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 lookup error: /usr/bin/../lib/julia/libcholmod.so: >>> undefined symbol: zpotrf_* >>> This is the output in REPL (followed by a crash), in IJulia I simply get >>> a popup saying the kernel died. >>> >>> On Tuesday, December 16, 2014 10:34:27 AM UTC+1, Andrei Berceanu wrote: >>>> >>>> Ok, so here is the output from versioninfo() from inside the Julia REPL: >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> *Julia Version 0.3.3Commit b24213b (2014-11-23 20:19 UTC)Platform >>>> Info: System: Linux (x86_64-unknown-linux-gnu) CPU: Intel(R) Xeon(R) >>>> CPU X5650 @ 2.67GHz WORD_SIZE: 64 BLAS: libblas LAPACK: >>>> liblapack LIBM: libm LLVM: libLLVM-3.3* >>>> >>>> and here is the output of `pacman -Qi julia blas lapack` >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> *Name : juliaVersion : 2:0.3.3-1Description : >>>> High-level, high-performance, dynamic programming languageArchitecture : >>>> x86_64URL : http://julialang.org/ >>>> <http://julialang.org/>Licenses : GPLGroups : >>>> NoneProvides : NoneDepends On : arpack fftw git gmp >>>> libunwind mpfr pcre zlib lapackOptional Deps : gnuplot: If using the >>>> Gaston Package from julia [installed]Required By : NoneOptional For : >>>> NoneConflicts With : NoneReplaces : NoneInstalled Size : 54741.00 >>>> KiBPackager : Alexander F Rødseth <[email protected]>Build Date : >>>> Thu 27 Nov 2014 01:54:38 PM CETInstall Date : Thu 11 Dec 2014 05:47:45 >>>> PM >>>> CETInstall Reason : Explicitly installedInstall Script : YesValidated By >>>> : SignatureName : blasVersion : 3.5.0-1Description : >>>> Basic Linear Algebra SubprogramsArchitecture : x86_64URL : >>>> http://www.netlib.org/lapack <http://www.netlib.org/lapack>Licenses >>>> : >>>> customGroups : NoneProvides : NoneDepends On : >>>> gcc-libsOptional Deps : NoneRequired By : lapack suitesparseOptional >>>> For : NoneConflicts With : NoneReplaces : NoneInstalled Size : >>>> 375.00 KiBPackager : Ronald van Haren <[email protected]>Build >>>> Date : Mon 27 Jan 2014 09:46:21 PM CETInstall Date : Tue 06 May 2014 >>>> 05:38:07 PM CESTInstall Reason : Installed as a dependency for another >>>> packageInstall Script : NoValidated By : SignatureName : >>>> lapackVersion : 3.5.0-1Description : Linear Algebra >>>> PACKageArchitecture : x86_64URL : >>>> http://www.netlib.org/lapack >>>> <http://www.netlib.org/lapack>Licenses : customGroups : >>>> NoneProvides : NoneDepends On : blas=3.5.0Optional Deps : >>>> NoneRequired By : arpack julia python-numpy python2-numpy >>>> suitesparseOptional For : NoneConflicts With : NoneReplaces : >>>> NoneInstalled Size : 15612.00 KiBPackager : Ronald van Haren >>>> <[email protected]>Build Date : Mon 27 Jan 2014 09:46:09 PM >>>> CETInstall Date : Tue 06 May 2014 05:38:07 PM CESTInstall Reason : >>>> Installed as a dependency for another packageInstall Script : NoValidated >>>> By : Signature* >>>> >>>> On Tuesday, December 16, 2014 2:16:10 AM UTC+1, Elliot Saba wrote: >>>>> >>>>> If you didn't compile, then ignore my second message and Joao's. >>>>> Running `versioninfo()` from the julia prompt will give some information >>>>> about your system configuration, and Valentin's question, (running >>>>> `pacman >>>>> -Qi julia blas lapack`) will be helpful to know the answer to as well. >>>>> -E >>>>> >>>>> On Mon, Dec 15, 2014 at 10:54 AM, Valentin Churavy <[email protected]> >>>>> wrote: >>>>>> >>>>>> A fellow archuser here. Under which circumstances does the error >>>>>> occur? Eg. what code are you executing? >>>>>> >>>>>> And what does >>>>>> pacman -Qi julia blas lapack >>>>>> output> >>>>>> >>>>>> On Monday, 15 December 2014 19:14:22 UTC+1, Andrei Berceanu wrote: >>>>>>> >>>>>>> Where do i need to type all this? I must mention that I did not >>>>>>> compile Julia from source, but used my distribution's (arch linux) >>>>>>> package >>>>>>> manager (pacman). >>>>>>> >>>>>>> On December 15, 2014 6:15:09 PM CET, Elliot Saba <[email protected]> >>>>>>> wrote: >>>>>>>> >>>>>>>> Ah, yes. If you haven't, try a `make -C deps distclean >>>>>>>> arpack-julia distclean-openblas distclean-suitesparse`, then `make >>>>>>>> cleanall` and finally `make`. >>>>>>>> -E >>>>>>>> >>>>>>>> On Mon, Dec 15, 2014 at 9:11 AM, João Felipe Santos < >>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>> You may need to clean and rebuild the dependencies as well as core >>>>>>>>> Julia. >>>>>>>>> >>>>>>>>> > On Dec 15, 2014, at 12:08 PM, Andrei Berceanu < >>>>>>>>> [email protected]> wrote: >>>>>>>>> > >>>>>>>>> > Hi all, >>>>>>>>> > >>>>>>>>> > I recently upgraded to Julia Version 0.3.3 on my Arch Linux box >>>>>>>>> and sometimes get this strange error, followed by a kernel crash - >>>>>>>>> what >>>>>>>>> gives? >>>>>>>>> > >>>>>>>>> > julia: symbol lookup error: /usr/bin/../lib/julia/libcholmod.so: >>>>>>>>> undefined symbol: zpotrf_ >>>>>>>>> > >>>>>>>>> > //A >>>>>>>>> >>>>>>>>> >>>>>>> -- >>>>>>> Sent from my Android device with K-9 Mail. Please excuse my brevity. >>>>>>> >>>>>>
