How to install the Genie Package in julia 1.6.2? - centos

I am trying to install Genie Package on Julia 1.6.2 on CentOS Linux release 7.7.1908 (Core).
But, getting the following error. Please guide me in resolving the Genie installation issue!
logs:
[root#srvr0 ~]# julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.6.2 (2021-07-14)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> versioninfo()
Julia Version 1.6.2
Commit 1b93d53fc4 (2021-07-14 15:36 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Core(TM) i7 CPU M 620 # 2.67GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-11.0.1 (ORCJIT, westmere)
Environment:
JULIA_DEPOT_PATH = /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6
JULIA_PROJECT = /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6
JULIA_LOAD_PATH = /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6
JULIA_PKG_DEVDIR = /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6
JULIA_HOME = /opt/julia/julia-1.6.2
JULIA_HISTORY = /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/logs/repl_history.jl
julia> using Pkg
julia> import Pkg; Pkg.precompile()
Precompiling project...
✗ MbedTLS
✗ Nettle_jll
✗ XML2_jll
✗ HTTP
✗ Nettle
✗ EzXML
✗ UrlDownload
✗ VersionCheck
✗ Genie
0 dependencies successfully precompiled in 89 seconds (47 already precompiled)
ERROR: The following 3 direct dependencies failed to precompile:
MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d]
Failed to precompile MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/MbedTLS/jl_Xqj7WF.
ERROR: LoadError: ArgumentError: Package MbedTLS_jll [c8ffd9c3-330d-5841-b78e-0817d7145fa1] is required but does not seem to be installed:
- Run `Pkg.instantiate()` to install all recorded dependencies.
Stacktrace:
[1] _require(pkg::Base.PkgId)
# Base ./loading.jl:1012
[2] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[3] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[4] include
# ./Base.jl:386 [inlined]
[5] 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:1235
[6] top-level scope
# none:1
[7] eval
# ./boot.jl:360 [inlined]
[8] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[9] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/MbedTLS/4YY6E/src/MbedTLS.jl:1
HTTP [cd3eb016-35fb-5094-929b-558a96fad6f3]
Failed to precompile HTTP [cd3eb016-35fb-5094-929b-558a96fad6f3] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/HTTP/jl_Yyye6x.
ERROR: LoadError: ArgumentError: Package MbedTLS_jll [c8ffd9c3-330d-5841-b78e-0817d7145fa1] is required but does not seem to be installed:
- Run `Pkg.instantiate()` to install all recorded dependencies.
Stacktrace:
[1] _require(pkg::Base.PkgId)
# Base ./loading.jl:1012
[2] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[3] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[4] include
# ./Base.jl:386 [inlined]
[5] 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:1235
[6] top-level scope
# none:1
[7] eval
# ./boot.jl:360 [inlined]
[8] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[9] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/MbedTLS/4YY6E/src/MbedTLS.jl:1
ERROR: LoadError: LoadError: Failed to precompile MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/MbedTLS/jl_gvFbMy.
Stacktrace:
[1] error(s::String)
# Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
# Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
# Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
# Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[7] include(mod::Module, _path::String)
# Base ./Base.jl:386
[8] include(x::String)
# HTTP /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/HTTP.jl:1
[9] top-level scope
# /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/HTTP.jl:33
[10] include
# ./Base.jl:386 [inlined]
[11] 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:1235
[12] top-level scope
# none:1
[13] eval
# ./boot.jl:360 [inlined]
[14] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[15] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/IOExtras.jl:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/HTTP.jl:1
Genie [c43c736e-a2d1-11e8-161f-af95117fbd1e]
Failed to precompile Genie [c43c736e-a2d1-11e8-161f-af95117fbd1e] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/Genie/jl_vquqzS.
ERROR: LoadError: ArgumentError: Package MbedTLS_jll [c8ffd9c3-330d-5841-b78e-0817d7145fa1] is required but does not seem to be installed:
- Run `Pkg.instantiate()` to install all recorded dependencies.
Stacktrace:
[1] _require(pkg::Base.PkgId)
# Base ./loading.jl:1012
[2] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[3] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[4] include
# ./Base.jl:386 [inlined]
[5] 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:1235
[6] top-level scope
# none:1
[7] eval
# ./boot.jl:360 [inlined]
[8] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[9] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/MbedTLS/4YY6E/src/MbedTLS.jl:1
ERROR: LoadError: LoadError: Failed to precompile MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/MbedTLS/jl_InozY8.
Stacktrace:
[1] error(s::String)
# Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
# Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
# Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
# Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[7] include(mod::Module, _path::String)
# Base ./Base.jl:386
[8] include(x::String)
# HTTP /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/HTTP.jl:1
[9] top-level scope
# /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/HTTP.jl:33
[10] include
# ./Base.jl:386 [inlined]
[11] 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:1235
[12] top-level scope
# none:1
[13] eval
# ./boot.jl:360 [inlined]
[14] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[15] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/IOExtras.jl:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/HTTP/aTjcj/src/HTTP.jl:1
ERROR: LoadError: Failed to precompile HTTP [cd3eb016-35fb-5094-929b-558a96fad6f3] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/HTTP/jl_A9Y88m.
Stacktrace:
[1] error(s::String)
# Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
# Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
# Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
# Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[7] include
# ./Base.jl:386 [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:1235
[9] top-level scope
# none:1
[10] eval
# ./boot.jl:360 [inlined]
[11] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[12] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/UrlDownload/30tLC/src/UrlDownload.jl:1
ERROR: LoadError: Failed to precompile UrlDownload [856ac37a-3032-4c1c-9122-f86d88358c8b] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/UrlDownload/jl_zopYYu.
Stacktrace:
[1] error(s::String)
# Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
# Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
# Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
# Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[7] include
# ./Base.jl:386 [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:1235
[9] top-level scope
# none:1
[10] eval
# ./boot.jl:360 [inlined]
[11] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[12] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/VersionCheck/IzZOn/src/VersionCheck.jl:1
ERROR: LoadError: LoadError: Failed to precompile VersionCheck [a637dc6b-bca1-447e-a4fa-35264c9d0580] to /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/compiled/v1.6/VersionCheck/jl_gmYXFo.
Stacktrace:
[1] error(s::String)
# Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
# Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
# Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
# Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
# Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
# Base ./loading.jl:923
[7] include(mod::Module, _path::String)
# Base ./Base.jl:386
[8] include(x::String)
# Genie /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/Genie/Qtv4L/src/Genie.jl:4
[9] top-level scope
# /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/Genie/Qtv4L/src/Genie.jl:12
[10] include
# ./Base.jl:386 [inlined]
[11] 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:1235
[12] top-level scope
# none:1
[13] eval
# ./boot.jl:360 [inlined]
[14] eval(x::Expr)
# Base.MainInclude ./client.jl:446
[15] top-level scope
# none:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/Genie/Qtv4L/src/Configuration.jl:1
in expression starting at /opt/julia/julia-1.6.2/share/julia/stdlib/v1.6/packages/Genie/Qtv4L/src/Genie.jl:1
Stacktrace:
[1] pkgerror(msg::String)
# Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:55
[2] precompile(ctx::Pkg.Types.Context; internal_call::Bool, strict::Bool, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
# Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1265
[3] precompile
# /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:921 [inlined]
[4] #precompile#196
# /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:919 [inlined]
[5] precompile()
# Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:919
[6] top-level scope
# REPL[16]:1
julia>


First follow what instructions tell your to do
julia> using Pkg
julia> Pkg.instantiate()
If that doesn't resolve the error add MbedTLS. You should install
julia> ]
pkg> add MbedTLS
pkg> add Genie#master

Related

Segmentation violation detected on run

I'm new to MATLAB and I get the following crash information when running GISTIC2 based on MCR. No problem running that algorithm in other machine we are using.
------------------------------------------------------------------------
Segmentation violation detected at Thu Jul 8 23:01:05 2021
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : 0x21 (class 4, depth 24)
Default Encoding : UTF-8
GNU C Library : 2.31 stable
MATLAB Architecture: glnxa64
MATLAB Root : /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83
MATLAB Version : 8.3.0.532 (R2014a)
Operating System : Linux 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10 UTC 2021 x86_64
Processor ID : x86 Family 143 Model 96 Stepping 1, AuthenticAMD
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : The X.Org Foundation (12009000), display :0
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 0000000000000000 RBX = 00007f7790b2c190
RCX = 0000000000000000 RDX = 0000000000000000
RSP = 00007f77f2becde8 RBP = 00007f77ec0376c0
RSI = 000000003e07c725 RDI = 0000000000000000
R8 = 0000000000000007 R9 = 00312d3634363031
R10 = 00007f77f2becc70 R11 = 0000000000000000
R12 = 0000000000000000 R13 = 00007f77f2bed180
R14 = 0000000000000000 R15 = 0000000000000000
RIP = 00007f7807063675 EFL = 0000000000010283
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00007f7807063675 /lib/x86_64-linux-gnu/libc.so.6+01619573
[ 1] 0x00007f77f588ec18 /lib/x86_64-linux-gnu/libX11.so.6+00134168 XLoadQueryFont+00000056
[ 2] 0x00007f77f870adf0 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwuix.so+00261616
[ 3] 0x00007f77f870baae /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwuix.so+00264878
[ 4] 0x00007f77f870bd29 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwuix.so+00265513
[ 5] 0x00007f77f8e5d143 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00663875 _Z21wm_SetUnadjWindowFontP10WinRec_tagP6mxFont+00000083
[ 6] 0x00007f77f8e5d74b /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00665419 _Z22wm_GetDeviceFontExtentP10WinRec_tagP6mxFontPKcdP6mwrect+00000315
[ 7] 0x00007f77f8e78fff /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00778239 uiGetDeviceFont+00000815
[ 8] 0x00007f77f8e79171 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00778609 _Z15uiSetWindowFontP10WinRec_tagP6mxFont+00000017
[ 9] 0x00007f77f8e5d013 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00663571 _Z16wm_SetWindowFontP10WinRec_tagP6mxFont+00000083
[ 10] 0x00007f77a5d81195 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05001621
[ 11] 0x00007f77f8e9489d /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00891037 _ZN11gui_objects10tickpicker12nicefyLimitsERNS0_14AxisDescriptorENS0_8AxisTypeE+00000173
[ 12] 0x00007f77f8e94cc3 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwgui.so+00892099 _ZN11gui_objects10tickpicker12nicefyLimitsERNS0_14AxisDescriptorE+00000019
[ 13] 0x00007f77a5d816d9 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05002969
[ 14] 0x00007f77a5ce57df /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+04364255
[ 15] 0x00007f77a5cd0b1f /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+04279071
[ 16] 0x00007f77a5dd4740 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05343040
[ 17] 0x00007f77a5dd427c /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05341820
[ 18] 0x00007f77a5dc72b0 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05288624
[ 19] 0x00007f77f746bded /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwudd.so+00634349
[ 20] 0x00007f77f7465153 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwudd.so+00606547 _ZN11UDInterface15notifyPropEventEP16UDDatabaseClientPK10UDPropInfoPK11UDEventInfoP7UDEvent+00000115
[ 21] 0x00007f77f7468671 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwudd.so+00620145 _ZN11UDInterface4setEEP16UDDatabaseClientP10UDPropInfoPvP13UDErrorStatus+00000593
[ 22] 0x00007f77a5dd15b6 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05330358
[ 23] 0x00007f77a5dcbadd /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05307101
[ 24] 0x00007f77a5dca0d0 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05300432
[ 25] 0x00007f77a5db06f5 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05195509
[ 26] 0x00007f77a5dbdfd0 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05251024
[ 27] 0x00007f77a5db7408 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05223432
[ 28] 0x00007f77a5dbe432 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05252146
[ 29] 0x00007f77a5dc3113 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhg.so+05271827 hgSet+00001107
[ 30] 0x00007f77a6c80742 /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwhgbuiltins.so+00345922
...
[125] 0x00007f77fba703bf /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwmcr.so+00365503
[126] 0x00007f77fba6b28f /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/bin/glnxa64/libmwmcr.so+00344719
[127] 0x00007f78070d3609 /lib/x86_64-linux-gnu/libpthread.so.0+00038409
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as /home/lcj/matlab_crash_dump.29508-1 **
Segmentation fault (core dumped)
After renaming the libstdc++.so.6 library to libstdc++.so.6.old in ~/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83/sys/os/glnxa64, I got the following crash information.
------------------------------------------------------------------------
Segmentation violation detected at Sat Jul 10 23:22:39 2021
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : 0x21 (class 4, depth 24)
Default Encoding : UTF-8
GNU C Library : 2.31 stable
MATLAB Architecture: glnxa64
MATLAB Root : /home/lcj/Biosoft/GISTIC2/MATLAB_Compiler_Runtime/v83
MATLAB Version : 8.3.0.532 (R2014a)
Operating System : Linux 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10 UTC 2021 x86_64
Processor ID : x86 Family 143 Model 96 Stepping 1, AuthenticAMD
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : The X.Org Foundation (12009000), display :0
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 0000000000000000 RBX = 00007f26c0b99880
RCX = 0000000000000000 RDX = 0000000000000000
RSP = 00007f2720dcede8 RBP = 00007f271c0376c0
RSI = 000000003e07c725 RDI = 0000000000000000
R8 = 0000000000000007 R9 = 00312d3634363031
R10 = 00007f2720dcec70 R11 = 0000000000000000
R12 = 0000000000000000 R13 = 00007f2720dcf180
R14 = 0000000000000000 R15 = 0000000000000000
RIP = 00007f2735246675 EFL = 0000000000010283
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
Caught "std::exception" Exception message is:
FatalException
Error:FatalException
Any clues to solve this errors?

Converting a cell row to a cell column

I have a matrix B (1 * 5 cell) I want to change it to B (5 * 1 cell) knowing that each element of the matrix contains (1 * 18 cell) and each is a cell
original matrix
[1] [2] [3] [4] [5]`
[1] (1*18 cell) (1*18 cell) (1*18 cell) (1*18 cell) (1*18 cell)
My goal is:
1) convert line from B to column% I try to use C = A (:); And C = B. '
2) make B a cellless matrix with cell2mat% Error using cell2mat (line 53)
Can not support cell arrays containing cell arrays or objects.
The desired output is:
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] ... [18]
[1] 2 1.5 1.69 1.02 1 1.36 1 2 1.67 1.20 1.36 ...
[2] 2 1.53 1.99 1 1.36 1 2 1 1 1.99 1.02 ...
[3] 1.02 1 1.36 1.3 2 1.67 1.20 1.36 1.99 2 1.5 ...
[4] 2 1.53 1.99 1 1.36 1 2 1 1 1.36 1.99 ...
[5] 1.5 1.69 1.02 1.2 1.36 1 2 1 1.36 1.5 1.5 ...
thanks

You can just use cat (combined with {} indexing to create a comma-separated list) to concatenate all of the cell arrays in B along the first dimension
out = cat(1, B{:});
If you want the result to no longer be a cell, use cell2mat on the output
cell2mat(out)

Perl module GSSAPI core dumps with kerberos 1.14

I am trying to compile GSSAPI PERL module with kerberos and I'm getting a core dump while testing it. Here are the details:
GSSAPI version: 0.28
KERBEROS: 1.14
PERL: 5.22
OS: SunOS kangaroo 5.11 11.2 sun4v sparc sun4v
While running the tests for GSSAPI, I get a core dump
sv_app#kangaroo:…rc/trunk/perl-5.22/GSSAPI-0.28$ make test
PERL_DL_NONLAZY=1 "/u01/sv/app/10.00/perl/product/perl-5.22.0/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/1constants.t ..... ok
t/2status.t ........ ok
t/checkoids.t ...... ok
t/importnames.t .... ok
t/indicatemechs.t .. 1/5 # KRB5 old Mechtype, Kerberos 5, SPNEGO
t/indicatemechs.t .. ok
t/inquire_cred.t ... Failed 6/6 subtests
t/pod.t ............ skipped: Test::Pod 1.00 required for testing POD
t/test.t ........... ok
t/zbugfixes.t ...... 1/3 #
Stack Trace from core dump:
t#1 (l#1) program terminated by signal BUS (invalid address alignment)
0x0007fffefcbec2d0: get_value_vt+0x0010: ldx [%i3 + 8], %i1
(dbx) where
current thread: t#1
=>[1] get_value_vt(0x1006b9ca0, 0xffffffff7fffe7d0, 0xffffffff7fffe7c8, 0x11, 0x0, 0x0), at 0x7fffefcbec2d0
[2] profile_get_string(0x1006b9ca0, 0x7fffefcbf9ab0, 0x7fffefcbf9b08, 0x0, 0x0, 0xffffffff7fffe8a8), at 0x7fffefcbec420
[3] k5_kt_client_default_name(0x1003746b0, 0xffffffff7fffe968, 0x0, 0x0, 0xffffffffffed59e8, 0x12a400), at 0x7fffefcbd50b0
[4] krb5_kt_client_default(0x1003746b0, 0x1005734a0, 0xffffffff7fffeafc, 0x0, 0xffffffff7fffef8c, 0x0), at 0x7fffefcb63678
[5] acquire_init_cred(0x1003746b0, 0xffffffff7fffef8c, 0x0, 0x0, 0x0, 0x100573450), at 0x7fffefd53c878
[6] acquire_cred_context(0x1003746b0, 0xffffffff7fffef8c, 0x0, 0x0, 0x100573450, 0x1), at 0x7fffefd53cc04
[7] krb5_gss_acquire_cred_from(0x0, 0x0, 0x78, 0x0, 0x1, 0x0), at 0x7fffefd53d880
[8] gss_add_cred_from(0xffffffff7fffef8c, 0x100362470, 0x78, 0x100362410, 0x100362470, 0x0), at 0x7fffefd51d61c
[9] gss_acquire_cred_from(0xffffffff7ffff188, 0x0, 0x1, 0x0, 0xffffffff7fffefd0, 0x0), at 0x7fffefd51cf50
[10] gss_acquire_cred(0xffffffff7ffff188, 0x0, 0x78, 0x0, 0x1, 0xffffffff7ffff198), at 0x7fffefd51cb84
[11] XS_GSSAPI__Cred_acquire_cred(0x28, 0x0, 0x0, 0x38, 0x30, 0x8), at 0x7fffefd808a08
[12] Perl_pp_entersub(0x38, 0x2, 0x20000, 0x1004b3310, 0x100000, 0x7), at 0x100116408
[13] Perl_runops_standard(0x100169260, 0x1006ca470, 0x1006ca470, 0x10034c000, 0x10034c, 0x10034c5e0), at 0x100109c04
[14] S_run_body(0x100000, 0x10034c, 0x10034c, 0x0, 0x0, 0x10034d460), at 0x100054fc0
[15] perl_run(0x10034d, 0xffffffff7ffff488, 0x100000, 0x1, 0x0, 0x10034b000), at 0x100054c20
[16] main(0x2, 0xffffffff7ffff6c8, 0x10034b, 0x10034d000, 0x10034b, 0x10034bb80), at 0x1000261f0
(dbx) frame 1
0x0007fffefcbec2d0: get_value_vt+0x0010: ldx [%i3 + 8], %i1
(dbx) regs
current thread: t#1
current frame: [1]
g0-g1 0x0000000000000000 0x0000000000000000
g2-g3 0x0000000000000000 0x0000000000000000
g4-g5 0x000000000000004b 0x0007fffefcbf9af5
g6-g7 0x0000000000000000 0x0007fffefea02a40
o0-o1 0x0000000000000000 0xffffffff7fffe7d0
o2-o3 0xffffffff7fffe708 0x0000000000000000
o4-o5 0x0000000000000000 0x0000000000000000
o6-o7 0xffffffff7fffde51 0x0007fffefcbec368
l0-l1 0x0000000000000000 0x0000000000000000
l2-l3 0x0000000000000000 0x0000000000000000
l4-l5 0x0000000000000000 0x0000000000000000
l6-l7 0x0000000000000000 0x0000000000000011
i0-i1 0x00000001006b9ca0 0xffffffff7fffe7d0
i2-i3 0xffffffff7fffe7c8 0x0000000000000011
i4-i5 0x0000000000000000 0x0000000000000000
i6-i7 0xffffffff7fffdf11 0x0007fffefcbec420
y 0x0000000000000000
ccr 0x0000000000000000
pc 0x0007fffefcbec2d0:get_value_vt+0x10 ldx [%i3 + 8], %i1
npc 0x0007fffefcbec2d4:get_value_vt+0x14 call %i1
(dbx) examine 0xffffffff7fffe7d0/i
0xffffffff7fffe7d0: illtrap 0x7fffe
krb5-1.14/src/util/profile/prof_get.c
/* Look up a relation in a vtable profile and return the first value in the
* result. */
static errcode_t
get_value_vt(profile_t profile, const char *const *names, char **ret_value)
{
errcode_t retval;
char **vtvalues;
retval = profile->vt->get_values(profile->cbdata, names, &vtvalues);
if (retval)
return retval;
*ret_value = strdup(*vtvalues);
if (*ret_value == NULL)
retval = ENOMEM;
profile->vt->free_values(profile->cbdata, vtvalues);
return retval;
}

ld linker script producing huge binary

I'm using binutils-2.21.53.0.1-6.fc16.x86_64.
I have a small object file, hello.o with just enough "stuff" to have contents in all sections:
Section Headers:
[Nr] Name Type Address Offset
Size EntSize Flags Link Info Align
[ 0] NULL 0000000000000000 00000000
0000000000000000 0000000000000000 0 0 0
[ 1] .text PROGBITS 0000000000000000 00000040
000000000000005d 0000000000000000 AX 0 0 4
[ 2] .rela.text RELA 0000000000000000 00000808
0000000000000060 0000000000000018 15 1 8
[ 3] .data PROGBITS 0000000000000000 000000a0
0000000000000000 0000000000000000 WA 0 0 4
[ 4] .bss NOBITS 0000000000000000 000000a0
0000000000000053 0000000000000000 WA 0 0 32
[ 5] .rodata PROGBITS 0000000000000000 000000a0
000000000000000f 0000000000000000 A 0 0 1
[ 6] .data.rel.local PROGBITS 0000000000000000 000000b0
0000000000000008 0000000000000000 WA 0 0 8
[ 7] .rela.data.rel.lo RELA 0000000000000000 00000868
0000000000000018 0000000000000018 15 6 8
[ 8] .data.rel PROGBITS 0000000000000000 000000b8
0000000000000008 0000000000000000 WA 0 0 8
[ 9] .rela.data.rel RELA 0000000000000000 00000880
0000000000000018 0000000000000018 15 8 8
[10] .comment PROGBITS 0000000000000000 000000c0
000000000000002d 0000000000000001 MS 0 0 1
[11] .note.GNU-stack PROGBITS 0000000000000000 000000ed
0000000000000000 0000000000000000 0 0 1
[12] .eh_frame PROGBITS 0000000000000000 000000f0
0000000000000058 0000000000000000 A 0 0 8
[13] .rela.eh_frame RELA 0000000000000000 00000898
0000000000000030 0000000000000018 15 12 8
[14] .shstrtab STRTAB 0000000000000000 00000148
0000000000000085 0000000000000000 0 0 1
[15] .symtab SYMTAB 0000000000000000 00000610
00000000000001b0 0000000000000018 16 11 8
[16] .strtab STRTAB 0000000000000000 000007c0
0000000000000045 0000000000000000 0 0 1
If I use -pie and no linker script, the results are as expected:
$ ld -pie -Map hello_pie.map -o hello_pie.elf hello.o
$ ll hello_pie.elf
-rwxrwx---. 1 jreinhart jreinhart 3453 Mar 13 23:44 hello_pie.elf
However, if I include any sort of linker script, the output size explodes:
$ cat 1.ld
SECTIONS
{
}
$ ld -T 1.ld -pie -Map hello_pie.map -o hello_pie.elf hello.o
$ ll hello_pie.elf
-rwxrwx---. 1 jreinhart jreinhart 2100070 Mar 13 23:45 hello_pie.elf
As you can see, this file became huge.
Note that this appears to happen because the .text section insists on starting at offset 0x200000 in the file:
$ readelf -l -S hello_pie.elf
There are 19 section headers, starting at offset 0x200400:
Section Headers:
[Nr] Name Type Address Offset
Size EntSize Flags Link Info Align
[ 0] NULL 0000000000000000 00000000
0000000000000000 0000000000000000 0 0 0
[ 1] .text PROGBITS 0000000000000000 00200000 <--- Why?
000000000000005d 0000000000000000 AX 0 0 4
[ 2] .rodata PROGBITS 000000000000005d 0020005d
000000000000000f 0000000000000000 A 0 0 1
[ 3] .eh_frame PROGBITS 0000000000000070 00200070
0000000000000058 0000000000000000 A 0 0 8
[ 4] .interp PROGBITS 00000000000000c8 002000c8
000000000000000f 0000000000000000 A 0 0 1
[ 5] .dynsym DYNSYM 00000000000000d8 002000d8
0000000000000078 0000000000000018 A 6 2 8
[ 6] .dynstr STRTAB 0000000000000150 00200150
0000000000000014 0000000000000000 A 0 0 1
[ 7] .hash HASH 0000000000000168 00200168
0000000000000028 0000000000000004 A 5 0 8
[ 8] .rela.dyn RELA 0000000000000190 00200190
0000000000000078 0000000000000018 A 5 0 8
[ 9] .data.rel.local PROGBITS 0000000000000208 00200208
0000000000000008 0000000000000000 WA 0 0 8
[10] .data.rel PROGBITS 0000000000000210 00200210
0000000000000008 0000000000000000 WA 0 0 8
[11] .dynamic DYNAMIC 0000000000000218 00200218
00000000000000f0 0000000000000010 WA 6 0 8
[12] .got PROGBITS 0000000000000308 00200308
0000000000000018 0000000000000008 WA 0 0 8
[13] .got.plt PROGBITS 0000000000000320 00200320
0000000000000018 0000000000000008 WA 0 0 8
[14] .bss NOBITS 0000000000000340 00200338
0000000000000053 0000000000000000 WA 0 0 32
[15] .comment PROGBITS 0000000000000000 00200338
000000000000002c 0000000000000001 MS 0 0 1
[16] .shstrtab STRTAB 0000000000000000 00200364
000000000000009a 0000000000000000 0 0 1
[17] .symtab SYMTAB 0000000000000000 002008c0
0000000000000258 0000000000000018 18 19 8
[18] .strtab STRTAB 0000000000000000 00200b18
000000000000004e 0000000000000000 0 0 1
Key to Flags:
W (write), A (alloc), X (execute), M (merge), S (strings), l (large)
I (info), L (link order), G (group), T (TLS), E (exclude), x (unknown)
O (extra OS processing required) o (OS specific), p (processor specific)
Elf file type is DYN (Shared object file)
Entry point 0x0
There are 5 program headers, starting at offset 64
Program Headers:
Type Offset VirtAddr PhysAddr
FileSiz MemSiz Flags Align
PHDR 0x0000000000000040 0x0000000000200040 0x0000000000000000
0x0000000000000118 0x0000000000000118 R E 8
INTERP 0x00000000002000c8 0x00000000000000c8 0x00000000000000c8
0x000000000000000f 0x000000000000000f R 1
[Requesting program interpreter: /lib/ld64.so.1]
LOAD --> 0x0000000000200000 0x0000000000000000 0x0000000000000000
0x0000000000000338 0x0000000000000393 RWE 200000
DYNAMIC 0x0000000000200218 0x0000000000000218 0x0000000000000218
0x00000000000000f0 0x00000000000000f0 RW 8
GNU_STACK 0x0000000000000000 0x0000000000000000 0x0000000000000000
0x0000000000000000 0x0000000000000000 RW 8
This has been happening regardless of the contents of my linker script. Any ideas what's going on?

I ran into this same problem today when learning about linker scripts. SIZEOF_HEADERS was the magic bullet to solve it. Here is my simple source file to build the object I'm linking:
.section .text
.global _start
_start:
mov $1, %eax
mov $8, %ebx
int $0x80
With the following linker script, I get a 2+ MB executable:
SECTIONS
{
. = 0x400000;
.text : { *(.text) }
}
If I add +SIZEOF_HEADERS, as shown below, I get a 568-byte executable:
SECTIONS
{
. = 0x400000 + SIZEOF_HEADERS;
.text : { *(.text) }
}
Per the LD documentation, this function returns the size of the output file's headers. Manually setting the offset to include the header size also yields a 568-byte executable:
SECTIONS
{
. = 0x400078;
.text : { *(.text) }
}
If I move .text even further down, the executable starts to expand. The following yields a 65984-byte executable:
SECTIONS
{
. = 0x410000;
.text : { *(.text) }
}
So basically, from what I can tell, it appears that:
The first output section appears to share a memory page with the output file headers. If the first section overlaps with the headers, LD emits a full page of pad bytes before outputting the first section to avoid a conflict
To fix this, set the output address for the first output section to X + SIZEOF_HEADERS. This is what the built-in linker script for LD does (you can take a look by running "ld --verbose")

Try the following command line option with ld (or gcc):
-z max-page-size=0x1000

By default ld page-aligns input sections. Since your kernel enforces superpages (pages of 2MB = 0x200000 bytes) your .text section gets aligned at offset 0x200000. It seems like a bug in ld as it should use offset 0x0000000 instead (see EDIT below for a possible explanation)
To prevent this alignment which creates a bigger file, you can use the --nmagic flag to ld to prevent it from page-aligning your .text section although it has side effects (it also disables linking against shared libraries). Be careful though to align other sections (.data, .rodata,...) to 2M pages because they can't live in the same page as .text since all these sections require different access bits.
EDIT: thinking about it, we all expect accesses to virtual address 0x00000000 to generate an exception (segfault). To do so, I see two possibilities: either the kernel maps a page with no access rights (r/w/x) or (more likely) it simply doesn't map anything (no page mapped => segfault) and the linker must know that somehow... that could explain why ld skips the first page which is at address zero. This is TBC.

how to add extra column that counts the occurance of each character in a cellarray using matlab

I need to write a code that it add extra column for the number of occurance of the characters in each cell for the fourth column for the cellarray GO :
GO:
'GO:0008150' [1] [1] 'a'
'GO:0016740' [2] [2] 'b'
'GO:0006412' [2] [2] 'b'
'GO:0016787' [2] [3] 'c'
'GO:0006810' [2] [4] 'd'
'GO:0016787' [3] [3] 'c'
'GO:0004672' [3] [3] 'c'
'GO:0016779' [3] [3] 'c'
'GO:0005215' [3] [3] 'c'
'GO:0006810' [3] [4] 'd'
'GO:0004386' [3] [4] 'd'
'GO:0003774' [3] [4] 'd'
'GO:0016298' [3] [4] 'd'
'GO:0016192' [3] [5] 'e'
'GO:0006412' [3] [2] 'b'
'GO:0005215' [3] [3] 'c'
'GO:0006810' [4] [4] 'd'
'GO:0004386' [4] [4] 'd'
'GO:0003774' [4] [4] 'd'
'GO:0016298' [4] [4] 'd'
'GO:0030533' [4] [4] 'd'
'GO:0030533' [4] [4] 'd'
'GO:0016192' [4] [5] 'e'
The resulted GO cellarray should be as follows (starting from 0 value):
GO:
'GO:0008150' [1] [1] 'a' '0'
'GO:0016740' [2] [2] 'b' '0'
'GO:0006412' [2] [2] 'b' '1'
'GO:0016787' [2] [3] 'c' '0'
'GO:0006810' [2] [4] 'd' '0'
'GO:0016787' [3] [3] 'c' '1'
'GO:0004672' [3] [3] 'c' '2'
'GO:0016779' [3] [3] 'c' '3'
'GO:0005215' [3] [3] 'c' '4'
'GO:0006810' [3] [4] 'd' '1'
'GO:0004386' [3] [4] 'd' '2'
'GO:0003774' [3] [4] 'd' '3'
'GO:0016298' [3] [4] 'd' '4'
'GO:0016192' [3] [5] 'e' '0'
'GO:0006412' [3] [2] 'b' '2'
'GO:0005215' [3] [3] 'c' '5'
'GO:0006810' [4] [4] 'd' '5'
'GO:0004386' [4] [4] 'd' '6'
I tried the following code but it doesn't work anyway:
x3=[]; % for saving the resulted numbers
z=0:length(GO); % will take the numbers from this matrix
z=z';
for j=1:length(num2alph)
for k=1:length(GO)
for i=1:length(GO)
if isequal(GO{i,4},num2alph{j})
x3{i}=z(k);
else
end
end
end
end
x3=x3';
GO1=[GO x3];
where cellarray num2alph (which will compare it with the fourth column of GO array to build the numering column)is:
'a'
'b'
'c'
'd'
'e'
'f'
'g'
'h'
'i'
'j'
'k'
also I need to map the last 2 columns with each other to be in the same cell , for example:
'a' '0' ===> a0
'b' '2' ===> b2
any advice
thx

This should do the trick:
un = unique(GO(:,4));
results = zeros(size(GO(:,4)));
for ii = 1:numel(un)
inds = strcmp(GO(:,4), un(ii));
count = max(0, cumsum(inds)-1);
results(inds) = count(inds);
end
GO = [GO num2cell(results)]

cellhist, an user defined function, can really be your friend here. It seems to fix exactly your needs.