Re: [easybuild] [ANN] EasyBuild v4.9.1

As can be seen in the description of the PR that added this: https://github.com/easybuilders/easybuild-easyconfigs/pull/19940 the problem was detected on ARM only, but I would recommend rebuilding regardless of arch. It is a bug that might cause problems if not fixed.

[easybuild] Re: pod5-file-format-0.3.10 eb

;s discuss the issue privately, to avoid spamming this generic mailing list. Regards Ehsan -Original Message- From: easybuild-requ...@lists.ugent.be On Behalf Of Åke Sandgren Sent: donderdag 4 april 2024 15:37 To: easybuild@lists.ugent.be Subject: [easybuild] Re: pod5-file-format-0.3.1

[easybuild] Re: pod5-file-format-0.3.10 eb

Yes, I finished that one yesterday. Haven't had time to make a PR of it yet though. From: easybuild-requ...@lists.ugent.be on behalf of Borut Rozman Sent: Thursday, April 4, 2024 14:45 To: easybuild@lists.ugent.be Subject: [easybuild] pod5-file-format-0

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

b OK... I will try to updatet libibverbs , isn't it ? I will let you know ! Thanks ! quim Missatge de Åke Sandgren mailto:ake.sandg...@umu.se>> del dia dv., 15 de març 2024 a les 13:49: ConnectX-3 gets dropped in MOFED 5.1, but MOFED 4.9 LTS will still

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

nstalling foss-2023a.eb in another cluster with : > > $lspci | grep -i mellanox > > 86:00.0 Infiniband controller: *Mellanox*Technologies MT27800 Family > [ConnectX-5] > > > > Thank you for any hint ! > > quim > > > Missatge de Åke Sandgren <mailto:ake.sandg..

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

Well, RH7 is deprecated, and that's an OFED 3.3 stack. They (UCX devs) probably didn't even come close to developing on something that old. So IBV_ACCESS_ON_DEMAND doesn't exist in that old distro. I strongly suggest updating, either both OS and OFED stack or just upgrade to the latest MOFED st

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

lling foss-2023a.eb Dear Ake, How can I check this? Thank you! El vie, 15 mar 2024, 7:58, Åke Sandgren mailto:ake.sandg...@umu.se>> escribió: No there is no bug there. Which MOFED stack version are you using? Or does your system lack Infiniband?

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

No there is no bug there. Which MOFED stack version are you using? Or does your system lack Infiniband? From: easybuild-requ...@lists.ugent.be on behalf of Joaquim Jornet Somoza Sent: Thursday, March 14, 2024 16:02 To: easybuild@lists.ugent.be Subject:

Re: [easybuild] EB modules for AMD ROCm?

We have 5.6.0 in an PR, see https://github.com/easybuilders/easybuild-easyconfigs/pull/18772 and it's dependencies. I haven't had time to do extensive testing of it but what little I've tried does at least work. It's not a proper toolchain yet though. Fr

[easybuild] Re: Will rebuilding GCCcore cause jobs to fail?

Depends on you setup. If you use something like a plain NFS (or other direct remote FS) for building/installing into then it will be gone the whole time. Using a CMVFS setup (like we do) with a separate FS for the actual build/install phase, it will be gone for <1s at most. I.e., we use a NFS ba

[easybuild] Re: Specifying optimization in easyconfigs

Start by looking at https://docs.easybuild.io/version-specific/toolchain-opts/ for the various toolchainopts you can set. The definition of them are in easybuild-framework/easybuild/toolchains/compiler/intel_compilers.py and easybuild-framework/easybuild/toolchains/compiler/inteliccifort.py toolc

Re: [easybuild] Bowtie2 2.3.5.1 with gcc 11.3.0

11.3.0 Hi Ake, But howcome that I was able to compile GCC 8.3 : GCC: GCC/8.3.0, GCC/11.2.0, GCC/11.3.0 Those versions did compile on my system? Borut On Wed, 2023-10-25 at 08:45 +, Åke Sandgren wrote: > Building GCC 10.3 on a Ubuntu 22.04 system would require some > difficult patching

Re: [easybuild] Bowtie2 2.3.5.1 with gcc 11.3.0

Building GCC 10.3 on a Ubuntu 22.04 system would require some difficult patching, it's just too old for the OS and binutils used so don't even try. From: easybuild-requ...@lists.ugent.be on behalf of Borut Rozman Sent: Wednesday, October 25, 2023 10:32

[easybuild] Re: Bowtie2 2.3.5.1 with gcc 11.3.0

Why build such an old version of Bowtie2? We have Bowtie2-2.4.5-GCC-11.3.0.eb already. From: easybuild-requ...@lists.ugent.be on behalf of Borut Rozman Sent: Tuesday, October 24, 2023 19:19 To: easybuild@lists.ugent.be Subject: [easybuild] Bowtie2 2.3.5

Re: [easybuild] Error trying to create new EC for TINKER 8.10.3

It probably failed on something else before that, you need to go hunting in the output log. From: easybuild-requ...@lists.ugent.be on behalf of Loris Bennett Sent: Thursday, October 12, 2023 17:02 To: easybuild Subject: [easybuild] Error trying to creat

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

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

[easybuild] Re: Gromacs build issue : GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb

FYI, GROMACS/2023.1 is now merged, so PR 18171 should be good to use. From: easybuild-requ...@lists.ugent.be on behalf of Åke Sandgren Sent: Tuesday, June 27, 2023 7:27 To: easybuild@lists.ugent.be Subject: [easybuild] Re: Gromacs build issue : GROMACS

[easybuild] Re: Gromacs build issue : GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb

Yeah, known (but not well documented) problem with jammy and old CUDA related packages. You need to stick to 2022a toolchain with CUDA 11.7.0 on Jammy. I'm currently working on getting GROMACS/2023.1 ready for 2022a with CUDA 11.7.0 where this is not a problem. It'll take a while longer before I

Re: [easybuild] EC for medaka 1.8.0

Last one I have is for 1.7.1 with foss/2021b From: easybuild-requ...@lists.ugent.be on behalf of Loris Bennett Sent: Tuesday, May 30, 2023 16:11 To: easybuild Subject: [easybuild] EC for medaka 1.8.0 Hi, Does anyone have a working EC for medaka 1.8.0?

[easybuild] Re: Managing Site-specific Easyconfigs

We use the hooks system to handle almost all of the site changes. There is some examples in the contrib dir. We also have our own repo of things (both easyconfigs/blocks and of course the hooks). The easyconfigs/blocks there are usually only kept until they appear in the next release.

Re: [easybuild] file-5.43-GCCcore-11.3.0.eb failure: __NR_statx undeclared

Which OS is this? I see no problems on Ubuntu 20.04 or 22.04 From: easybuild-requ...@lists.ugent.be on behalf of Loris Bennett Sent: Wednesday, May 24, 2023 8:24 To: easybuild Subject: [easybuild] file-5.43-GCCcore-11.3.0.eb failure: __NR_statx undeclar

Re: [easybuild] [GROMACS/2019.4-foss-2019a] Double precision version by default?

GROMACS-2019.4-foss-2019a.eb is not part of the EasyBuild repo so there might be something different in the local version compared to for instance GROMACS-2019.3-foss-2019b.eb which do build single/double + mpi/no-mpi versions gmx (single precision, no mpi) gmx_d (double precision, no mpi) gmx_m

Re: [easybuild] problem building the attached EB file

Your ESMPy-8.0.1-intel-2021b.eb is wrong. Compare the list of dependencies with ESMPy-8.0.1-intel-2020b.eb from the EB release. Both the one for SciPy-bundle and ESMF is wrong, they are both trying to use an incorrect toolchain. On 4/28/22 22:55, mohammed shambakey wrote: Hi I'm new to eas

Re: [EXTERNAL] [easybuild] Limiting access to licensed software by groups.

We use ACL's instead for this, through hooks: === def parse_hook(ec): if ec.name == 'VASP' or ec.name == 'VASP-data' or ec.name == 'ORCA': ec.log.info("[parse hook] Enforcing umask 007") os.umask(int('007', 8)) update_build_option('umask', '007') def post_install_hook(self, *args, *

Re: [easybuild] OpenMPI: --with-slurm needed or not

On 2/2/22 15:21, Loris Bennett wrote: Hi Alex, Thanks for the clarification. Would it be worth expanding the comment in the OpenMPI EC to make this clear, at least for v4 and later? And what is the current thinking with regards to building PMIx support for Slurm? There seem to be 4 main op

Re: [easybuild] PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb: test_gpipe.py fails

pabilities=6.1,7.5 --buildpath=/dev/shm > --tmpdir=/scratch/eb-build --from-pr 14496 > > it failed in the same way. > > Cheers, > > Loris > > Åke Sandgren writes: > >> Reg the cuda-enabled openmpi problem, see PR >> https://github.com/easybuilders/easyb

Re: [easybuild] PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb: test_gpipe.py fails

Reg the cuda-enabled openmpi problem, see PR https://github.com/easybuilders/easybuild-easyconfigs/pull/14496 On 12/21/21 1:34 PM, Loris Bennett wrote: > Hi, > > I am running > > eb PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb --robot > --cuda-compute-capabilities=6.1,7.5 --buildpath=/dev/shm >

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

On 12/2/21 8:20 PM, Ole Holm Nielsen wrote: > Hi Åke, > > 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

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

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-11.2.0 my trivial > MPI test code works correctly: > > $ ml OpenMPI > $ ml > > C

Re: [easybuild] CP2K-7.1-foss-2020b.eb - undefined reference to 'dfftw_plan_with_nthreads_'

ion, so I’m CC’ing him. >> >> On 5. Oct 2021, at 09:32, Alan O'Cais wrote: >> >> I think Åke is right from looking at >> https://groups.google.com/g/cp2k/c/H7K8vR3vEto . You probably need that flag >> to trigger the linking to the fftw3_threads library.

Re: [easybuild] CP2K-7.1-foss-2020b.eb - undefined reference to 'dfftw_plan_with_nthreads_'

You do know that there is a CP2K-7.1-foss-2020b-psmp.eb available already? that one also have toolchainopts openmp=true On 10/5/21 8:58 AM, Loris Bennett wrote: > Hi, > > I am trying to build CP2K 7.1 via > > CP2K-7.1-foss-2020b.eb > > whereby we use the following in a hook > > # Build

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

First of all, check the Result log: tmp/eb-jcym6or4/easybuild-OpenBLAS-0.3.12-20210528.152213.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: >>

Re: [easybuild] Github integration failing: could not read from remote repository

Yeah, I might have misread the actual problem. Concentrating too much on the ongoing EUM'21... On 1/29/21 2:44 PM, Loris Bennett wrote: > Hi Åke, > > Åke Sandgren writes: > >> Looks like a problem with your github token, not your ssh key. > > You may well be right

Re: [easybuild] Github integration failing: could not read from remote repository

Looks like a problem with your github token, not your ssh key. On 1/29/21 1:20 PM, Loris Bennett wrote: > Hi Jakob, > > Jakob Schiøtz writes: > >> Hi Loris, >> >> I have seen problems like that if the right modules are not installed in the >> Python installation used by Easybuild, i.e. the syst

Re: [easybuild] Compilation error for QuantumESPRESSO-6.6-intel-2020a.eb

On 12/18/20 9:30 PM, Joaquim Jornet Somoza wrote: > Dear all,  > > I am trying to compile the latest stable version of QuantumESPRESSO > using the intel/2020a  > toolchain, modifying the eb file found in the git repository: > > https://github.com/easybuilders/easybuild-easyconfigs/blob/develop

Re: [easybuild] gnu/stubs-32.h: No such file or directory

That one comes from libc6-dev-i386 or similar for RH based systems. On 12/1/20 2:28 PM, Loris Bennett wrote: > Hi, > > I am getting the following error with the foss-2020a toolchain: > > /usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file or > directory > 7 | # incl

Re: [easybuild] Looking for a COMSOL easyblock

I have these available: Comsol-5.2a.eb Comsol-5.3.0.248.eb COMSOL-5.3.0.260.eb COMSOL-5.3.1.348.eb COMSOL-5.4.0.225.eb if that would help, but I we're not adding MATLAB as a dep in those. On 9/29/20 2:51 PM, Ole Holm Nielsen wrote: > Dear Easybuilders, > > I have been asked to install a module

Re: [easybuild] Non-binary dependencies for PackedBinary?

You could put it under a toolchain to make it all somewhat simpler since it will need Python... And it should then have a dependency on the corresponding version of SciPy-Bundle which contains numpy. On 9/29/20 1:31 PM, Loris Bennett wrote: > Hi, > > If I have a program available as a packed bin

Re: [easybuild] Boost.Python for CUDA?

On 8/24/20 3:48 PM, Loris Bennett wrote: > Hi, > > based on > > > https://github.com/easybuilders/easybuild-easyconfigs/blob/ac0b95d3074b89d422e64446e5d5f0cc8f2035a3/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2019.1.2-intelcuda-2019b-Python-3.7.4.eb > > I am trying to build a FOSS version. How

Re: [easybuild] FFmpeg with CUDA?

There is a FFmpeg-4.1-fosscuda-2018b.eb in our installed tree. Not quite sure if it actually enabled CUDA in the build though. On 6/29/20 1:40 PM, Loris Bennett wrote: > Hi, > > I see that EB provides several versions of FFmpeg, but none which use > CUDA. Is this just because no-one has felt the

Re: [easybuild] missing lapack library

foss uses openblas for lapack/blas library, so you need to tell xtb to use -lopenblas for both of them. On 3/6/20 11:02 PM, Daniel Placencia Alvarez wrote: > > Dear Easybuilders, > I am trying to add support for the XTB software in EasyBuild. As a toolchain > I am using foss-2019a, in the docu

Re: [easybuild] Slurm/MPI error on importing tensorflow

On 2/28/20 1:59 PM, Loris Bennett wrote: > Åke Sandgren writes: > >> On 2/19/20 8:21 AM, Loris Bennett wrote: >>> OK, so you have the various PMIx versions installed both within *and* >>> separate from EB - that's the bit I was missing. It is obviously a &g

Re: [easybuild] Dependencies between OpenMPI, PMIx, and Slurm

On 2/20/20 1:01 PM, Loris Bennett wrote: > Åke Sandgren writes: > >> On 2/13/20 4:32 PM, Loris Bennett wrote: >>> PS: Slightly strangely, EB has a patch for PMIx 2.2.1 but no actual EC: >> >> Now available in >> https://github.com/easybuilders/easybuil

Re: [easybuild] Re: ``eb foss-2018a.eb -r --rebuild'' failed.

On 2/20/20 8:36 AM, Hongyi Zhao wrote: > Åke Sandgren 于2020年2月20日周四 下午3:21写道： >> >> glibc from EasyBuild has nothing to do with this, and you should >> probably not use it ever. > > But I want to compile a toolchain which include glibc, so than it can >

Re: [easybuild] Re: ``eb foss-2018a.eb -r --rebuild'' failed.

glibc from EasyBuild has nothing to do with this, and you should probably not use it ever. Please just make the change I mentioned and try to build GCCcore-.6.4.0.eb again. -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46

Re: [easybuild] Re: ``eb foss-2018a.eb -r --rebuild'' failed.

On 2/20/20 2:32 AM, Hongyi Zhao wrote: > Alan O'Cais 于2020年2月19日周三 下午9:47写道： >> >> Hi Hongsheng, >> >> Judging by your other emails to the list you got past this issue. For the >> sake of closing the thread, can you tell us what the problem was? > > > No, I cannot solve any of these issues.

Re: [easybuild] ``eb Python-3.7.4-GCCcore-8.3.0.eb -r'' stuck at the last step.

On 2/20/20 2:26 AM, Hongyi Zhao wrote: > Why it's so time expensive? BTW, even I compile python separately, it > use less time. A quick guess is that you don't use the same optimization levels that EasyBuild does. -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@h

Re: [easybuild] ``eb Python-3.7.4-GCCcore-8.3.0.eb -r'' stuck at the last step.

On 2/19/20 12:26 PM, Hongyi Zhao wrote: > Hi, > > I try with the following command: > > --- > $ eb Python-3.7.4-GCCcore-8.3.0.eb -r > == temporary log file in case of crash /tmp/eb-qHmcnW/easybuild-8DQbUx.log > == resolving dependencies ... > == processing EasyBuild easyconfig > /home/

Re: [easybuild] Slurm/MPI error on importing tensorflow

On 2/19/20 8:21 AM, Loris Bennett wrote: > OK, so you have the various PMIx versions installed both within *and* > separate from EB - that's the bit I was missing. It is obviously a > slightly clunky solution, but, as you say, not much maintenance needed > once it has been set up. I think this

Re: [easybuild] Slurm/MPI error on importing tensorflow

is no reason to change that until Slurm actually supports a newer version... On 2/18/20 4:20 PM, Loris Bennett wrote: > Åke Sandgren writes: > >> Since Slurm is built with the system compiler you should also build its >> PMIx/UCX builds with the system compiler (and the corr

Re: [easybuild] Slurm/MPI error on importing tensorflow

Since Slurm is built with the system compiler you should also build its PMIx/UCX builds with the system compiler (and the corresponding libevent in case you don't use the system version), and keep them separate from the EB installation. (Also check the compatibility matrix for PMIx.) Build Slurm

Re: [easybuild] Dependencies between OpenMPI, PMIx, and Slurm

On 2/17/20 9:42 AM, Loris Bennett wrote: > OK, thanks for that. Now I think I get it. Just to be absolutely clear > and apologies in advance for nitpicking, but the PMIx v2 you use is > 2.2.1, as also referenced in your parse hook. However, in your Slurm > config you have > > --with-pmix=/l

Re: [easybuild] Dependencies between OpenMPI, PMIx, and Slurm

On 2/17/20 10:22 AM, Loris Bennett wrote: > Åke Sandgren writes: > >> Might depend on version of OpenMPI > > https://pmix.org/support/faq/which-environments-include-support-for-pmix/ > > just says > > Open MPI v2.x: PMIx v1.2 > Open MPI v3.x: PMIx

Re: [easybuild] Dependencies between OpenMPI, PMIx, and Slurm (was: [easybuild] Advice about Slurm in OpenMPI EC outdated?)

On 2/13/20 4:32 PM, Loris Bennett wrote: > PS: Slightly strangely, EB has a patch for PMIx 2.2.1 but no actual EC: Now available in https://github.com/easybuilders/easybuild-easyconfigs/pull/9877 -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone

Re: [easybuild] Dependencies between OpenMPI, PMIx, and Slurm (was: [easybuild] Advice about Slurm in OpenMPI EC outdated?)

On 2/13/20 4:32 PM, Loris Bennett wrote: > Hi Åke, > > I see you that in your parse_hook you have > > if ec.name == 'OpenMPI': > ... > if LooseVersion(ec.version) >= LooseVersion('2.1'): > pmix_version = '1.2.5' > ucx_version = '1.4.0' >

Re: [easybuild] Advice about Slurm in OpenMPI EC outdated?

Yeah, the comment in that easyconfig is due for a rewrite. You could also look at https://github.com/easybuilders/easybuild-framework/pull/2777 for more ways to handle this. On 2/13/20 1:37 PM, Loris Bennett wrote: > Hi, > > In > > OpenMPI-4.0.2-GCC-9.2.0-2.32.eb > > it says > > # to enab

Re: [easybuild] How does 'noqanda' work?

On 2/6/20 9:29 AM, Kenneth Hoste wrote: > Dear Loris, > > On 04/02/2020 08:39, Loris Bennett wrote: >> Hi, >> >> I am still struggling with CPLEX.  I have added a missing entry to >> qanda, which seems to get me through the pre-install dialog. >> >> What I am not sure about is the how noqanda w

Re: [easybuild] How does 'noqanda' work?

On 2/6/20 2:06 PM, Åke Sandgren wrote: > > > On 2/6/20 9:29 AM, Kenneth Hoste wrote: >> Dear Loris, >> >> On 04/02/2020 08:39, Loris Bennett wrote: >>> Hi, >>> >>> I am still struggling with CPLEX.  I have added a missing entry to &g

Re: [easybuild] disabling defaultprec in iccifort toolchain

But ROOT is not a pythonpackage it is cmakemake, so that "should" not be the problem. On 2/4/20 10:11 AM, Mikael Öhman wrote: > I recognize this type of error; it's exactly what you get in > pythonpackages under intel with Python @ GCCcore where it picks up GCC > as the linker command, but tries t

Re: [easybuild] disabling defaultprec in iccifort toolchain

The intel build may still need the configure_FftwFromMkl_28.patch, ROOT-v5_recent-ifort.patch and possibly the ROOT-v5.34.26_libX.patch like the ROOT-6.10.08-intel-2017b-Python-2.7.14.eb does. On 2/4/20 6:21 AM, Jack Perdue wrote: > Howdy all, > > I'm trying to build a ROOT/6.14.06/intel-2018b-Py

Re: [easybuild] fixed-installdir-naming-scheme

On 12/16/19 6:05 PM, Yann Sagon wrote: > My $MODULEPATH contains after loading fosscuda/2019b: > > /opt/ebmodules/all/MPI/GCC/8.3.0/OpenMPI/3.1.4:/opt/ebmodules/all/Compiler/GCC/8.3.0:/opt/ebmodules/all/Compiler/GCCcore/8.3.0 For a standard HMNS loading fosscuda/2019b should show (in your case

Re: [easybuild] Building Rmpi: "PMI2_Init failed to intialize. Return code: 14"

On 12/6/19 6:31 PM, Will Furnass wrote: >> So you install PMIx using EasyBuild? I think I'm right in saying that > Slurm also depends on PMIx (and PMIx itself depends on hwloc). Out of > curiosity, how do you manage Slurm depending on PMIx given you have > multiple PMIx builds but only one Slu

Re: [easybuild] Building Rmpi: "PMI2_Init failed to intialize. Return code: 14"

On 12/6/19 3:59 PM, Will Furnass wrote: > Hi all, > > We're using EasyBuild 4.0.0 on a Centos 7 + Slurm 19.05 system. We're > able to build and use 'foss-2019a' EasyBuild toolchain (which includes > OpenMPI 3.1.3) using the libpmi2 provided by the Slurm folks (by > uncommenting "configopts = '

Re: [easybuild] Specifying partition for job-backend 'Slurm'

On 12/5/19 4:46 PM, Loris Bennett wrote: > Åke Sandgren writes: > >> On 12/5/19 11:40 AM, Loris Bennett wrote: >>> I have tried this with >>> >>> #!/bin/bash >>> >>> #SBATCH --job-name=easybuild_gpu >>> #SBATCH --nta

Re: [easybuild] Specifying partition for job-backend 'Slurm'

On 12/5/19 11:40 AM, Loris Bennett wrote: > I have tried this with > > #!/bin/bash > > #SBATCH --job-name=easybuild_gpu > #SBATCH --ntasks=4 > #SBATCH --time=12:00:00 > #SBATCH --mem-per-cpu=1G > #SBATCH --partition=gpu > #SBATCH --qos=medium > > srun eb Keras-2.2.4-fosscuda-

Re: [easybuild] Assistance with build

On 12/5/19 10:43 AM, Kenneth Hoste wrote: > On 05/12/2019 10:33, Ricardo Gregorio wrote: >> Hi Ake >> >> Thank you for taking your time to reply. >> >> As I had mentioned, this is all new to me and I am trying to >> understand the concept and mechanisms of EasyBuild. >> >> You said you are worki

Re: [easybuild] Specifying partition for job-backend 'Slurm'

It's really the env vars to sbatch you should look at, that's what is used to submit jobs. On 12/4/19 10:53 AM, Alan O'Cais wrote: > Sorry,  https://slurm.schedmd.com/srun.html#lbAH > > On Wed, 4 Dec 2019 at 10:36, Alan O'Cais > wrote: > > Hi Loris, > > Yo

Re: [easybuild] Specifying partition for job-backend 'Slurm'

If you're building a single easyconfig you could also just make a small submit file that runs eb the same way you would do manually, and send it to the right node. On 12/4/19 10:23 AM, Loris Bennett wrote: > Hi, > > With Kenneth's help I have realised/remembered that I need to compile > Keras / T

Re: [easybuild] building Python through gc3pie

On 12/2/19 3:32 PM, Jure Pečar wrote: > On Mon, 2 Dec 2019 11:14:26 +0100 > Riccardo Murri wrote: > >> Looks like EB is not cleaning up `PYTHONPATH` correctly? Settings of >> the build environment (EB + GC3Pie) should not leak into the package >> being built (i.e., Python3)... > > Yes, agree

Re: [easybuild] Modifying CXXFLAGS in hook?

ld only change opts related to configure step. build step opts should be done in pre_build_hook On 11/27/19 1:29 PM, Loris Bennett wrote: > Åke Sandgren writes: > >> What does your hooks look like? > > def pre_configure_hook(self, *args, **kwargs): > > "&quo

Re: [easybuild] Modifying CXXFLAGS in hook?

What does your hooks look like? And in what hook are you trying to do this? (Which i'll see when you show me the hook ...) On 11/27/19 10:19 AM, Loris Bennett wrote: > Hi Åke, > > Åke Sandgren writes: > >> You might need to add it to the configopts (preconfigopts). Not s

Re: [easybuild] Replacing Intel compiler option -ftz with -no-ftz

Or perhaps add a "noprec" option that does NOT set any precision flags at all, leaving it up to the easyconfig to specify? On 11/19/19 3:17 PM, Åke Sandgren wrote: > Yeah, I think we have to add an option for this in > toolchains/compiler/inteliccifort.py > > Kenneth

Re: [easybuild] Replacing Intel compiler option -ftz with -no-ftz

Yeah, I think we have to add an option for this in toolchains/compiler/inteliccifort.py Kenneth, any thoughts on that? On 11/19/19 3:12 PM, Loris Bennett wrote: > Hi Bart, > > Thanks for the information. I'll try 'precise'. However, the developer > of the program I need to compile (Siesta) exp

Re: [easybuild] OpenMPI-2.1.0-GCC-6.3.0-2.28.eb + Slurm 19.05.3-2: pmi.h and pmi2.h not found

You should nbot set --with-pmi to anything when /usr is the base, just use --with-pmi and stuff will find the include files correctly, or at least should On 11/14/19 11:53 AM, Alan O'Cais wrote: > Looks to me like you should be using: > --with-pmi=/usr  > It needs to find the headers and the libra

Re: [easybuild] difficulties installing FFTW-3.3.8-gompi-2018b.eb

The framework test directory contain things that are used only for testing EasyBuild itself and should be ignored. And there has been a couplke of syntactic changes between EB 3.8.1 and 4.0 which explains the differens between those two versions of gompi-2018b.eb, and in EB 4 the location of the e

Re: [easybuild] difficulties installing FFTW-3.3.8-gompi-2018b.eb

Not trying to answer your actual question here. If you're going to use --module-depends-on and --module-syntax=Tcl it's probably better to set that in the easyconfig.cfg file so you don't forget. On 10/23/19 10:38 AM, douglas.scofi...@ebc.uu.se wrote: > Hi, new to EasyBuild as is our center (UPPMA

Re: [easybuild] R, BLAS/LAPACK, C/Fotran interfacing and GCC >= 7

by > EasyBuild. The whole stack that supports R, and R is built with the same > toolbox. > > John Dey > > On 6/27/19, 1:09 PM, "easybuild-requ...@lists.ugent.be on behalf of Åke > Sandgren" ake.sandg...@hpc2n.umu.se> wrote: > > Ohhh that one's evil

Re: [easybuild] R, BLAS/LAPACK, C/Fotran interfacing and GCC >= 7

Ohhh that one's evil... On 6/27/19 6:30 PM, Jack Perdue wrote: > Howdy all, > > Saw an interesting aricle on LWN: > > https://lwn.net/Articles/791393/ > > (subscription required unless you wait a week). > > More details here: > > https://developer.r-project.org/Blog/public/2019/05/15/gfortran

Re: [easybuild] libsoup and libresolv

I'd say that this is a bug in CentOS resolv.h. Each include file should make sure to have all it depends on for types etc defined by including the required include files. The C7 resolv.h seem to not do that... On 6/4/19 12:18 PM, Joachim Hein wrote: > Hi, > > i got a libsoup easyconfig from a me

Re: [easybuild] INTERFACE64 for OpenBLAS?

This should have gone to the list... On 6/3/19 8:39 AM, Åke Sandgren wrote: > I'd say not to bother with OpenMolcas using foss, you need ilp64 > scalapack too if i remember correctly, and that means MKL only. > > The OpenBLAS build does not generate an ilp64 version of the

Re: [easybuild] Openblas(foss) matrix issue

Yes, 8396 fixes the tests from Openblas_matrix_issue for all our archs. Waiting for test results from a user that had problems with OpenBLAS/0.3.1 too. On 5/28/19 5:14 PM, Pablo Escobar Lopez wrote: > thank you Carlos! You did a great job figuring out this fix :) > > I can confirm that after appl

Re: [easybuild] Openblas(foss) matrix issue

On 5/8/19 7:56 PM, Kenneth Hoste wrote: > Thank you for reporting back on this Thomas! > > It's good to hear that the issue can be resolved by using a newer > version of OpenBLAS, but it's also frustrating... > > This is clearly a bug in OpenBLAS that could have been prevented. > I haven't stu

Re: [easybuild] Openblas(foss) matrix issue

We have a bug report for various OpenBLAS versions too, but I haven't had time to invesstigate it. Parts of it may be SkylakeX related. On 5/7/19 6:32 PM, Mikael Öhman wrote: > Hi Thomas, > > I can also confirm these issues. I tried rebuilding OpenBLAS+R after the > fix in #7180, but I still saw

Re: [easybuild] meson for foss-2019a toolchain

On 4/30/19 1:25 AM, Dey, John F wrote: > I am having issues with Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb.  Has > any built this? Yes, had no problems. What do you see? -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46

Re: [easybuild] QuantumESPRESSO:

It should work, I had no problems with it. But let's verify some things. Which version of EasyBuild are you using? On 4/1/19 4:31 PM, Loris Bennett wrote: > Hi, > > I have build QuantumESPRESSO using > > QuantumESPRESSO-6.3-foss-2018b.eb > > > %%

Re: [easybuild] override sanity check for futures with Python 2.7

https://github.com/easybuilders/easybuild-easyconfigs/pull/7961 On 3/26/19 3:47 PM, Åke Sandgren wrote: > Ok, I have dask 1.1.4 for fosscuda/2018b with Python 2.7.15 done. > Based on the existing dask-1.0.0-intel-2018b-Python-3.6.6.eb > > I'll PR it and you can take a look if t

Re: [easybuild] override sanity check for futures with Python 2.7

Ok, I have dask 1.1.4 for fosscuda/2018b with Python 2.7.15 done. Based on the existing dask-1.0.0-intel-2018b-Python-3.6.6.eb I'll PR it and you can take a look if there is something you think is missing. On 3/26/19 3:02 PM, Yann Sagon wrote: > Excellent, this was what I was looking for! > > Th

Re: AW: [easybuild] Accessing environment variables in easyconfig

On 3/12/19 1:25 PM, Loris Bennett wrote: > This is not for MDCS - we don't have that. This is also the setup we > had working on our previous cluster, but where we didn't use Easybuild. > >> If you install matlab using >> env LM_LICENSE_FILE=port@host eb MATLAB...eb then the LM_LICENSE_FILE is

Re: AW: [easybuild] Accessing environment variables in easyconfig

On 3/12/19 12:00 PM, Dr. Stefan Harfst wrote: > Dear Loris, > > one way to achieve what you want is to use the modxxxfooter parameters in the > eb-file (untested): > > modluafooter = 'setenv("MCR_CACHE_ROOT", pathJoin("/scratch", > pathJoin(os.getenv("USER"), "mcr_cache")))' > modtclfooter = 's

Re: [easybuild] MATLAB: Adding update to ISOs

You would really have to check what the installation for the update does. On 2/28/19 10:05 AM, Loris Bennett wrote: > Hi Kenneth, > > The problem is that the updates contain files like > > R2018b_Update_2/glnxa64/aeroblks_glnxa64.enc > R2018b_Update_1/glnxa64/aeroblks_glnxa64.enc > R2018

Re: [easybuild] Lmod clean up

use if (mode() == "unload") ? On 2/27/19 11:09 AM, Joachim Hein wrote: > Hi, > > This is more an Lmod than an Easybuild question, I hope it still ok to ask > here. We have a package that needs an executable to be run when the module > is loaded, which we succeeded in. However when there is a

Re: [easybuild] Building foss-2019a fails in binutils-2.31.1.eb (Skylake node)

What is the actual error? Look in /tmp/eb-dyNH9x/easybuild-binutils-2.31.1-20190220.140138.qdBpn.log On 2/20/19 2:18 PM, Ole Holm Nielsen wrote: > I'm trying to build the foss-2019a toolchain with EB 3.8.1 on a new > Intel Skylake node (40 cores + hyperthreading = 80 cores) but it fails > in binu

Re: [easybuild] Distributed vs. local easyconfigs

for OpenMPI which you would be willing to share? > > Cheers, > > Loris > > > Åke Sandgren writes: > >> This is where easyhooks is your friend. >> >> Especially if it is something you want to do for all OpenMPI builds >> (with variations depending

Re: [easybuild] Distributed vs. local easyconfigs

willing to share? > > Cheers, > > Loris > > > Åke Sandgren writes: > >> This is where easyhooks is your friend. >> >> Especially if it is something you want to do for all OpenMPI builds >> (with variations depending on versions). >> >> We add e

Re: [easybuild] Distributed vs. local easyconfigs

This is where easyhooks is your friend. Especially if it is something you want to do for all OpenMPI builds (with variations depending on versions). We add extra dependencies to OpenMPI and change configure flags to enable external PMIx/UCX for instance. And add extra env vars to the module file

Re: [easybuild] Massive Datasets as easyconfigs

For large data sets it doesn't quite make sense to use EB's setup. EB downloads the "source" into its own source repository and then unpacks it. But that downloades "source" will, in this case, just waste space. It's probably better to just download and unpack the dataset on a file system that is l

Re: [easybuild] Future of Python at GCCcore level?

Whatever gets done, please make sure that the current method of having Python at the intel/foss level is retained. There are too much python code out there and we need the additional speed of using Intel compiler for Python. On 12/13/18 9:35 PM, Bart Oldeman wrote: > Hi Mikael, > > you could actu

Re: [easybuild] Java module - how to use?

And to get the Java/1.8 to pick that up, you need to rebuild Java-1.8.eb with the new version number. On 10/29/18 7:27 PM, Jack Perdue wrote: > Ooops... just noticed you said _191/2 not _181. > > In that case, you might try: > >   eb --try-software-version=1.8.0_192 (wherever)/Java/Java-1.8.0_18

Re: [easybuild] Consistency across toolchains.

On 10/11/2018 09:32 AM, Jakob Schiøtz wrote: > > >> On 11 Oct 2018, at 9:17, Miguel Dias Costa wrote: >> >> I suppose the question then is whether there is an issue with libvdwxc >> always using FFTW and the rest of GPAW using the FFTW wrappers to Intel MKL, >> but I don't see why that woul

Re: [easybuild] Need to set an environment variable pointing to a dependency

On 10/10/2018 09:54 AM, Jakob Schiøtz wrote: > Hi all, > > I am making an easyconfig (WIP PR #6984), and to solve an issue I need to set > an environment variable pointing to a library in a dependency. The variably > logically belongs in this module, not in the dependency, as it is a quirk o

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