build error :"libsuitesparse_wrapper\"\n/usr/lib64/libcholmod.so.2: undefined symbol: amd_printf") #34667

yzcj105 · 2020-02-05T05:48:40Z

I've tried to compile julia. However, I've received the following error. I've tried gcc 5 gcc 7 gcc 9 . all failed.

It's related to /usr/lib64/libcholmod.so.2 file.

I've tried several versions.
v.1.3.0
v.1.3.1
v.1.4.0-rc1

error during bootstrap:
LoadError("sysimg.jl", 16, LoadError("/mnt/home/jchen/usr/julia/usr/share/julia/stdlib/v1.3/SuiteSparse/src/SuiteSparse.jl", 24, LoadError("/mnt/home/jchen/usr/julia/usr/share/julia/stdlib/v1.3/SuiteSparse/src/umfpack.jl", 66, 
ErrorException("error compiling top-level scope: could not load library **\"libsuitesparse_wrapper\"\n/usr/lib64/libcholmod.so.2: undefined symbol: amd_printf"))))**
rec_backtrace at /mnt/home/jchen/usr/julia/src/stackwalk.c:94
jl_throw at /mnt/home/jchen/usr/julia/src/task.c:224
jl_rethrow_with_add at /mnt/home/jchen/usr/julia/src/codegen.cpp:791
jl_compile_linfo at /mnt/home/jchen/usr/julia/src/codegen.cpp:1205
jl_compile_method_internal at /mnt/home/jchen/usr/julia/src/gf.c:1881
...
main at /mnt/home/jchen/usr/julia/ui/repl.c:217
__libc_start_main at /usr/lib64/libc.so.6 (unknown line)
_start at /mnt/home/jchen/usr/julia/usr/bin/julia (unknown line)

*** This error might be fixed by running `make clean`. If the error persists, try `make cleanall`. ***
make[1]: *** [/mnt/home/jchen/usr/julia/usr/lib/julia/sys.ji] Error 1
make: *** [julia-sysimg-ji] Error 2

The text was updated successfully, but these errors were encountered:

yzcj105 · 2020-02-05T05:53:01Z

I've also tried to download binary julia package. When first run, there comes out some errors.

> 
┌ Error: Error during initialization of module CHOLMOD
│   exception =
│    could not load library "libsuitesparse_wrapper"
│    /usr/lib64/libcholmod.so.2: undefined symbol: amd_printf
│    Stacktrace:
│     [1] __init__() at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/SuiteSparse/src/cholmod.jl:130
└ @ SuiteSparse.CHOLMOD /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/SuiteSparse/src/cholmod.jl:176
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.3.1 (2019-12-30)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia>
>

ViralBShah · 2020-02-05T06:15:47Z

For the binary release, do you have some LD_LIBRARY_PATH or other environment settings that are interfering? It is not finding the right headers when you are compiling and the right library when you are using binaries for the same AMD library which ships with suitesparse.

Also presumably you are using BINARYBUILDER=0, because at least for 1.4, it shouldn't try to build it by default.

yzcj105 · 2020-02-05T06:23:35Z

For the binary release, do you have some LD_LIBRARY_PATH or other environment settings that are interfering? It is not finding the right headers when you are compiling and the right library when you are using binaries for the same AMD library which ships with suitesparse.

Yes. I've setup LD_LIBRARY_PATH.
including /usr/lib64 folder, which contains libcholmod.so.2.

It seems very risky to remove that folder from LD_LIBRARY_PATH

For the binary version, if I alias julia='LD_LIBRARY_PATH="" ./julia' it works.
However, when I try to add packages. There will be errors like the following.

ERROR: SystemError: opening file "/mnt/home/jchen/.julia/registries/General/Registry.toml": No such file or directory
Stacktrace:
[1] #systemerror#44(::Nothing, ::typeof(systemerror), ::String, ::Bool) at ./error.jl:134
[2] systemerror at ./error.jl:134 [inlined]
[3] #open#512(::Bool, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(open), ::String) at ./iostream.jl:254
[4] #open at ./none:0 [inlined]
[5] open(::String, ::String) at ./iostream.jl:310
[6] #open#271(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(open), ::typeof(Pkg.TOML.parse), ::String, ::Vararg{String,N} where N) at ./io.jl:296
[7] open at ./io.jl:296 [inlined]
[8] parsefile at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/ext/TOML/src/TOML.jl:50 [inlined]
[9] #read_registry#128(::Bool, ::typeof(Pkg.Types.read_registry), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1075
[10] read_registry at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1070 [inlined]
[11] clone_or_cp_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1047
[12] clone_or_cp_registries at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1013 [inlined] (repeats 2 times)
[13] clone_default_registries() at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:963
[14] find_registered!(::Pkg.Types.EnvCache, ::Array{String,1}, ::Array{Base.UUID,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1244
[15] registry_resolve!(::Pkg.Types.EnvCache, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:880
[16] #add#25(::Bool, ::Pkg.BinaryPlatforms.Linux, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.add), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:95
[17] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/API.jl:72
[18] do_add!(::Dict{Symbol,Any}, ::Array{Pkg.Types.PackageSpec,1}, ::Dict{Symbol,Any}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/REPLMode.jl:505
[19] #invokelatest#1(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Base.invokelatest), ::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:709
[20] invokelatest(::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:708
[21] do_cmd!(::Pkg.REPLMode.Command, ::REPL.LineEditREPL) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/REPLMode.jl:412
[22] #do_cmd#23(::Bool, ::typeof(Pkg.REPLMode.do_cmd), ::REPL.LineEditREPL, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/REPLMode.jl:391
[23] do_cmd at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/REPLMode.jl:387 [inlined]
[24] (::Pkg.REPLMode.var"#28#31"{REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/REPLMode.jl:619
[25] #invokelatest#1 at ./essentials.jl:709 [inlined]
[26] invokelatest at ./essentials.jl:708 [inlined]
[27] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/REPL/src/LineEdit.jl:2306
[28] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/REPL/src/REPL.jl:1045
[29] run_repl(::REPL.AbstractREPL, ::Any) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/REPL/src/REPL.jl:201
[30] (::Base.var"#770#772"{Bool,Bool,Bool,Bool})(::Module) at ./client.jl:382
[31] #invokelatest#1 at ./essentials.jl:709 [inlined]
[32] invokelatest at ./essentials.jl:708 [inlined]
[33] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:366
[34] exec_options(::Base.JLOptions) at ./client.jl:304
[35] _start() at ./client.jl:460

yzcj105 · 2020-02-05T06:29:47Z

LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.6.1810 (Core)
Release: 7.6.1810
Codename: Core

The so file is soft linked to

/usr/lib64/ libcholmod.so.2.0.1

yzcj105 · 2020-02-05T06:34:13Z

readelf -a libcholmod.so.2

https://gist.github.com/yzcj105/f45c29c96a64d57a41a31da286be2387

ViralBShah · 2020-02-05T06:35:48Z

It would be better paste that long output from readelf in a gist. It seems here that you are doing something non-standard with libcholmod - and doesn't appear to be a julia build problem.

yzcj105 · 2020-02-05T06:49:34Z

I do not have su/sudo. So I am not able to change or modify the /usr/lib64 folder.
In my home dir I've installed the package manager homebrew.
And use module load command to load or switch different gcc packages

ViralBShah · 2020-02-05T07:10:21Z

It would help to understand why you need a different libcholmod instead of the one provided by Julia.

yzcj105 · 2020-02-05T07:12:40Z

It's my institute's cluster. I do not know why it is in that folder, either.

ViralBShah · 2020-02-05T07:16:07Z

I see - so you perhaps need some other libraries in /usr/lib64 and it also includes a suitesparse installation, which is somehow interfering with the Julia one when you build.

Can you try using the generic Julia binaries and avoid compiling anything (and also remove the LD_LIBRARY_PATH)? At least that will tell us if Julia works. You can then troubleshoot from there.

yzcj105 · 2020-02-05T16:25:30Z

It works. But when add packages, there is additional errors

registry add General
Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: SystemError: opening file "/mnt/home/jchen/.julia/registries/General/Registry.toml": No such file or directory

I've checked the ownership and permissions of the .julia folder recursively. drwxrwxr-x

I tried to delete .julia folder and restart julia. I got

(v1.3) pkg> add Colors
Cloning default registries into ~/.julia
Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: IOError: open: permission denied (EACCES)

ViralBShah · 2020-02-05T17:54:28Z

Ok, but building from source won't help you with these errors. I wonder if these are issues with NFS or some distributed filesystem.

Perhaps this is a question to ask on discourse to further resolve.

ViralBShah added building Build system, or building Julia or its dependencies sparse Sparse arrays labels Feb 5, 2020

ViralBShah closed this as completed Feb 5, 2020

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build error :"libsuitesparse_wrapper\"\n/usr/lib64/libcholmod.so.2: undefined symbol: amd_printf") #34667

build error :"libsuitesparse_wrapper\"\n/usr/lib64/libcholmod.so.2: undefined symbol: amd_printf") #34667

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build error :"libsuitesparse_wrapper\"\n/usr/lib64/libcholmod.so.2: undefined symbol: amd_printf") #34667

build error :"libsuitesparse_wrapper\"\n/usr/lib64/libcholmod.so.2: undefined symbol: amd_printf") #34667

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