


Although in theory merged easyconfig PRs may require recent changes in 
easyblocks and/or framework, they often don't, and then "eb --from-pr" 
works fine.


regards,

Kenneth

On 26/05/2023 11:54, Ole Holm Nielsen wrote:

Hi Terje,

Thanks a lot, I have copied out the .eb files I needed.

Best regards,
Ole

On 5/26/23 11:36, Terje Kvernes wrote:

Hi Ole,

Simon and the rest of the Bear Research Software Group have a complete 
tree of easyconfigs under 
https://github.com/bear-rsg/bear-eb/tree/main/easyconfigs and in there you will find the missing dependencies. You either can clone this tree locally and add it to your robots search path, or copy out the dependencies you need manually.


On 26 May 2023, at 10:48, Ole Holm Nielsen 
 wrote:


Hi Simon,

Fantastic, thanks a lot for the quick answer!  However, when I try to 
build the module I encounter some missing prerequisites:


ERROR: Missing dependencies: autograd/1.5-foss-2021b, 
libctl/4.5.1-foss-2021b, Harminv/1.4.1-foss-2021b, 
MPB/1.11.1-foss-2021b, libGDSII/0.21-foss-2021b (no easyconfig file 
or existing module found)


How can I resolve this issue?

Thanks,
Ole


On 5/26/23 10:39, Simon Branford wrote:

Hi Ole,
Yes, we have an easyconfig for 1.25 - see 
https://github.com/bear-rsg/bear-eb/blob/main/easyconfigs/m/Meep/Meep-1.25.0-foss-2021b.eb> Regards,

Simon
-Original Message-
From: easybuild-requ...@lists.ugent.be 
 On Behalf Of Ole Holm Nielsen

Sent: 26 May 2023 09:29
To: easybuild 
Subject: [easybuild] EB file for building a recent version of Meep?
CAUTION: This email originated from outside the organisation. Do not 
click links or open attachments unless you recognise the sender and 
know the content is safe.
We have a user request for installing the Meep module.  However, the 
versions of Meep in EasyBuild are very old:
https://docs.easybuild.io/version-specific/supported-software/#meep> The .eb files would build an old version Meep-1.4.3-intel-2020a.eb 
from an obsolete source, or old version 
Meep-1.6.0-intel-2018a-Python-2.7.14.eb

with Python 2.7 :-(
The current release of Meep is 1.26:
https://github.com/NanoComp/meep/releases and installation instructions are in https://meep.readthedocs.io/en/latest/Installation/> Question: Has anyone looked at writing an .eb file for a recent 
version of Meep with modern compilers and Python3?

Thanks,
Ole
--
Ole Holm Nielsen
PhD, Senior HPC Officer
Department of Physics, Technical University of Denmark

Re: [easybuild] next EasyBuild conf call: Wed 23 May 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at Notes are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230524 
.


Next call in planned for Wed 7 June 2023 at 15:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 23/05/2023 20:02, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 23 May 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* progress on 2023a update of common toolchains;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 23 May 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 23 May 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* progress on 2023a update of common toolchains;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 10 May 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230510 



Next call is planned for Wed 24 May 2023 at 08:00 UTC (10:00 CEST), see 
also https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 10/05/2023 09:59, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for *today* Wed 10 May 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* 2023a update of common toolchains;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 10 May 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for *today* Wed 10 May 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* 2023a update of common toolchains;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] EasyBuild 5.0 Working Group Meeting

[Kenneth Hoste]

Hi Alexandre,

On 03/05/2023 13:28, Strube, Alexandre wrote:
Simon, next time, maybe could you announce a couple days earlier, so I 
can make way on my calendar? You know, germans…


The timing was actually already mentioned in Simon's EasyBuild 5.0 talk 
at EUM'23 (see https://easybuild.io/eum23/eum23_005_EasyBuild_5.0.pdf).


I asked Simon to also send an email to the mailing list (and post a 
message on Slack), mostly as a reminder to try and make sure we got some 
good attendance (which we did in the end, with 8 people present for the 
meeting).


Date & time for the next meetings of the EasyBuild 5.0 working group are 
already planned, see 
https://github.com/easybuilders/easybuild/wiki/EasyBuild-5.0-working-group .


If you want me to, I can add you to the repeating calendar invite as 
well (let me know via Slack if that's the case).



regards,

Kenneth



Sorry, can’t attend - meeting here :-(


On 3. May 2023, at 09:32, Simon Branford  wrote:

And yes, I forgot an important detail: We will be using the EB conf 
call Zoom for this – so*https://umu.zoom.us/j/561463243 
*
*From:*easybuild-requ...@lists.ugent.be 
*On Behalf Of*Simon Branford

*Sent:*02 May 2023 18:16
*To:*easybuild@lists.ugent.be
*Subject:*[easybuild] EasyBuild 5.0 Working Group Meeting
Hi all,
During the recent EasyBuild User Meeting (https://easybuild.io/eum23 
), I presented on the plans for EasyBuild 
5.0 (https://easybuild.io/eum23/#easybuild5 
).
To work towards this, we are forming a working group for developing 
EasyBuild 5.0. The working group will meet on the first Wednesday of 
each month for the next few weeks. This means that the first meeting 
for this working group is at 14:00 CEST (https://time.is/CEST 
) tomorrow (Wednesday 3^rd May).

Regards,
Simon

Re: [easybuild] next EasyBuild conf call: Wed 15 Mar 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230412


Next conf call is scheduled for Wed 10 May 2023 (15:00 UTC, 17:00 CEST).

There will be no usual EasyBuild conf call on Wed 26 Apr 2023 due to the 
EasyBuild User Meeting (EUM'23) that week, see https://easybuild.io/eum23 .



regards,

Kenneth

On 11/04/2023 22:43, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 12 Apr 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 12 Apr 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

and now with the correct subject...

(hat tip Thomas HS)

On 11/04/2023 22:43, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 12 Apr 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 15 Mar 2023 at 15:00 UTC (17:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 12 Apr 2023 at
15:00 UTC (17:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] 6th EasyBuild User Survey (please participate!)

[Kenneth Hoste]

Dear EasyBuilders,

This is a final reminder to fill out the EasyBuild User Survey ASAP, if 
you haven't already.


https://www.surveymonkey.com/r/6th_easybuild_user_survey

We are keeping the survey open a little longer because we're very close 
to hitting 100 participants, and I would really like to see us reach 
that target!


Please consider spending ~15min of your time *today* to fill out the 
survey...



regards,

Kenneth

On 01/03/2023 08:54, Kenneth Hoste wrote:

Dear EasyBuilders,

By annual tradition, we are doing a survey to get a better view on the 
EasyBuild community.


This is the 6th time we are doing the EasyBuild User Survey, and it 
would be great if you are willing to participate (again)!


Please take ~15 min of your time to fill it out:

 https://www.surveymonkey.com/r/6th_easybuild_user_survey>> 
In addition, please consider sharing the survey link with friends or 
colleagues who you know are using EasyBuild but may not be subscribed to 
this mailing list.
It would be great if we could (again) have more responses than last time 
(105 for 5th user survey)...


The survey will be closed on Fri 31 March 2023.

Results will be made public shortly after and will also be discussed 
during my "EasyBuild" State of the Union" talk at the next EasyBuild 
User Meeting [1].



regards,

Kenneth


[1] 
https://easybuild.io/eum>

[easybuild] Re: [eum] 8th EasyBuild User Meeting (EUM'23) - Mon-Wed 24-26 April 2023 in London (UK)

[Kenneth Hoste]

Dear EasyBuilders,

The program of the 8th EasyBuild User Meeting (EUM'23) at Imperial 
College London on 24-26 April 2023 is now complete, see


https://easybuild.io/eum23/#program

Recent additions include a remote presentation on recent developments in 
ReFrame, a site presentation by Imperial College London on how EasyBuild 
has helped them, and a second keynote presentation on Wed 26 April by 
the infamous Martyn Guest.


For practical reasons, the registration closes **this Sunday, 2 April 
2023**, so if you plan to attend EUM'23 (physically or remotely), please 
register ASAP!


https://event.ugent.be/registration/eum23


In addition, please don't forget to fill out the EasyBuild User Survey, 
which is still open until the end of this week (Fri 31 March 2023)


https://www.surveymonkey.com/r/6th_easybuild_user_survey

We're close to 100 participants in the survey, please help us reach that 
goal if you haven't filled out the survey yet!



Finally, we are also organising an EasyBuild + EESSI workshop/tutorial 
in conjunction with EUM'23, on Thu 27 + Fri 28 April 2023, at the same 
venue.

For more information, see

https://easybuild.io/eb-eessi-uk-workshop-2023-04

Unfortunately we can only support physical attendance for this workshop 
(although we'll make an effort to record the entire session).


Attendance to this workshop is free, but registration is required:

https://event.ugent.be/registration/ebuk202304

Seats are limited, and running out quickly!
Registration for this workshop will close on 9 April 2023.



regards,

Kenneth

On 14/03/2023 11:29, Kenneth Hoste wrote:

Dear EasyBuilders,

The program for the 8th EasyBuild User Meeting (EUM'23) in London (24-26 
April 2023) is now almost complete:


 https://easybuild.io/eum23/#program>> 
It includes a keynote by Ian Cutress (a.k.a. TechTechPotato), talks on 
EasyBuild 5.0, an update on the EESSI project and EasyBuild on LUMI, a 
tutorial session on best practices for contributing to EasyBuild and on 
the EasyBuild framework, etc.
One or two additional talks will be added to the program in the coming 
days.


Please register if you are planning to attend (physically or virtually):

 https://event.ugent.be/registration/eum23

Deadline for registration is Sunday 2 April 2023.

regards,

Kenneth

PS: Also don't forget to fill out the EasyBuild User Survey - see 
https://www.surveymonkey.com/r/6th_easybuild_user_survey>> 


On 09/02/2023 19:55, Kenneth Hoste wrote:

Dear EasyBuilders,

We're pleased to announce that the registration for the 8th annual 
EasyBuild User Meeting (EUM'23) is now open.


** Event page **

https://easybuild.io/eum23>>> ** Venue & dates **

Imperial College London, UK
Mon 24 April - Wed 26 April 2023


** Organization **

Jörg Saßmannshausen (Imperial College London, UK)
Simon Branford (University of Birmingham, UK)
Jasper Grimm (University of York, UK)
Adam Huffman (Big Data Institute, Oxford, UK)
Kenneth Hoste (HPC-UGent, Belgium)


** Registration **

Attendance is free, but registration is required for practical purposes.

Register via: https://event.ugent.be/registration/eum23

Registration closes on Sun 2 April 2023.


** Agenda **

The agenda is currently still fairly empty, but is actively being 
worked out. We will gradually extend it in the coming days and weeks.


If you have a suggestion for a talk, presenter, or topic (e.g. a 
tutorial on a particular topic),
or if you would like to give talk yourself about your experiences with 
EasyBuild, or about other tools or topics somewhat related to 
EasyBuild, please contact e...@lists.ugent.be (or one of the organisers 
via Slack).


For more information, please consult 
https://easybuild.io/eum23 .



** Question & suggestions **

For questions or suggestions related to the EasyBuild User Meeting, 
please email e...@lists.ugent.be, or contact one of the organisers in 
the EasyBuild Slack.



regards,

Jörg, Simon, Jasper, Adam, Kenneth
EUM'23 organisers

Re: [easybuild] next EasyBuild conf call: Wed 29 Mar 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

Notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230329 
.


Next conf call is scheduled for Wed 12 April 2023 at 15:00 UTC (17:00 
CEST), see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 28/03/2023 20:53, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 29 Mar 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments (incl. PRs to EasyBuild documentation)

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 29 Mar 2023 at 08:00 UTC (10:00 CEST)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 29 Mar 2023 at
08:00 UTC (10:00 CEST).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments (incl. PRs to EasyBuild documentation)

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] [ANN] EasyBuild v4.7.1

[Kenneth Hoste]

On 20/03/2023 18:34, Kenneth Hoste wrote:

Dear EasyBuilders,

It's my pleasure to announce the release of EasyBuild v4.7.1 [1].

Read on to learn why this is the EasyBuild release to date.


This should have said "the best EasyBuild release to date".

Just wanted to make that clear, in case somebody was confused about that...



Trust us, we checked with ChatGPT on this: it's true...


...



regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.7.1

[Kenneth Hoste]

Dear EasyBuilders,

It's my pleasure to announce the release of EasyBuild v4.7.1 [1].

Read on to learn why this is the EasyBuild release to date.
Trust us, we checked with ChatGPT on this: it's true...

Do ignore any attempts to distract from this release, including a new 
version of a generative AI that is causing some concerns about the dawn 
of The Singularity, while the most recent EasyBuild version it knows 
about is EasyBuild 4.5.3 (I mean, come on...).



The executive summary for this release:

  - Various small enhancements and bug fixes to EasyBuild framework, 
easyblocks, and easyconfigs;


  - Easyconfigs for various recent software versions: AlphaFold 2.3.0, 
HDF5 1.14.0, networkx 3.0, TensorFlow v2.11.0, Trilinos 13.4.1, ...;


  - Additional easyconfigs using the latest 2022b toolchains, incl. 
SciPy-bundle 2023.02 with gfbf/2022b (subtoolchain of foss/2022b);


  - Support for installing 99 new software applications and libraries;


EasyBuild v4.7.1 is primarily a bugfix and update release, but it also 
includes various minor enhancements.


Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.7.1)



## Highlighted enhancements

[enhancements that (may) warrant updating existing installations are 
marked with (***)]


- add support for %(start_dir)s easyconfig template;

- add pre/post extension hook that is triggered before/after individual 
extension installations;


- enforce absolute paths as start dir of extensions;

- updates and enhancements for various generic easyblocks: GoPackage, 
MesonNinja, PythonPackage;


- updates and enhancements for various software-specific easyblocks: 
EasyBuildMeta, ELPA, Maple, Mathematica, NAMD, pybind11, Python, 
QScintilla, scipy, TensorFlow, Trilinos;


- (***) add additional extensions to Python 3.10.8 (required for scipy 
test suite) [3];


- (***) add extensions to Perl 5.32.1 [3];

- (***) add additional extensions to R 4.2.1 [3];

- (***) add additional extensions to Bioconductor 3.15 [3];

- (***) enhance OpenFold 1.0.1 for standalone usage;

- (***) add SDL2 dependency for FFmpeg 5.0.1 to build ffplay;

- (***) add ffnvcodec build dependency to all recent FFmpeg easyconfigs;

- (***) set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs;

- (***) add missing zstd dep to Boost;


## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are 
marked with (***)]


- restore initial environment before processing each easystack item 
(support for easystack files is still experimental);


- various fixes and improvements for the EasyBuild framework test suite;

- (***) fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage 
extensions;


- (***) fix checking of CUDA/ROCR-Runtime dependencies for Clang to 
determine default build targets;


- (***) fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x;

- bug fixes for various generic easyblocks: CMakeMake, 
CMakePythonPackage, PythonPackage, PythonBundle;


- bug fixes for various software-specific easyblocks: FlexiBLAS, netCDF, 
NVHPC, PyTorch;


- (***) add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug;

- (***) add missing pmix patch to OpenMPI 4.1.1 easyconfig used in 
iomkl/2021a and iomkl/2021b;


- (***) replace obsolete pycrypto with pycryptodome in Python 3.10.x 
easyconfigs;


- (***) update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs 
(since deap 1.3.1 is broken) [3];


- (***) replace src include path with installation dir for HDF5;

- (***) use GCC as toolchain for serial variants of HDF5, since it has a 
FORTRAN API;


- (***) add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2;

- (***) fix postinstallcmds in shovill easyconfigs;

- (***) add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1

- (***) add alternative checksum for spatial 7.3-14 extension in R 4.1.x 
easyconfigs;


- (***) enable -fPIC in GEOS 3.11.1 (required by GDAL);

- add alternative checksum for UCX 1.13.1 after source tarball was 
changed in-place (without actual code changes);


- rename some software names in existing easyconfigs, or archive these 
easyconfigs, to avoid case-insensitive name clashes;




## Supported software

Support for installing 99 (!) new software packages has been added, 
including (but not limited to):


  CatLearn
  Cellpose
  chemprop
  cuSPARSELt
  DensPart
  dorado
  fastjet
  finder
  genomepy
  grid
  Health-GPS
  HiCMatrix
  Inferelator
  kineto
  LASSO-Python
  netMHCII
  PfamScan
  plot1cell
  PyTorch-Ignite
  rapidNJ
  scArches
  scib
  smfishHmrf
  Strainberry
  VirSorter2
  YODA

  => This brings the total number of supported software packages to 
2,995 (excluding extensions)!

 An up-to-date list of supported software is 

[easybuild] next EasyBuild conf call: Wed 15 Mar 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 15 Mar 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] Which toolchain to use on AMD EPYC 9004 "Genoa"?

[Kenneth Hoste]

On 14/03/2023 11:04, Ole Holm Nielsen wrote:

On 2/15/23 15:30, Jure Pečar wrote:

On Wed, 15 Feb 2023 15:26:26 +0100
Ole Holm Nielsen  wrote:


Is "foss" also the preferred toolchain on AMD Rome and Genoa?


For now, yes.

There's some work going on to create a toolchain around amd compilers but
it's questionable how much you gain as all features these compilers and
libs bring eventually end up in upstream llvm and gcc.

So for Genoa look for upcoming foss toolchain built around gcc 13. For
Rome and Milan existing ones with gcc 11 and 12 are already working fine.


Sorry for my late reply.  The latest GCC in EasyBuild is 12.2.0.  Is 
there any way to build GCC 13 with EasyBuild so that we can test AMD Genoa?


There is no official release yet of GCC 13.x, but you could take the 
easyconfig file for the latest GCC(core), and use a release candidate 
for GCC 13.x if you want to start experimenting with it.


Usually when there's a new GCC release, we have an easyconfig PR for 
that version available soon after.



Obviously, a lot of other modules are needed as well, so when can a foss 
toolchain with GCC 13 be hoped for?


We're always a bit reluctant to pick up the first dot release of a new 
major compiler version (like 13.1) since we've learned the hard way that 
quite a bit get fixed in the first bugfix release (13.2 for example).


So for foss/2023a, we'll likely go with GCC 12.3 rather than 13.1, 
unless there are good (technical) reasons not to.


CUDA compatibility is a minor factor as well: initially foss/2023a could 
be CPU-only, until a CUDA release that is compatible with whatever GCC 
version is used in that foss version is available.
This is part of the reason for moving away from fosscuda towards 
foss+CUDA in recent foss versions.



regards,

Kenneth



Thanks,
Ole

[easybuild] Re: [eum] 8th EasyBuild User Meeting (EUM'23) - Mon-Wed 24-26 April 2023 in London (UK)

[Kenneth Hoste]

Dear EasyBuilders,

The program for the 8th EasyBuild User Meeting (EUM'23) in London (24-26 
April 2023) is now almost complete:


https://easybuild.io/eum23/#program

It includes a keynote by Ian Cutress (a.k.a. TechTechPotato), talks on 
EasyBuild 5.0, an update on the EESSI project and EasyBuild on LUMI, a 
tutorial session on best practices for contributing to EasyBuild and on 
the EasyBuild framework, etc.

One or two additional talks will be added to the program in the coming days.

Please register if you are planning to attend (physically or virtually):

https://event.ugent.be/registration/eum23

Deadline for registration is Sunday 2 April 2023.

regards,

Kenneth

PS: Also don't forget to fill out the EasyBuild User Survey - see 
https://www.surveymonkey.com/r/6th_easybuild_user_survey



On 09/02/2023 19:55, Kenneth Hoste wrote:

Dear EasyBuilders,

We're pleased to announce that the registration for the 8th annual 
EasyBuild User Meeting (EUM'23) is now open.


** Event page **

https://easybuild.io/eum23>> 


** Venue & dates **

Imperial College London, UK
Mon 24 April - Wed 26 April 2023


** Organization **

Jörg Saßmannshausen (Imperial College London, UK)
Simon Branford (University of Birmingham, UK)
Jasper Grimm (University of York, UK)
Adam Huffman (Big Data Institute, Oxford, UK)
Kenneth Hoste (HPC-UGent, Belgium)


** Registration **

Attendance is free, but registration is required for practical purposes.

Register via: https://event.ugent.be/registration/eum23

Registration closes on Sun 2 April 2023.


** Agenda **

The agenda is currently still fairly empty, but is actively being worked 
out. We will gradually extend it in the coming days and weeks.


If you have a suggestion for a talk, presenter, or topic (e.g. a 
tutorial on a particular topic),
or if you would like to give talk yourself about your experiences with 
EasyBuild, or about other tools or topics somewhat related to EasyBuild, 
please contact e...@lists.ugent.be (or one of the organisers via Slack).


For more information, please consult 
https://easybuild.io/eum23 .



** Question & suggestions **

For questions or suggestions related to the EasyBuild User Meeting, 
please email e...@lists.ugent.be, or contact one of the organisers in the 
EasyBuild Slack.



regards,

Jörg, Simon, Jasper, Adam, Kenneth
EUM'23 organisers

Re: [easybuild] next EasyBuild conf call: Wed 1 Mar 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Hi all,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230301 
.


Next call is planned for Wed 15 March 2023 at 16:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 28/02/2023 19:46, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 1 Mar 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] 6th EasyBuild User Survey (please participate!)

[Kenneth Hoste]

Dear EasyBuilders,

By annual tradition, we are doing a survey to get a better view on the 
EasyBuild community.


This is the 6th time we are doing the EasyBuild User Survey, and it 
would be great if you are willing to participate (again)!


Please take ~15 min of your time to fill it out:

https://www.surveymonkey.com/r/6th_easybuild_user_survey

In addition, please consider sharing the survey link with friends or 
colleagues who you know are using EasyBuild but may not be subscribed to 
this mailing list.
It would be great if we could (again) have more responses than last time 
(105 for 5th user survey)...


The survey will be closed on Fri 31 March 2023.

Results will be made public shortly after and will also be discussed 
during my "EasyBuild" State of the Union" talk at the next EasyBuild 
User Meeting [1].



regards,

Kenneth


[1] https://easybuild.io/eum

[easybuild] next EasyBuild conf call: Wed 1 Mar 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 1 Mar 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 15 Feb 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Hi all,

Notes of today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230215 
.


Next call is scheduled for Wed 1 March 2023 at 09:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 14/02/2023 20:42, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 15 Feb 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 15 Feb 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 15 Feb 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] 8th EasyBuild User Meeting (EUM'23) - Mon-Wed 24-26 April 2023 in London (UK)

[Kenneth Hoste]

Dear EasyBuilders,

We're pleased to announce that the registration for the 8th annual 
EasyBuild User Meeting (EUM'23) is now open.


** Event page **

https://easybuild.io/eum23


** Venue & dates **

Imperial College London, UK
Mon 24 April - Wed 26 April 2023


** Organization **

Jörg Saßmannshausen (Imperial College London, UK)
Simon Branford (University of Birmingham, UK)
Jasper Grimm (University of York, UK)
Adam Huffman (Big Data Institute, Oxford, UK)
Kenneth Hoste (HPC-UGent, Belgium)


** Registration **

Attendance is free, but registration is required for practical purposes.

Register via: https://event.ugent.be/registration/eum23

Registration closes on Sun 2 April 2023.


** Agenda **

The agenda is currently still fairly empty, but is actively being worked 
out. We will gradually extend it in the coming days and weeks.


If you have a suggestion for a talk, presenter, or topic (e.g. a 
tutorial on a particular topic),
or if you would like to give talk yourself about your experiences with 
EasyBuild, or about other tools or topics somewhat related to EasyBuild, 
please contact e...@lists.ugent.be (or one of the organisers via Slack).


For more information, please consult https://easybuild.io/eum23 .


** Question & suggestions **

For questions or suggestions related to the EasyBuild User Meeting, 
please email e...@lists.ugent.be, or contact one of the organisers in the 
EasyBuild Slack.



regards,

Jörg, Simon, Jasper, Adam, Kenneth
EUM'23 organisers

Re: [easybuild] next EasyBuild conf call: Wed 1 Feb 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The notes for today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230201 
.


Next call is scheduled at Wed 15 Feb 2023 at 16:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 31/01/2023 22:50, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 1 Feb 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* update on porting of EasyBuild docs to MarkDown (done!);

* source tarballs provided by GitHub will change;
   see 
https://github.blog/changelog/2023-01-30-git-archive-checksums-may-change/ + https://github.com/orgs/community/discussions/45830>> 
* Q



Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 1 Feb 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 1 Feb 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments + outlook to next EasyBuild release;

* update on porting of EasyBuild docs to MarkDown (done!);

* source tarballs provided by GitHub will change;
  see 
https://github.blog/changelog/2023-01-30-git-archive-checksums-may-change/ 
+ https://github.com/orgs/community/discussions/45830


* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] EasyBuild documentation migrated to MarkDown (MkDocs)

[Kenneth Hoste]

Dear EasyBuilders,

I'm pleased to announce that the migration of the EasyBuild 
documentation to MarkDown + MkDocs has been completed.


This effort has been discussed for a long time, and was finally 
kickstarted in October 2022.
It's the first major revamp of the EasyBuild documentation since it was 
created in


The EasyBuild documentation at https://docs.easybuild.io now has a very 
different look, is better organised, and has a significantly better 
search function.
The documentation sources in MarkDown are located in a dedicated 
repository at https://github.com/easybuilders/easybuild-docs .


The content is largely identical to the "old" documentation (which was 
rendered using Sphinx, with the .rst sources located in the 'docs' 
subdirectory of the https://github.com/easybuilders/easybuild repository).
However, we hope that completing this migration can be the starting 
point for thoroughly revising, updating, and extending the EasyBuild 
documentation.


Automatic redirects have been put in place to try and ensure that you 
won't run into any broken links, even if they still point to the old 
structure of the documentation, or use an outdated URL that starts with 
'https://easybuild.readthedocs.io/' .


The EasyBuild tutorial (https://tutorial.easybuild.io) is currently 
still a separate website - we may integrate that into the EasyBuild 
documentation (since both are rendered with MkDocs).



Thanks a lot to Simon Branford and James Carpenter, both from the 
University of Birmingham, for their extensive involvement in this 
migration effort, as well as to anyone else who has contributed to it 
(directly or indirectly).


If you notice any problems, or have some suggestions for 
changes/enhancments, please report them via 
https://github.com/easybuilders/easybuild-docs/issues, or open a pull 
request.



regards,

Kenneth

Re: [easybuild] next EasyBuild conf call: Wed 18 Jan 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Hi all,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230118 



Next bi-weekly conf call is planned on Wed 1 Feb 2023 at 09:00 UTC, see 
also https://github.com/easybuilders/easybuild/wiki/Conference-calls.



regards,

Kenneth

On 17/01/2023 22:41, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 18 Jan 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments;

* update on porting of EasyBuild docs to MarkDown;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] next EasyBuild conf call: Wed 18 Jan 2023 at 16:00 UTC (17:00 CET)

[Kenneth Hoste]

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 18 Jan 2023 at
16:00 UTC (17:00 CET).

You can join the conf call via https://tiny.cc/eb_conf_call .

Current agenda:

* overview of recent developments;

* update on porting of EasyBuild docs to MarkDown;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth

[easybuild] [ANN] EasyBuild v4.7.0

[Kenneth Hoste]

Dear EasyBuilders,

I'm happy to announce the release of EasyBuild v4.7.0 [1].

Since the start of 2023, we have managed to hold back on releasing 
EasyBuild v4.7.0, but we can't keep it from you any longer, since this 
beyond any doubt is the best EasyBuild release to date.


Hopefully you did not fall for the silly attempts to distract you from 
this release, like some open source software projects making a lot of 
fuss of something trivial like a new logo, or people celebrating just 
another lap around the sun for some reason...



The executive summary for EasyBuild v4.7.0:

  - running EasyBuild on top of Python 2 is deprecated;

  - various minor bug fixes and enhancements to EasyBuild framework, 
including support for generating documentation in MarkDown format;


  - enhancements and changes to the (still experimental) support for 
easystack files;


  - two new generic easyblocks, for installing (bundles of) Julia 
packages: JuliaPackage and JuliaBundle;


  - various minor bug fixes and enhancements to existing easyconfigs 
and easyblocks;


  - easyconfigs for the 2022b update of the common toolchains: 
foss/2022b and intel/2022b;


  - support for installing 107 (!) new software applications and 
libraries, and updated versions of already supported software;




EasyBuild v4.7.0 is primarily a feature release, but it also includes 
various minor bug fixes and enhancements.


Highlights for this release are listed below. More details are available 
in the release notes [2] which includes links to the respective pull 
requests for more detailed information.


(this information is also available at 
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.7.0)



## Highlighted enhancements

[enhancements that (may) warrant updating existing installations are 
marked with (***)]


- also run unit tests with Python 3.11;

- add support for checksums specified in external checksums.json file;

- take into account custom configuration options specified in easystack 
files - see also https://docs.easybuild.io/en/latest/Easystack-files.html;


- add support for using --output-format=md (MarkDown);

- add support for postinstallmsgs;

- add gfbf as subtoolchain of foss;

- make iimkl toolchain aware of intel-compilers;

- add generic easyblocks for installing (bundle of) Julia packages: 
JuliaPackage + JuliaBundle;


- updates and enhancements for various generic easyblocks, incl. 
ConfigureMake, PythonPackage;


- (***) updates and enhancements for various software-specific 
easyblocks: BerkeleyGW, Clang, Clang-AOMP, ESMF, libxml2, LLVM, OpenCV, 
OpenMPI, PETSc, QScintill, TensorFlow, Xmipp;



## Prominent bug fixes & changes

[bug fixes or changes that (may) warrant reinstalling easyconfigs are 
marked with (***)]


- print deprecation warning with running EasyBuild with Python 2;

- various tweaks to docstrings and help messages to fix problems with 
auto-generated documentation in MarkDown format;


- vendor distutils.version.LooseVersion as easybuild.tools.LooseVersion 
(since distutils is deprecated in Python 3.10, to be removed in Python 
3.12);


- auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0;

- use -march=x86-64 -mtune=generic instead of -xSSE2 when using Intel 
oneAPI compilers;


- drop support for easystack files using 'software' top-level key;

- make PythonPackage easyblock compatible with --sanity-check-only by 
loading module early during sanity check step;


- (***) update HDF5 easyblock to use --enable-threadsafe configure 
option to make C API thread safe;


- (***) bug fixes for various software-specific easyblocks: ANSYS, 
Clang, MRtrix, PyTorch;



## Supported software


New version of common toolchains: foss/2022b, intel/2022b

Support for installing 107 new software packages has been added, 
including (but not limited to):


  Alfred
  bamFilters
  CAT-BAT
  CloudCompare
  COBRApy
  CUDA-Samples
  DeepLabCut
  DRAGMAP
  ESM-2
  HighFive
  IJulia
  KaHIP
  LHAPDF
  Magics
  MEMOTE
  MONAI
  MOOSE
  MultilevelEstimators
  napari
  nf-core-mag
  OmegaFold
  pyccel
  PyDamage
  pyWannier90
  scvi-tools
  SELFIES
  SISSO++
  spaCy
  Squidpy
  TBA
  trimesh
  UCX-ROCm

  => This brings the total number of supported software packages to 
2,904 (excluding extensions)!

 An up-to-date list of supported software is available at [3].


Various software updates have been added, including (but not limited to):

  AOCC 4.0.0
  CDO 2.1.1
  CubeGUI/CubeLib/CubeWriter 4.8
  CUDA 11.8.0 + 12.0.0
  deepdiff 5.8.1
  FLANN 1.9.1
  GATK 4.3.0.0
  GDCM 3.0.20
  Ghostscript 10.0.0
  GRASS 8.2.0
  JasPer 4.0.0
  libspatialite 5.0.1
  LLVM 15.0.5
  Mesa 22.2.4
  mold 1.7.1
  MRChem 1.1.1
  ncbi-vdb 3.0.0
  nglview 3.0.3
  nodejs 18.12.1
  Octave 7.1.0
  OpenFOAM 10
  OpenFold 1.0.1
  OpenMolcas 22.10
  OpenStackClient 6.0.0
  PAPI 7.0.0,
  PETSc 3.17.4
  pyproj 3.4.0
  Python 3.10.8
  PyTorch 1.12.1
  PyTorch-Geometric 2.1.0
  QGIS 3.28.1
  Qt5 5.15.7
  

Re: [easybuild] PythonBundle and use_pip_requirement

[Kenneth Hoste]

Hi Arnau,

When using PythonBundle, you should specify 'sources' for specific 
extensions in exts_list (not "top-level").



regards,

Kenneth

On 09/01/2023 14:53, Arnau wrote:

Dear all,

I'd like to install a bunch of python packages from a requirements.txt 
instead of listing each of them as extension. So I'd like to use the 
use_pip_requirement option.


According to the doc :

install using ‘python -m pip install –requirement’. The sources is 
expected to be the requirements file.


but as soon as I add the sources to point to the requirements file EB 
complains with the error:


" List of sources for bundle itself must be empty, found 
['requirements.txt']"


If I do not add any sources at all, it does not install anythings at all.

so, what is the correct way of using this option in a PythonBundle?

(eb 4.6.2)

TIA,
Arna

Re: [easybuild] next EasyBuild conf call: Wed 4 Jan 2023 at 09:00 UTC (10:00 CET)

[Kenneth Hoste]

Hi all,

Notes on today's conf call are available at 
https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20230104 
.


Next call is planned for Wed 18 Jan 2023 at 16:00 UTC, see also 
https://github.com/easybuilders/easybuild/wiki/Conference-calls



regards,

Kenneth

On 03/01/2023 21:19, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wed 4 Jan 2023 at
09:00 UTC (10:00 CET).

You can join the conf call via 
https://tiny.cc/eb_conf_call .


Current agenda:

* overview of recent developments + outlook to EasyBuild v4.7.0;

* update on porting of EasyBuild docs to MarkDown;

* Q


Suggestions for additional topics are always welcome!

More information on the EasyBuild conf calls is available at
https://github.com/easybuilders/easybuild/wiki/Conference-calls .

regards,

Kenneth