[easybuild] Will rebuilding GCCcore cause jobs to fail?

long is a module gone when rebuilding it with "eb XXX.eb --rebuild"? Is it during the entire rebuilding process? Or during the "installation" step? Or just during the few seconds where EasyBuild writes "creating module"? Bets regards Jakob -- Jakob Schiøt

[easybuild] CUDA on machine with OmniPath

a completely different module tree for these few nodes, but if it is necessary then we will have to. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark

[easybuild] Specifying optimization in easyconfigs

Hi folks, I have noticed that in the intel/2023 toolchain (and subchains), optimization has very wisely been set to a moderate level (-O2 -ftz -fp-speculation=safe -fp-model precise). By setting the toolchain option 'opt' to True, -O2 is changed to -O3 for a very moderate gain in performance.

[easybuild] ASE added to 2023a in wrong toolchain level

Hi folks, Somebody added an ASE easybuild to foss/2023a a few weeks ago (PR #18777). However, ASE should be at the gfbf/2023a level, it was moved to that level in 2022b. An easyconfig is available in PR #18874. How should this be handled? Best regards Jakob

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

Hi, > On 11 Oct 2023, at 19.42, Kenneth Hoste wrote: > > Is it CUDA 11.8 that doesn't support GCC 12.x, or the other way around? It's the CUDA compiler that complains that it does not work with a GCC greater than 11.X. It may be possible to ignore it. I'll try out the patch, and see if I

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

that hack stuff until it works? I guess I can just use an older toolchain for machine learning until then, but it would be nice to have... Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark

[easybuild] Invoking the right Intel MPI compiler

and mpiicpx. And mpiicc warns me that I should use the new OneAPI compilers... How do I do that for MPI code? (Note that I am not building modules, I am building my own code as a developer, but using the EasyBuild modules with toolchains etc) Best regards Jakob -- Jakob Schiøtz, professor, Ph.D

[easybuild] Re: Problems with foss/2022a and OmniPath

/lib/libpython3.10.so.1.0(PyModule_ExecDef+0x6f)[0x2b540f8b849f] [a022:229451] [11] /home/modules/software/Python/3.10.4-GCCcore-11.3.0/lib/libpython3.10.so.1.0(+0x1adff9)[0x2b540f8b8ff9] ... -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800

[easybuild] Problems with foss/2022a and OmniPath

environment variables to set to get the right MCA (assuming that the MCA is indeed the culprit)? It is two different codes both giving a segmentation fault during MPI_Init() or MPI_Init_thread(), and both work with foss/2020b but fail with foss/2022a. With my best regards Jakob -- Jakob Schiøtz

[easybuild] numba for foss/2022a

not feel qualified to hack it. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark

[easybuild] Problems building SciPy-bundle-2022.05-intel-2022a.eb

gist.github.com/schiotz/b8cb4aded9fce183261fc5ae31202a40 Does anybody have any suggestions for what could be wrong? EasyBuild 4.6.1 on a machine with Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark

Re: [easybuild] Github integration - token error despite successful push

was wrong when it tried to read the token. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark > On 9 Aug 2022, at 11.52, Loris Bennett wrote: > > Loris Bennett writes: > >> Lor

Re: [easybuild] Github integration - token error despite successful push

Hi all, One thing that I have seen going wrong is that keyring should be available in the Python version that EasyBuild runs internally. That may very well be an old, system-installed Python. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University

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

Sorry for sending this to the mailing list instead of personally to Ole! Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark > On 7 Dec 2021, at 13.13, Jakob Schiøtz wrote: > > > > Hej Ole, >

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

Hej Ole, To muligheder: 1) Prøv at sætte disse tre environment variable: export OMPI_MCA_osc='^ucx' export OMPI_MCA_pml='^ucx' 'export OMPI_MCA_btl='^openib' 2) Prøv at bygge med eb --filter-deps=UCX OpenMPI-4.0.5-GCC-10.2.0.eb --force og derefter sætte export OMPI_MCA_btl=^openib Mvh

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

> >> I'd also suggest to join Slack as discussions there are potentially faster. > > I'll take a look - are there instructions for Slack? Once can join here https://easybuild-slack.herokuapp.com/ Jakob

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

es without optimization, except for a few critical files where -O2 seems to be turned on manually. I'll assume that your suggestions will fix this. All in all, I am not impressed! :-) Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-28

Re: [easybuild] Toolchain question

> On 4 Mar 2021, at 20.36, Kenneth Hoste wrote: > > Hi Jakob, > > On 04/03/2021 15:10, Jakob Schiøtz wrote: >> Hi, >> I am making an .eb file for POV-RAY, and would love to move it down from >> foss/intel 2020b to GCCcore-10.2.0. Unfortunately, one of t

[easybuild] Toolchain question

with intel/2020b (the iccifort/2020.4.304 toolchain, probably)? It is a binary, not a library needing to be linked by other packages. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http

[easybuild] multi_deps

. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

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

, the error message makes it more likely to be your private key missing. That is the file ~/.ssh/id_rsa NOT the file ~/.ssh/id_rsa.pub (the PRIVATE key must be available on your computer, the public key is on GitHub). Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical

[easybuild] Re: Conflicting Python versions when building IPython

Hi again, I realize now that Python 2.7 is only a build dependency of OpenPGM, which prevents it from being a real conflict. But still unfortunate to have to install an obsolete python version to build it. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical

[easybuild] Conflicting Python versions when building IPython

on Python-2.7.18-GCCcore-10.2.0.eb Will this not cause two conflicting Python packages to be loaded (conflicting as in the binary python will be the one last loaded, and perhaps PYTHONPATH will also be a mess)? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical

[easybuild] SciPy-bundle-2020.11-intel-2020b fails numpy test suite.

regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/ extract-of-log.log Description: extract-of-log.log

Re: [easybuild] SciPy-bundle-2020.11-intel-2020b fails numpy test suite.

> On 15 Dec 2020, at 09.56, Kenneth Hoste wrote: > > [ ... ] > Can you check how similar those problems are to what we see on AMD Rome, see > https://github.com/easybuilders/easybuild-easyconfigs/issues/11836 ? Thank you very much for your quick reply. Yes, it is the same test that fails.

[easybuild] Running tests in an EasyConfig

before any of the "extensions" were installed, i.e. before anything was really done. Ideally, I would like to run the test at the very end after installing all the packages, but running it after the main package is installed is also fine. Best regards Jakob -- Jakob Schiøtz

Re: [easybuild] Running tests in an EasyConfig

> On 14 Dec 2020, at 11.16, Kenneth Hoste wrote: > > Hi Jakob, > > On 14/12/2020 11:07, Jakob Schiøtz wrote: >>> On 14 Dec 2020, at 09.48, Kenneth Hoste wrote: >>> >>> Dear Jakob, >>> >>> On 14/12/2020 09:28, Jakob Schiøtz wrote:

Re: [easybuild] Running tests in an EasyConfig

> On 14 Dec 2020, at 09.48, Kenneth Hoste wrote: > > Dear Jakob, > > On 14/12/2020 09:28, Jakob Schiøtz wrote: >> Hi EasyBuilders, >> I am trying to run the test suite of a Python package (ASE), that I install >> as a PythonBundle. However, the t

Re: [easybuild] Tk-8.6.10-GCCcore-9.3.0.eb fails due to download issue

This seems to affect all downloads from Sourceforge today. /Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/ > On 22 Jun 2020, at 10.40, Ole Holm Nielsen wrote: > >

Re: [easybuild] Github integration - fatal: Could not read from remote repository

> > For the token I have the 'repo' and 'gists' scopes enabled (the gist bit > works). Is there some setting on the repository itself that needs > tweaking? Is your SSH key set up correctly? You can try like this: $ ssh g...@github.com X11 forwarding request failed on channel 0 PTY allocation

Re: [easybuild] Github token not found

the solution was installing some package systemwise, probably python2-keyring, but I honestly cannot remember it. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz

Re: [easybuild] Q about PythonPackage/Bundle: PyTorch-Geometric

> On 20 Feb 2020, at 09.39, Sebastian Potthoff > wrote: > > Hi, > > follow-up question: If I create a generic PythonBundle, like > "PyTorch-Extensions" what version number would one use? > > Is it allowed to skip the version? Otherwise I would think of something like > 2019a or 2019.01 or

Re: [easybuild] Problems building scikit-image with intel/2019b

Dear John, It worked for me with foss/2019b. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/ > On 3 Feb 2020, at 18.00, Dey, John F wrote: > > sci

Re: [easybuild] Disabling parallel build in a EasyConfig file?

Thank you very much, Terje! maxparallel = 1 did the job! /Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/ > On 2 Feb 2020, at 20.17, Terje Kvernes wrote: > >

[easybuild] Disabling parallel build in a EasyConfig file?

EasyConfig? Obviously, the correct solution would be to fix the upstream Autotools-generated Makefile, but that is beyond me. /Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

[easybuild] Problems building scikit-image with intel/2019b

ux-x86_64-3.7/skimage/feature/_cascade.o -MMD -MF build/temp.linux-x86_64-3.7/skimage/feature/_cascade.o.d -fopenmp" failed with exit status 4 -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] Cuda supporting toolchains - continued

does not use EasyBuild. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/ > On 27 Nov 2019, at 12.07, Caspar van Leeuwen > wrote: > > Dear all, &

Re: [easybuild] Question about multi_deps and Python

> On 15 Nov 2019, at 15.57, Kenneth Hoste wrote: > > On 15/11/2019 13:15, Jakob Schiøtz wrote: >> Dear Easybuilders, >> In the GCCcore-8.2.0 toolchain, some Python packages were common for Python >> 3 and Python 2, with the "multi_deps" keyword, for exam

[easybuild] Question about multi_deps and Python

f Python 2 for those only using Python 3. Is that the new style? Should I do the same when I make a new easyconfig for Pillow (and possibly other Python packages), i.e. just make it a Python 3 package? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical

Re: [easybuild] Canonical way of creating new file?

Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

[easybuild] Several versions of a dependency

and the Travis CI self test still complains. Have I misunderstood what I should do, or is this just not possible? Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

[easybuild] OpenBLAS + Skylake CPU - what is the status?

to this issue. Any help/guidelines would be appreciated. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] cannot find -lpthread

probably somewhere else in the Python .eb file that you are using - but I am just guessing here... Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] Openblas(foss) matrix issue

> On 8 May 2019, at 11:20, Jakob Schiøtz wrote: > > > >> On 7 May 2019, at 18:12, Thomas Eylenbosch >> wrote: >> >> >> Can someone try to reproduce the error with the R/Python(foss/2018b) >> modules. Or can someone give me feedback on this

Re: [easybuild] Openblas(foss) matrix issue

6148 CPU @ 2.40GHz) and a Broadwell (Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz). I cannot reproduce the problem, the test (check.py) succeeds on both machines. Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http:

Re: [easybuild] Python in the 2019a toolchains.

Apr 2019, at 16:43, Kenneth Hoste wrote: > > Dear Jakob, > > On 08/04/2019 11:48, Jakob Schiøtz wrote: >> Hi, >> What is the status for Python in the 2019a toolchains? I see no Python >> easyconfig for the foss/2019a and intel/2019a toolchains, but there is one >

[easybuild] Python in the 2019a toolchains.

, presumably because they benefit from being in the full toolchains. But where do they live now, in some scientific python bundle, I presume? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http

Re: [easybuild] TensorFlow with GPU support.

olchains option. > > > Jack Perdue > Lead Systems Administrator > High Performance Research Computing > TAMU Division of Research > j-per...@tamu.eduhttp://hprc.tamu.edu > HPRC Helpdesk: h...@hprc.tamu.edu > > On 3/26/19 8:26 AM, Jakob Schiøtz wrote: >> Dea

[easybuild] TensorFlow with GPU support.

on CUDA explicitly. Is there a reason not to do it this way? I guess I could try to make a .eb file inspired on the existing ones doing just that - or have I overlooked something? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800

Re: [easybuild] Problems building with CMake

/easybuild-easyconfigs/pull/7569 Thanks again for your help. Jakob > On 12 Mar 2019, at 14:04, Jakob Schiøtz wrote: > > > >> On 12 Mar 2019, at 11:03, Paul Melis wrote: >> >> Hi Jakob, >> >> Whoops, sorry, didn't read your post in enough detail. I s

Re: [easybuild] Problems building with CMake

ul > > ----- Original Message - > From: "Jakob Schiøtz" > To: "easybuild" > Sent: Tuesday, 12 March, 2019 10:35:36 > Subject: Re: [easybuild] Problems building with CMake > >> On 12 Mar 2019, at 10:25, Paul Melis wrote: >> >> You need to

Re: [easybuild] Problems building with CMake

r tool. > > Tell CMake where to find the compiler by setting either the environment > variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path > to the compiler, or to the compiler name if it is in the PATH. > > and the same for the C and Fortran c

[easybuild] Problems building with CMake

build_obj/icpc I have no idea where it gets that idea from. Has anybody seen something like that before, or have any hint as to where I should be looking? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, D

Re: [easybuild] Canonical approach for local exts_list?

ate will recursively resolve dependencies and create output that can > be cut/paste into an EasyConfig. > > [ ] Now *that* is really useful! Thank you very much. Could this perhaps either be integrated into EasyBuild, or made installable as an EasyBuild module? Best regard

Re: [easybuild] 2019a update of common toolchains

gt; > by simply >> > updating to the latest version of these dependencies. >> > >> > >> > The 2019a toolchain definitions will also be discussed during >> the >> > EasyBuild conf call this Wed

Re: [easybuild] Re: Configuring ELPA according to the cpu

asybuilders/easybuild-easyblocks/blob/master/easybuild/easyblocks/f/fftw.py#L124 >> . >> This really is beyond what's possible in an easyconfig file, you need custom >> code to deal with this... >> regards, >> Kenneth >> On 11/01/2019 12:48, Jakob Schiøtz wrote: >

[easybuild] Re: Configuring ELPA according to the cpu

Dear all, I did not get any response to this before Christmas. Does anybody have any ideas that might help me? Best regards Jakob > On 18 Dec 2018, at 15:00, Jakob Schiøtz wrote: > > Hi, > > I am trying to build the newest version of ELPA (Eigenvalue SoLvers for > Pet

[easybuild] Configuring ELPA according to the cpu

the unsupported versions instead of just doing the right thing. But that is beyond my control. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

[easybuild] Python links to libncurses, not libncursesw

es/__init__.py", line 94, in wrapper return func(stdscr, *args, **kwds) File "", line 1, in AttributeError: '_curses.window' object has no attribute 'get_wch' On other machines (e.g. my Macbook), this does not produce an error. Best regards Jakob -- Jakob Schiøtz, professo

Re: [easybuild] Warning against Python 3.7

> On 23 Nov 2018, at 8:17, Kenneth Hoste wrote: > > Dear Jakob, > > On 22/11/2018 22:34, Jakob Schiøtz wrote: >> Hi, >> I know that Python 3.7 was dropped in the last release of EasyBuild due to >> issues with some packages. >> There are still pa

[easybuild] Warning against Python 3.7

with Python 3.6.X also in the next release of EasyBuild. Of course I may be overlooking something significant :-) /Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] PythonBundle breakage

he newest easyblocks as well. Thanks for your help! Jakob > >> Jakob >> -- >> Jakob Schiøtz, professor, Ph.D. >> Department of Physics >> Technical University of Denmark >> DK-2800 Kongens Lyngby, Denmark >> http://www.fysik.dtu.dk/~schiotz/ -- J

Re: [easybuild] PythonBundle breakage

for more information. > > Let me know if that does the trick... Yes, that worked! I guess I will just add that line to my .bashrc. Thank you very much! Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] PythonBundle breakage

YTHONPATH after loading the eb module. Maybe that is not the correct way to do it? Jakob > > > regards, > > Kenneth > > On 21/11/2018 10:38, Jakob Schiøtz wrote: >> Dear all, >> I just git-pulled the develop branch for easybuild-easyblocks and >> easybuild-easyconfi

[easybuild] PythonBundle breakage

elopment/easybuild-easyblocks/easybuild/easyblocks/generic/pythonbundle.py", line 47, in extra_options extra_vars = Bundle.extra_options(extra_vars) TypeError: extra_options() takes no arguments (1 given) Was it an error pulling easybuild-easyblocks? Is there an update that only works with

Re: [easybuild] Modules not shown by 'module av'

> On 20 Nov 2018, at 14:27, Kenneth Hoste wrote: > > Dear Jakob, > > On 20/11/2018 13:57, Jakob Schiøtz wrote: >> Hi, >> I very often have problems with the lmod cache, as if it suddenly stop >> updating and new modules are no longer listed. In

Re: [easybuild] Modules not shown by 'module av'

98 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > > -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] Python dependencies for ASE

rtment > The Max Planck Institute for the Structure and Dynamics of Matter (MPSD) > Bldg. 99 (CFEL) > Luruper Chaussee 149 > 22761 Hamburg > > Nano-Bio Spectroscopy group > Departamento de Física de Materiales > Universidad del País Vasco (UPV/EHU) > Donostia-San Sebastián, Gipuzkoa, Spain -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] Trouble linking Pillow/intel-2018b with libtiff

> On 19 Oct 2018, at 12:49, Jakob Schiøtz wrote: > > Dear Alan, > > Thank you very much indeed for your detailed answers. > >> On 19 Oct 2018, at 10:25, Alan O'Cais wrote: >> >> Hi Jakob, >> >> It is always possible to shadow the LiBTIFF

Re: [easybuild] Trouble linking Pillow/intel-2018b with libtiff

s build with GCC. I am using an Intel python, and I can see that linkage happens with icc not with gcc. So I do not think this is the problem. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] Trouble linking Pillow/intel-2018b with libtiff

his was discussed as far as I know. > > Cheers, > Ben > > > On Thu, Oct 18, 2018 at 10:10 AM Jakob Schiøtz wrote: > Thanks, > > It is undoubtedly the same problem, in this case it is CentOS 7.4 not CentOS > 6. > > Is there a reason that --enable-ld-version-

Re: [easybuild] Trouble linking Pillow/intel-2018b with libtiff

pt solved the > problem. > > Miguel > > On Thu, Oct 18, 2018 at 7:17 PM Jakob Schiøtz wrote: > Hi, > > I am trying to make easyconfigs for scikit-image and Pillow with intel/2018b. > For previous versions, the foss and intel easyconfigs are identical (a part >

[easybuild] Trouble linking Pillow/intel-2018b with libtiff

cannot help noticing that with the 2018b toolchains it has been moved to the GCCcore-7.3.0 toolchain instead of intel/foss 2017b for the previous versions. Could that have any influence on this problem? And can anyone suggest a solution? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D

Re: [easybuild] Consistency across toolchains.

things to load FFTW, I will be able to get it to work. Best regards Jakob > On 11 Oct 2018, at 16:02, Jakob Schiøtz wrote: > > > >> On 11 Oct 2018, at 14:17, Miguel Costa wrote: >> >> >> >> On Thu, 11 Oct 2018, 15:36 Jakob Schiøtz, wrote: >&

Re: [easybuild] Consistency across toolchains.

> On 11 Oct 2018, at 12:47, Jakob Schiøtz wrote: > > We have an open issue discussing it on the gpaw gitlab page. And here I intended to cut-and-paste the link, but forgot the paste part :-) https://gitlab.com/gpaw/gpaw/issues/163 -- Jakob Schiøtz, professor, Ph.D. Department o

Re: [easybuild] Consistency across toolchains.

> On 11 Oct 2018, at 9:42, Åke Sandgren wrote: > > > > 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

Re: [easybuild] Consistency across toolchains.

, this is where the problem is. It causes core dumps. According to the libvdwxc developer, this is because MKL and FFTW use the same internal function names for incompatible functions (I assume some internal functions called by the official API functions). > Or did I misunderstand? > >

[easybuild] Consistency across toolchains.

including libvdwxc, and is thus superfluous. What do you guys think? Best regards Jakob The work-in-progress PR is here: https://github.com/easybuilders/easybuild-easyconfigs/pull/6984 -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby

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

> On 10 Oct 2018, at 13:28, Åke Sandgren wrote: > > > > 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

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

t thing instead. Best regards Jakob > > > regards, > > Kenneth > > >> Best regards >> Jakob >> -- >> Jakob Schiøtz, professor, Ph.D. >> Department of Physics >> Technical University of Denmark >> DK-2800 Kongens Lyngby, Denmark >&

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

nking GPAW with FFTW before MKL almost works, but unfortunately the Python code does some unholy stuff and tries to find the FFTW library itself, picks up MKL and crases. Setting GPAW_FFTWSO overrrules this. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Tech

Re: [easybuild] X11 stack with foss/2018b breaks other programs.

I forgot to add that I already did the PR, it is #6963 Jakob > On 5 Oct 2018, at 11:19, Jakob Schiøtz wrote: > > At least for me, having fontconfig depend on linux-util instead of LibUUID > solves exactly that problem (version `UUID_1.0' not found). > > Obviously, that is

Re: [easybuild] X11 stack with foss/2018b breaks other programs.

kob > > > > On 5 Oct 2018, at 10:17, Alan O'Cais wrote: > > > > This was discussed on the mailing list recently (see > > https://lists.ugent.be/wws/arc/easybuild/2018-09/msg00015.html) but someone > > needs to open a PR... > > > > On Fri, 5 Oct

Re: [easybuild] X11 stack with foss/2018b breaks other programs.

> > * rebuild X11 on top of that changed fontconfig > > * check whether the problem is fixed > > > > regards, > > Kenneth > > On 05/10/2018 10:27, Jakob Schiøtz wrote: >> Thanks for the reference. Unfortunately, I have no clue what they are >>

Re: [easybuild] X11 stack with foss/2018b breaks other programs.

; > > > regards, > > Kenneth > > On 05/10/2018 10:27, Jakob Schiøtz wrote: >> Thanks for the reference. Unfortunately, I have no clue what they are >> talking about in that thread. :-( >> Is the LibUUID module included to work around the bug they ment

Re: [easybuild] X11 stack with foss/2018b breaks other programs.

ntly (see > https://lists.ugent.be/wws/arc/easybuild/2018-09/msg00015.html) but someone > needs to open a PR... > > On Fri, 5 Oct 2018 at 10:00, Jakob Schiøtz wrote: > Dear all, > > We use matplotlib with Tkinter support. Until foss/2018a that worked just > fine, but w

[easybuild] X11 stack with foss/2018b breaks other programs.

to a folder containing a library with the same name as another program expects to find elsewhere. But that may be very difficult to fix, getting rid of LibUUID might be a good start. :-) Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK

Re: [easybuild] Python ulimit workaround (issue 6484)

OK, I’ll make a patch right away. Jakob > On 4 Oct 2018, at 15:56, Kenneth Hoste wrote: > > > > On 04/10/2018 15:50, Jakob Schiøtz wrote: >> Hi again, >> The newest Python easybuilds (3.6.6 and 3.7.0 with all toolchains) do not >> contain these lines:

[easybuild] Python ulimit workaround (issue 6484)

ulimit_unlimited = True Is that on purpose, or is it a regression? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

Re: [easybuild] Right version of Python with xxx/2018b toolchains.

Thanks, I will begin submitting PRs. :-) Jakob > On 4 Oct 2018, at 14:17, Kenneth Hoste wrote: > > Hi Jakob, > > On 04/10/2018 13:40, Jakob Schiøtz wrote: >> Dear all, >> Am I right in remembering that the correct version of Python to use with the >> foss

[easybuild] Right version of Python with xxx/2018b toolchains.

. Should I add 3.6.6 while adding ASE and matplotlib, or should I use 3.7.0 in this case (or in all cases?). Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/

[easybuild] matplotlib now sets MPLBACKEND=Agg

will have to be modified. Setting MPLBACKEND in interactive scripts may not be a good idea, since on Linux you want TkAgg but on macOS you want MacOSX. Best regards Jakob -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark

Re: [easybuild] Cuda supporting toolchains

al to the latter approach since it allows > more flexibility of CUDA version without redefining an entire > toolchain (which then requres everything to be rebuilt (e.g. Python) > whether they need CUDA or not). > > Jack Perdue > Lead Systems Administrator > High Performance Researc

[easybuild] Recovering after removal of Tkinter from Python.

-easyconfigs/pull/5658 containing the new Tkinter easyconfig for Python 3.6.3 and fixes the matplotlib and ASE easyconfigs to depend on Tkinter explicitly. I assume that with a fix to an easyblock it is too late to make it into 3.5.1 ? Best regards Jakob -- Jakob Schiøtz, professor, Ph.D

Re: [easybuild] Fixing an easyconfig

> On 16 Jan 2018, at 14:42, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: > > Dear Jakob, > > On 16/01/2018 14:37, Jakob Schiøtz wrote: >> Hi, >> >> One of my colleagues found an error in one of the easyconfigs that I >> recently made (ASE, t is

[easybuild] Fixing an easyconfig

with an updated version number (patch1 or something)? The latter clearly prevents any doubt about which version is which, but it also implies that all software depending on this package need to be updated to prevent them from pulling in the broken version. Best regards Jakob -- Jakob

Re: [easybuild] TensorFlow with GPU support.

> On 8 Jan 2018, at 20:27, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: > > On 08/01/2018 15:48, Jakob Schiøtz wrote: >> Hi Kenneth, >> >> I have now tested your TensorFlow 1.4.0 eb on our machines with a real-world >> script. It works, but it runs th

Re: [easybuild] TensorFlow with GPU support.

oppose that. > > > regards, > > Kenneth > >> >> Best regards >> >> Jakob >> >> >>> On 4 Jan 2018, at 15:29, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: >>> >>> Dear Jakob, >>> >>> O

Re: [easybuild] TensorFlow with GPU support.

and depends on CUDA and friends)? Best regards Jakob > On 5 Jan 2018, at 16:10, Jakob Schiøtz <schi...@fysik.dtu.dk> wrote: > > > >> On 5 Jan 2018, at 15:18, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: >> >> On 05/01/2018 14:13, Jakob Schiøtz wrot

Re: [easybuild] TensorFlow with GPU support.

> On 5 Jan 2018, at 15:18, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: > > On 05/01/2018 14:13, Jakob Schiøtz wrote: >> Hi again, >> >> Yes, I have overlooked that - I just switched my repo to your branch and >> tried to build :-) >> &

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