Re: [easybuild] MATLAB: ISOs no longer available?

-- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark, Fysikvej Building 309, DK-2800 Kongens Lyngby, Denmark E-mail: ole.h.niel...@fysik.dtu.dk Homepage: http://dcwww.fysik.dtu.dk/~ohnielse/ Mobile: (+45) 5180 1620

Re: [easybuild] What is the meaning of --cuda-compute-capabilities ?

umbers: https://developer.nvidia.com/cuda-gpus. Great, thanks a lot for sharing your insights! EasyBuild developers: Could you kindly add the above two URLs to the documentation at https://docs.easybuild.io/en/latest/version-specific/help.html ? Best regards, Ole -- Ole Holm Nielsen PhD, Seni

[easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

1 cpu tests failed: //tensorflow/core/common_runtime:graph_constructor_test == 2021-05-26 15:30:49,721 easyblock.py:298 INFO Closing log for application name TensorFlow version 2.4.1 Can anyone suggest a fix for this issue? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department

[easybuild] What is the meaning of --cuda-compute-capabilities ?

separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) This makes me none the wiser! Can anyone tell me what these numeric values are supposed to mean, and how I pick the right values for the GPUs in my nodes? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department

Re: [easybuild] Build fails for OpenBLAS-0.3.12-GCC-10.2.0.eb on Intel Ice Lake processors

n I tell OpenBLAS that we have an Intel Ice Lake CPU? It seems that OpenBLAS doesn't know about Ice Lake nor Cascade Lake :-( https://github.com/xianyi/OpenBLAS/blob/develop/TargetList.txt Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of

Re: [easybuild] Build fails for OpenBLAS-0.3.12-GCC-10.2.0.eb on Intel Ice Lake processors

-20210528.152213.BZayz.log and figure out what the actual problem is. On 5/28/21 3:26 PM, Ole Holm Nielsen wrote: Hi Simon, On 5/28/21 2:50 PM, Simon Branford wrote: OpenBLAS recently added IceLake detection: https://github.com/xianyi/OpenBLAS/pull/3233 Thanks a lot for the info!  It seems that Ice Lake

Re: [easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

. For each of those (2) tests there should be some more detailed output Search for "At least 2 gpu tests failed" and look below. FYI: Setting EASYBUILD_TMPDIR to a large directory is not required. Temporary files are usually small. Am 27.05.21 um 13:02 schrieb Ole Holm Nielsen: On 5/27/2

Re: [easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

On 5/27/21 10:46 AM, Alexander Grund wrote: > Alexandre: should we look for patterns like "No space left on device" in the Bazel output and highlight them better, perhaps with a concrete suggestion to use --tmpdir to avoid the usage of /tmp? We could in general put something into EasyBuild,

Re: [easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

I can gzip it and send you an URL? Thanks, Ole FYI: Setting EASYBUILD_TMPDIR to a large directory is not required. Temporary files are usually small. Am 27.05.21 um 13:02 schrieb Ole Holm Nielsen: On 5/27/21 10:46 AM, Alexander Grund wrote:  > Alexandre: should we look for patterns like &

Re: [easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

On 5/27/21 10:46 AM, Alexander Grund wrote: /home/modules/software/binutils/2.35-GCCcore-10.2.0/bin/ld.gold: fatal error: bazel-out/k8-opt/bin/tensorflow/core/common_runtime/graph_constructor_test: No space left on device What device might that be?  As shown above, I have quite a bit of disk

Re: [easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

-fosscuda-2019b-Python-3.7.4.eb --robot --cuda-compute-capabilities=6.1,7.5 --buildpath=/dev/shm --tmpdir=/scratch/eb-build Yes, I configured that with: export EASYBUILD_BUILDPATH=/run/user/$UID/eb_build ulimit -s 2000240 export EASYBUILD_TMPDIR=/scratch/$USER Thanks, Ole -- Ole Holm Nielsen PhD

Re: [easybuild] Build failure with PyTorch-1.7.1-fosscuda-2020b.eb

, but perhaps it rings a bell for Alexander (in CC). There are a couple of fixes related to PyTorch that will be included in the upcoming EasyBuild v4.4.0 release (which will be released tomorrow hopefully), so keep an eye out for that... regards, Kenneth On 01/06/2021 09:56, Ole Holm Nielsen wrote

Re: [easybuild] Build failure with PyTorch-1.7.1-fosscuda-2020b.eb

for the update Ole! regards, Kenneth On 03/06/2021 07:42, Ole Holm Nielsen wrote: Hi Kenneth, I can confirm that with EasyBuild v4.4.0 the PyTorch 1.8.1 installation went smoothly and without any problems: $ eb PyTorch-1.8.1-foss-2020b.eb -r Best regards, Ole On 6/1/21 5:13 PM, Kenneth Hoste wrote

Re: [easybuild] Build failure with PyTorch-1.7.1-fosscuda-2020b.eb

(CI tests are failing currently), but you can try installing that using "eb --from-pr 12814". regards, Kenneth On 03/06/2021 10:17, Alexander Grund wrote: There is an open PR in the easyconfigs repo. Check that :) Am 03.06.21 um 10:16 schrieb Ole Holm Nielsen: Our users

Re: [easybuild] ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 2.6+ or 3.5+)

om easybuild.tools.config import build_option File "/home/modules/software/EasyBuild/4.4.0/lib/python3.6/site-packages/easybuild/tools/config.py", line 47, in from easybuild.base.frozendict import FrozenDictKnownKeys ModuleNotFoundError: No module named 'easybuild.base.frozendict' On 04/06/

Re: [easybuild] ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 2.6+ or 3.5+)

On 6/4/21 2:22 PM, Kenneth Hoste wrote: Hi Ole, On 04/06/2021 14:09, Ole Holm Nielsen wrote: On 6/4/21 1:54 PM, Kenneth Hoste wrote: Please try running this, which will probably reveal the problem:     python3 -O -m easybuild.main $ python3 -O -m easybuild.main Traceback (most recent call

Re: [easybuild] ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 2.6+ or 3.5+)

On 6/4/21 2:41 PM, Kenneth Hoste wrote: On 04/06/2021 14:36, Ole Holm Nielsen wrote: $ ls -la /home/modules/software/EasyBuild/4.4.0/lib/python3.6/site-packages/easybuild/base total 172 drwxr-xr-x. 3 modules modules   147 Jun  4 07:30 . drwxr-xr-x. 8 modules modules   137 Jun  3 09:42 .. -rw

Re: [easybuild] Build failure with PyTorch-1.7.1-fosscuda-2020b.eb

Hi Alexander, On 6/4/21 1:46 PM, Alexander Grund wrote: == ERROR: test_process_group_as_module_member (__main__.C10dProcessGroupSerialization) -- Traceback

[easybuild] ERROR: No compatible 'python' command found via $PATH (EasyBuild requires Python 2.6+ or 3.5+)

+6b4b10ec.x86_64 Is there a fix for the inability to locate the python command? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark, Fysikvej Building 309, DK-2800 Kongens Lyngby, Denmark E-mail: ole.h.niel...@fysik.dtu.dk Homepage: http

Re: [easybuild] Build fails for OpenBLAS-0.3.12-GCC-10.2.0.eb on Intel Ice Lake processors

Hi Simon, On 5/28/21 2:50 PM, Simon Branford wrote: OpenBLAS recently added IceLake detection: https://github.com/xianyi/OpenBLAS/pull/3233 Thanks a lot for the info! It seems that Ice Lake gets detected as CPUTYPE_SKYLAKEX? This has been patched in EasyBuild for OpenBLAS 0.3.12 and

Re: [easybuild] TensorFlow build fails in //tensorflow/core/common_runtime:graph_constructor_test

rflow/core/platform/liberror.a', configuration: </tt><tt>f6bc5b6107d950b9fac2186352cdfdfe45c6815016e3edc9f32af940b50d30a6, </tt><tt>execution platform: @local_execution_config_platform//:platform] </tt><tt>ERROR: </tt><tt>/run/user/983/

[easybuild] Build fails for OpenBLAS-0.3.12-GCC-10.2.0.eb on Intel Ice Lake processors

n I tell OpenBLAS that we have an Intel Ice Lake CPU? It seems that OpenBLAS doesn't know about Ice Lake nor Cascade Lake :-( https://github.com/xianyi/OpenBLAS/blob/develop/TargetList.txt Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark,

[easybuild] Build failure with PyTorch-1.7.1-fosscuda-2020b.eb

-zAAAvr/tmpnh77Vl/lib/python3.8/site-packages:$PYTHONPATH && cd test && PYTHONUNBUFFERED=1 /home/modules/software/Python/3.8.6-GCCcore-10.2.0/bin/python run_test.py --verbose -x distributed/rpc/test_process_group_agent test_quantization " exited with exit code 1 and ou == 2021-06

[easybuild] Build of SciPy-bundle-2020.11-intel-2020b.eb fails on AMD Rome node

AssertionError(_build_err_msg()) E AssertionError: E Arrays are not almost equal to 6 decimals EACTUAL: array([2.+1.j, 1.+2.j], dtype=complex64) EDESIRED: array([nan+nanj, nan+nanj], dtype=complex64) E AssertionError: E Arrays

[easybuild] Build fails of OpenMPI/4.0.5-GCC-10.2.0 on AMD EPYC node

em on our own cluster. Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

Re: [easybuild] Build fails of OpenMPI/4.0.5-GCC-10.2.0 on AMD EPYC node

On 12-03-2021 10:35, Ole Holm Nielsen wrote: Thanks a lot for pointing at the solution.  I have asked the sysadmin if he can install the libnl3-devel RPM.  Hopefully that will resolve the issue for us. I can report that after installing the libnl3-devel RPM and rebuilding the libfabric

[easybuild] EB module for AFLOW - Automatic FLOW for Materials Discovery?

Dear Easybuilders, I have received a request to provide the software AFLOW - Automatic FLOW for Materials Discovery (http://aflow.org) with an installation page at http://aflow.org/install-aflow/ Question: Has anyone been working on an EB module for AFLOW? Thanks a lot, Ole -- Ole Holm

Re: [easybuild] Build fails of OpenMPI/4.0.5-GCC-10.2.0 on AMD EPYC node

additional feedback on this is welcome (in particular in the GitHub issue). regards, Kenneth On 11/03/2021 16:11, Ole Holm Nielsen wrote: Dear EasyBuilders, I'm trying to get EasyBuild modules up and running on an external cluster with AMD EPYC 7351 and running CentOS 7.6.  With EB 4.3.3 I can't

Re: [easybuild] Re: UCX ibv_create_cq and UCP worker errors on nodes with EL8 OS and Omni-Path fabric

MPI binaries on multiple clusters but set this on OmniPath: OMPI_MCA_btl='^openib' OMPI_MCA_osc='^ucx' OMPI_MCA_pml='^ucx' to disable UCX and openib at runtime. If you include UCX in EB's OpenMPI it will not compile in "openib" so the first one of those three would not be

Re: [easybuild] ORCA 5.0.1 fails in testing ("There are not enough slots")

-easyblocks/pull/2611 <https://github.com/easybuilders/easybuild-easyblocks/pull/2611> and the linked issues. For an immediate fix, you just need to limit the number of cores used for the build, e.g. use the eb option `--parallel=12` On Mon, 15 Nov 2021 at 09:06, Ole Holm N

Re: [easybuild] Re: UCX ibv_create_cq and UCP worker errors on nodes with EL8 OS and Omni-Path fabric

Hi Åke, On 12/3/21 08:27, Åke Sandgren wrote: On 02-12-2021 14:18, Åke Sandgren wrote: On 12/2/21 2:06 PM, Ole Holm Nielsen wrote: These are updated observations of running OpenMPI codes with an Omni-Path network fabric on AlmaLinux 8.5:: Using the foss-2021b toolchain and OpenMPI/4.1.1-GCC

[easybuild] OpenPMIx PMIx important security issue

installed PMIx modules? Can anyone give the exact command used to rebuild any given PMIx module including the mentioned PRs? Slurm users: Check if your Slurm has been built with PMIx support by: $ srun --mpi=list in which case you must rebuild Slurm without PMIx! Thanks, Ole -- Ole Holm Nielsen

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

Dear Kenneth, On 9/28/23 10:49, Kenneth Hoste wrote: 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

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

nox IB PCIe adapter lying around and mount it in my server? Or maybe a relatively new Omni-Path adapter? Would that make the OpenMPI EB module happy, and would the module work with our future nodes? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark,

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

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? Thanks, Ole On 28/09/2023 09:26, Ole Holm Nielsen wrote: It's interesting that while attempting

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

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

[easybuild] Module for netcdf4-python with the foss-2023a toolchain?

? We're using EB 4.8.1. Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

[easybuild] OpenMPI-4.1.5-GCC-12.3.0.eb Sanity check failed on AMD "Genoa" node

nce we now have used the latest GCC 12.3.0, and we have installed an OPA fabric, the problem would seem to be related to having the AMD "Genoa" hardware. Does anyone have suggestions for building OpenMPI successfully on this platform? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC

Re: [easybuild] Module for netcdf4-python with the foss-2023a toolchain?

looking at the PR now. If the test reports are all successful I will merge it and it will be part of the next EasyBuild release 4.8.2. If you want to install it before the next release you do this with `--from-pr`, e.g.: eb --from-pr 18731 Best, Sebastian On 02.10.23 13:51, Ole Holm Nielsen wrote

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

d: warning: /tmp/eb-74m3kzgo/ccy1Gkzg.o: missing .note.GNU-stack section implies executable stack / == 2023-09-25 16:13:04,293 easyblock.py:328 INFO Closing log for application name OpenBLAS version 0.3.21 Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

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

h Infiniband or Omni-Path, just plain Ethernet. -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

[easybuild] SOLVED: OpenMPI-4.1.5-GCC-12.3.0.eb Sanity check failed on AMD "Genoa" node

builds correctly and passes all its tests. Best regards, Ole On 10/3/23 09:51, 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, Omni-Path (OPA) fabric, and AlmaLinux 8.8 OS. I

Re: [easybuild] MPI jobs fail with intel toolchains after upgrade of EL8 Linux from 8.5 to 8.6

ive me permission to copy over the content of your email to create the issue. Thanks, Alan On Wed, 25 May 2022 at 10:54, Ole Holm Nielsen <mailto:ole.h.niel...@fysik.dtu.dk>> wrote: Hi Easybuilders, I'm testing the upgrade of our compute nodes from Almalinux 8.5 to 8.6 (t

Re: [easybuild] MPI jobs fail with intel toolchains after upgrade of EL8 Linux from 8.5 to 8.6

11:09, Ole Holm Nielsen wrote: Hi Alan, Thanks a lot for the feedback!  I've opened a new issue now: https://github.com/easybuilders/easybuild-easyconfigs/issues/15651 Best regards, Ole On 6/9/22 10:52, Alan O'Cais wrote: Ole, Can you please copy this over to an issue in https://github.

[easybuild] Build of Perl-5.34.1-GCCcore-11.3.0.eb fails due to updated version of Variable-Magic-0.62.tar.gz

': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), Can anyone suggest a workaround such as getting a copy of 0.62? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

Re: [easybuild] Build of Perl-5.34.1-GCCcore-11.3.0.eb fails due to updated version of Variable-Magic-0.62.tar.gz

fetched this tarball: https://cpan.metacpan.org/authors/id/V/VP/VPIT/Variable-Magic-0.62.tar.gz /Ole -Original Message- From: easybuild-requ...@lists.ugent.be On Behalf Of Ole Holm Nielsen Sent: 23 November 2022 12:17 To: easybuild@lists.ugent.be Subject: [easybuild] Build of Perl

Re: [easybuild] Force rebuild of module plus all dependencies

Hi Loris, On 12/2/22 08:27, Loris Bennett wrote: How do I force a total rebuild of, say, a foss toolchain for a different CPU architecture? Up to now I had a homogeneous cluster with Intel Xeon CPUs, now we have acquired some nodes with AMD Epyc CPUs for which I need to build software. I have

Re: [easybuild] Which toolchain to use on AMD EPYC 9004 "Genoa"?

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 g

Re: [easybuild] libxc-5.2.3-GCC-11.3.0.eb: Download incomplete

Hi Loris, I'm being hit by that libxc download problem too! It's very bad for the modules that we're trying to build :-( Should EB use this download URL in stead? https://gitlab.com/libxc/libxc/-/archive/5.2.3/libxc-5.2.3.tar.gz Thanks, Ole On 3/28/23 11:41, Loris Bennett wrote: The EC

Re: [easybuild] libxc-5.2.3-GCC-11.3.0.eb: Download incomplete

Hi Loris, It would be great if you could make a PR against libxc! I'm not that experienced with Git usage ;-) Thanks, Ole On 3/28/23 13:03, Loris Bennett wrote: Hi Ole, Ole Holm Nielsen writes: Hi Loris, I'm being hit by that libxc download problem too! It's very bad for the modules

[easybuild] Which toolchain to use on AMD EPYC 9004 "Genoa"?

s for sharing any advice and experiences! Best regards, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

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

-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

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

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] EB file for building a recent version of Meep?

, 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

[easybuild] Build failure of Rust-1.70.0-GCCcore-12.3.0.eb

st/2023-04-20/rust-std-1.69.0-x86_64-unknown-linux-gnu.tar.xz #=#=- # # == 2023-12-08 20:28:03,383 easyblock.py:328 INFO Closing log for application name Rust version 1.70.0 Can anyone suggest a fix? Thanks, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Te

Re: [easybuild] Build failure of Rust-1.70.0-GCCcore-12.3.0.eb

a lot! This command does the job: $ eb Rust-1.70.0-GCCcore-12.3.0.eb --include-easyblocks-from-pr=3038 On 8 December 2023 20:33:34 CET, Ole Holm Nielsen wrote: I'm trying to build Rust-1.70.0-GCCcore-12.3.0.eb but this fails because of a download failure. I don't know how t

[easybuild] EB modules for AMD ROCm?

about AMD's ROCm RPM packages? Thanks a lot, Ole -- Ole Holm Nielsen PhD, Senior HPC Officer Department of Physics, Technical University of Denmark

Re: [easybuild] Failure in UCX-1.14.1-GCCcore-12.3.0.eb when installing foss-2023a.eb

sa 72, 4a planta 20018 Donostia-San Sebastián, Gipuzkoa, Spain /External Collaborator./ Nano-Bio Spectroscopy group Departamento de Física de Materiales Universidad del País Vasco (UPV/EHU) Donostia-San Sebastián, Gipuzkoa, Spain The Max Planck Institute for the Structure and Dynamics of Matter (MP

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