Logo UNIGE Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic <http://www.unige.ch/stic>
and Dynamics of Matter (MPSD)
Bldg. 99 (CFEL)
Luruper Chaussee 149
22761 Hamburg, Germany
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communication
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Tél 022 379 77 37 | Bureau 151
www.u
-devel', 'rdma-core-devel')
How can I overcome this problem, thanks in advance
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communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch
* installing
*source* package liquidSVM ...\n** package liquidSVM successfu')
[sagon@node025 ~] $ view
/tmp/eb-57sk42/easybuild-R-3.6.2-20210115.113949.rQKDk.log
Details in https://gist.github.com/ysagon/a9f70577ed3e5e6a3f2d388e6c000f5c
Thanks for any clue!
Best
Yann
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Hi Kenneth,
Le 05.11.2020 à 19:26, Kenneth Hoste a écrit :
Dear Yann,
On 05/11/2020 17:46, Yann Sagon wrote:
to install the Python code, I should execute the following:
python setup.py build_ext --inplace
The easiest way to achieve this is by changing the installation
command via
Dear list,
I wanted to create an EB file for EMU:
http://www.popgen.dk/software/index.php/EMU
First of all, the EMU git repo doesn't provide a tag with the latest
version, this is why I hardcoded the download path, maybe I can do that
in a better way.
Second, to install the Python code, I
a version
for python 2.7.16 and Python 3.7.4? And what is the syntax?
Best
Yann
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communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.uni
Hello, sorry to bother you again about this issue. It's still not
working and I don't know if this specific to our instllation or if this
eb isn't working.
Thanks for any hint.
Yann
Le 01.07.2020 à 17:57, Yann Sagon a écrit :
Hello, please find attached the log. It's from a
--try-software
Hello, please find attached the log. It's from a --try-software-version=1.76
Best
Yann
Le 01.07.2020 à 17:40, John Dey a écrit :
are you getting errors about poetry
John Dey
j...@fuzzdog.com
On Jul 1, 2020, at 8:27 AM, Yann Sagon wrote:
Dear list,
I'm trying to build Biopython-1.75
Dear list,
I'm trying to build Biopython-1.75-foss-2019b-Python-2.7.16.eb with
EeasyBuild 4.2.1 and it fails with a LOT of errors in the tests (in the
log file) and failed with the install step.
I tried with version 1.76 which is the latest version for Python 2.7,
same error.
Is this a
Hello,
Le 17.04.2020 à 10:26, Kenneth Hoste a écrit :
This looks like a Boost module that was not installed with EasyBuild,
or was it?
Does it define the $EBROOTBOOST environment variable? If not, that
explains why "get_software_root" is failing for Boost...
ml show Boost
Dear list,
I was happy since a user sees FSL on eb is missing imcp:)
The version we had installed on our cluster is quite old, so I took the
opportunity to update it, with a version with CUDA support. Yes is see
it's still not provided with imcp. Anyway, i'm even not able to install
a newer
Dear Kenneth,
Le 17.12.2019 à 15:11, Kenneth Hoste a écrit :
Dear Yann,
On 17/12/2019 15:06, Yann Sagon wrote:
Dear list,
at the end of the TensorFlow installation, during the sanity check,
it have the following error:
== 2019-12-17 12:46:46,834 run.py:219 INFO running cmd: pip --version
0 requires sphinxcontrib-serializinghtml, which is not installed.
pytest 5.1.2 requires wcwidth, which is not installed.
(at easybuild/tools/run.py:529 in parse_cmd_output)
Any clue?
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com
Hello
Le 16.12.2019 à 19:09, Åke Sandgren a écrit :
On 12/16/19 6:05 PM, Yann Sagon wrote:
My $MODULEPATH contains after loading fosscuda/2019b:
/opt/ebmodules/all/MPI/GCC/8.3.0/OpenMPI/3.1.4:/opt/ebmodules/all/Compiler/GCC/8.3.0:/opt/ebmodules/all/Compiler/GCCcore/8.3.0
For a standard HMNS
Hello
Le 16.12.2019 à 17:41, Mikael Öhman a écrit :
Hi Yann,
This option only affects the install directory of the *software*,
modules are unaffected.
So, the completely unrelated problem is that you have not yet loaded
in your toolchains before trying to load a software.
Nop, it was
Dear list,
I'm sorry to bother you again, but it's still not very clear for me if I
should turn on or off this option.
I'm now using EB 4.1.0. When I went from 3.9.x to 4.0.x I didn't changed
this option, thus I had it set to true by default. It seems it was
working fine.
I'm using
act this is what I was already doing, but when I built pixman, the
rights were wrong on repositorypath directory and the eb wasn't written!
My bad, problem solved!
Thanks
Best
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communicat
Dear list,
I'm having the following issue when trying to build cairo.
[sagon@node025 openpose] $ eb
--configfiles=/opt/cluster/easybuild/dev.cfg cairo-1.16.0-GCCcore-8.3.0.eb
== temporary log file in case of crash /tmp/eb-AVpHdo/easybuild-5vTSb6.log
ERROR: Failed to process easyconfig
.
The Python-3.7.2 for foss-2019a was linked against an EB ssl instead of
the one from the system. And this wasn't working for this eb file in
particular because the ssl was too recent!
I rebuilt Python using system SSL and it's working!
Best
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Référent HPC
Division du
.py",
line 1117, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: unable to get local issuer certificate
(_ssl.c:1056)
As far as I guess, Python 3.7.2 is installed without SSL certificates
populated. I
Dear Kenneth,
> -Message d'origine-
> De : Kenneth Hoste
> Envoyé : mercredi, 7 août 2019 21:08
> À : Yann Sagon
> Cc : easybuild@lists.ugent.be
> Objet : Re: TR: [easybuild] Failed to compile CUDA 10.1.105 on CentOS7
>
> Dear Yann,
>
> The problem see
Sorry, I forgot to reply to the mailing list.
I still have the issue.
-Message d'origine-
De : Yann Sagon
Envoyé : mercredi, 31 juillet 2019 15:13
À : 'Kenneth Hoste'
Objet : RE: [easybuild] Failed to compile CUDA 10.1.105 on CentOS7
Dear Kenneth,
-Message d'origine-
De
Dear list,
I'm trying to compile fosscuda/2019b on a CentOS7 server using EB 3.9.3
It's failed and here are the relevant debug log:
== 2019-07-31 13:55:40,928 easyblock.py:2806 INFO Running method install_step
part of step install
== 2019-07-31 13:55:40,929 run.py:268 DEBUG run_cmd_qa: Output
On Tue, Jun 18, 2019 at 3:36 PM Yann Sagon wrote:
>
>
> Maybe I misunderstood, but I thought the required packages like setuptools
> are provided by the boostrap stage0?
>
> I installed python-setuptools
>
> then the error is ImportError: No module named future.utils
>
Hello
On Tue, Jun 18, 2019 at 2:41 PM Ole Holm Nielsen
wrote:
> On 6/18/19 2:25 PM, Yann Sagon wrote:
> > I'm trying to install EasyBuild as user in CentOS 7.6.
> >
> > I tried this procedure:
> >
> https://easybuild.readthedocs.io/en/latest/Installatio
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[image: Logo UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic
Dear Kenneth,
On Mon, Jun 17, 2019 at 10:31 AM Kenneth Hoste
wrote:
> Dear Yann,
>
> On 14/06/2019 21:12, Yann Sagon wrote:
> > Dear list,
> >
> > a user of our cluster wanted to have FSL 5.0.11 with CUDA support.
> >
> > Any clue how to do that?
Dear list,
a user of our cluster wanted to have FSL 5.0.11 with CUDA support.
Any clue how to do that? I have tried to add CUDA as dependency to the eb
file but of course it's not enough:)
Thanks
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[image: Logo UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de
Dear Kenneth,
On Tue, Jun 4, 2019 at 1:34 PM Kenneth Hoste wrote:
> Dear Yann,
>
> This is probably what you're looking for (it's a bit non-intuitive I
> guess):
>
> options = {'modulename': False}
>
> Using False should effectively skip the import check which is usually done.
>
Great, that
eb file [2]
What is the correct way to tell EB not to try to load this package during
sanity check?
Thanks
[1] https://cran.r-project.org/web/packages/RInside/index.html
[2] https://gist.github.com/ysagon/c2aa7846cdf8f68de53d4a3b04f5a17d
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Division
Z module file? If so then it should be able to find it in
> > PKG_CONFIG_PATH at configure time. If either of those is not the case
> > then you probably need Autotools as a builddep of your XZ/MRtrix
> > easyconfigs?
> >
> > On Fri, 24 May 2019 at 15:08, Yann Sagon >
t in case" with no change.
Best
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[image: Logo UNIGE] Yann Sagon
Référent HPC
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communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic
I'm using:
https://gist.github.com/ysagon/4e1b5f66450a467c0d8ec3765d5b456c
Any clue?
Best
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[image: Logo UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau
the dependencies of
Pango and LibUUID is not loaded as expected.
Any clue?
Best
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[image: Logo UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic
le of how to do it.
>
> Alan
>
> On Tue, 26 Mar 2019 at 14:02, Yann Sagon wrote:
>
>> Dear list,
>>
>> I'm trying to build dask for python 2.7.15 with the toolchain
>> fosscuda/2018b
>>
>> the Python extension "distributed" needs the
portError: No module named futures, (at
easybuild/framework/easyblock.py:2369 in _sanity_check_step)
Best
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[image: Logo UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic
ping!
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[image: Logo UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic
Dear Kennet, thanks for your answer.
On Fri, Mar 8, 2019 at 11:21 AM Kenneth Hoste
wrote:
> Dear Yann,
>
> On 07/03/2019 14:06, Yann Sagon wrote:
> > Dear list,
> >
> > sometime ago, I asked this question on the same list. I think I tried
> > the procedure but
UNIGE] Yann Sagon
Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151
www.unige.ch/stic
Dear Damian,
thanks, this should do the tricks!
Best
De : easybuild-requ...@lists.ugent.be de la
part de Alvarez, Damian
Envoyé : lundi, 11 février 2019 16:29
À : easybuild@lists.ugent.be
Objet : Re: [easybuild] cuda with cuda samples
Dear Yann,
I
automatically?
What is the best to compile them then? Should I go to the sample directory
and do it manually using make?
Best
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Référent HPC
Division du système et des technologies de l'information et de la
communication
Université de Genève | 24 rue Général-Dufour
Tél 022
-static) and rebuild
> > OpenMpi it should work.
> >
> > (https://github.com/open-mpi/ompi/issues/4338#issuecomment-384578916)
> >
> >
> > Best,
> >
> > Andreas
> >
> >
> > *Von:* easybuild-requ...@lists.ugent.be
> >
Dear list,
I installed foss/2018a without slurm specific flags (because I forgot) and
then I recompiled only openmpi with the following flags : --with-slurm
--with-pmi
I think there is no need to recompile something else, but I may be
mistaken. When I try to submit a job using srun, I have the
Dear Kenneth,
2018-04-30 11:32 GMT+02:00 Kenneth Hoste <kenneth.ho...@ugent.be>:
> Dear Yann,
>
> On 30/04/2018 11:28, Yann Sagon wrote:
> > I just noticed that building TF17 with cuda compute 6.0 and 6.1 doesn't
> > respect the job-cores = 12 that I have i
I just noticed that building TF17 with cuda compute 6.0 and 6.1 doesn't
respect the job-cores = 12 that I have in my config file. According to
htop, it's using ~28 cores
Best
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Chef d'équipe HPC
Division du système et des technologies de l'information et de la
oesn't ring a bell for me, but maybe some CUDA drivers are missing?
>
> Something is wrong here, libdevice.10.bc doesn't exist until CUDA 9.0
>
> --
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14
> Please let us know whether that helps, and whether you need to apply
> Mikael's patch as well or not.
>
>
> regards,
>
> Kenneth
>
> >
> > Best regards, Mikael
> >
> >
> >
> > On Wed, Apr 25, 2018 at 6:01 PM, Yann Sagon <yann.sa...
rFlow
> [2]
> https://github.com/easybuilders/easybuild-easyblocks/blob/develop/
> easybuild/easyblocks/t/tensorflow.py
>
> On 25/04/2018 15:12, Yann Sagon wrote:
> > Dear list,
> >
> > I'm very happy to see that TF is now available in eb as compiled from
> >
Dear list,
I'm very happy to see that TF is now available in eb as compiled from
source, not only the whl.
Unfortunately, I have an error when trying to build:
/opt/ebsofts/Core/GCCcore/6.4.0/bin/gcc -U_FORTIFY_SOURCE
-fstack-protector -Wall -B/opt/ebsofts/Core/GCCcore/6.4.0/bin
e-sciences
>
> John Dey
> j...@fuzzdog.com
>
> On Tue, Nov 21, 2017 at 12:37 AM, Kenneth Hoste <kenneth.ho...@ugent.be>
> wrote:
>
>> Dear Yann,
>>
>> On 21/11/2017 09:34, Yann Sagon wrote:
>>
>> Hello,
>>
>> I'm trying to build
ied to use --skip, but it seems it's starting from scratch and as there
are ~400 extensions, this is takes time.
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Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
;
> pablo.escobarlo...@unibas.ch>:
>
>> Hi Yann,
>>
>> Try doing this:
>>
>> prebuildopts = 'export SCRIPTDIR=%(installdir)s && '
>>
>> preinstallopts = 'export SCRIPTDIR=%(installdir)s && '
>>
>> Pablo.
>>
>>
not the correct way to set an env
variable with EB?
Any clue?
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Yann SAGON
Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
Thanks Damian and Kenneth,
I'm just stupid, I forgot to specify my usual config file, so it was indeed
installed in an other place:(
Sorry and thanks!
2017-05-02 16:30 GMT+02:00 Kenneth Hoste <kenneth.ho...@ugent.be>:
> On 02/05/2017 15:39, Yann Sagon wrote:
>
> Hello,
>
&g
/3.0.2
EasyBuild/3.1.0
I'm unable to find the file 3.1.2.lua.
How can I tell eb to not erase the temporary log file to see if there is
something obvious?
Thanks
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Yann SAGON
Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa
gt; Hello Yann,
>
> Not sure at all if you are hitting this, but there used to be a bazel
> build issue against the glibc of centos6.*
>
> Could it be this case?!
>
> F.
>
>
> Αποστολή από κινητό Samsung.
>
>
> ---- Αρχικό μήνυμα
> Από: Yann Sag
could be the difference between devtoolset and
foss/x and why it's not working?
Here is the issue that I have opened on github for Bazel:
https://github.com/bazelbuild/bazel/issues/2534
Many thanks
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1211 Genève 4 - Suisse
Tél. : +41
submitted to a
> scheduler?
>
> On Wed, Feb 22, 2017 at 5:36 AM Yann Sagon <yann.sa...@unige.ch> wrote:
>
>> Hello,
>>
>> I'm back again with my problem (I had a similar problem with Rmpi), maybe
>> someone has an idea of what is going on.
>
h may only be relevant to an
Open MPI developer):
PMI2_Job_GetId failed failed
--> Returned value (null) (14) instead of ORTE_SUCCESS
It worth be said that I have compiled OpenMPI with the following additional
flags:
configopts += '--with-slurm --with-pmi '
Thanks for any suggestion
--
Yann SA
': '-Python-%(pyver)s', 'version': '3.5.0',
'toolchain_inherited': True, 'hidden': False, 'build_only': False}
Any hint?
Thanks
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24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
ee the gist) , I have this error message:
https://gist.github.com/ysagon/c9c5a7207dc77278ead6e4b53dd66929
Best
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Yann SAGON
Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
someone want's to use it.
https://github.com/ysagon/easybuild-easyconfigs/blob/R-3.3.1-foss-2016a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb
Let me know if you want that I do a PR.
Best
2016-06-30 10:17 GMT+02:00 Yann Sagon <yann.sa...@unige.ch>:
> Hello,
>
> After some investiga
-type=OPENMPI"
--library=/opt/ebsofts/MPI/GCC/4.9.3-2.25/OpenMPI/1.10.2/R/3.3.1/lib64/R/library
--no-clean-on-error
without mpirun, it' failed with the test.
2016-06-29 18:00 GMT+02:00 Kenneth Hoste <kenneth.ho...@ugent.be>:
> Hi Yann,
>
> On 29/06/16 17:51, Yann Sagon wrot
Hello,
I'm trying to tweak the file
R-3.2.3-foss-2016a.eb
to install version 3.3.1 of R.
In this file, there is a list of non standard exts.
Rmpi seems to do some checking once installed and failed with orte_init.
Any clue?
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Ingénieur système HPC
24 Rue du Général-Dufour
1211
-
>
> echo "sysadmin know better bash than english" | sed s/min/mins/ \
> | 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
pragma.
[1]
https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/b/Biopython/Biopython-1.65-foss-2016a-Python-2.7.11.eb
Thanks
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Yann SAGON
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24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch
/sagon/easybuild/dev.cfg
ANTs-2.1.0rc3-goolf-1.5.14.eb --robot --try-toolchain=foss,2016a
--try-software-version=2.1.0
and I got this error:
ERROR: Failed to find easyconfig file 'ncurses-5.9-foss-2016a.eb'
Is there any obvious reason?
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Yann SAGON
Ingénieur système HPC
24 Rue du Général
gards,
> Bart
>
>
> On 12 April 2016 at 08:26, Yann Sagon <yann.sa...@unige.ch> wrote:
>
>> Thanks Ward,
>>
>> but, there are a lot of OpenMPI files (even if I don't need them all of
>> course) and what happens when I upgrade eb?
>>
>> 2016-0
nfigs of
> OpenMPI?
>
>
> Ward
>
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Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
, it's ugly. Is there any news on this topic?
Best
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Yann SAGON
Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
>
>
>
> You can override the paths that the sanity check uses, see
>
> http://easybuild.readthedocs.org/en/latest/Writing_easyconfig_files.html#sanity-check
>
>
>
Thanks, it's working fine like that (with override).
files? If yes, what would be cleaner, create a new easyblock or
override?
Thanks!
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Yann SAGON
Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4 - Suisse
Tél. : +41 (0)22 379 7737
yann.sa...@unige.ch - www.unige.ch
.
Created the diff : diff -u Makefile.o Makefile
> Gadget-2.0.7-makefile-hardcoding.patch
Error message: "Can't determine patch level for patch"
2015-07-02 17:51 GMT+02:00 Ward Poelmans <ward.poelm...@ugent.be>:
> Hi Yann,
>
> Welcome to Easybuild.
>
> On Thu,
of Gadget2 contains a directory named Gadget2, so I need to
instruct easybuild to cd to that directory. Is this possible or I need to
write my own easyblock? I'm using the easyblock MakeCp as there is no
configure.
Thanks
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Ingénieur système HPC
24 Rue du Général-Dufour
1211 Genève 4
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