Hi all,
For those who need to create EasyConfigs for R: I've updated the
generateEasyConfig.R generator for R 3.3.0 @
https://github.com/fgeorgatos/easybuild.experimental/tree/master/users/pneerincx/
Cheers,
Pi
> On 31 May 2016, at 14:47, Pieter Neerincx <[email protected]> wrote:
>
> Hi Pablo,
>
> On 29 May 2016, at 19:33, Pablo Escobar Lopez <[email protected]>
> wrote:
>>
>> Hi Pieter,
>>
>> This is the R-3.3.0 easyconfig I am using . I think the biggest change I had
>> to do was adding the XZ and PCRE deps
>> https://gist.github.com/anonymous/5380f4ed8ca853c4d1f41cca7fbafedb
>
> Check, I had something similar except I dropped LAPACK_LIBS:
>
> #preconfigopts = 'BLAS_LIBS=\"$LIBBLAS\" LAPACK_LIBS=\"$LIBLAPACK\"'
> preconfigopts = 'BLAS_LIBS=\"$LIBBLAS\"'
>
>> And this is what I get in the configure output:
>> https://gist.github.com/pescobar/dd8430e9eda17aec3eaa8c05483e89d1
>>
>> I think I get "LAPACK(generic)" because I have "lapack-devel" rpm installed
>> in my system.
>
> Check, I now have:
>
> Interfaces supported: tcltk
> External libraries: readline, BLAS(OpenBLAS), LAPACK(in blas), curl
> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
> Options enabled: shared R library, R profiling
>
> Capabilities skipped:
> Options not enabled: shared BLAS, memory profiling
>
> Tada: PNG support; finally!
>
>
>> Be aware that you should use a recent PCRE easyconfig
>> https://github.com/hpcugent/easybuild-easyconfigs/pull/2561
>
> Check already found that problem and fixed it, but....
>
>> And you should recompile you bzip2 module using latest easybuild/2.8. If you
>> had no problem with bzip2 maybe you have an rpm providing libbz2.so and you
>> are using this one instead of the bzip2 version provided by easybuild
>> https://github.com/hpcugent/easybuild-easyblocks/pull/910
>
> ... aha that was the cruelpit that resulted in the failure to build Rlib.so
> and provided a nice excuse to update EasyBuild from 2.7.0 -> 2.8.1 :).
>
> Redeployed bzip2 and all is well now.
> Thanks for the pointers to the fixes!
>
> Cheers,
>
> Pi
>
>> regards,
>> Pablo.
>>
>>
>>
>> 2016-05-29 17:32 GMT+02:00 Pieter Neerincx <[email protected]>:
>> Hi Kenneth and Pablo,
>>
>> Thanks for the intel'! This is indeed related. When I drop
>> LAPACK_LIBS="$LIBLAPACK" from the preconfigopts, I get "... BLAS(OpenBLAS),
>> LAPACK(in blas), ..." and the build no longer fails on compiling
>> libRlapack.so.
>> For the record this is for R 3.3.0.
>>
>> Unfortunately it now fails on libR.so itself :(. Looks like for some of the
>> dependencies there is no shared lib available.
>> This may be related to
>>
>> DEPRECATED AND DEFUNCT
>> • The previously included versions of zlib, bzip2, xz and PCRE have
>> been removed, so suitable external (usually system) versions are required
>> (see the ‘R Installation and Administration’ manual).
>>
>> To make a standard R 3.3.0 compile (on Centos 6.7) I now have:
>> * added some additional dependencies to the easyconfig that I previously did
>> not need to specify
>> * removed --enable-R-shlib from configure options
>> * Used this workaround:
>>
>> IFS=':' read -r -a list_of_dirs <<< "${CPATH}"
>> for path in ${list_of_dirs[@]}; do export CPPFLAGS="${CPPFLAGS:-}
>> -I${path}"; done
>>
>> IFS=':' read -r -a list_of_dirs <<< "${LIBRARY_PATH}"
>> for path in ${list_of_dirs[@]}; do export LDFLAGS="${LDFLAGS:-}
>> -L${path}"; done
>>
>> The good news is that the code to detect the presence of libpng has been
>> fixed. Previously the configure script would try to detect libpng twice:
>> * once using pkg-config as dependency for Cairo to enable the 'cairo' device.
>> * once without using pkg-config to enable the 'PNG' device.
>> The latter would fail miserably when libpng was not available from default
>> paths like in the case when deployed with EasyBuild elsewhere.
>>
>> So far I now have:
>>
>> Interfaces supported: tcltk
>> External libraries: readline, BLAS(OpenBLAS), LAPACK(in blas), curl
>> Additional capabilities: 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 also will play along and
>> compile...
>>
>> Cheers,
>>
>> Pi
>>
>>
>>
>>> On 28 May 2016, at 22:22, Pablo Escobar Lopez
>>> <[email protected]> wrote:
>>>
>>> Hi Pieter,
>>>
>>> maybe related? https://github.com/hpcugent/easybuild-easyconfigs/issues/1435
>>>
>>> Pablo
>>>
>>> 2016-05-28 16:23 GMT+02:00 Kenneth Hoste <[email protected]>:
>>> 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
>>>> and 2016a, but so far no luck. The build fails on compiling libRlapack.so.
>>>> After some digging I found out that I have for example as part of
>>>> foss/2015b:
>>>>
>>>> ScaLAPACK/2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0
>>>>
>>>> with a dependency on
>>>>
>>>> OpenBLAS/0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0
>>>>
>>>> The name suggests that LAPACK/3.5.0 is a dependency and will be loaded
>>>> too, but LAPACK is absent according to "module list", which makes sense as
>>>> none of the deployed module files specify LAPACK.
>>>> I also cannot find LAPACK back as OS dependency in the corresponding *.eb
>>>> easyconfigs... What am I missing here?
>>>
>>> The LAPACK sources are provided to OpenBLAS, which picks it up during
>>> the build and embeds the LAPACK symbols in the OpenBLAS library:
>>>
>>> $ nm $EBROOTOPENBLAS/lib/libopenblas.a | grep dgeev
>>> dgeev.o:
>>> 0000000000000000 T dgeev_
>>> dgeevx.o:
>>> 0000000000000000 T dgeevx_
>>> lapacke_dgeev.o:
>>> 0000000000000000 T LAPACKE_dgeev
>>> U LAPACKE_dgeev_work
>>> lapacke_dgeev_work.o:
>>> 0000000000000000 T LAPACKE_dgeev_work
>>> U dgeev_
>>> lapacke_dgeevx.o:
>>> 0000000000000000 T LAPACKE_dgeevx
>>> U LAPACKE_dgeevx_work
>>> lapacke_dgeevx_work.o:
>>> 0000000000000000 T LAPACKE_dgeevx_work
>>> U dgeevx_
>>>
>>>
>>> I was confused by this too initially, see
>>> https://github.com/xianyi/OpenBLAS/issues/203
>>>
>>>
>>> regards,
>>>
>>> Kenneth
>>>
>>>
>>>
>>> --
>>> Pablo Escobar López
>>> HPC systems engineer
>>> sciCORE, University of Basel
>>> SIB Swiss Institute of Bioinformatics
>>> http://scicore.unibas.ch
>>
>> -------------------------------------------------------------
>> phone: +31 6 143 66 783
>> e-mail: [email protected]
>> skype: pieter.online
>> -------------------------------------------------------------
>>
>>
>>
>>
>> --
>> Pablo Escobar López
>> HPC systems engineer
>> sciCORE, University of Basel
>> SIB Swiss Institute of Bioinformatics
>> http://scicore.unibas.ch
>
> -------------------------------------------------------------
> phone: +31 6 143 66 783
> e-mail: [email protected]
> skype: pieter.online
> -------------------------------------------------------------
>
-------------------------------------------------------------
phone: +31 6 143 66 783
e-mail: [email protected]
skype: pieter.online
-------------------------------------------------------------
