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