Re: [easybuild] REPOSITORYPATH broken in 4.5.0

2021-11-09 Thread Pablo Escobar Lopez
Hi Arnau, We had the same problem. Check this issue in github: https://github.com/easybuilders/easybuild-framework/issues/3892 Regards, Pablo. On Tue, Nov 9, 2021 at 12:35 PM Arnau wrote: > Hi all, > > we have been using the EB/git integration for while so, after a successful > compilation,

Re: [easybuild] icc, --modules-tool, --module-syntax

2019-11-25 Thread Pablo Escobar Lopez
On Mon, Nov 25, 2019 at 7:08 PM Marcelo Carignano wrote: > Hello there, > today I installed EasyBuild on a Cray XC50, installation went ok. > Then I tried to install CP2K by doing: > > > eb CP2K-6.1-intel-2018a.eb --modules-tool EnvironmentModulesC > --module-syntax Tcl --robot > > > and eb

Re: [easybuild] Singularity 3?

2019-09-10 Thread Pablo Escobar Lopez
On Tue, Sep 10, 2019 at 11:03 AM Loris Bennett wrote: > > Thanks for the information. I appreciate the security concerns, > although it seems to me that an EasyBuild version could be the best > solution. That way I can build a new version as soon as it comes out > and deploy it immediately,

Re: [easybuild] Singularity 3?

2019-09-09 Thread Pablo Escobar Lopez
Hi Loris In singularity 3.x the developers did a new implementation using golang instead of the python/C used in 2.x https://archive.sylabs.io/2018/02/singularity-golang/ This changed the build procedure for 3.x so the existing easyconfigs no longer work with 3.x . Someone would need to create

Re: [easybuild] Generic easyblock for Unpack+Cmd

2019-08-15 Thread Pablo Escobar Lopez
try to add this line to your easyconfig: unpack_options = '--strip-components=1' On Thu, Aug 15, 2019 at 4:29 PM Maik Schmidt wrote: > Hi Kenneth, > > I just tried that, but the problem is that I get the subdirectory from > the tar in my installdir when using "buildininstalldir". Just using >

Re: [easybuild] Generic easyblock for Unpack+Cmd

2019-08-15 Thread Pablo Escobar Lopez
you could also use the Tarball easyblock + postinstallcmds . e.g. https://gist.github.com/pescobar/5412f1fd889563f3600741a861047d3a On Thu, Aug 15, 2019 at 3:26 PM Maik Schmidt wrote: > Hi all, > > short question: which easyblock is best used for the case: > > - unpack to installdir first > >

Re: [easybuild] Openblas(foss) matrix issue

2019-05-29 Thread Pablo Escobar Lopez
OpenBLAS/0.3.1-GCC-7.3.0-2.30 > > So is the update command simply this one? > > eb --rebuild OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb > OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb > > Is the --force flag also required? > > I suppose that we do not have

Re: [easybuild] Openblas(foss) matrix issue

2019-05-28 Thread Pablo Escobar Lopez
nyi/OpenBLAS/commit/b14f44d2adbe1ec8ede0cdf06fb8b09f3c4b6e43 > (you > can get the patch by adding .patch at the end of the URL) > > Regards, > Carlos > > On Mon, May 27, 2019 at 6:15 PM Pablo Escobar Lopez < > pablo.escobarlo...@unibas.ch> wrote: > >> Hi, >

Re: [easybuild] Openblas(foss) matrix issue

2019-05-27 Thread Pablo Escobar Lopez
Hi, did anyone found a working patch or workaround for the matrix issue when using OpenBLAS-0.3.1 ? After a lot of try I couldn't pass the tests in https://github.com/eylenth/Openblas_matrix_issue when using

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

2019-03-04 Thread Pablo Escobar Lopez
On Tue, Feb 26, 2019 at 11:24 AM Kenneth Hoste wrote: > > One easy thing we could do is make the binutils easyblock check whether > both 'gcc' and 'g++' are present, and emit a clear warning if they're > missing? > That would help significantly, since pinpointing the underlying problem > is

Re: [easybuild] deprecating the 'goolf' and 'ictce' toolchains

2018-11-16 Thread Pablo Escobar Lopez
goolf/1.7.20 is my default toolchain. most of my installations use it I would like to move to foss as my default toolchain "soon" but I have more urgent tasks and I won't be able to do it in coming months. In any case I think I would survive if you deprecate it On Fri, Nov 16, 2018 at 12:06 AM

Re: [easybuild] installing lm-sensors

2018-05-04 Thread Pablo Escobar Lopez
t; installopts = 'PREFIX=%(installdir)s/' > installopts = 'ETCDIR=%(installdir)s/etc/' > > moduleclass = "lang" > > Yours sincerely, > > > > > *Joseph John * > > *Assistant Professor * > > *Department of Computer Science & Engineering * > *Rajagiri Sc

[easybuild] Re: iomkl-2018.02 toolchain. What OpenMPI version?

2018-03-27 Thread Pablo Escobar Lopez
btw, I forgot to mention that iomk-2018.02 would be based in https://github.com/easybuilders/easybuild-easyconfigs/pull/6077 On Tue, Mar 27, 2018 at 6:52 PM, Pablo Escobar Lopez < pablo.escobarlo...@unibas.ch> wrote: > Hi, > > I plan to send a PR for iomkl-2018.02 and I wanted to

[easybuild] iomkl-2018.02 toolchain. What OpenMPI version?

2018-03-27 Thread Pablo Escobar Lopez
Hi, I plan to send a PR for iomkl-2018.02 and I wanted to ask for advice about what OpenMPI version should be included so it's accepted upstream. Latest OpenMPI version is 3.0.0 and I personally prefer to avoid new major releases ending in x.0.0 unless there is a clear reason like a new feature

Re: [easybuild] problem building custom python3 module

2018-01-12 Thread Pablo Escobar Lopez
. 2018-01-12 9:27 GMT+01:00 Alan O'Cais <a.oc...@fz-juelich.de>: > Hmm, I wonder if you would be better off using modaltsoftname rather than > changing the name of the software, your approach could kick off some > problems with EBROOTPYTHON perhaps? > > Alan > > On 11

Re: [easybuild] TensorFlow with GPU support.

2018-01-04 Thread Pablo Escobar Lopez
Hi Jakob, I installed Tensorflow in my cluster few days ago modifying your easyconfigs. I have just sent two PR with the two easyconfigs I installed: https://github.com/easybuilders/easybuild-easyconfigs/pull/5590 https://github.com/easybuilders/easybuild-easyconfigs/pull/5591 I used cuDDN 6.0

Re: [easybuild] Configuration variables in easyconfig

2017-11-27 Thread Pablo Escobar Lopez
https://easybuild.readthedocs.io/en/latest/Configuration.html#configuration-file-s 2017-11-27 12:59 GMT+01:00 nan...@luis.uni-hannover.de < nan...@luis.uni-hannover.de>: > > Hello, > > is there any way to set easybuild env. variables, for example the > installation path, from within an >

Re: [easybuild] Installing pygraph

2017-11-17 Thread Pablo Escobar Lopez
Hi Joseph, If there is no available easyconfig in the official easybuild release the first thing you should check is if there is any pending pull request for this application which still hasn't been merged upstream: https://github.com/easybuilders/easybuild-easyconfigs/pulls If there is no pull

Re: [easybuild] Re: installing octave

2017-11-17 Thread Pablo Escobar Lopez 
Hi Joseph,

Have you tried to execute "rpm -qa | grep -i ssl" in the node where you are
trying to do the installation to double check that the packages are
installed? You should get something similar to this:

$ rpm -qa | grep -i ssl
openssl-libs-1.0.1e-60.el7_3.1.x86_64

Re: [easybuild] need help to write easyconfig file for fall3d

2017-07-25 Thread Pablo Escobar Lopez
I missed that probably you also want preconfigopts = 'export SCRIPTDIR=%(installdir)s && ' 2017-07-25 11:13 GMT+02:00 Pablo Escobar Lopez <pablo.escobarlo...@unibas.ch >: > Hi Yann, > > Try doing this: > > prebuildopts = 'export SCRIPTDIR=%(installdir)s &

Re: [easybuild] RE: support for tmolex and tcoffee

2017-06-12 Thread Pablo Escobar Lopez
Hi Shahzeb, here you have ;) https://github.com/hpcugent/easybuild-easyconfigs/pull/4709/files 2017-06-12 17:25 GMT+02:00 Kenneth Hoste : > Hi Shahzeb, > > On 12/06/2017 17:16, Siddiqui, Shahzeb wrote: > > I haven’t heard any response. Does anyone have easyconfig for

Re: [easybuild] Easybuild R.3.4.0 is available

2017-04-27 Thread Pablo Escobar Lopez
2017-04-27 14:25 GMT+02:00 Benjamin Evans : > > I noticed you have qiime in the list of installed modules. I know that a > full qiime from source easyconfig has been on the wishlist for a while. > > This one works for me even it's not "clean" to merge

Re: [easybuild] Bootstrap specific EasyBuild version

2017-04-05 Thread Pablo Escobar Lopez
p.s. I haven't specified it and probably it's not obvious for those not familiar with pip but during the "pip install" step you can choose which easybuild version you want to install E.g. $> pip install easybuild==3.0.0 2017-04-05 20:24 GMT+02:00 Pablo Escobar Lopez <

Re: [easybuild] Bootstrap specific EasyBuild version

2017-04-05 Thread Pablo Escobar Lopez
some time ago I did some testing to see how easybuild could be bootstrapped using conda. This should work in any machine even if you don't have a supported python version or a modules tool available $> curl -o /tmp/Miniconda2-latest-Linux-x86_64.sh

Re: [easybuild] R foss threads question

2017-02-02 Thread Pablo Escobar Lopez
Hi Jure, I have experienced similar issues in the past. I think this depends on the R library you use for parallelization but I don't remember the details. I suggest that you also define OPENBLAS_NUM_THREADS with the same value as OMP_NUM_THREADS. Defining both env vars with the same value

Re: [easybuild] Fwd: [Open MPI Announce] Open MPI v2.0.2 released

2017-02-01 Thread Pablo Escobar Lopez
btw, I have iomkl/2017.01 with OpenMPI/2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26 and I had to apply this patch to be able to compile it with slurm support https://www.mail-archive.com/users@lists.open-mpi.org/msg30048.html I suppose this is fixed in 2.0.2 2017-02-01 15:01 GMT+01:00 Kenneth Hoste

Re: [easybuild] HPL without OFED

2016-12-20 Thread Pablo Escobar Lopez
Hi David, You won't find many easyconfigs using the "-no-OFED" toolchains and goalf-1.1.0 is quite old. I don't think it's a good choice specially if you are starting a new installation. I would recommend that you use one of the foss toolchains (

Re: [easybuild] R extra packages

2016-12-17 Thread Pablo Escobar Lopez
Personally I would not recommend the approach of adding a dedicated easyconfig for each R package. I think it would be hard to maintain specially when defining the dependency chain. Have you look at this? https://github.com/fgeorgatos/easybuild.experimental/tree/master/users/pneerincx Using that

Re: [easybuild] How to hide modules at the Lmod level?

2016-11-19 Thread Pablo Escobar Lopez
2016-11-19 15:44 GMT+01:00 Ole Holm Nielsen : > > > IMHO, the --hidden option ought to be the EB default for all "system" > modules which are irrelevant to end users. > > I think that deciding what modules are irrelevant for users is something subjective which depends

Re: [easybuild] How to hide modules at the Lmod level?

2016-11-19 Thread Pablo Escobar Lopez
Hi Ole, I think Lmod 6.x doesn't support using a modulerc file. This feature was added in latest Lmod 7.0. See the changelog here https://github.com/TACC/Lmod What Lmod 6.x supports is hidding a module if the version in the module name starts by dot. e.g. a module like "zlib/.1.2.8" would be

Re: [easybuild] Has anyone created EB files for the Intel 2017 compilers?

2016-11-03 Thread Pablo Escobar Lopez
ion Developer > Adjunct Assistant Professor of Chemical and Biomolecular Engineering > Advanced Computing Center for Research and Education (ACCRE) > Vanderbilt University - Hill Center 201 > (615)-875-9137 > www.accre.vanderbilt.edu > > On Nov 3 2016, at 6:23 am, Pablo Escobar Lope

Re: [easybuild] easybuild -devel files for users?

2016-10-23 Thread Pablo Escobar Lopez
wouldn't make sense if compiler modules provide $CC $CXX and Co. by default? 2016-10-22 23:59 GMT+02:00 Alan O'Cais : > Maybe I'm misunderstanding but that is pretty much exactly why I 'created' > the trivial buildenv easyblock. The users just load the module that gets >

Re: [easybuild] FFTW dynamic libraries?

2016-10-13 Thread Pablo Escobar Lopez
neth Hoste <kenneth.ho...@ugent.be>: > Hi Pablo, > > On 13/10/16 11:48, Pablo Escobar Lopez wrote: > > Hi, > > I have noticed that FFTW-3.3.3-gompi-1.4.10.eb is not building the > dynamic FFTW libraries. For this I think the fix would be to change > configopts f

Re: [easybuild] How to build modules compiled for different hardware architectures?

2016-10-04 Thread Pablo Escobar Lopez
2016-10-04 11:49 GMT+02:00 Martin : > > > * Within R users are loading the module and doing install.packages() > on a random node, later they want to use that package on a script and it > gives "random" errors with illegal instruction depending on where it ran. > -- User

Re: Discontinuation of packages (Re: [easybuild] next EasyBuild conf call: *Thu* Sept 29th 2016, 5pm CET)

2016-09-30 Thread Pablo Escobar Lopez
2016-09-30 13:19 GMT+02:00 Kenneth Hoste : > > So, the idea of a middle ground popped into my head, something like this: > > $ eb --search ^foo > ... > * /path/to/foo-1.2.3.eb > * /path/to/foo-1.2.4.eb > > Note: additional matching archived easyconfigs were found, use "eb

Re: Discontinuation of packages (Re: [easybuild] next EasyBuild conf call: *Thu* Sept 29th 2016, 5pm CET)

2016-09-30 Thread Pablo Escobar Lopez
2016-09-30 12:32 GMT+02:00 Jack Perdue : > > Not saying they are well tested or the best builds but having > repos that you could enable/disable at will to search for easyconfigs > would be nice. > > I like the idea! Being able to define an extra list of git repos or local

Re: [easybuild] Python 2.6 usage poll

2016-09-19 Thread Pablo Escobar Lopez
rks fine for me and I also have the choice to use conda or not. regards, Pablo. 2016-09-19 2:44 GMT+02:00 Christopher Samuel <sam...@unimelb.edu.au>: > On 16/09/16 20:15, Pablo Escobar Lopez wrote: > > > I remember we have commented in some hackathon (while having some b

Re: [easybuild] Python 2.6 usage poll

2016-09-16 Thread Pablo Escobar Lopez
I remember we have commented in some hackathon (while having some beers I think) about the possibility of distributing easybuild as a self-contained app. Using something like mini-conda (http://conda.pydata.org/miniconda.html) with easybuild already installed on top of hit could do the trick. With

Re: [easybuild] COMSOL, Feko, ..

2016-08-17 Thread Pablo Escobar Lopez
here you have the one I use for Schrodinger https://github.com/hpcugent/easybuild-easyconfigs/pull/762 I suggest you to look for in the list of open pull requests. Maybe you can find some working or semi-working easyconfigs there which hasn't been merged yet

Re: [easybuild] Lua modules and Lmod

2016-08-11 Thread Pablo Escobar Lopez
Hi Maxime, maybe this simple example showing how to add a new cli flag to easybuild can help you as reference https://github.com/hpcugent/easybuild-framework/pull/1250/files regards, Pablo. 2016-08-11 15:51 GMT+02:00 Maxime Boissonneault < maxime.boissonnea...@calculquebec.ca>: > Hi Kenneth, >

Re: [easybuild] best easyblock for simple package installation (wget, untar, install)

2016-07-19 Thread Pablo Escobar Lopez
if you are downloading a tarball I think you want the "PackedBinary" easyblock 2016-07-19 13:56 GMT+02:00 Bernd Mohr : > Hi EasyBuilders, > > what would be the best EasyBlock to use for the installation of PACKAGE? > > Installation is as follows: > > a) wget

Re: [easybuild] Question about builddependencies and pkg-config

2016-06-23 Thread Pablo Escobar Lopez
2016-06-22 22:57 GMT+02:00 Jack Perdue : > On 06/22/2016 03:31 PM, McGough, Benjamin E wrote: > > I have been struggling with creating a clean environment in which to > build with EasyBuild and test easyconfigs. > > I wish I could be pardoned if I just left a: > > 8^) > >

Re: [easybuild] Where is the LAPACK dependency defined for the foss toolchains

2016-05-29 Thread Pablo Escobar Lopez
PNG, JPEG, TIFF, NLS, cairo, ICU > Options enabled: R profiling > > Capabilities skipped: > Options not enabled: shared BLAS, memory profiling > > Now lets see if the large list of additional (BioConductor and CRAN) > packages we had in a previous version of R

Re: [easybuild] Where is the LAPACK dependency defined for the foss toolchains

2016-05-28 Thread Pablo Escobar Lopez
Hi Pieter, maybe related? https://github.com/hpcugent/easybuild-easyconfigs/issues/1435 Pablo 2016-05-28 16:23 GMT+02:00 Kenneth Hoste : > Hi Pieter, > > On 28/05/16 15:04, Pieter Neerincx wrote: > > Hi all, > > > > I'm trying to build a new R with a recent foss

Re: [easybuild] SPAdes-3.7.1-goolf-1.4.10.eb FAILED

2016-04-22 Thread Pablo Escobar Lopez
I see this in your logs Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR) try adding bzip2 as a dependency in the spades easyconfig. 2016-04-22 19:29 GMT+02:00 Klima, Robert (NIH/NIAID) [C] < robert.kl...@nih.gov>: > Hi, > > My installation SPAdes-3.7.1-goolf-1.4.10.eb

Re: [easybuild] Using easybuild to manage different Python toolstacks

2016-03-18 Thread Pablo Escobar Lopez
as Alan suggests I think python bundle is the way to go for what you want. I would also suggest that if you want to assure reproducibility you should test your bundles in a machine without internet access. Some python libraries download extra dependencies during installation so if you run your

Re: [easybuild] adding local variables to module files

2016-02-29 Thread Pablo Escobar Lopez
I have this in some of my easyconfigs. It works for me with tcl modules, I haven't tried with lua syntax. I think you could also use $HOME or $USER or any other env var. It's not exactly what you ask of adding env vars which are local to the module file but maybe it helps... modextravars = {

Re: [easybuild] Building a life sciences sub-community and citation practices

2016-02-18 Thread Pablo Escobar Lopez
Hi Ben, To maintain different subsets of R and Python libraries I suggest you look at the "bundle" easyblock. This is how I am handling this now. Before I was using your approach of adding all the R libraries in the main R easyconfig but adding all the extensions in the main R easyconfig becomes

Re: [easybuild] Python packages?

2016-02-09 Thread Pablo Escobar Lopez
HI Elizabeth, There are different options to handle python packages in EB. You can use the "PythonPackage" easyblock or the "Bundle" easyblock. Personally I use PythonPackage for python apps without extra deps and Bundle for apps with many deps but this is quite subjective. Some examples:

[easybuild] EasyBuild Workshop, March 2, Basel

2016-02-05 Thread Pablo Escobar Lopez
Can I send some spam to the mailing list? :) As part of the eSCT training program, sciCORE, the scientific computing center at University of Basel is organizing a workshop on EasyBuild. The aim of the workshop is to learn, share information about and practice the EasyBuild software management

Re: [easybuild] Warning from EasyBuild 2.6.0

2016-02-05 Thread Pablo Escobar Lopez
dule vsc was already imported" and "Module easybuild > was already imported" warnings on this system? > > > K. > > > On 05/02/16 11:05, Pablo Escobar Lopez wrote: > > in case it helps, I have noticed that I only get these warnings in the > machine were i hav

Re: [easybuild] Warning from EasyBuild 2.6.0

2016-02-05 Thread Pablo Escobar Lopez
in case it helps, I have noticed that I only get these warnings in the machine were i have python-keyring installed. this is my output for the command that Kenneth asks (identical is the machine which triggers the warning and in the machine which doesn't trigger the warning) [escobar@login18

Re: [easybuild] ffmpeg versus FFmpeg

2016-01-19 Thread Pablo Escobar Lopez
to workaround this "issue" I install Lmod with "./configure --with-caseIndependentSorting=yes" ( https://github.com/TACC/Lmod/blob/master/configure#L1317) and I always use the tab-completion in Lmod 2016-01-18 22:59 GMT+01:00 Riccardo Murri : > (Elizabeth Fischer, Mon,

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

2016-01-14 Thread Pablo Escobar Lopez
in my opinion I would not include gcc5 in a toolchain which should be considered as "stable". Many developers haven't tried gcc5 yet so I think we would hit many new issues when trying to compile applications which have never been compiled with gcc5. For me in the bioinformatics field is a totally

Re: [easybuild] custom glibc

2015-12-14 Thread Pablo Escobar Lopez
I am also curious to know if someone has tried to use a custom glibc. 2015-12-12 11:29 GMT+01:00 Kenneth Hoste : > Hi Olaf, > > On 13/11/15 10:32, Olaf Walter wrote: > > Dear easybuilders, > > > > has anybody ever attempted to do an easybuild with a custom glibc? > >

Re: [easybuild] New to EasyBuild - problem installing

2015-10-21 Thread Pablo Escobar Lopez
Hola Oscar, installing scientific software as root is a non recommended practice that's why easybuild triggers an error and asks you not to do it. For testing you can use your standard account. What many easybuild users do once they use easybuild in production is having a dedicated user account

Re: [easybuild] ISC15???

2015-07-16 Thread Pablo Escobar Lopez
2015-07-15 17:24 GMT+02:00 Kenneth Hoste : > > I don't care much for German beer though. ;-) > > > hahahahah Jack be aware you should never ever start the beer flame with a belgian guy. It's much worse than the vim vs emacs discussion..even if everybody knows that the

Re: [easybuild] Incompatibilities with different CPUs

2015-07-14 Thread Pablo Escobar Lopez
Hi Martin, openblas will ignore the optarch option in easybuild but you can use something like this in the OpenBLAS easyconfig buildopts = 'TARGET=SANDYBRIDGE BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' here you have the list of supported targets in openblas

Re: [easybuild] Binary of a python package

2015-06-23 Thread Pablo Escobar Lopez
Hi Oliver, I tried to install that software doing "python setup.py install --user" and I cannot find anything in ~/.local/bin . I only get files in ~/.local/lib/python2.7/site-packages/ which is what easybuild is doing and then setting up PYTHONPATH in the modulefile, so when I load the misopy

Re: [easybuild] Easier way of installing R packages

2015-06-18 Thread Pablo Escobar Lopez
Hi Niek, I think many people in this list has suffer the R dependencies nightmare. I wrote an small scirpt which if you already have a R easyconfig will try to give you which are the latest versions available in R repos. It's not perfect but it helps a little bit at least. Here you have it in

[easybuild] updating mathematica easyblock. how to generate the "sources" file?

2015-04-14 Thread Pablo Escobar Lopez
Hi, I need to install Mathematica 10.0.2 which is not supported in easybuild so I will try to update the available easyblock and I have a doubt. I have a Mathematica iso which contains the installer. As far as I know Easybuild doesn't support reading .iso files and I am not sure which is the

Re: [easybuild] How to deal with dependencies for R

2015-03-31 Thread Pablo Escobar Lopez
Hi Martin, R extensions change quite often and the url also changes so the normal approach is "manual fix". In case it's useful for you I wrote this script some days ago to deal with this, it's not perfect and still requires some manual work but it works for ~90% of the R libraries so it saves

Re: [easybuild] will openmpi with infiniband support fall back to ethernet if infiniband not available? [bcc - adr][faked - adr]

2015-03-16 Thread Pablo Escobar Lopez
Hi John thanks for your feedback. I just asked this in the openmpi-users mailing list. You are right that's the right place to ask. Pablo. 2015-03-16 11:25 GMT+01:00 John Hearns : > I am thinking about trying to compile openmpi with infiniband support > (I would

Re: [easybuild] easybuild new user experience

2015-02-13 Thread Pablo Escobar Lopez
2015-02-11 17:09 GMT+01:00 Cook, Malcolm : > > > Fotis, I note your example name, "sandybridge", apparently encoded an > intel processor microarchitecture, NOT the name of a linux distribution > (such as c6 or c7 for releases of centOS, as proposed). I'm trying to >

Re: [easybuild] EasyBuild configuration

2014-11-21 Thread Pablo Escobar Lopez
Hi again Valeriu, in reply to your question about using your existing compiler modules, it's technically possible but as you probably have noticed it's not straightforward My suggestion would be to start using the default easybuild toolchains at least while you start testing and learning

Re: [easybuild] EasyBuild configuration

2014-11-21 Thread Pablo Escobar Lopez
Hi Valeriu, you can always add as many enviroment variables as you need using the options "modextravars" and "modextrapaths" in your easyconfigs. I paste here an example but if you grep for "modextra" in your easyconfigs folder you will find more. modextravars = { 'TRANSABYSS_PATH':

Re: [easybuild] Any easy way to get lots of CPAN modules for a Perl installation?

2014-11-20 Thread Pablo Escobar Lopez
Hi Tin I attach a quick and dirty script I use when I need to add extra perl libraries to my Perl easyconfig in case it's useful for you. The output is something like this: $> ./get-perl-package.sh Digest::SHA1 found a package for Digest::SHA1 :

Re: [easybuild] easybuild build problem

2014-11-18 Thread Pablo Escobar Lopez
Hi Vali, instead of using the bootstrap method I prefer to install easybuild like this: $> wget https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb $> git clone https://github.com/hpcugent/easybuild-easyconfigs.git $> git

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

2014-10-28 Thread Pablo Escobar Lopez
://www.biozentrum.unibas.ch 2014-10-28 12:06 GMT+01:00 Ward Poelmans <ward.poelm...@ugent.be>: > On Tue, Oct 28, 2014 at 12:04 PM, Pablo Escobar Lopez > <pablo.escobarlo...@unibas.ch> wrote: > > I verified it when I tried the workaround and it seems to work fine, at > > least in thi

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

2014-10-28 Thread Pablo Escobar Lopez
I verified it when I tried the workaround and it seems to work fine, at least in this case. Here is my build log == 2014-10-27 10:36:55,249 main.run INFO cmd "unset CC && unset CXX && make -j 1 " exited with exitcode 0 and output: cat: src/version_git.h: No such file or directory wget -q

Re: [easybuild] upgrade EB from 1.13 to 1.14

2014-09-09 Thread Pablo Escobar Lopez
2014-09-09 9:37 GMT+02:00 Arnau Bria : > > > > That worked like a charm! > > And for coming releases you don't even need to download a new easyconfig :) This is how I did my last upgrade: $> eb EasyBuild-1.13.0.eb --try-software-version=1.14.0 regards, Pablo. --

Re: [easybuild] New to EB, problems building goalf toolchain

2014-07-02 Thread Pablo Escobar Lopez
Hi Arnau there is one tip I forgot to tell you in my previous email. By default easybuild doesn't enable support for any queuing system in OpenMPI. I know at CRG you use SGE so I would recommend you to edit the openmpi easyconfig (if you are using goolf-1.4.10 that would be

Re: [easybuild] formula for toolchain versions???

2014-06-03 Thread Pablo Escobar Lopez
+1000 :) 2014-06-03 22:27 GMT+02:00 Kilian Cavalotti : > On Tue, Jun 3, 2014 at 1:11 PM, Heywood, Todd wrote: > > This is why I’m most interested in module hierarchies via integrating > Easybuild with Lmod. :-) > > I guess there's a lot of us waiting

Re: [easybuild] chmod after installation

2014-04-10 Thread Pablo Escobar Lopez
Hi Andreas, As long as I am aware this is not possible in an easyconfig, you need to go for easyblock, at least I have used an easyblock when I need something like this I also suggested to add this feature in this comment in github

Re: [easybuild] Module naming

2014-04-07 Thread Pablo Escobar Lopez
Hi Bart, I tried this custom naming scheme as it was working fine for me https://gist.github.com/anonymous/10016075 To configure it I followed the docs at https://github.com/hpcugent/easybuild/wiki/Using-a-custom-module-naming-scheme and then run easybuild with "eb

Re: [easybuild] Postprocessing Error

2014-03-19 Thread Pablo Escobar Lopez
Hi Keith, In case it's useful for you, I recently added this pull request https://github.com/hpcugent/easybuild-easyconfigs/pull/747 Pablo. 2014-03-18 23:45 GMT+01:00 Fotis Georgatos : > > Hi Ke*, > > On Mar 18, 2014, at 10:45 PM, Kenneth Hoste wrote: > > But it should

Re: [easybuild] Python and readline

2014-03-13 Thread Pablo Escobar Lopez
Hi all In case the informatiion is useful, for me readline is working fine. I cannot find the string "Failed to build these modules" in any of my build logs. I am using Python-2.7.5-goolf-1.4.10.eb and commented out the readline dependencies in the easyconfig file, so I am using the system

[easybuild] question about ictce toolchain versions numbers...

2014-03-11 Thread Pablo Escobar Lopez
Hi, I am trying to install ictce toolchain in my cluster. The files I have are: l_ccompxe_2013_sp1.2.144.tgz l_fcompxe_2013_sp1.2.144.tgz l_mkl_11.1.2.144.tgz l_mpi_p_4.1.3.049.tgz In the github repository I have found this pull request which contains mostly all these versions. The only change

Re: [easybuild] Toolchains

2014-03-06 Thread Pablo Escobar Lopez
Hi Keith toolchains are not installed by default, you need to build/install one toolchain and then use it to continue building more apps. You can list all the toolchain that easybuild supports by default with the command " eb --list-toolchains" to decide which one you want to use. I recommend

Re: [easybuild] module unload for toolchains?

2014-02-10 Thread Pablo Escobar Lopez
2014-02-10 17:14 GMT+01:00 Kenneth Hoste : > > > Which modules tool are you using (environment modules, Lmod, ...), and > which version? > personally, I have tested this behaviour with modules 3.2.10 and Lmod 5.2 > > Also: I agree with your amazement that simply

Re: [easybuild] module unload for toolchains?

2014-01-30 Thread Pablo Escobar Lopez
unload" on the same file, where the file has conditionals that load >> unloadewd/undefined dependencies, and also unload dependencies that are >> loaded/defined. Would running "module load" twice result in unloading? :-) >> >> Easybuild developers: this would be

Re: [easybuild] module unload for toolchains?

2014-01-30 Thread Pablo Escobar Lopez
maybe this is what you are looking for: https://github.com/hpcugent/easybuild-framework/issues/714#issuecomment-26036880 You can modify your modules like this or modify easybuild to automatically generate the modules like this. I think the place to tweak is here