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 Le
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 clear
Hi,
did anyone found a working patch or workaround for the matrix issue when
using OpenBLAS-0.3.1 ?
After a lot of try&error I couldn't pass the tests in
https://github.com/eylenth/Openblas_matrix_issue when using
https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easycon
/github.com/xianyi/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:
>
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
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
>
>
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
> P
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 ne
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, wit
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 sta
Hi
Anyone in the list has a working easyconfig for Gromacs 2020 + plumed 2.6 ?
crappy, hacky, dirty easyconfigs which would not be accepted upstream and
would make Kenneth scream are welcome. In fact are preferred ;)
thanks!
Pablo.
--
Pablo Escobar López
Linux/HPC systems engineer
sciCORE, Un
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, t
the bug is reported. quick woraround is upgrade to latest lmod stable
release
https://github.com/hpcugent/easybuild-framework/issues/772
you should also check this one
https://github.com/hpcugent/easybuild-framework/issues/773
2013/12/5 Garvey, Cormac T
>
> Hi all,
> I have lmod 5.2rc4 install
for
BioPython failed: BioPython failed to install, cmd 'python -c "import
biopython"' (stdin: None) output: Traceback (most recent call last):
2013/12/11 Pablo Escobar Lopez
> Hi,
>
> I am trying to add an extra library (extension) to my python install
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
https://github.com/hpcugent/easybui
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 a reasonable (optional) feature
>> req
Hi Franky
I think you would need to modify the block for vtune and fix the
sanity_check_step() function
https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/v/vtune.py#L91
Here you can see an example of how to do different checks depending on the
version of the app (v
I will attend also
2014-02-04 Bernd Mohr :
> I plan to listen in
> Bernd
>
> On Mon, Feb 03, 2014 at 10:18:05PM +0100, Kenneth Hoste wrote:
> > Hello EasyBuilders,
> >
> > The next EasyBuild conference call is planned for Tuesday Feb 4th
> > 2014, 3 - 3.30pm (CET), i.e. tomorrow, see
> > https:/
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 wrapping the module name
> in si
In case it's useful for anyone, there are some utilities to convert from
this shell scripts to modulefiles
https://github.com/TACC/Lmod/tree/master/contrib/converting_shell_to_module_files
regards,
Pablo.
2014-02-19 Kenneth Hoste :
> Hi Bart,
>
> The OpenFOAM libraries and binaries are (appar
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 you
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 i
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 packag
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 still look in the confi
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 --module-naming-scheme=JustApp
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
https://github.com/hpcugent/easybuild-easyconfigs/pull/795#issuec
+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 on that. :)
>
> Cheers,
> --
> Kilian
>
Hi Arnau :)
I think the dependencies are not being resolved because maybe you are not
using --robot option? Just try the same command line just adding --robot or
-r and let us know if it works.
by the way, if you are starting with easybuild from scratch and you are not
using any modules tool in
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 OpenMPI-1.6.4-GCC-4.7.
if you do a search with easybuild you will also get the PATH where all your
easyconfigs are located locally in your machine
[pub@login11 ~]$ eb --search blast
== temporary log file in case of crash
/scratch/easybuild-5Vexjc/easybuild-WanX0X.log
== Searching (case-insensitive) for 'blast' in
*/imp
Hi Arnau
If you already have EasyBuild working I think the easier aproach is to use
easybuild itself to install it. Kenneth always attach a easyconfig file
with the release announce email so you would only need to run "eb
newEBrelease.eb". That way you will have two different modules for your two
Hola Miguel :)
as you already mentioned neither LSF or slurm is officially supported yet,
anyway even if it were supported, I would suggest to start learning how
easybuild works without the --job option because that is not a widely
tested option. So I think it´s better to start learning how easyb
2014-08-25 18:00 GMT+02:00 Trey Dockendorf :
>
> towhee - http://sourceforge.net/projects/towhee/ - not sure what it's
> used for but requested by local Petroleum engineering users.
> tesseract - OCR application used by our local Digital Humanities group
> ior - I use this for benchmarking our par
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.
--
Pablo Escobar López
HPC sys
Hi,
Has anyone tried easybuild in centos 7 ?
any feedback before I start some testing with it?
thanks
Pablo.
--
Pablo Escobar López
HPC systems engineer
Biozentrum, University of Basel
Swiss Institute of Bioinformatics SIB
Email: pablo.escobarlo...@unibas.ch
Phone: +41 61 267 21 80
http://www
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 http://
21 80
http://www.biozentrum.unibas.ch
2014-10-28 12:06 GMT+01:00 Ward Poelmans :
> 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 toolc
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
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:
$> ./get-perl-package.sh Digest::SHA1
found a package for Digest::SHA1 :
https://cpan.metacpan.org/authors/id/G/GA/GAAS/D
Hi Valeriu,
you can always add as many enviroment variables as you need using the
options "modextravars" and "modextrapaths" in your easyconfigs.
I paste here an example but if you grep for "modextra" in your easyconfigs
folder you will find more.
modextravars = {
'TRANSABYSS_PATH': '$root',
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 easybuil
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
> understand the implications
Hi all,
This question is not strictly related to easybuild but I supposed someone
here could give me some feedback on the topic.
I am planning to upgrade my software stack (using easybuild of course :)
and now I will have machines without infiniband and machines with
infiniband, I would like to s
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 compile openmpi in one of the
Hi Malcom,
some time ago I sent a pull request for MACS
https://github.com/hpcugent/easybuild-easyconfigs/pull/1247
I suggest you to review the list of pending pull requests in github before
you start writting new easyconfigs
https://github.com/hpcugent/easybuild-easyconfigs/pulls
regards,
Pablo
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 you
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
reco
ng for perfect purity, so for me the above has always
> been the one and only way
> to deliver anything that requires .iso extraction (as opposed to manually
> creating a tarball).
>
> hope this helps in some way,
>
> F.
>
> On Apr 14, 2015, at 9:12 AM, 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 cas
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
mo
2015-06-24 10:58 GMT+02:00 Pieter Neerincx :
>
> Yesterday I started working on an R-script that generates an *.eb from an
> existing R installation. This is based on Stefano's code (Many thanks for
> sharing that!) and adds some commandline switches, help and code to figure
> out whether a packag
ok, thanks for your effort Pieter
2015-06-29 16:25 GMT+02:00 Pieter Neerincx :
>
> On Jun 29, 2015, at 3:37 PM, Pablo Escobar Lopez <
> pablo.escobarlo...@unibas.ch> wrote:
>
> >
> >
> > 2015-06-24 10:58 GMT+02:00 Pieter Neerincx :
> >
> >
Hola Armando,
That command line will install only the framework but you need to install
also the easyblocks and easyconfigs to have a fully working easybuild
setup. These are the three things you need to get installed (plus a
modules system like Lmod)
https://github.com/hpcugent/easybuild-framew
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
https://github.com/xianyi/OpenBLA
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 combination of a really
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 in
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?
>
>
>
> The GCC HOWTO documen
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
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, Jan 18, 2016 at 04:02:43PM
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 easy
d "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 have python-keyring installed.
>
&g
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 t
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:
https:
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 h
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 = {
'PYRO
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 eas
| sed 's/better bash/bash better/' # Yelling in a CERN forum
>
> --
> *From:* easybuild-requ...@lists.ugent.be [easybuild-requ...@lists.ugent.be]
> on behalf of Pablo Escobar Lopez [pablo.escobarlo...@unibas.ch]
> *Sent:* Friday, March
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 faile
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 toolchain. I've tried
> 2015b an
ities: 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 ver
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^)
>
> and walked away...
>
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 /PACKAGE_.tar.gz
> b) tar zxvf PACKAGE
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
ted now works 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 :
> On 16/09/16 20:15, Pablo Escobar Lopez wrote:
>
> > I remember we have commented in some hackathon (while having some beers
> > I think) abo
I use a similar solution. I have /soft/apps/arch1
/soft/apps/arch2/soft/apps/archN in a nfs server and I use autofs to
mount the right folder in /soft/apps in each compute node. This way the
path to access the software stack is the same in every machine (/soft/apps)
but each machines uses the r
have you tried "eb Python-3.5.2-foss-2016.04.eb
--try-toolchain=foss,2016.09 -r" ?
2016-09-29 8:55 GMT+02:00 Ole Holm Nielsen :
> I need to build Python 3.5 for the EB 2.9.0 toolchain foss-2016.09.
> I copied the file Python-3.5.2-foss-2016.04.eb and replaced 04 by 09.
>
> Unfortunately, irreso
ecome an issue.
> >
> > Thanks,
> > Ole
> >
> > On 09/29/2016 10:48 AM, Kenneth Hoste wrote:
> >> Hi Ole,
> >>
> >> On 29/09/16 10:37, Pablo Escobar Lopez wrote:
> >>> have you tried "eb Python-3.5.2-foss-2016.04.eb
>
I like what Joachim suggest about the "attic" concept. Old/deprecated
easyconfigs provided "as-is" but not included in the regular tests. I think
I suggested something similar in one of the conf calls.
About how to search in the legacy easyconfigs I would prefer a different
approach . What I would
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
folders for "eb --search
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
> --search ^foo --conside
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 feedback is that this
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 from
this:
common_configopts = "--enable-threads --enable-openmp --with-pic"
to
common_configopts = "--enable-threads --enable-openmp --with-pic
neth Hoste :
> 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 from this:
>
> common_configopts
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,
>
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
https://github.com/hpcugent/easybuild-e
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
> created and they can s
Hi Ole,
Could you share your iomkl easyconfig using the latest intel2017 compiler?
regards,
Pablo.
2016-11-03 12:07 GMT+01:00 Fotis Georgatos :
> Hi Ole, all,
>
> On Nov 2, 2016, at 2:33 PM, Ole Holm Nielsen
> wrote:
> > On 11/02/2016 12:52 PM, Åke Sandgren wrote:
> >> env INTEL_LICENSE_FILE=p
tant 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 Lopez <
> pablo.escobarlo...@uni
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 hidd
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 on the site/admin/users prefe
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
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 (
https://github.com/hpcugent/easybuild-easyconfigs/
age
>
> 4. Run the script generateEasyConfig.R (Any specific parameters you
> used)
>
> 5. Verify easyconfig for R packages and rebuild them with Easybuild
>
>
>
> *From:* easybuild-requ...@lists.ugent.be [mailto:easybuild-request@list
> s.ugent.be] *On
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 :
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 should
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
https://repo.continuum.io/miniconda/Miniconda2-la
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 :
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
https://github.com/hpcugent/easybuild-easyconf
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 these
> packages that they
Hi Yann,
Try doing this:
prebuildopts = 'export SCRIPTDIR=%(installdir)s && '
preinstallopts = 'export SCRIPTDIR=%(installdir)s && '
Pablo.
2017-07-25 10:38 GMT+02:00 Yann Sagon :
> Dear users,
>
> I'm trying to create an easyconfig file for fall3d.
>
> The first problem with this software i
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