Error with ode_def

Stephen · December 12, 2018, 1:41pm

using DifferentialEquations
f = @ode_def LotkaVolterra begin
  dx = a*x - b*x*y
  dy = -c*y + d*x*y
end a b c d

produce

ERROR: LoadError: LoadError: error compiling #ode_def_opts#1: error compiling symbols: error compiling _symbol: could not load library "libsymengine"
libsymengine.so: 无法打开共享对象文件: 没有那个文件或目录
Stacktrace:
 [1] ode_def_opts(::Symbol, ::Dict{Symbol,Bool}, ::Expr, ::Symbol, ::Vararg{Symbol,N} where N) at /home/rzhli/.julia/packages/ParameterizedFunctions/ozDxQ/src/ode_def_opts.jl:5
 [2] @ode_def(::LineNumberNode, ::Module, ::Any, ::Any, ::Vararg{Any,N} where N) at /home/rzhli/.julia/packages/ParameterizedFunctions/ozDxQ/src/macros.jl:11
in expression starting at untitled-eeb77f88afbc35d3ef7092e6a7f41371:2
in expression starting at untitled-eeb77f88afbc35d3ef7092e6a7f41371:2

ChrisRackauckas · December 12, 2018, 3:37pm

What does ]build SymEngine give you?

Stephen · December 13, 2018, 1:29am

oh, Hash Mismatch, what should I do?

Error: Error building `SymEngine`:
│ ERROR: LoadError: Hash Mismatch!
│   Expected sha256:   40f3d06abf45b571b23135a079d66827282e587be15d540874bb45dac163e2c7
│   Calculated sha256: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] (::getfield(BinaryProvider, Symbol("##141#143")){Bool,String,String,String})(::IOStream) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/Prefix.jl:571
│  [3] #open#294(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::getfield(BinaryProvider, Symbol("##141#143")){Bool,String,String,String}, ::String) at ./iostream.jl:369
│  [4] open at ./iostream.jl:367 [inlined]
│  [5] #verify#140(::Bool, ::Bool, ::String, ::Function, ::String, ::String) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/Prefix.jl:557
│  [6] #verify at ./none:0 [inlined]
│  [7] #download_verify#90(::Bool, ::Bool, ::Bool, ::Function, ::String, ::String, ::String) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/PlatformEngines.jl:543
│  [8] download_verify(::String, ::String, ::String) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/PlatformEngines.jl:528
│  [9] top-level scope at /home/rzhli/.julia/packages/SymEngine/sh7Yz/deps/build.jl:23
│  [10] include at ./boot.jl:317 [inlined]
│  [11] include_relative(::Module, ::String) at ./loading.jl:1044
│  [12] include(::Module, ::String) at ./sysimg.jl:29
│  [13] include(::String) at ./client.jl:392
│  [14] top-level scope at none:0
│ in expression starting at /home/rzhli/.julia/packages/SymEngine/sh7Yz/deps/build.jl:21
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1097

ChrisRackauckas · December 13, 2018, 4:36am

If you delete the binary from .julia/packages/SymEngine it should try to re-download and get you the new one. I assume you might’ve changed versions or something. I’m not sure what happened but something wrong happening with the download/install of that binary.

Stephen · December 13, 2018, 11:12am

I followed your instruction and re-build SymEngine, but it gives new error:

Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Installed SymEngine ─ v0.4.3
  Building SymEngine → `~/.julia/packages/SymEngine/sh7Yz/deps/build.log`
┌ Error: Error building `SymEngine`:
│ [ Info: Downloading https://github.com/JuliaMath/MPFRBuilder/releases/download/v4.0.1-3/build_MPFR.v4.0.1.jl to /home/rzhli/.julia/packages/SymEngine/sh7Yz/deps/symengine-0.3/downloads/build_40f3d06abf45b571b23135a079d66827282e587be15d540874bb45dac163e2c7.jl...
│ ┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
│ │   caller = ip:0x0
│ └ @ Core :-1
│ [ Info: Downloading https://github.com/JuliaMath/MPFRBuilder/releases/download/v4.0.1-3/MPFR.v4.0.1.x86_64-linux-gnu.tar.gz to /home/rzhli/.julia/packages/SymEngine/sh7Yz/deps/symengine-0.3/downloads/MPFR.v4.0.1.x86_64-linux-gnu.tar.gz...
│ ERROR: LoadError: LoadError: Could not download https://github.com/JuliaMath/MPFRBuilder/releases/download/v4.0.1-3/MPFR.v4.0.1.x86_64-linux-gnu.tar.gz to /home/rzhli/.julia/packages/SymEngine/sh7Yz/deps/symengine-0.3/downloads/MPFR.v4.0.1.x86_64-linux-gnu.tar.gz:
ErrorException("")
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] macro expansion at ./logging.jl:311 [inlined]
│  [3] #download#89(::Bool, ::Function, ::String, ::String) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/PlatformEngines.jl:487
│  [4] #download at ./none:0 [inlined]
│  [5] #download_verify#90(::Bool, ::Bool, ::Bool, ::Function, ::String, ::String, ::String) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/PlatformEngines.jl:567
│  [6] #download_verify at ./tuple.jl:0 [inlined]
│  [7] #install#129(::Prefix, ::String, ::Bool, ::Bool, ::Bool, ::Function, ::String, ::String) at /home/rzhli/.julia/packages/BinaryProvider/4F5Hq/src/Prefix.jl:314

…
there is more error message, but actually the file has been downloaded in /home/rzhli/.julia/packages/SymEngine/sh7Yz/deps/symengine-0.3/downloads/

ChrisRackauckas · December 13, 2018, 11:06pm

This was fixed by https://github.com/symengine/SymEngine.jl/pull/150 , but master hasn’t been released yet. Could you open an issue on their repo asking for them to tag an update?

Stephen · December 15, 2018, 4:58am

I’m new to github, I’m learning how to use it. Anyway, thank you so much

ChrisRackauckas · December 15, 2018, 5:19am

No problems, let me know if you need more explanation on any of that.

Stephen · December 16, 2018, 4:18am

problem solved since the SymEngine has been updated

ChrisRackauckas · December 16, 2018, 4:30am

Great! Glad it worked.

Tilstandsrommet · July 16, 2019, 10:29am

I got a very similar Error today doing the same LotkaVolterra example:

error compiling _symbol: could not load library "symengine"

Tilstandsrommet · July 17, 2019, 6:51am

a = symbols("a") produces the same error, so I guess there is something wrong with SymEngine.jl. Opened issue #168

sbacelar · July 20, 2019, 7:51pm

I have a similar error:

error compiling #ode_def_opts#1: error compiling symbols: error compiling _symbol: could not load library "libsymengine"
dlopen(libsymengine.dylib, 1): image not found

Stacktrace:
 [1] ode_def_opts(::Symbol, ::Dict{Symbol,Bool}, ::Expr, ::Symbol, ::Vararg{Symbol,N} where N) at /Users/sergiobacelar/.julia/packages/ParameterizedFunctions/1K9v5/src/ode_def_opts.jl:5
 [2] @ode_def(::LineNumberNode, ::Module, ::Any, ::Any, ::Vararg{Any,N} where N) at /Users/sergiobacelar/.julia/packages/ParameterizedFunctions/1K9v5/src/macros.jl:11

ChrisRackauckas · July 20, 2019, 11:01pm

Try rebuilding SymEngine

sbacelar · July 20, 2019, 11:18pm

I deleted SymEngine in .julia/packages and then rebuild it. But I still got an error. My version of SymEngine is 0.7.0 and Julia 1.1.1.

ChrisRackauckas · July 21, 2019, 8:36am

I need to see the error you get from import Pkg; Pkg.build("SymEngine") or I can’t help.

Anyways, I would highly recommend updating to the newer https://github.com/JuliaDiffEq/ModelingToolkit.jl (which cannot have these kinds of install problems since it’s a pure Julia library!)

sbacelar · July 21, 2019, 12:10pm

Thank you for your answer. The problem is now solved.
I got no errors when following your instructions to build SymEngine.
I updated DiffEqTutorials.jl (git pull origin master). And now it works fine but nevertheless, I will try your suggestion of using ModelingToolkit.jl.
Note: I have created a new cell in Jupyter with using SymEngine. Is it really necessary?