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
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