Test StructuralIdentifiability fails : libsingular not defined about structuralidentifiability.jl HOT 30 CLOSED

Thank you for reporting this! I did not encounter this issue before. Could you try

using Pkg
Pkg.add("Singular")

?
What will it say?

from structuralidentifiability.jl.

Same outcome! I installed Singular and updated the registries. My current >status is:
_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.7.1 (2021-12-22)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

(@v1.7) pkg> st
Status C:\Users\Denis\.julia\environments\v1.7\Project.toml
[165a45c3] DASKR v2.8.0
[e993076c] DASSL v2.6.0
[2445eb08] DataDrivenDiffEq v0.6.9
[f3b72e0c] DiffEqDevTools v2.28.0
[0c46a032] DifferentialEquations v7.0.0
[587475ba] Flux v0.12.8
[7073ff75] IJulia v1.23.2
[23fbe1c1] Latexify v0.15.9
[442fdcdd] Measures v0.3.1
[961ee093] ModelingToolkit v8.0.0
[8913a72c] NonlinearSolve v0.3.13
[09606e27] ODEInterfaceDiffEq v3.10.1
[1dea7af3] OrdinaryDiffEq v6.3.0
[91a5bcdd] Plots v1.25.4
[d330b81b] PyPlot v2.10.0
[bcd08a7b] Singular v0.5.8
[220ca800] StructuralIdentifiability v0.3.4
[c3572dad] Sundials v4.9.1
[8254be44] SymbolicRegression v0.6.16
[0c5d862f] Symbolics v4.2.3

(@v1.7) pkg>

from structuralidentifiability.jl.

By the same outcome you mean that you get libsingular not defined while precompiling Singular?

from structuralidentifiability.jl.

Quick question, does this happen on an Intel CPU or an Apple M1 chip?

from structuralidentifiability.jl.

Intel CPU

The error report is:

Info: Precompiling StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544]
└ @ Base loading.jl:1423
ERROR: LoadError: UndefVarError: libsingular not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base .\Base.jl:35
[2] top-level scope
@ C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:66
[3] include
@ .\Base.jl:418 [inlined]
[4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base .\loading.jl:1318
[5] top-level scope
@ none:1
[6] eval
@ .\boot.jl:373 [inlined]
[7] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[8] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:1
ERROR: LoadError: Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to C:\Users\Denis.julia\compiled\v1.7\Singular\jl_DF69.tmp.
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:997
[7] include
@ .\Base.jl:418 [inlined]
[8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base .\loading.jl:1318
[9] top-level scope
@ none:1
[10] eval
@ .\boot.jl:373 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[12] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\GroebnerBasis\89ud7\src\GroebnerBasis.jl:1
ERROR: LoadError: Failed to precompile GroebnerBasis [e39c9192-ea4d-5e15-9584-a488c6d614bd] to C:\Users\Denis.julia\compiled\v1.7\GroebnerBasis\jl_DA67.tmp.
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:997
[7] include
@ .\Base.jl:418 [inlined]
[8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base .\loading.jl:1318
[9] top-level scope
@ none:1
[10] eval
@ .\boot.jl:373 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[12] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\StructuralIdentifiability\SPeqW\src\StructuralIdentifiability.jl:1
Failed to precompile StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544] to C:\Users\Denis.julia\compiled\v1.7\StructuralIdentifiability\jl_D45D.tmp.

Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:997
[7] eval
@ .\boot.jl:373 [inlined]
[8] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
@ Base .\loading.jl:1196

from structuralidentifiability.jl.

I just tried the same package collection (albeit on v1.6.5) in a new environment, I did not observe the error. I don't have access to an Intel machine, on my mac 1.7.1 does not succeed installing Nemo, Singular and other such dependencies. What happens if you try

using Singular

?

Edit: Also, can you try a new environment like so:

>]activate .
>]add StructuralIdentifiability
>]test Structuralidentifiability

?

from structuralidentifiability.jl.

           _

_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.7.1 (2021-12-22)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

julia> Using Singular
ERROR: syntax: extra token "Singular" after end of expression
Stacktrace:
[1] top-level scope
@ none:1

julia>

from structuralidentifiability.jl.

julia> Using Singular
ERROR: syntax: extra token "Singular" after end of expression
Stacktrace:
[1] top-level scope
@ none:1

This is probably a typo, should be using, all lowercase @finmod

from structuralidentifiability.jl.

Sorry.
_
_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.7.1 (2021-12-22)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

julia> using Singular
[ Info: Precompiling Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c]
ERROR: LoadError: UndefVarError: libsingular not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base .\Base.jl:35
[2] top-level scope
@ C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:66
[3] include
@ .\Base.jl:418 [inlined]
[4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base .\loading.jl:1318
[5] top-level scope
@ none:1
[6] eval
@ .\boot.jl:373 [inlined]
[7] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[8] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:1
ERROR: Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to C:\Users\Denis.julia\compiled\v1.7\Singular\jl_30F0.tmp.
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:997

julia>

from structuralidentifiability.jl.

@finmod no worries.

So it seems that root cause is in Singular only. Do you have the LTS Julia installed? i think it's 1.6.5. Could be useful to try an older stable version.

Also, have you tried this?

>]activate .
>]add StructuralIdentifiability
>]test Structuralidentifiability

Then, if the error is in precompilation, I think running

using Pkg
Pkg.precompile("Singular")

may give details about the specific issue.

from structuralidentifiability.jl.

The problem is with Singular. The above command gives the sual error message. I do not have LTS 1.6.5 installed but it used to give me the same message. The failure to test StructuralIdentifiability has been around for quite some time. I just expected it would disappear with regular update of commits but it does not.


  _

_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.7.1 (2021-12-22)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

julia> using Singular
[ Info: Precompiling Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c]
ERROR: LoadError: UndefVarError: libsingular not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base .\Base.jl:35
[2] top-level scope
@ C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:66
[3] include
@ .\Base.jl:418 [inlined]
[4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base .\loading.jl:1318
[5] top-level scope
@ none:1
[6] eval
@ .\boot.jl:373 [inlined]
[7] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[8] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:1
ERROR: Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to C:\Users\Denis.julia\compiled\v1.7\Singular\jl_605B.tmp.
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:997

julia> import Pkg; Pkg.precompile()
Precompiling project...
✗ Singular
✗ GroebnerBasis
✗ StructuralIdentifiability
0 dependencies successfully precompiled in 17 seconds (334 already precompiled)

ERROR: The following 2 direct dependencies failed to precompile:

Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c]

Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to C:\Users\Denis.julia\compiled\v1.7\Singular\jl_91CC.tmp.
ERROR: LoadError: UndefVarError: libsingular not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base .\Base.jl:35
[2] top-level scope
@ C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:66
[3] include
@ .\Base.jl:418 [inlined]
[4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base .\loading.jl:1318
[5] top-level scope
@ none:1
[6] eval
@ .\boot.jl:373 [inlined]
[7] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[8] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:1

StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544]

Failed to precompile StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544] to C:\Users\Denis.julia\compiled\v1.7\StructuralIdentifiability\jl_AE7E.tmp.
ERROR: LoadError: UndefVarError: libsingular not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base .\Base.jl:35
[2] top-level scope
@ C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:66
[3] include
@ .\Base.jl:418 [inlined]
[4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base .\loading.jl:1318
[5] top-level scope
@ none:1
[6] eval
@ .\boot.jl:373 [inlined]
[7] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[8] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\Singular\nGiup\src\Singular.jl:1
ERROR: LoadError: Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to C:\Users\Denis.julia\compiled\v1.7\Singular\jl_B9E5.tmp.
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:997
[7] include
@ .\Base.jl:418 [inlined]
[8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base .\loading.jl:1318
[9] top-level scope
@ none:1
[10] eval
@ .\boot.jl:373 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude .\client.jl:453
[12] top-level scope
@ none:1
in expression starting at C:\Users\Denis.julia\packages\GroebnerBasis\89ud7\src\GroebnerBasis.jl:1
ERROR: LoadError: Failed to precompile GroebnerBasis [e39c9192-ea4d-5e15-9584-a488c6d614bd] to C:\Users\Denis.julia\compiled\v1.7\GroebnerBasis\jl_B496.tmp.
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base .\loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base .\loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base .\loading.jl:1013
[6] re

from structuralidentifiability.jl.

I have done Pkg> add Singular#master and it gives this. Obviously there are several compat problems. with GroebnerBasis which, I read, is now deprecated and replaced by Oscar.jl

           _

_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.7.1 (2021-12-22)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

julia>

(@v1.7) pkg> add Singular#master
Cloning git-repo https://github.com/oscar-system/Singular.jl.git
Updating git-repo https://github.com/oscar-system/Singular.jl.git
Updating registry at C:\Users\Denis\.julia\registries\General
Updating git-repo https://github.com/JuliaRegistries/General.git
Resolving package versions...
ERROR: Unsatisfiable requirements detected for package GroebnerBasis [e39c9192]:
GroebnerBasis [e39c9192] log:
├─possible versions are: 0.1.0-0.3.3 or uninstalled
├─restricted by compatibility requirements with Nemo [2edaba10] to versions: uninstalled
│ └─Nemo [2edaba10] log:
│ ├─possible versions are: 0.9.0-0.28.0 or uninstalled
│ └─restricted to versions 0.28 by Singular [bcd08a7b], leaving only versions 0.28.0
│ └─Singular [bcd08a7b] log:
│ ├─possible versions are: 0.9.1 or uninstalled
│ └─Singular [bcd08a7b] is fixed to version 0.9.1
└─restricted by compatibility requirements with StructuralIdentifiability [220ca800] to versions: 0.1.0-0.3.3 — no versions left
└─StructuralIdentifiability [220ca800] log:
├─possible versions are: 0.1.0-0.3.4 or uninstalled
├─restricted to versions * by an explicit requirement, leaving only versions 0.1.0-0.3.4
└─restricted by compatibility requirements with AbstractAlgebra [c3fe647b] to versions: 0.3.4 or uninstalled, leaving only versions: 0.3.4
└─AbstractAlgebra [c3fe647b] log:
├─possible versions are: 0.1.0-0.23.0 or uninstalled
└─restricted to versions 0.23 by Singular [bcd08a7b], leaving only versions 0.23.0
└─Singular [bcd08a7b] log: see above

(@v1.7) pkg>

from structuralidentifiability.jl.

I agree with @iliailmer - the problem seem to be in Singular.jl. @finmod , could you make an issue there?
I vaguely remember that there have been some issues in using Singular.jl on Windows machines (looks like @finmod is using Windows). If this is the case, one could make the Singular dependency optional and use this for Windows.

from structuralidentifiability.jl.

@finmod , could you make an issue there? Done. oscar-system/Singular.jl#538

from structuralidentifiability.jl.

Thank you! As they reply there, Singular is indeed not supported on Windows.
If you have some examples you wanted to try but do not have access to Mac/Linux machine, feel free to send them to me.
We will keep this in mind, in fact we have an issue to replace Singular with msolve (but have to check whether this will help for Windows)

from structuralidentifiability.jl.

I will stay tuned to this issue to help test that Pkg> test StructuralIdentifiability passes on all OS. The MTK tutorial is important for the visibility and dissemination of StructuralIdentifiability in the SciML ecosystem. It should rely on pure Julia code to avoid these OS controversies usually associated with wrapper packages for other languages.

from structuralidentifiability.jl.

The tutorial does look great BTW. It would be good to add something to the MTK docs to give it visibility. Maybe something in the ODESystem analysis portion.

from structuralidentifiability.jl.

Running the MTK tutorial and testing this package fail because of this libsingular not defined error. It has been there since the beginning. Would be good if this issue could finally be resolved so that one can give a real test of this excellent package.

           _

_ _ ()_ | Documentation: https://docs.julialang.org () | () () | _ _ | | __ _ | Type "?" for help, "]?" for Pkg help. | | | | | | |/ ` | | | | || | | | (| | | Version 1.7.1 (2021-12-22) / |__'|||'_| | Official https://julialang.org/ release |/ |

It may have issue on Linux too. Here is OS info I found (not IT person, just followed internet instructions - we have IT person to deal with systems)

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

We have Julia 1.6.5, and I did

julia> using Pkg
julia> Pkg.add("StructuralIdentifiability")

Got error message: (the successful ones weren't included.)

Precompiling project...
✗ CxxWrap
✗ libsingular_julia_jll
✗ Singular
✗ GroebnerBasis
✗ StructuralIdentifiability
178 dependencies successfully precompiled in 291 seconds
5 dependencies errored. To see a full report either run import Pkg; Pkg.precompile() or load the packages

Tried to add those 5 one-by-one as follows:

julia> using Pkg

julia> Pkg.add("CxxWrap")
Updating registry at ~/.julia/registries/General
Resolving package versions...
Updating ~/.julia/environments/v1.6/Project.toml
[1f15a43c] + CxxWrap v0.11.2
No Changes to ~/.julia/environments/v1.6/Manifest.toml

julia> Pkg.add("libsingular_julia_jll")
Resolving package versions...
Updating ~/.julia/environments/v1.6/Project.toml
[ae4fbd8f] + libsingular_julia_jll v0.15.6+0
No Changes to ~/.julia/environments/v1.6/Manifest.toml

julia> Pkg.add("Singular")
Resolving package versions...
Updating ~/.julia/environments/v1.6/Project.toml
[bcd08a7b] + Singular v0.5.8
No Changes to ~/.julia/environments/v1.6/Manifest.toml

julia> Pkg.add("GroebnerBasis")
Resolving package versions...
Updating ~/.julia/environments/v1.6/Project.toml
[e39c9192] + GroebnerBasis v0.3.3
No Changes to ~/.julia/environments/v1.6/Manifest.toml

julia> Pkg.add("StructuralIdentifiability")
Resolving package versions...
No Changes to ~/.julia/environments/v1.6/Project.toml
No Changes to ~/.julia/environments/v1.6/Manifest.toml

Then run the test case HIV.jl. Here is error message: (my home folder name replaced with xxxxx). There seems to be issues with versions of those 5 packages.

julia HIV.jl
ERROR: LoadError: LoadError: InitError: could not load library "/home/xxxxx/.julia/artifacts/b93c684e7135496a3c612fa8286c7e4ae50eb86d/lib/libcxxwrap_julia.so"
/opt/ohpc/pub/compiler/gcc/8.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/xxxxx/.julia/artifacts/b93c684e7135496a3c612fa8286c7e4ae50eb86d/lib/libcxxwrap_julia.so)
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
[2] init()
@ libcxxwrap_julia_jll ~/.julia/packages/libcxxwrap_julia_jll/iGjEb/src/wrappers/x86_64-linux-gnu-cxx03-julia_version+1.6.0.jl:9
[3] top-level scope
@ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
[4] top-level scope (repeats 2 times)
@ none:1
during initialization of module libcxxwrap_julia_jll
in expression starting at /home/xxxxx/.julia/packages/libsingular_julia_jll/ZydmZ/src/wrappers/x86_64-linux-gnu-cxx03.jl:4
in expression starting at /home/xxxxx/.julia/packages/libsingular_julia_jll/ZydmZ/src/libsingular_julia_jll.jl:2
ERROR: LoadError: Failed to precompile libsingular_julia_jll [ae4fbd8f-ecdb-54f8-bbce-35570499b30e] to /home/xxxxx/.julia/compiled/v1.6/libsingular_julia_jll/jl_e9eZgK.
Stacktrace:
[1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[2] top-level scope (repeats 2 times)
@ none:1
in expression starting at /home/xxxxx/.julia/packages/Singular/nGiup/src/Singular.jl:1
ERROR: LoadError: Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to /home/xxxxx/.julia/compiled/v1.6/Singular/jl_czCGbh.
Stacktrace:
[1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[2] top-level scope (repeats 2 times)
@ none:1
in expression starting at /home/xxxxx/.julia/packages/GroebnerBasis/89ud7/src/GroebnerBasis.jl:1
ERROR: LoadError: Failed to precompile GroebnerBasis [e39c9192-ea4d-5e15-9584-a488c6d614bd] to /home/xxxxx/.julia/compiled/v1.6/GroebnerBasis/jl_muKrzY.
Stacktrace:
[1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[2] top-level scope (repeats 2 times)
@ none:1
in expression starting at /home/xxxxx/.julia/packages/StructuralIdentifiability/bRtkP/src/StructuralIdentifiability.jl:1
ERROR: LoadError: Failed to precompile StructuralIdentifiability [220ca800-aa68-49bb-acd8-6037fa93a544] to /home/xxxxx/.julia/compiled/v1.6/StructuralIdentifiability/jl_VL89iY.
Stacktrace:
[1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
in expression starting at /home/xxxxx/Research/Reference/Identifiability/SIAN/StructuralIdentifiability.jl-master/examples/HIV.jl:7

from structuralidentifiability.jl.

@qchenmath
Thank you for reporting this! This is puzzling. What happens if you do using CxxWrap ?

from structuralidentifiability.jl.

@qchenmath Thank you for reporting this! This is puzzling. What happens if you do using CxxWrap ?

I am new to Julia, and honestly have no clue - also, our IT person installed Julia 1.6.5 yesterday.

ERROR: LoadError: InitError: could not load library "/home/xxxxx/.julia/artifacts/b93c684e7135496a3c612fa8286c7e4ae50eb86d/lib/libcxxwrap_julia.so"
/opt/ohpc/pub/compiler/gcc/8.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/xxxxx/.julia/artifacts/b93c684e7135496a3c612fa8286c7e4ae50eb86d/lib/libcxxwrap_julia.so)
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
[2] init()
@ libcxxwrap_julia_jll ~/.julia/packages/libcxxwrap_julia_jll/iGjEb/src/wrappers/x86_64-linux-gnu-cxx03-julia_version+1.6.0.jl:9
[3] top-level scope (repeats 2 times)
@ none:1
during initialization of module libcxxwrap_julia_jll
in expression starting at /home/xxxxx/.julia/packages/CxxWrap/OcN1Z/src/CxxWrap.jl:1
ERROR: Failed to precompile CxxWrap [1f15a43c-97ca-5a2a-ae31-89f07a497df4] to /home/xxxxx/.julia/compiled/v1.6/CxxWrap/jl_23N7Sq.
Stacktrace:
[1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385

from structuralidentifiability.jl.

@qchenmath This could be relevant, it seems that there is a C-compiler issue on your machine.

from structuralidentifiability.jl.

@qchenmath This could be relevant, it seems that there is a C-compiler issue on your machine.

Thanks. I have very limited permission on that machine (cluster), and will have to wait until our IT person gets back to me.

from structuralidentifiability.jl.

@qchenmath
I guess you can still try what was recommended in the thread @iliailmer pointed out: typing export LD_LIBRARY_PATH=/usr/local/lib:/usr/lib:/usr/local/lib64:/usr/lib64 in your command line. This should not require substantial permissions.

from structuralidentifiability.jl.

It didn't do anything. Still not working. Earlier, tried

strings libstdc++.so.6.0.25 | grep GLIBCXX

It shows that 3.4.26 can't be found - it has up to 3.4.25.

from structuralidentifiability.jl.

With the help of our IT staff, it worked on linux cluster.

1. Test a model on my MacPro M1 with 16G memory. Didn't finish after >16 hours. Use all memory from time to time.
2. On the cluster (Centos), assigned 20G memory, it finished in 7.8 hours.

from structuralidentifiability.jl.

I believe that having more memory may be quite important: on a relatively slow server but with 100G, I got the same model in less than two hours.

from structuralidentifiability.jl.

I believe that having more memory may be quite important: on a relatively slow server but with 100G, I got the same model in less than two hours.

Any estimate how much memory will be needed? I know it will depend the model's complexity. But will be great to know roughly how much memory will be needed. It will be extremely slow, if the server/cluster doesn't have enough memory. The I/O time will kill it.

from structuralidentifiability.jl.

A priori estimates are really hard to get. If you see that swap memory is being used, then it will likely to be very slow.

from structuralidentifiability.jl.

@finmod
The new release 0.4.0 works on Windows. Please let us know if you encounter any issues with it.

from structuralidentifiability.jl.

Great! test StructuralIdentifiability passes . It was a long time coming on Windows but it is here.

from structuralidentifiability.jl.