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 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. >>>>>>>>> >>>>>>>>
