Re: [easybuild] non-standard location of setup.py for easyconfig

Hi again, I just learned about `start_dir`, and the following seems to work: ('ESMpy', '7.1.0r', { 'source_tmpl': 'esmf_7_1_0r_src.tar.gz', 'source_urls': ['http://www.earthsystemmodeling.org/esmf_releases/public/ESMF_7_1_0r/'], 'checksums': ['ae9a5edb8d40

[easybuild] non-standard location of setup.py for easyconfig

Hi EasyBuilders, I'd like to add ESMpy to an easyconfig as a PythonPackage extension. The problem is that the `setup.py` is not in the root of the source archive, but instead in a subfolder `src/addon/ESMPy/`. Currently I have ('ESMpy', '7.1.0r', { 'source_tmpl': 'esmf_7_

Re: [easybuild] preparing R-3.6.1-foss-2019b

27;0.3-3', {'checksums': ['ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca']}), ('IRkernel', '1.0.2', {'checksums': ['976f63a3c76f03ec793213255022d7b9aa91c4dcd5aa1c90d35dfd72cc8b1810']}), in our in

Re: [easybuild] Inconsistent versions within one toolchain

Dear Kenneth, thanks for the explanation! Kenneth Hoste writes: Dear Andres, We've been keeping a close (automated) eye on which dependencies are used in recent common toolchains (foss* & intel*, since 2018a) in that respect: we have a test that verifies that there's only a single "varian

[easybuild] Inconsistent versions within one toolchain

Hey, I just noticed that library versions are not necessarily used consistently within one toolchain. For example, in foss-2018b, there's both Bison-3.0.4 and Bison-3.0.5: $  grep Bison */*/*.eb | grep foss-2018b b/bioawk/bioawk-1.0-foss-2018b.eb:builddependencies = [('Bison', '3.0

Re: [easybuild] Cannot find dependency with --minimal-toolchains and --hidden-deps

Thanks, Kenneth -- One thing you also need to take into account is that the tcsh-6.20.00-GCCcore-7.3.0.eb easyconfig must be available in your robot search path ("eb --search tcsh-6.20.00-GCCcore-7.3.0" should fine it). That's a known problem which we haven't gotten around to fixing yet, see

[easybuild] Cannot find dependency with --minimal-toolchains and --hidden-deps

Hi, I'm trying to build WRF-4.0.1 for foss-2018b. My easyconfig has (among other settings) toolchain = {'name': 'foss', 'version': '2018b'} builddependencies = [('tcsh', '6.20.00')] dependencies = [ ('JasPer', '2.0.14'), ('netCDF', '4.6.1'), ('netCDF-Fortran',

Re: [easybuild] Updated Lmod RPM package needed for EasyBuild v3.7.0

We just yesterday installed 7.8.1 from http://build.openhpc.community/OpenHPC:/1.3:/Update6:/Factory/CentOS_7/x86_64/lmod-ohpc-7.8.1-5.1.ohpc.1.3.6.x86_64.rpm, and everything's working smoothly. Cheers, Andreas André Gemünd writes: Dear Ole, maybe the OpenHPC for CentOS 7 package can be

Re: [easybuild] Re: installing octave

Dear Joseph, the package you have to install is called "openssl-devel" (at least on CentOS 7.2). This package has to be present in your image. The error message you're getting tells you that easybuild cannot find that package in your image. When, in your image, you look at the output of the com

Re: [easybuild] mpdboot in intel/2017a MPI

f mpiexec. > > Cheers, > John > > ----- Original Message - > From: "Andreas Hilboll" > To: "easybuild" > Sent: Wednesday, 15 November, 2017 18:34:16 > Subject: [easybuild] mpdboot in intel/2017a MPI > > Hi, > > I just noticed that

[easybuild] mpdboot in intel/2017a MPI

Hi, I just noticed that the intel/2017a MPI doesn't have the `mpdboot` binary. In the intel/2016a one it was present. Is this to be expected, or is there something wrong with my setup? If it is expected, what can I do when I have software relying on mpdboot in scripts? Cheers for your help,

Re: [easybuild] installing octave

Hi Joseph, you should rather install openssl development package through your distribution's package manager. As you can see in the error message, > One or more OS dependencies were not found: [('openssl-devel', > 'libssl-dev', 'libopenssl-devel')] EasyBuild is looking for a package in your dis

Re: [easybuild] Including pip in EasyBuild module

Hi Kennth, Kenneth Hoste writes: > Hi Andreas, > > On 25/08/2017 11:23, Andreas Hilboll wrote: >> PS: I should add that this is a Python3-based easyconfig, so there is no >> `pip` executable in Python/3.6.1-intel2017a; it is called `pip3`. Maybe >> the PythonPacka

Re: [easybuild] Including pip in EasyBuild module

PS: I should add that this is a Python3-based easyconfig, so there is no `pip` executable in Python/3.6.1-intel2017a; it is called `pip3`. Maybe the PythonPackage easyblock should somehow check if the correct pip is called pip or pip3?

[easybuild] Including pip in EasyBuild module

EasyBuild, eb complains that there are unallowed modules loaded. Cheers, Andreas [1] https://nbdime.readthedocs.io/ -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen NW1 / S3132 Ot

Re: [easybuild] Intel toolchain / architecture selection

Thanks, Åke, I just remember that our login nodes are KVM virtualized, which should be the reason for this behavior. I'll have my colleague look into libvirt configuration to hopefully fix that. To answer your question, the full /proc/cpuinfo is below. Cheers, Andreas Compute node: ---8<---

Re: [easybuild] Intel toolchain / architecture selection

Hi Kenneth, thanks for your answer! > By default, EasyBuild uses -xHost when building with the Intel compilers > to optimize for the processor architecture of the system you are > building on. Yes, that's what I thought. However, I'm a bit confused, because both CPUs are from the Xeon E-5 26X

[easybuild] Intel toolchain / architecture selection

Hi Easybuilders, when I build the Python-3.6.1-intel-2017a.eb easyconfig on the compute nodes of our cluster instead of the login node, I can only start the generated python executable on the compute nodes: [hilboll@login1 ~]$ module load Python [hilboll@login1 ~]$ python Please veri

Re: [easybuild] Regarding New weather application

l > >Please let us know if you have any planning for these above models. > >Thank You! > >Regards, >Satish Sherikar Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen NW1 / S3132 Otto-Ha

Re: [easybuild] patch just one R extension

Hi, it's in the documentation, see https://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html#common-easyconfig-parameters. Cheers, Andreas Jure Pečar writes: > Hi, > > I want to apply this patch to R data.table to get it to behave in civilized > manner: > > diff -ur data.tabl

Re: [easybuild] how to specify choices for dependencies?

tePackage.lua > and then use the > option modluafooter in easyconfig of emos. Not very nice, but should work. > > http://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html > > Best, > Gizo > > Quoting Andreas Hilboll mailto:hilb...@uni-bremen.de>>: > >

[easybuild] how to specify choices for dependencies?

ose any default - if either Python/2.7.11 or Python/3.5.1 are already loaded, chose the matching ecCodes module Is this somehow possible? Cheers, Andreas. [1] https://software.ecmwf.int/wiki/display/ECC [2] https://software.ecmwf.int/wiki/display/EMOS -- Dr. Andreas Hilboll Center for

[easybuild] Path to test scripts

Hi all, I'd like to use the `tests` option to include testing by a custom script. I'm unsure where to put such a script, and how to set its path in the EasyConfig. When I simply specify tests = ['run_my_test.sh'] I get the error message Test specifies invalid path: /home/eb/sources/Pn

Re: [easybuild] SHA1 checksums

Thanks a lot, Kenneth! I couldn't find this in the documentation. Where would be a good place to include this information, I could prepare a PR. Cheers, Andreas. Kenneth Hoste writes: > Hi Andreas, > > On 20/04/2017 19:13, Andreas Hilboll wrote: >> Hi all, >> &g

[easybuild] SHA1 checksums

Hi all, I'm writing an EasyConfig for some software which provides SHA1 checksums for their source packages. Is there a way to tell eb that the checksums are SHA1 instead of MD5? Cheers, Andreas.

[easybuild] Strategy for hiding modules

Hi all, when I started using EasyBuild, I didn't know about the option to hide modules. Slowly, the list of installed modules becomes too long for `module avail` to be useful for the user. So I would like to hide modules. The question is, how should I do this? 1. Re-generate all modules (can I

Re: [easybuild] FPATH variable overwritten by imkl module

Agreed, Kenneth, see https://github.com/hpcugent/easybuild-easyblocks/pull/1140 Cheers, Andreas. Kenneth Hoste writes: > Hi Andreas, > > On 16/03/2017 14:23, Andreas Hilboll wrote: >> Hi, >> >> I'm using ZSH as my shell. Apparently ZSH uses an environmen

[easybuild] FPATH variable overwritten by imkl module

H variable. I'd appreciate any suggestions how to deal with this problem. Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen NW1 / S3132 Otto-Hahn-Allee 1

Re: [easybuild] Support for ROOT and/or Julia?

config for Julia here: > > http://www.siliconslick.com/easybuild/easyconfigs/ada/ Great, thanks a lot, I'll give it a try. Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) U

[easybuild] Support for ROOT and/or Julia?

Hi, has anyone here worked on installing ROOT (https://root.cern.ch/) and/or Julia (http://julialang.org/)? Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen

Re: [easybuild] A question on Intel 2017 cluster edition

PS: I put the easyconfigs here: https://gist.github.com/andreas-h/9a0b3fc50fd1445fecb6ece8cd367a83 HTH, Andreas Andreas Hilboll writes: > Hi Exequiel, > > I did this some months ago; it is possible to get somewhere with > specifying the 'components'. (However, now

Re: [easybuild] A question on Intel 2017 cluster edition

only a big tar.gz file with Intel Cluster Edition, how > could I separate the required parts to use easyconfigs file for icc, ifort, > imkl, etc. > > Cheers and a great 2017! -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - I

Re: [easybuild] Python extensions from .whl

b/raw/efe52f557b289c7b322e633ed31e9568f4675004/easybuild-eKoEuJ.log, easybuild 3.0.1 still tries to use setup.py ?) Cheers, Andreas. Kenneth Hoste writes: > Hi Andreas, > > On 27/12/2016 19:12, Andreas Hilboll wrote: >> Hi all, >> >> I'm trying to create an easyconfig for jupy

[easybuild] How to install .whl from pypi

ld that I want to install this extension from the Wheel? Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen NW1 / S3132 Otto-Hahn-Allee 1 D-28359 Bremen Germany +

Re: [easybuild] Python extension installation using pip (was: Python extensions from .whl)

Sorry, the subject line was wrong ... Andreas Hilboll writes: > Hi all, > > I'm trying to create an easyconfig for jupyterhub 0.7. I copied the > existing 0.6.1 easyconfig and bumped the version number, so it now reads > >easyblock = 'Bundle' >name

[easybuild] Python extensions from .whl

ng bdist_egg Aborting implicit building of eggs. Use `pip install .` to install from source. (at easybuild/tools/run.py:438 in parse_cmd_output) == 2016-12-27 19:07:51,707 easyblock.py:2499 WARNING build failed (first 300 chars): cmd " /home/eb/software/Python/3.5.1-intel-2016a/bin/pytho

Re: [easybuild] How to specify the source file name with URL parameters for Python extensions

Hi Kenneth, Kenneth Hoste writes: > Hi Andreas, > > On 22/12/16 23:14, Andreas Hilboll wrote: >> Hi, >> >> I'm trying to add the ecmwf-api-client >> (https://software.ecmwf.int/wiki/display/WEBAPI/Downloads) to my custom >> Python easyconfig. I cu

[easybuild] How to specify the source file name with URL parameters for Python extensions

it, but maybe there's a cleaner solution? Anyways, let me take the time to thank you for all the amazing work you're doing! EasyBuild really is an invaluable resource for setting up our cluster with low manpower in short time -- thanks! Have a merry Christmas! Best, Andreas --

Re: [easybuild] Setting environment variables

;' > > There are a lot of ready for use configs that you could just grep under your > EB installation > ~/lib/python2.6/site-packages/easybuild_easyconfigs-2.8.0-py2.6.egg/easybuild/easyconfigs > > Cheers, > Gizo > > On Friday, June 24, 2016 15:34 CEST, Andreas Hilbo

Re: [easybuild] How to name easyconfigs for alternative build options

Ward Poelmans writes: > On 01-07-16 10:53, Andreas Hilboll wrote: >> >> How should I go about naming the easyconfig, so that in the end I have >> two distinct module files, one with 'nonetcdf' somewhere in its name? > > The current approach is to use a versi

[easybuild] How to name easyconfigs for alternative build options

abled. How should I go about naming the easyconfig, so that in the end I have two distinct module files, one with 'nonetcdf' somewhere in its name? Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute o

[easybuild] Setting environment variables

mehow, but I couldn't find any reference to this in http://easybuild.readthedocs.io/en/latest/eb_a.html. Any pointers would be greatly appreciated ... Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute o

Re: [easybuild] Extending an easyconfig

also hit the problem > you're seeing... Here you go: https://github.com/hpcugent/easybuild-easyconfigs/issues/2983 Cheers, Andreas -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) Uni

Re: [easybuild] Extending an easyconfig

em easyconfig (and maybe easyblock > too, depends), or just enhance the existing WRF easyconfig/easyblock to > include WRF-Chem. > > I'm not sure if the latter would actually make any sense though... Actually, I think it would. I'll look into extending the existing wrf easy

[easybuild] Extending an easyconfig

clude the chemistry code Does EasyBuild foresee a mechanism to extend easyconfigs, so that I can build on the existing WRF easyconfig? Or do I have to make a seperate WRF-Chem easyconfig by copy-pasting and amending the existing WRF? Cheers, Andreas. -- Dr. Andreas Hilboll Center for M

Re: [easybuild] Supporting WRF 3.8

Hi Kenneth, Kenneth Hoste writes: > Hi Andreas, > > On 20/04/16 20:44, Andreas Hilboll wrote: >> Okay, it seems I have the regexp now. Now I need to fiddle with the >> patches ... but that should be okay. I'll submit a PR once I'm done. > > Any luck? I gu

Re: [easybuild] Packaging of Intel compilers

e same is true for tbb, ipp, vtune,... We will need to fine tune the > easyconfigs for these with components to trim back the installations (or we > just use the specific tarballs rather than the bundle). > > On 22 April 2016 at 15:21, Andreas Hilboll > mailto:hilb...@uni-bremen.d

Re: [easybuild] Packaging of Intel compilers

tel... > > There's currently no supported to install the whole Parallel Studio > suite in one go, although that could be looked into... > > > regards, > > Kenneth > > On 22/04/16 14:20, Andreas Hilboll wrote: >> Hi EasyBuilders, >> >> I'm t

[easybuild] Packaging of Intel compilers

181.x86_64.rpm - intel-mkl-common-181-11.3.2-181.noarch.rpm - intel-mkl-devel-181-11.3.2-181.i486.rpm - intel-mkl-devel-181-11.3.2-181.x86_64.rpm I'd appreciate some guidance in building the impi and imkl easyconfigs from these rpm files. Any ideas? Cheers, Andreas. -- Dr. Andreas Hilb

Re: [easybuild] Supporting WRF 3.8

> IRC channel on the FreeNode IRC network... Okay, it seems I have the regexp now. Now I need to fiddle with the patches ... but that should be okay. I'll submit a PR once I'm done. Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM)

Re: [easybuild] Supporting WRF 3.8

, how would I ensure that EasyBuild automatically picks the correct easyblock depending on the version? But maybe I should start working on the right regexp ... ;) Sunny greetings, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND -

[easybuild] Supporting WRF 3.8

toolchain, the correct option would be 34. Is this as bad as it looks, or does the run_cmd_qa function already provide the necessary features to deal with this? Any help would be appreciated, but I do understand that probably this is pretty screwed up ... Sunny greetings, Andreas. -- Dr. Andreas

Re: [easybuild] Problems installing: ImportError on pkg_resources

> I would recommended considering 'foss' instead (in particular > foss/2016a), although it depends on your needs. Doing that now, as goolf didn't compile properly. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - A

Re: [easybuild] Problems installing: ImportError on pkg_resources

Thanks again, Kenneth! Your fix solved my issue, and I'm now installing goolf =) Cheers, Andreas. Kenneth Hoste writes: > Hi Andreas, > > On 19/04/16 19:33, Andreas Hilboll wrote: >> Hi Kenneth, >> >>> Is this a recent version of the bootstrap script? Wh

Re: [easybuild] How to update easybuild?

Sorry for the noise, I overlooked the conf.py file in the docs/ directory. Everything looks fine, and I'll do the PR now. Cheers, Andreas. Andreas Hilboll writes: > Hi Kenneth, > > I basically copied your email into the Installation.rst file, see my > branch at https://git

Re: [easybuild] How to update easybuild?

couldn't find the Sphinxdoc Makefile in the repo. Is there an easy way to build the documentation locally on my machine? Otherwise, I can submit the PR as-is ... Cheers, Andreas. Kenneth Hoste writes: > Hi Andreas, > > On 19/04/16 17:17, Andreas Hilboll wrote: >>

Re: [easybuild] Problems installing: ImportError on pkg_resources

you prefer me opening an issue for this? If so, against which repository (easybuild or easybuild-framework)? Cheers, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen

Re: [easybuild] How to update easybuild?

Would you consider a PR I could prepare to include this in the documentation? Cheers, Andreas. Kenneth Hoste writes: > Hi Andreas, > > On 19/04/16 17:17, Andreas Hilboll wrote: >> Hi easybuild experts, >> >> I'm wondering what is the canonical method to update th

[easybuild] Problems installing: ImportError on pkg_resources

kages/ distribute-0.6.49-py2.7.egg easy-install.pth setuptools-0.6c11-py2.7.egg-info setuptools.pth site.py site.pyc Or is it an issue that the packages are in the lib folder while my Python might expect them to be in lib64? Confused greetings, Andreas. -- Dr. Andreas Hilboll Center for

[easybuild] How to update easybuild?

cumentation, so I'm asking here ... Thanks for your helping me use this great software, Andreas. -- Dr. Andreas Hilboll Center for Marine Environmental Sciences (MARUM) - AND - Institute of Environmental Physics (IUP) University of Bremen U3145 Otto-Hahn-Allee 1 D-