[easybuild] Re: R renders with Xlib instead of cairo

[Adam Huffman]

Hi Davide,


I've found that you need explicitly to set the bitmap type to "Cairo" in 
.Rprofile e.g.


options(bitmapType='cairo')


or you could set that system-wide.


Cheers,

Adam


From: easybuild-requ...@lists.ugent.be  on 
behalf of Vanzo, Davide 
Sent: 12 June 2017 23:30:04
To: easybuild@lists.ugent.be
Subject: [easybuild] R renders with Xlib instead of cairo

We provide R 3.3.3 built with both intel and foss toolchains and in both cases 
we observe that the bitmap type is set to "Xlib" instead of "cairo", as it 
should be since the cairo capability is TRUE. Here it is for the unbelievers:

> capabilities("png")
png
TRUE
> capabilities("cairo")
cairo
TRUE
> capabilities("X11")
X11
TRUE
> options('bitmapType')
$bitmapType
[1] "Xlib"

According to the R documentation [A] the default should be "cairo" since it is 
available.
Do you think it is a bug in R or something relative to how it has been built?

[A] https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/x11.html


--
Davide Vanzo, PhD
Application Developer
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT

[easybuild] R renders with Xlib instead of cairo

[Vanzo, Davide]

We provide R 3.3.3 built with both intel and foss toolchains and in both cases 
we observe that the bitmap type is set to "Xlib" instead of "cairo", as it 
should be since the cairo capability is TRUE. Here it is for the unbelievers:

> capabilities("png")
png
TRUE
> capabilities("cairo")
cairo
TRUE
> capabilities("X11")
X11
TRUE
> options('bitmapType')
$bitmapType
[1] "Xlib"

According to the R documentation [A] the default should be "cairo" since it is 
available.
Do you think it is a bug in R or something relative to how it has been built?

[A] https://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/x11.html


--
Davide Vanzo, PhD
Application Developer
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

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

[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 these
> packages that they mind sharing or submitting a pull request.
>
>
> I'm not aware of easyconfigs for these software packages yet.
>
> Maybe this is a good opportunity to try and compose one yourself?
> See the existing examples for already supported software, and the
> documentation at [1] and [2].
>
>
> regards,
>
> Kenneth
>
> PS: See you at the HPCKP meeting in San Sebastian later this week!
>
> [1] http://easybuild.readthedocs.io/en/latest/Writing_
> easyconfig_files.html
> [2] http://easybuild.readthedocs.io/en/latest/version-specific/
> generic_easyblocks.html
>
>
>
> Thanks
>
>
>
>
>
>
>
> *From:* easybuild-requ...@lists.ugent.be [mailto:easybuild-request@
> lists.ugent.be ] *On Behalf Of *Siddiqui,
> Shahzeb
> *Sent:* Tuesday, June 6, 2017 2:20 PM
> *To:* easybuild@lists.ugent.be
> *Subject:* [easybuild] support for tmolex and tcoffee
>
>
>
> Hi,
>
>
>
> I was wondering if there is support for tmolex and tcoffee. They are
> distributed as binary files (.bin).
>
>
>
> http://www.cosmologic.de/turbomole/tmolex.html
> 
>
> http://www.cosmologic.de/support-download/downloads/tmolex-client.html
> 
>
> http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD
> 
>
>
>
> Anyone have any easyconfig files for these?
>
>
>
>
>
>
>
> Shahzeb Siddiqui
>
> HPC Linux Engineer
>
> B2220-447.2
>
> Groton, CT
>
>
>
>
>


-- 
Pablo Escobar López
HPC systems engineer
sciCORE, University of Basel
SIB Swiss Institute of Bioinformatics
http://scicore.unibas.ch

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

[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 mind sharing or submitting a pull request.




I'm not aware of easyconfigs for these software packages yet.

Maybe this is a good opportunity to try and compose one yourself?
See the existing examples for already supported software, and the 
documentation at [1] and [2].



regards,

Kenneth

PS: See you at the HPCKP meeting in San Sebastian later this week!

[1] http://easybuild.readthedocs.io/en/latest/Writing_easyconfig_files.html
[2] 
http://easybuild.readthedocs.io/en/latest/version-specific/generic_easyblocks.html



Thanks

*From:*easybuild-requ...@lists.ugent.be 
[mailto:easybuild-requ...@lists.ugent.be] *On Behalf Of *Siddiqui, Shahzeb

*Sent:* Tuesday, June 6, 2017 2:20 PM
*To:* easybuild@lists.ugent.be
*Subject:* [easybuild] support for tmolex and tcoffee

Hi,

I was wondering if there is support for tmolex and tcoffee. They are 
distributed as binary files (.bin).


http://www.cosmologic.de/turbomole/tmolex.html 



http://www.cosmologic.de/support-download/downloads/tmolex-client.html 



http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD 



Anyone have any easyconfig files for these?

Shahzeb Siddiqui

HPC Linux Engineer

B2220-447.2

Groton, CT

[easybuild] RE: support for tmolex and tcoffee

[Siddiqui, Shahzeb]

I haven't heard any response. Does anyone have easyconfig for these packages 
that they mind sharing or submitting a pull request.

Thanks



From: easybuild-requ...@lists.ugent.be 
[mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Siddiqui, Shahzeb
Sent: Tuesday, June 6, 2017 2:20 PM
To: easybuild@lists.ugent.be
Subject: [easybuild] support for tmolex and tcoffee

Hi,

I was wondering if there is support for tmolex and tcoffee. They are 
distributed as binary files (.bin).

http://www.cosmologic.de/turbomole/tmolex.html
http://www.cosmologic.de/support-download/downloads/tmolex-client.html
http://www.tcoffee.org/Projects/tcoffee/index.html#DOWNLOAD

Anyone have any easyconfig files for these?



Shahzeb Siddiqui
HPC Linux Engineer
B2220-447.2
Groton, CT

Re: [easybuild] Xvfb

[Markus Geimer]

Davide,

> Thanks a lot!

You're welcome.

> If it works do you mind if I upload to the EB repo?

When I said it works for me, I basically meant "it builds and produces
an Xvfb executable" ;-)  Unfortunately, the guy who requested it is
currently on vacation, so I can't ask him whether it really works.  But
if you have some test case and it is working for you, of course, go
ahead and open a PR.

Markus


> On Jun 10 2017, at 3:14 am, Markus Geimer  wrote:
>
> Davide,
>
> > Does anybody have (or have tried) to build Xvfb?
> > I need it and I would rather not reinvent the wheel or help to
> finish it
> > if possible.
>
> You can get it by building the XServer package. Here is an easyconfig
> that is working for me, including one support package that is not yet
> in EB: https://gist.github.com/geimer/f375a45bbfe85309aaf1d720d464d80f
>
> You may have to tweak toolchains/versions according to your environment.
>
> Hth,
> Markus

--
Dr. Markus Geimer
Juelich Supercomputing Centre
Institute for Advanced Simulation
Forschungszentrum Juelich GmbH
52425 Juelich, Germany

Phone:  +49-2461-61-1773
Fax:+49-2461-61-6656
E-Mail: m.gei...@fz-juelich.de
WWW:http://www.fz-juelich.de/jsc




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt