There is an AUR pkgbuild, but since Julia is in community we can not depend on that. But yeah the system BLAS seems to be at fault. I added the Arch maintainer of Julia to the conversation.
@Alexander. There seems to be an issue with the BLAS implementation for Julia. Would it be possible to use OpenBLAS either via moving the pkgbuild from the aur to community or build Julia with USE_SYSTEM_BLAS=0? On Wednesday, 17 December 2014 23:26:54 UTC+1, Tony Kelman wrote: > > Might be a good idea to package OpenBLAS for Arch, if you can't find an > existing PKGBUILD. > > > On Tuesday, December 16, 2014 2:22:10 PM UTC-8, Milan Bouchet-Valat wrote: > > Le mardi 16 décembre 2014 à 13:27 -0800, Elliot Saba a écrit : > > I think the problem here is that we might be using something that > > requires a certain version of BLAS or LAPACK, or possibly a patched > > LAPACK or something. We get a patched LAPACK when we build OpenBLAS. > > I've directly included Andreas in this reply, as he's the kind of guy > > that would have a good idea as to what's going on here. > I don't think Julia needs a patched LAPACK, at least it builds fine on > Fedora with the system's LAPACK. It's the one from OpenBLAS, not the > reference LAPACK, but it worked fine too with Julia 0.3.0 when I used > the latter (though it was slower). > > FWIW the Fedora package sets USE_SYSTEM_*=1 for everything, except > libuv, Rmath and libm. Additional flags are > LIBBLAS=-lopenblasp LIBBLASNAME=libopenblasp.so.0 LIBLAPACK=-lopenblasp > LIBLAPACKNAME=libopenblasp.so.0 USE_BLAS64=0 > > Maybe using Julia's version of SuiteSparse together with the system > BLAS/LAPACK does not work? > > > Also, do you imply it worked fine with 0.3.2, and started randomly > failing only with 0.3.3? > > > Regards > > > > On Tue, Dec 16, 2014 at 10:03 AM, Valentin Churavy > > <v.ch...@gmail.com> wrote: > > So I narrowed it down to combining the system's blas with > > Julia's suitesparse. In the tests I made laplack has no > > influence. Should I file an issue against Julia or with the > > Archlinux package? What are the Fedora packages bundling? > > > > > > USE_SYSTEM_BLAS=1 \ > > USE_SYSTEM_SUITESPARSE=0 \ > > > > > > On Tuesday, 16 December 2014 18:07:23 UTC+1, Valentin Churavy > > wrote: > > Ok setting > > USE_SYSTEM_BLAS=0 \ > > USE_SYSTEM_LAPACK=0 \ > > USE_SYSTEM_SUITESPARSE=0 \ > > > > Make the problem go away. So it is the interaction > > between the system blas/lapack and the built > > suitesparese. Are there any patches that julia carries > > over suitesparse 4.4.1? > > > > > > On Tuesday, 16 December 2014 17:28:28 UTC+1, Valentin > > Churavy wrote: > > So using > > > > > > make \ > > USE_SYSTEM_LLVM=0 \ > > USE_SYSTEM_LIBUNWIND=1 \ > > USE_SYSTEM_READLINE=0 \ > > USE_SYSTEM_PCRE=1 \ > > USE_SYSTEM_LIBM=1 \ > > USE_SYSTEM_OPENLIBM=0 \ > > USE_SYSTEM_OPENSPECFUN=0 \ > > USE_SYSTEM_BLAS=1 \ > > USE_SYSTEM_LAPACK=1 \ > > USE_SYSTEM_FFTW=1 \ > > USE_SYSTEM_GMP=1 \ > > USE_SYSTEM_MPFR=1 \ > > USE_SYSTEM_ARPACK=1 \ > > USE_SYSTEM_SUITESPARSE=0 \ > > USE_SYSTEM_ZLIB=1 \ > > USE_SYSTEM_GRISU=0 \ > > USE_SYSTEM_RMATH=0 \ > > USE_SYSTEM_LIBUV=0 \ > > USE_SYSTEM_UTF8PROC=0 \ > > USE_MKL=0 \ > > USE_BLAS64=0 \ > > USE_LLVM_SHLIB=0 > > > > > > leads to the error observed by me and Andrei, > > can anybody not using Arch try that out? > > > > On Tuesday, 16 December 2014 17:07:55 UTC+1, > > Valentin Churavy wrote: > > So building it from the PKGBUILD leads > > to the same error. I am now building > > it with the same make options from the > > tar.gz on the Julia download page. > > > > > > Andrei we probably have to build other > > parts that interact with suitesparse > > from source instead of using the Arch > > ones. But if the problem persists > > while using the tarball, then at least > > other people on non-Arch distros can > > try to see if it works for them and > > which interaction leads to the error. > > > > > > For the time being you can call > > full(A) on your sparse matrix to > > convert it to a dense matrix and > > circumvent the problem > > > > On Tuesday, 16 December 2014 16:52:18 > > UTC+1, Andrei Berceanu wrote: > > So if your suspicion is > > correct, setting > > USE_SYSTEM_SUITESPARSE=1 > > should fix this, right? > > Let me know how it goes :) > > > > On Tuesday, December 16, 2014 > > 3:19:43 PM UTC+1, Valentin > > Churavy wrote: > > So your system setup > > is exactly the same > > (except me running on > > CPU: Intel(R) Core(TM) > > i5-2520M CPU @ > > 2.50GHz) and I can > > conform that the > > following code > > > > > > A = sparse([rand() + > > rand() * im for i in > > 1:100, j in 1:100]) > > B = [rand() + rand() > > * im for i in 1:100] > > A\B > > > > > > leads to the following > > error: > > julia: symbol lookup > > error: > /usr/bin/../lib/julia/libcholmod.so: undefined symbol: zpotrf_ > > > > > > pacman > > -Qo > /usr/lib/libcholmod.so > > /usr/lib/libcholmod.so > > is owned by > > suitesparse 4.4.1-1 > > > > > > but the PKGBUILD > > at > https://projects.archlinux.org/svntogit/community.git/tree/trunk/PKGBUILD?h=packages/julia > > tells me that the Julia package was build with USE_SYSTEM_SUITESPARSE=0 > > > > > > I am currently > > building the Julia > > from the PKGBUILD in > > order to confirm that > > these build-options > > lead to the problem. > > > > > > Best, > > Valentin > > > > On Tuesday, 16 > > December 2014 11:59:51 > > UTC+1, Andrei Berceanu > > wrote: > > I now have a > > more accurate > > description of > > when the error > > happens. If I > > try to solve > > the following > > linear system > > > > A > > 1681x1681 sparse > matrix with 8321 Complex{Float64} entries: > > [1 , > 1] = -10.95+0.001im > > [2 , > 1] = 0.415415-0.909632im > > [42 , > 1] = 1.0+0.0im > > [1 , > 2] = 0.415415+0.909632im > > [2 , > 2] = -10.56+0.001im > > [3 , > 2] = 0.415415-0.909632im > > [43 , > 2] = 1.0+0.0im > > [2 , > 3] = 0.415415+0.909632im > > [3 , > 3] = -10.19+0.001im > > [4 , > 3] = 0.415415-0.909632im > > ⋮ > > [1638, > 1679] = 1.0+0.0im > > [1678, > 1679] = 0.415415-0.909632im > > [1679, > 1679] = -10.19+0.001im > > [1680, > 1679] = 0.415415+0.909632im > > [1639, > 1680] = 1.0+0.0im > > [1679, > 1680] = 0.415415-0.909632im > > [1680, > 1680] = -10.56+0.001im > > [1681, > 1680] = 0.415415+0.909632im > > [1640, > 1681] = 1.0+0.0im > > [1680, > 1681] = 0.415415-0.909632im > > [1681, > 1681] = -10.95+0.001im > > > > B > > 1681-element > Array{Complex{Float64},1}: > > > 0.525444+0.850828im > > > 0.644642+0.764485im > > > -0.658926-0.752208im > > > -0.653119+0.757256im > > > -0.684803+0.728728im > > > 0.499568-0.866275im > > > -0.362176-0.93211im > > > 0.87001+0.493034im > > > -0.616929-0.787019im > > > 0.698366-0.715741im > > > -0.275131-0.961407im > > > -0.984546-0.175127im > > > -0.857186+0.515007im > > ⋮ > > > > -0.148487-0.988914im > > > 0.860544-0.509376im > > > -0.929042+0.369975im > > > -0.812528-0.582923im > > > -0.972683-0.232138im > > > -0.449449+0.893306im > > > -0.929623-0.368512im > > > 0.950785+0.309852im > > > -0.309421-0.950925im > > > 0.115447+0.993314im > > > 0.685855+0.727738im > > > -0.215699+0.97646im > > > > A\B > > julia: symbol > > > > ...
