Help on error: symbol lookup error -libcholmod.so - dpotrf_ in Mixedmodels

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

Help on error: symbol lookup error -libcholmod.so - dpotrf_ in Mixedmodels

Yonghee Lee-2
Hi! I got an error during sparse Cholesky computation related Mixed Models. So I ran test for MixedModels and I got the same error as below: 
 
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

There has been no problem, but it comes up suddenly. 
There might be some problems in the library libcholmod, but I have no idea to fix this.

If anyone can help solving this problem, I will appreciate!!
Yonghee Lee 

-------------------------------------------- error message and system info -----------------------------------------  
julia> Base.Pkg.test("MixedModels")
INFO: Testing MixedModels
PASSED: plsonescalar.jl
PASSED: plsonevector.jl
PASSED: plstwoscalar.jl
PASSED: plstwovector.jl
PASSED: plsdiagnested.jl
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_
======================================[ ERROR: MixedModels ]======================================

failed process: Process(`/usr/bin/julia /home/ylee19067/.julia/v0.3/MixedModels/test/runtests.jl`, ProcessExited(127)) [127]

==================================================================================================
INFO: No packages to install, update or remove
ERROR: MixedModels had test errors
 in error at error.jl:21
 in test at pkg/entry.jl:718
 in anonymous at pkg/dir.jl:28
 in cd at ./file.jl:20
 in cd at pkg/dir.jl:28
 in test at pkg.jl:67

julia> versioninfo(true)
Julia Version 0.3.11
Commit 483dbf5 (2015-07-27 06:18 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
  WORD_SIZE: 64
           Ubuntu 14.04.3 LTS
  uname: Linux 3.13.0-62-generic #102-Ubuntu SMP Tue Aug 11 14:29:36 UTC 2015 x86_64 x86_64
Memory: 31.36642074584961 GB (27138.046875 MB free)

  BLAS: libopenblas (NO_LAPACK NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: liblapack.so.3
  LIBM: libopenlibm
  LLVM: libLLVM-3.3
Environment:
  TERM = xterm
  XDG_SESSION_PATH = /org/freedesktop/DisplayManager/Session2
  XDG_SEAT_PATH = /org/freedesktop/DisplayManager/Seat0
  DEFAULTS_PATH = /usr/share/gconf/ubuntu.default.path
  PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
  MANDATORY_PATH = /usr/share/gconf/ubuntu.mandatory.path
  NODE_PATH = /usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript

  COMPIZ_BIN_PATH = /usr/bin/


$ wajig show julia
Package: julia                    
State: installed
Automatically installed: no
Version: 0.3.11-trusty1
Priority: extra
Section: science
Maintainer: Debian Julia Team <[hidden email]>
Architecture: amd64
Uncompressed Size: 67.1 M
Depends: libc6 (>= 2.17), libdouble-conversion1, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6),
         liblapack3 | liblapack.so.3, libopenblas-base, libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.0),
         liblapack3 | libatlas3-base, libpcre3 (>= 8.31), libfftw3-3, libcholmod1.7.1 |
         libcholmod2.1.2, libumfpack5.4.0 | libumfpack5.6.2, libgmp10 (>= 5.1.3), libarpack2,
         librmath-julia-dev, libmpfr4, git
PreDepends: multiarch-support
Suggests: ess (>= 12.09-1~), julia-doc
Conflicts: julia

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: Help on error: symbol lookup error -libcholmod.so - dpotrf_ in Mixedmodels

Andreas Noack
How did you install Julia? Did you use the official PPA https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases If not, I'd suggest that you uninstall, add the official repo, update, and install julia again.

On Sun, Aug 23, 2015 at 4:28 PM, Yonghee Lee <[hidden email]> wrote:
Hi! I got an error during sparse Cholesky computation related Mixed Models. So I ran test for MixedModels and I got the same error as below: 
 
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

There has been no problem, but it comes up suddenly. 
There might be some problems in the library libcholmod, but I have no idea to fix this.

If anyone can help solving this problem, I will appreciate!!
Yonghee Lee 

-------------------------------------------- error message and system info -----------------------------------------  
julia> Base.Pkg.test("MixedModels")
INFO: Testing MixedModels
PASSED: plsonescalar.jl
PASSED: plsonevector.jl
PASSED: plstwoscalar.jl
PASSED: plstwovector.jl
PASSED: plsdiagnested.jl
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_
======================================[ ERROR: MixedModels ]======================================

failed process: Process(`/usr/bin/julia /home/ylee19067/.julia/v0.3/MixedModels/test/runtests.jl`, ProcessExited(127)) [127]

==================================================================================================
INFO: No packages to install, update or remove
ERROR: MixedModels had test errors
 in error at error.jl:21
 in test at pkg/entry.jl:718
 in anonymous at pkg/dir.jl:28
 in cd at ./file.jl:20
 in cd at pkg/dir.jl:28
 in test at pkg.jl:67

julia> versioninfo(true)
Julia Version 0.3.11
Commit 483dbf5 (2015-07-27 06:18 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
  WORD_SIZE: 64
           Ubuntu 14.04.3 LTS
  uname: Linux 3.13.0-62-generic #102-Ubuntu SMP Tue Aug 11 14:29:36 UTC 2015 x86_64 x86_64
Memory: 31.36642074584961 GB (27138.046875 MB free)

  BLAS: libopenblas (NO_LAPACK NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: liblapack.so.3
  LIBM: libopenlibm
  LLVM: libLLVM-3.3
Environment:
  TERM = xterm
  XDG_SESSION_PATH = /org/freedesktop/DisplayManager/Session2
  XDG_SEAT_PATH = /org/freedesktop/DisplayManager/Seat0
  DEFAULTS_PATH = /usr/share/gconf/ubuntu.default.path
  PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
  MANDATORY_PATH = /usr/share/gconf/ubuntu.mandatory.path
  NODE_PATH = /usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript

  COMPIZ_BIN_PATH = /usr/bin/


$ wajig show julia
Package: julia                    
State: installed
Automatically installed: no
Version: 0.3.11-trusty1
Priority: extra
Section: science
Maintainer: Debian Julia Team <[hidden email]>
Architecture: amd64
Uncompressed Size: 67.1 M
Depends: libc6 (>= 2.17), libdouble-conversion1, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6),
         liblapack3 | liblapack.so.3, libopenblas-base, libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.0),
         liblapack3 | libatlas3-base, libpcre3 (>= 8.31), libfftw3-3, libcholmod1.7.1 |
         libcholmod2.1.2, libumfpack5.4.0 | libumfpack5.6.2, libgmp10 (>= 5.1.3), libarpack2,
         librmath-julia-dev, libmpfr4, git
PreDepends: multiarch-support
Suggests: ess (>= 12.09-1~), julia-doc
Conflicts: julia

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: Help on error: symbol lookup error -libcholmod.so - dpotrf_ in Mixedmodels

Yonghee Lee-2

Dear Andreas, Thanks for your comment!

I installed Julia from the official PPA and also already tried to remove Julia completely, but the problem persisted.

I found very similar  issue for JuliaBox: 

https://github.com/JuliaLang/JuliaBox/issues/221

I tried same codes in the issue and got the same error:

julia> B1 = sprandn(100,100,0.1);
julia> B2 = speye(100);
julia> x  = kron(B2,B1)\randn(100*100);
julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

But, for me, it is not easy to understand the issue and still don't know what to do. 
It looks the problem comes from chnage in versions of SuiteSparse

I will move my question to USER group since I think now it is not appropriate to STAT group.

Thanks
Yonghee Lee

2015년 8월 25일 화요일 오전 10시 27분 20초 UTC+9, Andreas Noack 님의 말:
How did you install Julia? Did you use the official PPA <a href="https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Flaunchpad.net%2F~staticfloat%2F%2Barchive%2Fubuntu%2Fjuliareleases\46sa\75D\46sntz\0751\46usg\75AFQjCNEdS4KUWgrUjn7uo01v3xXQjHjvdA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Flaunchpad.net%2F~staticfloat%2F%2Barchive%2Fubuntu%2Fjuliareleases\46sa\75D\46sntz\0751\46usg\75AFQjCNEdS4KUWgrUjn7uo01v3xXQjHjvdA&#39;;return true;">https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases If not, I'd suggest that you uninstall, add the official repo, update, and install julia again.

On Sun, Aug 23, 2015 at 4:28 PM, Yonghee Lee <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="f9veigezBwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">drag...@...> wrote:
Hi! I got an error during sparse Cholesky computation related Mixed Models. So I ran test for MixedModels and I got the same error as below: 
 
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

There has been no problem, but it comes up suddenly. 
There might be some problems in the library libcholmod, but I have no idea to fix this.

If anyone can help solving this problem, I will appreciate!!
Yonghee Lee 

-------------------------------------------- error message and system info -----------------------------------------  
julia> Base.Pkg.test("MixedModels")
INFO: Testing MixedModels
PASSED: plsonescalar.jl
PASSED: plsonevector.jl
PASSED: plstwoscalar.jl
PASSED: plstwovector.jl
PASSED: plsdiagnested.jl
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_
======================================[ ERROR: MixedModels ]======================================

failed process: Process(`/usr/bin/julia /home/ylee19067/.julia/v0.3/MixedModels/test/runtests.jl`, ProcessExited(127)) [127]

==================================================================================================
INFO: No packages to install, update or remove
ERROR: MixedModels had test errors
 in error at error.jl:21
 in test at pkg/entry.jl:718
 in anonymous at pkg/dir.jl:28
 in cd at ./file.jl:20
 in cd at pkg/dir.jl:28
 in test at pkg.jl:67

julia> versioninfo(true)
Julia Version 0.3.11
Commit 483dbf5 (2015-07-27 06:18 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
  WORD_SIZE: 64
           Ubuntu 14.04.3 LTS
  uname: Linux 3.13.0-62-generic #102-Ubuntu SMP Tue Aug 11 14:29:36 UTC 2015 x86_64 x86_64
Memory: 31.36642074584961 GB (27138.046875 MB free)

  BLAS: libopenblas (NO_LAPACK NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: liblapack.so.3
  LIBM: libopenlibm
  LLVM: libLLVM-3.3
Environment:
  TERM = xterm
  XDG_SESSION_PATH = /org/freedesktop/DisplayManager/Session2
  XDG_SEAT_PATH = /org/freedesktop/DisplayManager/Seat0
  DEFAULTS_PATH = /usr/share/gconf/ubuntu.default.path
  PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
  MANDATORY_PATH = /usr/share/gconf/ubuntu.mandatory.path
  NODE_PATH = /usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript

  COMPIZ_BIN_PATH = /usr/bin/


$ wajig show julia
Package: julia                    
State: installed
Automatically installed: no
Version: 0.3.11-trusty1
Priority: extra
Section: science
Maintainer: Debian Julia Team <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="f9veigezBwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">pkg-jul...@....debian.org>
Architecture: amd64
Uncompressed Size: 67.1 M
Depends: libc6 (>= 2.17), libdouble-conversion1, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6),
         liblapack3 | liblapack.so.3, libopenblas-base, libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.0),
         liblapack3 | libatlas3-base, libpcre3 (>= 8.31), libfftw3-3, libcholmod1.7.1 |
         libcholmod2.1.2, libumfpack5.4.0 | libumfpack5.6.2, libgmp10 (>= 5.1.3), libarpack2,
         librmath-julia-dev, libmpfr4, git
PreDepends: multiarch-support
Suggests: ess (>= 12.09-1~), julia-doc
Conflicts: julia

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="f9veigezBwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">julia-stats...@googlegroups.com.
For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;">https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: Help on error: symbol lookup error -libcholmod.so - dpotrf_ in Mixedmodels

Yonghee Lee-2
I installed Julia by compiling source and the error goes away!

Thanks for comments..

Yonghee Lee

2015년 8월 26일 수요일 오후 8시 15분 38초 UTC+9, Yonghee Lee 님의 말:

Dear Andreas, Thanks for your comment!

I installed Julia from the official PPA and also already tried to remove Julia completely, but the problem persisted.

I found very similar  issue for JuliaBox: 

<a href="https://github.com/JuliaLang/JuliaBox/issues/221" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Fgithub.com%2FJuliaLang%2FJuliaBox%2Fissues%2F221\46sa\75D\46sntz\0751\46usg\75AFQjCNHx_jiXvVwWIpnGCrtb4sklw5-djA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Fgithub.com%2FJuliaLang%2FJuliaBox%2Fissues%2F221\46sa\75D\46sntz\0751\46usg\75AFQjCNHx_jiXvVwWIpnGCrtb4sklw5-djA&#39;;return true;">https://github.com/JuliaLang/JuliaBox/issues/221

I tried same codes in the issue and got the same error:

julia> B1 = sprandn(100,100,0.1);
julia> B2 = speye(100);
julia> x  = kron(B2,B1)\randn(100*100);
julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

But, for me, it is not easy to understand the issue and still don't know what to do. 
It looks the problem comes from chnage in versions of SuiteSparse

I will move my question to USER group since I think now it is not appropriate to STAT group.

Thanks
Yonghee Lee

2015년 8월 25일 화요일 오전 10시 27분 20초 UTC+9, Andreas Noack 님의 말:
How did you install Julia? Did you use the official PPA <a href="https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Flaunchpad.net%2F~staticfloat%2F%2Barchive%2Fubuntu%2Fjuliareleases\46sa\75D\46sntz\0751\46usg\75AFQjCNEdS4KUWgrUjn7uo01v3xXQjHjvdA&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Flaunchpad.net%2F~staticfloat%2F%2Barchive%2Fubuntu%2Fjuliareleases\46sa\75D\46sntz\0751\46usg\75AFQjCNEdS4KUWgrUjn7uo01v3xXQjHjvdA&#39;;return true;">https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases If not, I'd suggest that you uninstall, add the official repo, update, and install julia again.

On Sun, Aug 23, 2015 at 4:28 PM, Yonghee Lee <[hidden email]> wrote:
Hi! I got an error during sparse Cholesky computation related Mixed Models. So I ran test for MixedModels and I got the same error as below: 
 
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

There has been no problem, but it comes up suddenly. 
There might be some problems in the library libcholmod, but I have no idea to fix this.

If anyone can help solving this problem, I will appreciate!!
Yonghee Lee 

-------------------------------------------- error message and system info -----------------------------------------  
julia> Base.Pkg.test("MixedModels")
INFO: Testing MixedModels
PASSED: plsonescalar.jl
PASSED: plsonevector.jl
PASSED: plstwoscalar.jl
PASSED: plstwovector.jl
PASSED: plsdiagnested.jl
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_
======================================[ ERROR: MixedModels ]======================================

failed process: Process(`/usr/bin/julia /home/ylee19067/.julia/v0.3/MixedModels/test/runtests.jl`, ProcessExited(127)) [127]

==================================================================================================
INFO: No packages to install, update or remove
ERROR: MixedModels had test errors
 in error at error.jl:21
 in test at pkg/entry.jl:718
 in anonymous at pkg/dir.jl:28
 in cd at ./file.jl:20
 in cd at pkg/dir.jl:28
 in test at pkg.jl:67

julia> versioninfo(true)
Julia Version 0.3.11
Commit 483dbf5 (2015-07-27 06:18 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
  WORD_SIZE: 64
           Ubuntu 14.04.3 LTS
  uname: Linux 3.13.0-62-generic #102-Ubuntu SMP Tue Aug 11 14:29:36 UTC 2015 x86_64 x86_64
Memory: 31.36642074584961 GB (27138.046875 MB free)

  BLAS: libopenblas (NO_LAPACK NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: liblapack.so.3
  LIBM: libopenlibm
  LLVM: libLLVM-3.3
Environment:
  TERM = xterm
  XDG_SESSION_PATH = /org/freedesktop/DisplayManager/Session2
  XDG_SEAT_PATH = /org/freedesktop/DisplayManager/Seat0
  DEFAULTS_PATH = /usr/share/gconf/ubuntu.default.path
  PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
  MANDATORY_PATH = /usr/share/gconf/ubuntu.mandatory.path
  NODE_PATH = /usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript

  COMPIZ_BIN_PATH = /usr/bin/


$ wajig show julia
Package: julia                    
State: installed
Automatically installed: no
Version: 0.3.11-trusty1
Priority: extra
Section: science
Maintainer: Debian Julia Team <[hidden email].debian.org>
Architecture: amd64
Uncompressed Size: 67.1 M
Depends: libc6 (>= 2.17), libdouble-conversion1, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6),
         liblapack3 | liblapack.so.3, libopenblas-base, libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.0),
         liblapack3 | libatlas3-base, libpcre3 (>= 8.31), libfftw3-3, libcholmod1.7.1 |
         libcholmod2.1.2, libumfpack5.4.0 | libumfpack5.6.2, libgmp10 (>= 5.1.3), libarpack2,
         librmath-julia-dev, libmpfr4, git
PreDepends: multiarch-support
Suggests: ess (>= 12.09-1~), julia-doc
Conflicts: julia

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to julia-stats...@googlegroups.com.
For more options, visit <a href="https://groups.google.com/d/optout" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;">https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: Help on error: symbol lookup error -libcholmod.so - dpotrf_ in Mixedmodels

Andreas Noack
Good to hear that. We have occasionally had some problems with the cholmod libraries provided by linux distributions so either compiling from source or using the generic linux binaries can be the solution.

On Wed, Aug 26, 2015 at 10:27 AM, Yonghee Lee <[hidden email]> wrote:
I installed Julia by compiling source and the error goes away!

Thanks for comments..

Yonghee Lee

2015년 8월 26일 수요일 오후 8시 15분 38초 UTC+9, Yonghee Lee 님의 말:

Dear Andreas, Thanks for your comment!

I installed Julia from the official PPA and also already tried to remove Julia completely, but the problem persisted.

I found very similar  issue for JuliaBox: 


I tried same codes in the issue and got the same error:

julia> B1 = sprandn(100,100,0.1);
julia> B2 = speye(100);
julia> x  = kron(B2,B1)\randn(100*100);
julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

But, for me, it is not easy to understand the issue and still don't know what to do. 
It looks the problem comes from chnage in versions of SuiteSparse

I will move my question to USER group since I think now it is not appropriate to STAT group.

Thanks
Yonghee Lee

2015년 8월 25일 화요일 오전 10시 27분 20초 UTC+9, Andreas Noack 님의 말:
How did you install Julia? Did you use the official PPA https://launchpad.net/~staticfloat/+archive/ubuntu/juliareleases If not, I'd suggest that you uninstall, add the official repo, update, and install julia again.

On Sun, Aug 23, 2015 at 4:28 PM, Yonghee Lee <[hidden email]> wrote:
Hi! I got an error during sparse Cholesky computation related Mixed Models. So I ran test for MixedModels and I got the same error as below: 
 
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_

There has been no problem, but it comes up suddenly. 
There might be some problems in the library libcholmod, but I have no idea to fix this.

If anyone can help solving this problem, I will appreciate!!
Yonghee Lee 

-------------------------------------------- error message and system info -----------------------------------------  
julia> Base.Pkg.test("MixedModels")
INFO: Testing MixedModels
PASSED: plsonescalar.jl
PASSED: plsonevector.jl
PASSED: plstwoscalar.jl
PASSED: plstwovector.jl
PASSED: plsdiagnested.jl
/usr/bin/julia: symbol lookup error: /usr/bin/../lib/x86_64-linux-gnu/julia/libcholmod.so: undefined symbol: dpotrf_
======================================[ ERROR: MixedModels ]======================================

failed process: Process(`/usr/bin/julia /home/ylee19067/.julia/v0.3/MixedModels/test/runtests.jl`, ProcessExited(127)) [127]

==================================================================================================
INFO: No packages to install, update or remove
ERROR: MixedModels had test errors
 in error at error.jl:21
 in test at pkg/entry.jl:718
 in anonymous at pkg/dir.jl:28
 in cd at ./file.jl:20
 in cd at pkg/dir.jl:28
 in test at pkg.jl:67

julia> versioninfo(true)
Julia Version 0.3.11
Commit 483dbf5 (2015-07-27 06:18 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
  WORD_SIZE: 64
           Ubuntu 14.04.3 LTS
  uname: Linux 3.13.0-62-generic #102-Ubuntu SMP Tue Aug 11 14:29:36 UTC 2015 x86_64 x86_64
Memory: 31.36642074584961 GB (27138.046875 MB free)

  BLAS: libopenblas (NO_LAPACK NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: liblapack.so.3
  LIBM: libopenlibm
  LLVM: libLLVM-3.3
Environment:
  TERM = xterm
  XDG_SESSION_PATH = /org/freedesktop/DisplayManager/Session2
  XDG_SEAT_PATH = /org/freedesktop/DisplayManager/Seat0
  DEFAULTS_PATH = /usr/share/gconf/ubuntu.default.path
  PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
  MANDATORY_PATH = /usr/share/gconf/ubuntu.mandatory.path
  NODE_PATH = /usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript

  COMPIZ_BIN_PATH = /usr/bin/


$ wajig show julia
Package: julia                    
State: installed
Automatically installed: no
Version: 0.3.11-trusty1
Priority: extra
Section: science
Maintainer: Debian Julia Team <[hidden email]>
Architecture: amd64
Uncompressed Size: 67.1 M
Depends: libc6 (>= 2.17), libdouble-conversion1, libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.6),
         liblapack3 | liblapack.so.3, libopenblas-base, libstdc++6 (>= 4.6), zlib1g (>= 1:1.2.0),
         liblapack3 | libatlas3-base, libpcre3 (>= 8.31), libfftw3-3, libcholmod1.7.1 |
         libcholmod2.1.2, libumfpack5.4.0 | libumfpack5.6.2, libgmp10 (>= 5.1.3), libarpack2,
         librmath-julia-dev, libmpfr4, git
PreDepends: multiarch-support
Suggests: ess (>= 12.09-1~), julia-doc
Conflicts: julia

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "julia-stats" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.