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Error building 'Clp' cannot generate deps.jl #90

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Will-Gorman opened this issue May 13, 2020 · 17 comments
Closed

Error building 'Clp' cannot generate deps.jl #90

Will-Gorman opened this issue May 13, 2020 · 17 comments

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@Will-Gorman
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I am trying to install and build Clp on my system but am receiving an error:

┌ Error: Error building `Clp`:
│ ERROR: LoadError: LibraryProduct(nothing, ["libClp"], :libClp, "Prefix(/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] #write_deps_file#165(::Bool, ::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /global/home/users/gorman_will/.julia/packages/BinaryProvider/GeAtj/src/Products.jl:419
│  [3] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│  [4] top-level scope at none:0
│  [5] include at ./boot.jl:317 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1044
│  [7] include(::Module, ::String) at ./sysimg.jl:29
│  [8] include(::String) at ./client.jl:392
│  [9] top-level scope at none:0
│ in expression starting at /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/build.jl:144
└ @ Pkg.Operations /global/software/sl-7.x86_64/sources/julia-1.0.3/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1097

I am thinking this might have something to do with potentially needing a custom installation, but am not sure..

Julia session info:

julia> versioninfo()
Julia Version 1.0.3
Platform Info:
  OS: Linux (x86_64-redhat-linux)
  CPU: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, sandybridge)
Environment:
  JULIA_DIR = /global/software/sl-7.x86_64/modules/langs/julia/1.0.3

Package version in my project:

julia> Pkg.status()
    Status `~/.julia/environments/v1.0/Project.toml`
  [e2554f3b] Clp v0.8.0
  [e2685f51] ECOS v0.11.0
  [4076af6c] JuMP v0.21.2
  [eadc2687] Pandas v1.4.0
  [438e738f] PyCall v1.91.4
@blegat
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blegat commented May 14, 2020 •
edited
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Can you give the output of

$ julia /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/build.jl --verbose

@Will-Gorman
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Yes here was the output first:

[gorman_will@n0002 ~]$ julia /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/build.jl --verbose
ERROR: LoadError: ArgumentError: Package BinaryProvider not found in current path:
- Run `import Pkg; Pkg.add("BinaryProvider")` to install the BinaryProvider package.

Stacktrace:
 [1] require(::Module, ::Symbol) at ./loading.jl:823
 [2] include at ./boot.jl:317 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1044
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] exec_options(::Base.JLOptions) at ./client.jl:266
 [6] _start() at ./client.jl:425
in expression starting at /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/build.jl:5

I updated BinaryProvider but that didn't allow me to build Clp (received the same error). But, then your command did generate a new output when I re-ran it shown below.

[gorman_will@n0002 ~]$ julia /global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/build.jl --verbose
[ Info: Found a valid dl path libClp.so while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClp.so matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClp.so cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/usr/lib/libClp.so"
└    /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /globa                                                                           l/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so)
[ Info: Found a valid dl path libClp.so.1 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClp.so.1 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClp.so.1 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/usr/lib/libClp.so.1"
└    /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /globa                                                                           l/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1)
[ Info: Found a valid dl path libClp.so.1.14.6 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClp.so.1.14.6 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClp.so.1.14.6 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/usr/lib/libClp.so.1.14.6"
└    /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /globa                                                                           l/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1.14.6                                                                           )
[ Info: Found a valid dl path libClpSolver.so while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClpSolver.so matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClpSolver.so cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/usr/lib/libClpSolver.so"
└    /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /glo                                                                           bal/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.s                                                                           o)
[ Info: Found a valid dl path libClpSolver.so.1 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClpSolver.so.1 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClpSolver.so.1 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/usr/lib/libClpSolver.so.1"
└    /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /glo                                                                           bal/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.s                                                                           o.1)
[ Info: Found a valid dl path libClpSolver.so.1.14.6 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClpSolver.so.1.14.6 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/li                                                                           bClpSolver.so.1.14.6 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/                                                                           cX6R7/deps/usr/lib/libClpSolver.so.1.14.6"
└    /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /glo                                                                           bal/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.s                                                                           o.1.14.6)
[ Info: Found a valid dl path libCoinUtils.so while looking for libClp
[ Info: Found a valid dl path libCoinUtils.so.3 while looking for libClp
[ Info: Found a valid dl path libCoinUtils.so.3.11.3 while looking for libClp
[ Info: Found a valid dl path libOsi.so while looking for libClp
[ Info: Found a valid dl path libOsi.so.1 while looking for libClp
[ Info: Found a valid dl path libOsi.so.1.13.5 while looking for libClp
[ Info: Found a valid dl path libOsiClp.so while looking for libClp
[ Info: Found a valid dl path libOsiClp.so.1 while looking for libClp
[ Info: Found a valid dl path libOsiClp.so.1.14.6 while looking for libClp
[ Info: Found a valid dl path libOsiCommonTests.so while looking for libClp
[ Info: Found a valid dl path libOsiCommonTests.so.1 while looking for libClp
[ Info: Found a valid dl path libOsiCommonTests.so.1.13.5 while looking for libC                                                                           lp
[ Info: Found a valid dl path libopenblas.0.3.9.so while looking for libClp
[ Info: Found a valid dl path libopenblas.so while looking for libClp
[ Info: Found a valid dl path libopenblas.so.0 while looking for libClp
[ Info: Could not locate libClp inside /global/home/users/gorman_will/.julia/pac                                                                           kages/Clp/cX6R7/deps/usr/lib
[ Info: Destination file /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/downloads/Clp.v1.17.6.x86_64-linux-gnu-libgfortran3-cxx03.tar.gz already exists, verifying...
[ Info: Hash cache is consistent, returning true
[ Info: Installing /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/downloads/Clp.v1.17.6.x86_64-linux-gnu-libgfortran3-cxx03.tar.gz into /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr
[ Info: Removing files installed by manifests/Clp.v1.17.6.x86_64-linux-gnu-libgfortran3-cxx03.list
[ Info:   bin/clp removed
[ Info:   Culling empty directory bin
[ Info:   include/coin/CbcOrClpParam.cpp removed
[ Info:   include/coin/CbcOrClpParam.hpp removed
[ Info:   include/coin/ClpCholeskyBase.hpp removed
[ Info:   include/coin/ClpCholeskyDense.hpp removed
[ Info:   include/coin/ClpCholeskyMumps.hpp removed
[ Info:   include/coin/ClpCholeskyPardiso.hpp removed
[ Info:   include/coin/ClpConfig.h removed
[ Info:   include/coin/ClpConstraint.hpp removed
[ Info:   include/coin/ClpConstraintLinear.hpp removed
[ Info:   include/coin/ClpConstraintQuadratic.hpp removed
[ Info:   include/coin/ClpDualRowDantzig.hpp removed
[ Info:   include/coin/ClpDualRowPivot.hpp removed
[ Info:   include/coin/ClpDualRowSteepest.hpp removed
[ Info:   include/coin/ClpDummyMatrix.hpp removed
[ Info:   include/coin/ClpDynamicExampleMatrix.hpp removed
[ Info:   include/coin/ClpDynamicMatrix.hpp removed
[ Info:   include/coin/ClpEventHandler.hpp removed
[ Info:   include/coin/ClpFactorization.hpp removed
[ Info:   include/coin/ClpGubDynamicMatrix.hpp removed
[ Info:   include/coin/ClpGubMatrix.hpp removed
[ Info:   include/coin/ClpInterior.hpp removed
[ Info:   include/coin/ClpLinearObjective.hpp removed
[ Info:   include/coin/ClpMatrixBase.hpp removed
[ Info:   include/coin/ClpMessage.hpp removed
[ Info:   include/coin/ClpModel.hpp removed
[ Info:   include/coin/ClpNetworkMatrix.hpp removed
[ Info:   include/coin/ClpNode.hpp removed
[ Info:   include/coin/ClpNonLinearCost.hpp removed
[ Info:   include/coin/ClpObjective.hpp removed
[ Info:   include/coin/ClpPEDualRowDantzig.hpp removed
[ Info:   include/coin/ClpPEDualRowSteepest.hpp removed
[ Info:   include/coin/ClpPEPrimalColumnDantzig.hpp removed
[ Info:   include/coin/ClpPEPrimalColumnSteepest.hpp removed
[ Info:   include/coin/ClpPESimplex.hpp removed
[ Info:   include/coin/ClpPackedMatrix.hpp removed
[ Info:   include/coin/ClpParameters.hpp removed
[ Info:   include/coin/ClpPdcoBase.hpp removed
[ Info:   include/coin/ClpPlusMinusOneMatrix.hpp removed
[ Info:   include/coin/ClpPresolve.hpp removed
[ Info:   include/coin/ClpPrimalColumnDantzig.hpp removed
[ Info:   include/coin/ClpPrimalColumnPivot.hpp removed
[ Info:   include/coin/ClpPrimalColumnSteepest.hpp removed
[ Info:   include/coin/ClpQuadraticObjective.hpp removed
[ Info:   include/coin/ClpSimplex.hpp removed
[ Info:   include/coin/ClpSimplexDual.hpp removed
[ Info:   include/coin/ClpSimplexNonlinear.hpp removed
[ Info:   include/coin/ClpSimplexOther.hpp removed
[ Info:   include/coin/ClpSimplexPrimal.hpp removed
[ Info:   include/coin/ClpSolve.hpp removed
[ Info:   include/coin/Clp_C_Interface.h removed
[ Info:   include/coin/Idiot.hpp removed
[ Info:   include/coin/OsiClpSolverInterface.hpp removed
[ Info:   lib/libClp.la removed
[ Info:   lib/libClp.so removed
[ Info:   lib/libClp.so.1 removed
[ Info:   lib/libClp.so.1.14.6 removed
[ Info:   lib/libClpSolver.la removed
[ Info:   lib/libClpSolver.so removed
[ Info:   lib/libClpSolver.so.1 removed
[ Info:   lib/libClpSolver.so.1.14.6 removed
[ Info:   lib/libOsiClp.la removed
[ Info:   lib/libOsiClp.so removed
[ Info:   lib/libOsiClp.so.1 removed
[ Info:   lib/libOsiClp.so.1.14.6 removed
[ Info:   lib/pkgconfig/clp.pc removed
[ Info:   lib/pkgconfig/osi-clp.pc removed
[ Info:   logs/Clp.log removed
[ Info:   logs/relink_to_rpath_clp.log removed
[ Info:   logs/relink_to_rpath_libClp.so.1.14.6.log removed
[ Info:   logs/relink_to_rpath_libClpSolver.so.1.14.6.log removed
[ Info:   logs/update_linkage_clp_libClp.so.1.log removed
[ Info:   logs/update_linkage_clp_libClpSolver.so.1.log removed
[ Info:   logs/update_linkage_clp_libCoinUtils.so.3.log removed
[ Info:   logs/update_linkage_clp_libopenblas.so.log removed
[ Info:   logs/update_linkage_libClp.so.1.14.6_libCoinUtils.so.3.log removed
[ Info:   logs/update_linkage_libClp.so.1.14.6_libopenblas.so.log removed
[ Info:   logs/update_linkage_libClpSolver.so.1.14.6_libClp.so.1.log removed
[ Info:   logs/update_linkage_libClpSolver.so.1.14.6_libCoinUtils.so.3.log removed
[ Info:   logs/update_linkage_libClpSolver.so.1.14.6_libopenblas.so.log removed
[ Info:   logs/update_linkage_libOsiClp.so.1.14.6_libClp.so.1.log removed
[ Info:   logs/update_linkage_libOsiClp.so.1.14.6_libCoinUtils.so.3.log removed
[ Info:   logs/update_linkage_libOsiClp.so.1.14.6_libOsi.so.1.log removed
[ Info:   logs/update_rpath_clp_libClpSolver.so.1.log removed
[ Info:   logs/update_rpath_libClp.so.1.14.6_libopenblas.so.log removed
[ Info:   logs/update_rpath_libClpSolver.so.1.14.6_libClp.so.1.log removed
[ Info:   logs/update_rpath_libOsiClp.so.1.14.6_libClp.so.1.log removed
[ Info:   share/coin/doc/Clp/AUTHORS removed
[ Info:   share/coin/doc/Clp/LICENSE removed
[ Info:   share/coin/doc/Clp/README removed
[ Info:   share/coin/doc/Clp/clp_addlibs.txt removed
[ Info:   Culling empty directory share/coin/doc/Clp
[ Info:   share/licenses/Clp/LICENSE removed
[ Info:   Culling empty directory share/licenses/Clp
[ Info:   manifests/Clp.v1.17.6.x86_64-linux-gnu-libgfortran3-cxx03.list removed
[ Info: Found a valid dl path libClp.so while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so"
└    /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so)
[ Info: Found a valid dl path libClp.so.1 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1"
└    /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1)
[ Info: Found a valid dl path libClp.so.1.14.6 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1.14.6 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1.14.6 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1.14.6"
└    /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so.1.14.6)
[ Info: Found a valid dl path libClpSolver.so while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so"
└    /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so)
[ Info: Found a valid dl path libClpSolver.so.1 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1"
└    /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1)
[ Info: Found a valid dl path libClpSolver.so.1.14.6 while looking for libClp
[ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1.14.6 matches our search criteria of libClp
┌ Info: /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1.14.6 cannot be dlopen'ed
│   dlopen_result =
│    could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1.14.6"
└    /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClpSolver.so.1.14.6)
[ Info: Found a valid dl path libCoinUtils.so while looking for libClp
[ Info: Found a valid dl path libCoinUtils.so.3 while looking for libClp
[ Info: Found a valid dl path libCoinUtils.so.3.11.3 while looking for libClp
[ Info: Found a valid dl path libOsi.so while looking for libClp
[ Info: Found a valid dl path libOsi.so.1 while looking for libClp
[ Info: Found a valid dl path libOsi.so.1.13.5 while looking for libClp
[ Info: Found a valid dl path libOsiClp.so while looking for libClp
[ Info: Found a valid dl path libOsiClp.so.1 while looking for libClp
[ Info: Found a valid dl path libOsiClp.so.1.14.6 while looking for libClp
[ Info: Found a valid dl path libOsiCommonTests.so while looking for libClp
[ Info: Found a valid dl path libOsiCommonTests.so.1 while looking for libClp
[ Info: Found a valid dl path libOsiCommonTests.so.1.13.5 while looking for libClp
[ Info: Found a valid dl path libopenblas.0.3.9.so while looking for libClp
[ Info: Found a valid dl path libopenblas.so while looking for libClp
[ Info: Found a valid dl path libopenblas.so.0 while looking for libClp
[ Info: Could not locate libClp inside /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib
ERROR: LoadError: LibraryProduct(nothing, ["libClp"], :libClp, "Prefix(/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr)") is not satisfied, cannot generate deps.jl!
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] #write_deps_file#165(::Bool, ::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /global/home/users/gorman_will/.julia/packages/BinaryProvider/GeAtj/src/Products.jl:419
 [3] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
 [4] top-level scope at none:0
 [5] include at ./boot.jl:317 [inlined]
 [6] include_relative(::Module, ::String) at ./loading.jl:1044
 [7] include(::Module, ::String) at ./sysimg.jl:29
 [8] exec_options(::Base.JLOptions) at ./client.jl:266
 [9] _start() at ./client.jl:425
in expression starting at /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/build.jl:144

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blegat commented May 14, 2020 •
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Could you give the output of

$ strings /lib64/libstdc++.so.6 | grep GLIBCXX

as well as

$ julia -e 'using BinaryProvider; @show platform_key_abi()'

@Will-Gorman
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First output:

[gorman_will@n0002 ~]$ strings /lib64/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_DEBUG_MESSAGE_LENGTH

second:

platform_key_abi() = Linux(:x86_64, libc=:glibc, compiler_abi=CompilerABI(:gcc4, :cxx03))

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blegat commented May 14, 2020

Do ] build Clp then ] test Clp work on Julia v1.4?

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This is an instance of julia on a supercomputer I don't have full control over. I will ask to see if it can be updated to Julia v1.4.

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blegat commented May 15, 2020

In theory, the same binaries are used in Julia v1.4 and Julia v1.0 but they use different ways to get them. In Julia v1.0, we use BinaryBuilder and in Julia v1.4, we simply install the _jll packges with Pkg.
@giordano any idea why this is failing ? Is this selecting the wrong library versions ? Or is this setup not supported and gcc need to be updated on their redhat system ?

@giordano
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This is an instance of julia on a supercomputer I don't have full control over. I will ask to see if it can be updated to Julia v1.4.

Do you have a chance to just download Julia from https://julialang.org/downloads/ and use it? You don't require sysadmin intervention for this if you have enough space on disk to download and unpack the archive.

@Will-Gorman
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I tried downloading and unpacking the archive but it failed out. I'm not really sure the cause but I will just need to wait to see what the sys administrators can do. Thx for your help

[gorman_will@n0000 gorman_will]$ tar -xvzf julia-1.4.1-linux-x86\_64.tar.gz
julia-1.4.1/
julia-1.4.1/LICENSE.md
julia-1.4.1/lib/
julia-1.4.1/lib/julia/
julia-1.4.1/lib/julia/libgit2.so
julia-1.4.1/lib/julia/libcamd.so.2
julia-1.4.1/lib/julia/libmbedcrypto.so.3
julia-1.4.1/lib/julia/libgmp.so
julia-1.4.1/lib/julia/libamd.so
julia-1.4.1/lib/julia/libpcre2-8.so.0
julia-1.4.1/lib/julia/libumfpack.so
julia-1.4.1/lib/julia/libmbedtls.so.2.16.0
julia-1.4.1/lib/julia/libmpfr.so
julia-1.4.1/lib/julia/libsuitesparseconfig.so.5.4.0
julia-1.4.1/lib/julia/libopenlibm.so.2
julia-1.4.1/lib/julia/libsuitesparseconfig.so.5
julia-1.4.1/lib/julia/libgit2.so.28
julia-1.4.1/lib/julia/libcamd.so.2.4.6
julia-1.4.1/lib/julia/libmbedx509.so
julia-1.4.1/lib/julia/libcolamd.so.2
julia-1.4.1/lib/julia/libssh2.so.1
julia-1.4.1/lib/julia/libz.so.1
julia-1.4.1/lib/julia/libmbedtls.so
julia-1.4.1/lib/julia/libgit2.so.0.28.2
julia-1.4.1/lib/julia/libquadmath.so.0
julia-1.4.1/lib/julia/libcurl.so.4
julia-1.4.1/lib/julia/libamd.so.2
julia-1.4.1/lib/julia/libcolamd.so.2.9.6
julia-1.4.1/lib/julia/libcurl.so
julia-1.4.1/lib/julia/libopenblas64_.0.3.5.so

gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

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Will-Gorman commented May 19, 2020 •
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I have been able to build the Clp package now on the system. It required loading the gcc/9.2.0 module from the SMF. However, even though I can now load the module on the system, I am receiving an error when implementing my optimization algorithm which suggests that something might be going wrong in the build still. I should say this is still using Julia v1.0.

julia> using JuMP, Clp

julia> m = Model(Clp.Optimizer)
ERROR: error compiling #Optimizer#1: could not load library "/global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so"
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/deps/usr/lib/libClp.so)
Stacktrace:
 [1] Clp.Optimizer() at /global/home/users/gorman_will/.julia/packages/Clp/cX6R7/src/MOI_wrapper/MOI_wrapper.jl:46
 [2] _instantiate_and_check(::Type) at /global/home/users/gorman_will/.julia/packages/MathOptInterface/RmalA/src/instantiate.jl:56
 [3] #instantiate#35(::Type{Float64}, ::Bool, ::Function, ::Type) at /global/home/users/gorman_will/.julia/packages/MathOptInterface/RmalA/src/instantiate.jl:107
 [4] (::getfield(MathOptInterface, Symbol("#kw##instantiate")))(::NamedTuple{(:with_bridge_type, :with_names),Tuple{DataType,Bool}}, ::typeof(MathOptInterface.instantiate), ::Type) at ./none:0
 [5] #set_optimizer#96(::Bool, ::Function, ::Model, ::Type) at /global/home/users/gorman_will/.julia/packages/JuMP/MnJQc/src/optimizer_interface.jl:66
 [6] (::getfield(JuMP, Symbol("#kw##set_optimizer")))(::NamedTuple{(:bridge_constraints,),Tuple{Bool}}, ::typeof(set_optimizer), ::Model, ::Type) at ./none:0
 [7] #Model#16(::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Type, ::Type) at /global/home/users/gorman_will/.julia/packages/JuMP/MnJQc/src/JuMP.jl:234
 [8] Model(::Type) at /global/home/users/gorman_will/.julia/packages/JuMP/MnJQc/src/JuMP.jl:233
 [9] top-level scope at none:0

@giordano
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If you pin BinaryProvider to v0.5.8 you should be able to install the package without much more work from you. See JuliaPackaging/BinaryProvider.jl#194

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blegat commented May 19, 2020

The latest version of Clp requires at least BinaryProvider v0.5.9 as otherwise you get the same segfault as CSDP when dlclosing OpenBLAS64.
Fixing BinaryProvider to v0.5.8 will therefore downgrade Clp.jl but that may sill work for you.

@Will-Gorman
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I just needed to delete the old compiled version of Clp and re-install and compile while making sure the gcc module was loaded. Thank you for all your help on this problem! I am going to go ahead and close this issue.

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blegat commented May 20, 2020

So it worked with the latest version of Clp right?

@Will-Gorman
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Yes, that's right

@giordano
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@Will-Gorman can I ask you what's the content of your Julia init file (.julia/config/startup.jl)? In JuliaPackaging/BinaryProvider.jl#194 (comment) it was reported that that file might be the culprit.

@Will-Gorman
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@giordano I am not sure what file you are looking for. I don't have a config folder in my .julia setup...

Happy to show the file if I can find it.

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