[easybuild] Lmod no autoswap error customization

Hi all, If you use Lmod as your module system, you can either allow or disable 'auto swap'. If you want to mimic Tmod behaviour as close as possible, you usually don't want this to happen. A user might get confused by it (especially in a flat module tree). However, Lmod gives out a rather

Re: [easybuild] configure: error: cannot run C compiled programs.

Hi Satish, On Mon, Jan 30, 2017 at 11:57 AM, Satish Sherikar wrote: > > Currently i am installing NCL, HDF5 applications everytime it is giving same > error. > > can you please help me to resolve this issue. > > I have attached log file for the same. Can you also post

Re: [easybuild] Extended package documentation

On 14-02-17 20:08, Kenneth Hoste wrote: > > I feel this sort of terse key/value style could be useful, but only for > single-line info (e.g. homepage, contact, etc.). > > For things like 'description' and 'usage', I'm not sure this would be > useful or sensible. > > So, maybe what you're

Re: [easybuild] Python-2.7.12-foss-2016b undefined references

On 18-01-17 22:16, Vanzo, Davide wrote: > Ward, > the symbols exist in the libreadline.a, not in libncurses.a as you can > see here: > > $ readelf --syms > /usr/software/software/Compiler/GCC/5.4.0-2.26/libreadline/6.3/lib/libreadline.a > | grep

Re: [easybuild] Python-2.7.12-foss-2016b undefined references

Hi Davide, On Wed, Jan 18, 2017 at 9:05 PM, Vanzo, Davide wrote: > When trying to build Python-2.7.12-foss-2016b it fails with the error below. > > = > /usr/software/software/Compiler/GCC/5.4.0-2.26/libreadline/6.3/lib/libreadline.a >

Re: [easybuild] LUA modules: whatis statement split up across multiple lines when printed

On Thu, Jan 19, 2017 at 10:38 PM, Ben Roberts wrote: > This is a problem for me and my site as we prepare our lists of modules by > looking at the output of “module whatis”. While we could post-process that > output, it is somewhat tedious and error prone to have to do so.

[easybuild] Build gcc with up to date cloog and ppl

Hello all, I want to make a new eb for gcc that builds with the latest cloog and ppl. The problem is that I need to apply a patch to ppl before building in stage 2. And that's a problem (I think). Currently, the sources of gcc, cloog, ppl, ... are all extracted in the same directory and just

Re: [easybuild] Re: Build gcc with up to date cloog and ppl

I've made a pull request (#667). It now search first in the directory of the current easyconfig, then robot and as last the sources directory. Ward On Mon, Jul 15, 2013 at 11:45 AM, Fotis Georgatos wrote: > > Hi Jens, Ward, > > On Jul 15, 2013, at 11:31 AM, jens timmerman

Re: [easybuild] More than 1 admin

s approach are more than welcome! > > Einen guten Rutsch ins neue Jahr! As they say in German, > Bart > > > > -- > Dr. Bart Verleye > Centre for e-Research > Level G, Room 409-G21 > 24 SYMONDS ST > Auckland 1010 > New Zealand > +64 (0) 9 923 9740 ext 897

Re: [easybuild] CMake built, but does not run

On Mon, Feb 24, 2014 at 5:24 PM, Heywood, Todd wrote: > From: , Todd Heywood > > Reply-To: "easybuild@lists.ugent.be" > > > Date: Monday,

Re: [easybuild] GCC

n error (at easybuild/framework/easyblock.py:1897 > in > get_class): Failed to import easyblock for EB_gcc because of module issue: > ' > -- ir. Ward Poelmans Center for Molecular Modeling Ghent University Technologiepark 903, B-9052 Zwijnaarde Belgium Tel: +32 9 264 65 76 Fax: +32 9 264 66 97 E-mail: ward.poelm...@ugent.be http://molmod.UGent.be/

Re: [easybuild] Install problem

On Mon, Mar 31, 2014 at 11:36 PM, Bart Verleye wrote: > > Is this something in the eb file that is wrong, or a small error in EB? Hi, I don't see any errors in your ebconfig file. Can you send (or pastebin/github gist) the full debug output of the build? Ward

Re: [easybuild] A patch containing a new file

On Fri, Apr 4, 2014 at 3:03 PM, Kenneth Hoste wrote: > prebuildopts = ["cd hmm && ", "cd phmm && "] s/prebuildopts/premakeopts/ everywhere ;-) We should rename that one. Ward

Re: [easybuild] Request pull for 1000+ easyconfigs or --try-toolchain???

s this huge PR, it would be better to redirect our efforts to ECv2. Ward -- ir. Ward Poelmans Center for Molecular Modeling Ghent University Technologiepark 903, B-9052 Zwijnaarde Belgium Tel: +32 9 264 65 76 E-mail: ward.poelm...@ugent.be http://molmod.UGent.be/

Re: [easybuild] easyconfig list

; find how to list the easyconfig file list. > > Regards, > Ahmed. -- ir. Ward Poelmans Center for Molecular Modeling Ghent University Technologiepark 903, B-9052 Zwijnaarde Belgium Tel: +32 9 264 65 76 E-mail: ward.poelm...@ugent.be http://molmod.UGent.be/

Re: [easybuild] easyconfig list

> Yup. > > Is there option to pass to eb? > > Ahmed. > > -Original Message- > From: Ward Poelmans [mailto:ward.poelm...@ugent.be] > Sent: 14 July 2014 12:18 > To: easybuild@lists.ugent.be > Subject: Re: [easybuild] easyconfig list > > Hi Ahmed, > > Do you mean

Re: [easybuild] CMake-3.3.0-intel-2014b : problem building

On Tue, Oct 28, 2014 at 11:10 AM, Pablo Escobar wrote: > recently I wrote a FreeBayes easyconfig and I had to add this to the > easyconfig to avoid that error > > # workaround to avoid the error "The C compiler identification is unknown" > prebuildopts = "unset CC && unset

Re: [easybuild] CMake-3.3.0-intel-2014b : problem building

On Tue, Oct 28, 2014 at 12:04 PM, Pablo Escobar Lopez wrote: > I verified it when I tried the workaround and it seems to work fine, at > least in this case. That's because you are using a gcc toolchain and it is in the path. I suspect this would fall back to system

Re: [easybuild] CMake-3.3.0-intel-2014b : problem building

On Wed, Oct 29, 2014 at 12:05 PM, Backeljauw Franky wrote: > We’ve managed to get CMake to build on our local filesystem, but when I load > it, it falls back to the system installed gcc instead of the intel toolchain: > /tmp/hello_world> cmake . > --

Re: [easybuild] CMake-3.3.0-intel-2014b : problem building

On Wed, Oct 29, 2014 at 3:40 PM, Backeljauw Franky wrote: >> Well, you have to tell it about icc/icpc. By default, CMake will look >> for gcc and if it finds gcc, it will use it. EB sets several env >> variables to point CMake in the right direction (CC, CXX,

Re: [easybuild] Install extensions to already installed package

On Tue, Dec 2, 2014 at 3:04 PM, Backeljauw Franky wrote: > > Just a small question: is it possible to install extensions to a package > instead of using a separate easyconfig-file? > E.g., I want to install some extra python modules to an already install >

Re: [easybuild] no sqlite3 in python builds

On Thu, Jan 22, 2015 at 9:57 PM, Heywood, Todd wrote: > I have built Python2 and Python3 using standard easyconfigs and the goolf > toolchain. But they don¹t include the sqlite3 module: Hi Todd, We're aware of the issue [1]. If you want to fix it, it should be as simple as

Re: [easybuild] easybuild new user experience

On Wed, Feb 11, 2015 at 2:32 AM, Stuart Barkley wrote: > I've been looking at easybuild for a little while now and it appears > to be a suitable framework for a good portion of our needs. Welcome to EB! > My cluster does not have direct access to the Internet so I can't use >

Re: [easybuild] Rebuild modulefiles

On Fri, Mar 6, 2015 at 1:55 PM, wrote: > Can one only rebuild a modulefile without going through a whole build? > I've already built quite a lot of software and not keen on rebuilding > everything just to recreate the modulefiles. Not yet, but it's on the todo list:

Re: [easybuild] Issue with v2.0.0? (can not import _bdist_rpm)

On Sun, Mar 8, 2015 at 5:20 PM, Timothy Brown wrote: > == 2015-03-08 10:08:53,646 bootstrap_eb.run ERROR EasyBuild crashed with an > error (at easybuild/tools/run.py:384 in parse_cmd_output): cmd " python > setup.py install

Re: [easybuild] Re:

On Mon, Mar 9, 2015 at 5:07 PM, Don Moore wrote: > eb gmpolf-1.4.8.eb -r > Fail: > from openBlas .. > ideas? > -/Don Can you send the --debug logs again? Ward

Re: [easybuild] MKLROOT in modulefiles

On Wed, Apr 1, 2015 at 4:28 PM, Inigo Aldazabal Mensa wrote: > > I noticed this as it already caused me a couple of conflicts with the > canonical MKLROOT definition. Or am I missing something? Hi Inigo, You're correct. The fix is already made but not yet merged:

Re: [easybuild] Adding files to the repository

On Wed, Apr 29, 2015 at 5:15 PM, Backeljauw Franky wrote: > I tried with a patch as in “diff -ru -NB” but that tells me it cannot > determine the patch level… That should do the trick. Does the patch work if you try to apply it manually? Autodetecting the patch

Re: [easybuild] Adding files to the repository

On Thu, Apr 30, 2015 at 10:06 AM, Backeljauw Franky wrote: > The main.filetools module seems to have a problem with the fact that the > file build.conf does not exist at first… Yes because it cannot derive the patch level for a non-existing file. You will have to

Re: [easybuild] EasyBuild newbie question

It is on our wish/todo list. Kenneth can correct me but I don't think there is currently somebody working on this. > Am I on the right track with all this? You sure are! Good luck with the new system. Ward -- ir. Ward Poelmans Center for Molecular Modeling Ghent University Technologiepark

Re: [easybuild] Re: [easybuidl] intel vs gnu toolchains, easyconfigs explosion (was: Intel toolchains and mpiicc/mpiicpc/mpiifort)

On Thu, Jun 4, 2015 at 10:02 AM, Kenneth Hoste wrote: > Version numbers are very confusing with the Intel tools (and EB doesn't make > it any better...). > > The 2015 versions of the Intel tools are currently only in the most recent > intel/ictce toolchains, i.e.

Re: [easybuild] EasyConfig repos?

On Sat, Jun 6, 2015 at 7:13 PM, Jack Perdue wrote: > > Any plans for adding web-based repos for easyconfig files? > > e.g. > EASYBUILD_ROBOT=/http/www.siliconslick.com/easybuild/eb_repos_cleaned/ada > > which would resolve to (via EB framework): Hi Jack, I've thought about

Re: [easybuild] (Recursive) github checkout with easybuild

there is a possibility to configure or write an easyblock to > do a recursive github checkout instead of fetching files. I wanted to follow > this instructions: > > https://github.com/ekg/freebayes#obtaining > > What possibilities do I have and what is the most straight-forward way? >

Re: [easybuild] (Recursive) github checkout with easybuild

On Wed, Jun 10, 2015 at 11:33 AM, Stolpe, Oliver wrote: > How do I skip the fetching step in an EasyBlock, which seems to be mandatory? The fetching step will be skipped if all files in `sources` can be found locally ;) Ward

Re: [easybuild] (Recursive) github checkout with easybuild

On Wed, Jun 10, 2015 at 12:01 PM, Stolpe, Oliver wrote: > Ok, can I somehow execute commands before it tries to do the fetching step? > What is about the 'skipsteps' parameter for the config file? I can't get from > the manual what values it accepts. Can I trick it by

Re: [easybuild] Sending text to the command line during installation

ter > pressing yes. Is there already support in EasyBuild for sending text to the > command line during installation? > > Thanks, > Niek -- ir. Ward Poelmans Center for Molecular Modeling Ghent University Technologiepark 903, B-9052 Zwijnaarde Belgium Tel: +32 9 264 65 76 E-mail: ward.poelm...@ugent.be http://molmod.UGent.be/

Re: [easybuild] how to set dependency to not use compiler?

Hi Niek, On Tue, Jun 16, 2015 at 7:11 PM, Niek de Klein wrote: > ERROR: Irresolvable dependencies encountered: Weblogo/2.8.2-goolf-1.7.20 > > when it should be using Weblogo/2.8.2. > > My dependencies in the HOMER.eb file look like this: > > dependencies = [ >

Re: [easybuild] 2015b common toolchains

On Fri, Jun 19, 2015 at 12:05 PM, Martin wrote: > I'm not sure wether it should be part of the toolchain but to me "base > tools/libs" should somehow be standardized on. I'm thinking along the lines > of xz, bzip and such (I'm more along the lines of: Provide an environment

Re: [easybuild] wget GCC issue

On Fri, Jun 26, 2015 at 3:47 PM, Stolpe, Oliver wrote: > Hello List, > > I got another issue and wondered whether this is intentional or if there is > a workaround for this. I am using easybuild on a debian right now. A lot of > tools were compiled with the goolf-1.4.10

Re: [easybuild] wget GCC issue

On Fri, Jun 26, 2015 at 7:04 PM, Todd Gamblin wrote: > In Spack, the compilers don't actually have to be loaded, so your new > compilers stay out of the way of the system software. The stuff compiled > with Spack gets RPATH'd, so it knows how to find its libraries -- in the >

Re: [easybuild] cd to a directory with easybuild

Hi Yann, Welcome to Easybuild. On Thu, Jul 2, 2015 at 5:46 PM, Yann Sagon wrote: > I'm trying to write my first easyconfig file (for Gadget2). Once untarred, > the source of Gadget2 contains a directory named Gadget2, so I need to > instruct easybuild to cd to that

Re: [easybuild] cd to a directory with easybuild

On Thu, Jul 2, 2015 at 6:05 PM, Yann Sagon wrote: > I have copied the Makefile in my work directory as Makefile.o and Makefile > Modified the Makefile. > Created the diff : diff -u Makefile.o Makefile > > Gadget-2.0.7-makefile-hardcoding.patch > > Error message: "Can't determine

Re: [easybuild] next EasyBuild conf call: Wed July 8th, 3pm CET

On Wed, Jul 8, 2015 at 5:58 PM, Jack Perdue wrote: > But _something_ needs to be done to make sure that toolchains > in EB can keep up with compiler/MPI/mathlib releases. So basically you would like a way to generate a toolchain with the gcc, icc, ifort, imkl, impi, ... of

Re: [easybuild] (g)awk and easybuild

On Fri, Jul 10, 2015 at 4:26 PM, Stolpe, Oliver wrote: > > $ gawk > gawk: symbol lookup error: > /tools/easybuild/software/libreadline/6.3-foss-2015a/lib/libreadline.so.6: > undefined symbol: PC Dear Oliver, Please try this:

Re: [easybuild] conflicts with system libraries

On Fri, Jul 31, 2015 at 5:49 AM, Riccardo Murri wrote: > > Am I doing something wrong here? Is there a well-known solution/fix? Hi Riccardo, It's a known issue: https://github.com/hpcugent/easybuild-easyconfigs/pull/1670 I still have to divide into the exact cause of

Re: [easybuild] difference between `--filter-deps` and `--hide-deps` ?

On Fri, Jul 31, 2015 at 2:35 PM, Riccardo Murri wrote: > What's exactly the difference between the two? Does "filter" consider > the dependency satisfied (hence, skip building), whereas "hide" still > builds it but does not provide a module file? The --hide-deps will

Re: [easybuild] Installations that require non-trivial patches

On Fri, Jul 24, 2015 at 4:55 PM, wrote: > > The first program is GROMACS that I need to patch with plumed. I need to have > the GROMACS files un-tared, and then run the plumed patch command in their > directory. During the patching plumed suggests several versions of GROMACS

Re: [easybuild] Tarball Easyblock sanity_check fails

On Mon, Aug 10, 2015 at 4:39 PM, Stolpe, Oliver wrote: > When I comment out the sanity_check part, then it complains that lib and > lib64 are missing, but I there is nothing to check for easybuild and I > didn't request them? > > Sanity check failed: no dir of

Re: [easybuild] install from git clone

On Fri, Aug 28, 2015 at 2:42 PM, Niek de Klein wrote: > git clone https://github.com/voutcn/megahit.git They have releases so you can simplify use https://github.com/voutcn/megahit/archive/v1.0.2.tar.gz as source url? Ward

Re: [easybuild] GCC-4.9.3-binutils-2.25 : invalid ELF header

On Tue, Sep 1, 2015 at 4:44 PM, Backeljauw Franky wrote: > > > The one I found back is about "CMake-3.3.0-intel-2014b : problem building” > also on this mailing list, dated 28 October 2014. > It was an issue with GPFS 3.5.0-20, currently we have GPFS 4.1.0-8, so

Re: [easybuild] 2015b toolchains : non-GCC- and GCC-versions

On Wed, Sep 2, 2015 at 2:50 PM, Backeljauw Franky wrote: > I guess the first one can go (since it’s just a dependency to build > binutils/2.25 as you mentioned below), but what’s the difference between > GCC-4.9.3-binutils-2.25 and GCC-4.9.3-2.25? M4/1.4.17 is

Re: [easybuild] 2015b toolchains : non-GCC- and GCC-versions

On Wed, Sep 2, 2015 at 2:56 PM, Bode, Brett wrote: > How do you handle the binutils dependency for other software (like mpich)? I > have been using the GCC-4.9.2-binutils-2.25 version on a haswell node. > Binutils is required to build GCC, but it is also required to build

Re: [easybuild] Sourceforge download

quot;"" > > toolchain = {'name': 'goolf', 'version': '1.7.20'} > toolchainopts = {'pic': True, 'usempi': True} > > > sources = [SOURCELOWER_TAR_BZ2] > source_urls = [('http://sourceforge.net/projects/rnaseqassembly/', > 'download')] > > > files_to_copy = [('Assemble','bin/')] > > moduleclass = 'bio' > > > > -- dr. ir. Ward Poelmans Center for Molecular Modeling Ghent University Technologiepark 903, B-9052 Zwijnaarde Belgium Tel: +32 9 264 65 76 E-mail: ward.poelm...@ugent.be http://molmod.UGent.be/

Re: [easybuild] Maintaining patches

k passes. Ward -- dr. ir. Ward Poelmans High Performance Computing infrastructure unit Ghent University Krijgslaan 281 S9 B-9000 Gent Belgium Tel: +32 9 264 4817 http://www.ugent.be/hpc

Re: [easybuild] Use of environment variables (CC, etc.) in patched configure scripts

On Tue, Oct 13, 2015 at 7:57 PM, Ward Poelmans <ward.poelm...@ugent.be> wrote: > On Tue, Oct 13, 2015 at 6:58 PM, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: >> No, but you can do the reverse (as you already know, I think), using the >> 'unwanted_env_vars' easyconfig p

Re: [easybuild] GNU toolchain

GCC, we only mean to use that binutils once as it was built using the system GCC. The flaw is that you try to load the GCC module itself while you should be loading the GNU module. But the naming is indeed confusing. Ward -- dr. ir. Ward Poelmans High Performance Computing infrastructure unit Ghe

Re: [easybuild] GROMACS-5.1-intel-2015b-hybrid.eb: error in test

On 28-10-15 09:46, Backeljauw Franky wrote: > Actually, we are not getting compilation errors when building GROMACS itself. > It only fails in the testing phase. > But when we do this step manually, after having loaded the necessary modules, > it works fine. > So that gives us the impression

Re: [easybuild] cannot build old GCC on recent Ubuntu

On 29-10-15 02:37, Riccardo Murri wrote: > 2. have `EB_GCC` supply `MAKEINFO=missing` in all stages when the >build-dependencies are ignored. > > If you don't have 1. then build will fail on all distributions that have > texinfo >= 5.0.0; but 2. is needed because `builddependencies` are >

Re: [easybuild] cannot build old GCC on recent Ubuntu

On 30-10-15 10:41, Martin wrote: > On Thu, Oct 29, 2015 at 2:37 AM, Riccardo Murri > wrote: > > > Why, oh why, would you need a GCC that old on a recent system? > > To compile code that was known to compile correctly with GCC 4.5 and

Re: [easybuild] [ANN] EasyBuild v2.5.0

>>> >>>(iii) install EasyBuild v2.5.0 from PyPI, using one of the >>> standard Python installation tools (easy_install, pip, ...) >>> >>>(iv) update your Git working copies of the different EasyBuild >>> repositories >>> >>> &g

Re: [easybuild] Intel-2016.xx toolchains

Hi Franky, On 22-12-15 12:02, Backeljauw Franky wrote: > > I’ve just installed EasyBuild 2.5.0 and noticed there are several > intel-2016b.xx toolchains now: Yes, that's because we haven't decided about which one is going to be intel/2016a. Kenneth was going to send a mail about it but he

Re: [easybuild] mpiicc and mpiifort, and --cleanup-builddir

upoldbuild” in > the easyconfig doesn’t seem quite right as this seems related to previous > builds, but maybe I’m missing something here. You need --disable-cleanup-builddir. Ward -- dr. ir. Ward Poelmans High Performance Computing infrastructure unit Ghent University Krijgslaan 281 S9 B-9000 Gent Belgium Tel: +32 9 264 4817 http://www.ugent.be/hpc

Re: [easybuild] foss/2016a and intel/2016a common toolchains

On 11-01-16 21:50, Kenneth Hoste wrote: > ** GCC 4.9.3 vs GCC 5.3.0 ** > > The question here is if we stay with the latest release of GCC v4.x, > which as it happens is still the same version as the one included in the > 2015b toolchains, or if we make the jump to GCC 5.x. > > My personal

Re: [easybuild] Problems with installation of Clang under Cent OS 6.6/6.7

tests... Ward? >> >> I’m inclined to agree, however it’s good to have a better understanding if >> that introduces an “unsafe" situation. >> Basically, if behaviour is the same like it used to be with clang/3.3, it >> may be OK to disable as default even if impe

Re: [easybuild] Python packages?

On 08-02-16 22:50, Elizabeth Fischer wrote: > Is there any documentation on how EasyBuild interacts with Python > packages? I see there's an EasyBuild for matplotlib, but not for > basemap. What is the recommended way to go about installing stuff? > Pure EasyBuild? EasyBuild + PIP? EasyBuild

Re: [easybuild] configure flag for openmpi

Hi Yann, Just add the options to the `configopts` string in the easyconfigs of OpenMPI? Ward

Re: [easybuild] binutils for foss/2016a

On 03-05-16 17:00, Heywood, Todd wrote: > *** static library > /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a > is not portable! That's weird. It seems -fPIC is needed when compiling zlib. Very strange that this didn't happen automatically. On what system are

Re: [easybuild] [ANN] EasyBuild v2.8.1

On 30-05-16 13:47, Kenneth Hoste wrote: > I'm happy to announce the release of EasyBuild version 2.8.1 [1]. > Yes, that's right, EasyBuild v2.8.0 just got even better! This really doesn't capture the importance of this release. In its continuous quest for world dominance, EasyBuild took an

Re: [easybuild] Option --dep-graph

On 03-06-16 13:13, nan...@luis.uni-hannover.de wrote: > > Hi, > > I get the following error when I try to use the option -dep-graph, thought I > have installed all necessary packages following the doc > >> eb foss-2016a.eb -r --dep-graph ~/foss-2016a.eb.png > == temporary log file in case

Re: [easybuild] eb --job

On 03-06-16 16:27, Riccardo Murri wrote: >>> Can you please provide me with the full `qstat -f` output for a >>> completed job? >> >> it is here > > Thanks! (And thanks to Ward as well, who provided another example) > > One quetion more: this is very similar to what PBSPro provides with its >

Re: [easybuild] ccache support in EasyBuild?

For ordinary EasyBuild use, I agree it's quite useless. However, when creating new easyblocks/easyconfigs, it can be quite handy to speed things up. Usually, it will involved build the same software several times until the new easyblock fully works. Ward

Re: [easybuild] 2016b toolchains: proposal & test results

On 30-06-16 13:52, Backeljauw Franky wrote: > Hi Kenneth, > > Two small questions: > > * Why don’t you condiser GCC 6.1 (or GCC 6.0) to be part of “all the > latest & greatest”? > * Is it necessary to have identical version of GCC for the foss and > intel toolchains? Well, you could

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

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 versionsuffix for this. In the `nonetcdf` you simple add: versionsuffix =

Re: [easybuild] OpenFOAM module file

On 05-07-16 13:01, Erik Smeets wrote: > > The problem in our opinion would be that a user wouldn't return to a clean > environment when unloading the modules. Furthermore, this complicates > switching between different versions. What's your thought on this and how do > you approach these

Re: [easybuild] How to setup EB in the global /etc/profile.d/ ?

On 13-10-16 15:20, Ole Holm Nielsen wrote: > On 10/13/2016 01:54 PM, Ward Poelmans wrote: >> On 13-10-16 13:48, Ole Holm Nielsen wrote: >> >> For loading Easybuild by default, I would use a Lmod default collection. > > Could you possibly offer a specific exam

Re: [easybuild] How to setup EB in the global /etc/profile.d/ ?

On 13-10-16 13:48, Ole Holm Nielsen wrote: > I would like to enable the EB/Lmod modules to all users in a global > bash/tcsh setup script. On CentOS 7.2 initialization is done using > scripts in /etc/profile.d/ > > Basically I want every user shell to execute these commands: > > export

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

On 04-01-17 11:01, Kenneth Hoste wrote: > > > On 04/01/2017 02:41, Jack Perdue wrote: >> On 01/03/2017 06:55 PM, Exequiel Sepúlveda wrote: >>> >>> 1.- Why are GCC and binutils needed on the easyconfigure file >>> intel-2017.00.eb >> >> See other response. Additionally, the Intel compilers

Re: [easybuild] Training session at S3IT: GC3Pie for programmers, January 23--27, 2017

Hi Riccardo, On 10-01-17 13:10, Riccardo Murri wrote: > > S3IT is glad to announce a training session "GC3Pie for programmers". > It is targeted at current and prospective users who want to develop their > own scripts and workflows using GC3Pie. Any chance of streaming/recording the training?

Re: [easybuild] mpi4py on OpenMPI 2.x (foss/2017a)

Hi Joachim, On 11-04-17 15:39, Joachim Hein wrote: > Hi, > > I have a user with MPI4PY issues. MPI4PY out of the box wants to have a > multi threaded MPI library, which is not supported in OpenMPI 1.x on IB. So > building on top of foss/2016b and foss/2016a is not an option. foss/2017a is

Re: [easybuild] GPG signing RPM in EasyBuild

On 04-04-17 14:32, Siddiqui, Shahzeb wrote: > Exactly, if there is a way to store GPG key like a GitHub token we could > get this to work. > I might be missing something here but why can't we handle the GPG key id as an ordinary commandline argument? The ID of GPG key is not sensitive

Re: [easybuild] building mxnet

On 27-06-17 11:41, Jure Pečar wrote: > On Mon, 8 May 2017 12:27:55 +0200 > Just haswell remaining ... and boom. Sanity check for python fails with: > > == 2017-06-27 11:05:27,003 extension.py:181 WARNING Extension: MXNet failed > to install, cmd >

Re: [easybuild] Spider output - whatis vs help

On 04-07-17 08:43, Alvarez, Damian wrote: > I think there is no reason to break backwards compatibility. But we still can > make it better adding templates like %(pyver)s and allowing whatis to be > defined using them. For instance: > > whatis = ["Homepage: %s" % homepage, "Description: %s" %

Re: [easybuild] Strategy for hiding modules

If you're still interested, the isVisible() hook has been merged. An example on how to use it can be found at https://github.com/TACC/Lmod/pull/276/files You can dynamically hide a module based on any criteria of your desire, time, toolchain version, ... Ward On 07-04-17 14:32, Alan O'Cais

Re: [easybuild] Software/easyconfigs update avail check

On 04-05-17 10:39, Jens Timmerman wrote: > > On 04/05/2017 08:31, Henkel, Andreas wrote: >> Hi, >> >> Recently we started using eb for our new cluster. Yesterday, in our group >> meeting a question was raised concerning updates and security patches for >> installed software similar to apt

Re: [easybuild] building mxnet

On 02-05-17 17:13, Jure Pečar wrote: > On Tue, 2 May 2017 15:36:27 +0200 > Ward Poelmans <wpoel...@gmail.com> wrote: > >> Hi Jure, >> >> There are now an easyblock [1] and easyconfig [2] for MXNet. >> >> Can you give them a spin? > > Nice ...

Re: [easybuild] building mxnet

On 25-01-17 11:51, Jure Pečar wrote: > > Hi all, > > I'm trying to build mxnet thru EasyBuild. It's quite a challenge ... Hi Jure, There are now an easyblock [1] and easyconfig [2] for MXNet. Can you give them a spin? [1] https://github.com/hpcugent/easybuild-easyconfigs/pull/4346 [2]

Re: [easybuild] Local user intstallation

You can decide to hide a module based on it's full name, short name or path to the module file. So yes. Ward On 28-06-17 09:55, Alan O'Cais wrote: > So you're saying you can select to hide all modules called > Core/Compiler/MPI (in a HMNS) which you pick up > from $EB_GLOBAL_PREFIX/modules/all

Re: [easybuild] zlib is not statically linked

On 20-09-17 10:56, Philippart Raphaël wrote: > I’m trying to install the package ROOT and bam-readcount. I have in the > 2 scenarii the same error :  > > zlib is not statically linked in > /cm/shared/apps/easyb/.local/easybuild/software/binutils/2.25-GCCcore-4.9.3/bin/addr2line: >

Re: [easybuild] Mesa and vglrun

On 22-09-17 13:39, alexi.riv...@chalmers.se wrote: > So I'm wondering if there are any recommendations for how to compile software > with 3D-acceleration? Hi Alexi, The Mesa easyconfig of EasyBuild currently doesn't build with support for hardware 3D acceleration. It requires the presence of a

Re: [easybuild] zlib is not statically linked

Hi Raphaël, On 25-09-17 09:33, Philippart Raphaël wrote: > Do you have an explanation for my zlib problem and his statically link > problem ? > I deleted in the .eb the zlib’s dependency and I have the same result  I'm seeing things like: checking for library containing zlibVersion... no

Re: [easybuild] custom glibc

On 24-08-17 15:53, Jure Pečar wrote: > > Hi all, > > I found this thread from about two years ago: > www.mail-archive.com/easybuild@lists.ugent.be/msg01795.html > > Have things changed since? Would newer glibc still present a pain from > easybuild point of view? Not really. It's not

Re: [easybuild] VMD-1.9.3-intel-2016b-Python-2.7.12.eb segfaults

Hi John, On 18-12-17 15:52, John Donners wrote: > > the problem seems to be in LLVM compiled with the intel compiler when > used as backend for Mesa. > It can be circumvented when using > > GALLIUM_DRIVER=swr vmd > > but that is slower, so not preferrable. Did anyone get VMD running with >

Re: [easybuild] next EasyBuild conf call: Wed Dec 12th 2018 (*today*), 5pm CET

On 13/12/18 00:46, Jack Perdue wrote: > I think that would be wonderful if we could just > give the user the option of flat or hierarchical instead > of imposing one or the other on all of them. Just add all the modules paths to $MODULELIST and you've switched from hierarchical to flat, no? Ward

Re: [easybuild] Retrospectively hiding modules / hiding by default

On 23/11/18 10:57, Ole Holm Nielsen wrote: > > It's also possible to hide modules by configuring Lmod, see the > isVisibleHook function in > https://lmod.readthedocs.io/en/latest/170_hooks.html We hide modules from older toolchain with the hooks:

Re: [easybuild] Fix incorrect paths in modules

On 14/01/19 11:07, Loris Bennett wrote: > > I assume easiest solution is just to rebuild all the module files as > user 'build'. Is that correct? Yes, paths may be put in all kind of places. The only way to be sure is to rebuild. Ward

Re: [easybuild] Non-standard PATH?

Hi Loris, On 27/03/19 13:35, Loris Bennett wrote: > > However, the binaries are not directly under 'bin', but in the > subdirectories shown below: > > [build@admin bin]$ tree -L 1 > . > ├── em64t-unknown-linux-gnu > ├── em64t-unknown-linux-gnu_mpi > ├── em64t-unknown-linux-gnu_smp > ├──

Re: [easybuild] Specifying location of configure

On 22/02/19 14:49, Loris Bennett wrote: > Hi, > > Just writing my first easyconfigs from scratch. The first went OK, but > with the second, 'configure' is not in the root of the tarball, but in > the subdirectory 'src'. I assume this is described the documentation, > but I wasn't able to find

Re: [easybuild] Checksum errors while installing GCCcore 6.4.0

Hi Sona, On 13/03/19 10:22, Ms. Sona CP wrote: > I am getting this checksum error message while installing GCCcore-6.4.0 > file. > I have cross checked the easyconfig files but couldn;t find a solution. > Can any one please help with this? > I have attached my log file. It's a bit of a cryptic

Re: [easybuild] CP2K psmp?

Hi Loris, On 17/06/19 16:23, Loris Bennett wrote: > > Is there any particular reason why the buildopts don't just specify, say, > > VERSION="sopt popt ssmp psmp" > There is no specific reason for this. I shouldn't be very hard to adjust the easyblock to accept this. Ward

Re: [easybuild] CP2K-6.1-intel-2018a.eb builds broken version?

Hi Loris, On 25/06/19 11:02, Loris Bennett wrote: > According to the following page > > https://www.cp2k.org/dev:compiler_support > > CP2K is broken ("fails at runtime") if built with the Intel 18.0.1 > compiler. However, that is the compiler version used for the easyconfig > >

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