Using Meta/Facebook Prophet with Conda/PyCall

General Usage
,
1

Hi,

I run into problems when trying to run the example code from:

What I did:

import Pkg
ENV["PYTHON"]=""
Pkg.build("PyCall")

Restarted the Julia CLI, then:

import Pkg

Pkg.add("Conda")
using Conda
Conda.runconda(`update -y conda`)
Conda.add("pandas")
Conda.add("prophet")

and

julia> using Conda

julia> using PyCall

julia> pd = pyimport("pandas")
PyObject <module 'pandas' from '/home/ftournier/.julia/conda/3/x86_64/lib/python3.12/site-packages/pandas/__init__.py'>

julia> pro = pyimport("prophet")
Importing matplotlib failed. Plotting will not work.
Importing plotly failed. Interactive plots will not work.
PyObject <module 'prophet' from '/home/ftournier/.julia/conda/3/x86_64/lib/python3.12/site-packages/prophet/__init__.py'>

julia> m = pro.Prophet()
PyObject <prophet.forecaster.Prophet object at 0x7fd6beece6f0>

julia> df = pd.read_csv("https://raw.githubusercontent.com/facebook/prophet/main/examples/example_wp_log_peyton_manning.csv")
PyObject               ds          y
0     2007-12-10   9.590761
1     2007-12-11   8.519590
2     2007-12-12   8.183677
3     2007-12-13   8.072467
4     2007-12-14   7.893572
...          ...        ...
2900  2016-01-16   7.817223
2901  2016-01-17   9.273878
2902  2016-01-18  10.333775
2903  2016-01-19   9.125871
2904  2016-01-20   8.891374

[2905 rows x 2 columns]

Next step failed:

julia> m.fit(df)
14:55:24 - cmdstanpy - INFO - Chain [1] start processing
14:55:24 - cmdstanpy - INFO - Chain [1] done processing
14:55:24 - cmdstanpy - ERROR - Chain [1] error: error during processing Operation not permitted
Optimization terminated abnormally. Falling back to Newton.
14:55:24 - cmdstanpy - INFO - Chain [1] start processing
14:55:24 - cmdstanpy - INFO - Chain [1] done processing
14:55:24 - cmdstanpy - ERROR - Chain [1] error: error during processing Operation not permitted
ERROR: PyError ($(Expr(:escape, :(ccall(#= /home/jska/.julia/packages/PyCall/1gn3u/src/pyfncall.jl:43 =# @pysym(:PyObject_Call), PyPtr, (PyPtr, PyPtr, PyPtr), o, pyargsptr, kw))))) 
[15267] signal 11 (1): Segmentation fault
in expression starting at none:0
PyErr_CheckSignals at /usr/local/src/conda/python-3.12.11/Modules/signalmodule.c:1771 [inlined]
PyObject_Repr at /usr/local/src/conda/python-3.12.11/Objects/object.c:544
pystring at /home/jska/.julia/packages/PyCall/1gn3u/src/PyCall.jl:243
show at /home/jska/.julia/packages/PyCall/1gn3u/src/exception.jl:39
showerror at ./errorshow.jl:30 [inlined]
#showerror#1026 at ./errorshow.jl:97
showerror at ./errorshow.jl:95
unknown function (ip: 0x7f6b381018a2)
show_exception_stack at ./errorshow.jl:996
display_error at ./client.jl:117
jfptr_display_error_11782.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1055 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
repl_display_error at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:414
print_response at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:431
#70 at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:405
jfptr_YY.70_10215.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
with_repl_linfo at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:678
jfptr_with_repl_linfo_10303.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
print_response at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:403
do_respond at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:1037
jfptr_do_respond_10366.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1055 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
#126 at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:1444
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1055 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
#30 at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:1711
jfptr_YY.30_8323.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
macro expansion at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:2861 [inlined]
macro expansion at ./lock.jl:273 [inlined]
#282 at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:2851
jfptr_YY.282_8870.1 at /opt/jska-tmp/julia-1.11.6/share/julia/compiled/v1.11/REPL/u0gqU_QBeOa.so (unknown line)
jl_apply at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
start_task at /cache/build/tester-amdci4-12/julialang/julia-release-1-dot-11/src/task.c:1202
Allocations: 1056136 (Pool: 1055206; Big: 930); GC: 2
Segmentation fault

I’m not familiar with using Python under Julia so I may have done something wrong.

2

Can you try PythonCall.jl instead? It is the more mature way to call Python from Julia, PyCall.jl was an earlier package with less robust design.

In this specific case, I think you might be running into threading issues like thread safety · Issue #882 · JuliaPy/PyCall.jl · GitHub

3

I managed to install PythonCall, but I still have an error:

julia> using CondaPkg

julia> using PythonCall

julia> CondaPkg.add("Pandas")
    CondaPkg Found dependencies: /home/jska/.julia/environments/v1.11/CondaPkg.toml
    CondaPkg Found dependencies: /home/jska/.julia/packages/PythonCall/avYrV/CondaPkg.toml
    CondaPkg Initialising pixi
             │ /home/jska/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /home/jska/.julia/environments/v1.11/.CondaPkg
Created /home/jska/.julia/environments/v1.11/.CondaPkg/pixi.toml
    CondaPkg Wrote /home/jska/.julia/environments/v1.11/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ prophet = "*"
             │ libstdcxx-ng = ">=3.4,<14.0"
             │ pandas = "*"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = ">=3.8,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             └ description = "automatically generated by CondaPkg.jl"
    CondaPkg Installing packages
             │ /home/jska/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /home/jska/.julia/environments/v1.11/.CondaPkg/pixi.toml
The default environment has been installed.

julia> CondaPkg.add("prophet")

julia> pd = pyimport("pandas")
Python: <module 'pandas' from '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/pandas/__init__.py'>

julia> pro = pyimport("prophet")
Importing matplotlib failed. Plotting will not work.
Importing plotly failed. Interactive plots will not work.
Python: <module 'prophet' from '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/__init__.py'>

julia> df = pd.read_csv("https://raw.githubusercontent.com/facebook/prophet/main/examples/example_wp_log_peyton_manning.csv")
Python:
              ds          y
0     2007-12-10   9.590761
1     2007-12-11   8.519590
2     2007-12-12   8.183677
3     2007-12-13   8.072467
4     2007-12-14   7.893572
...          ...        ...
2900  2016-01-16   7.817223
2901  2016-01-17   9.273878
2902  2016-01-18  10.333775
2903  2016-01-19   9.125871
2904  2016-01-20   8.891374

[2905 rows x 2 columns]

julia> m = pro.Prophet()
Python: <prophet.forecaster.Prophet object at 0x7f02760b2a50>

julia> m.fit(df)
17:55:06 - cmdstanpy - INFO - Chain [1] start processing
17:55:06 - cmdstanpy - INFO - Chain [1] done processing
17:55:06 - cmdstanpy - ERROR - Chain [1] error: error during processing Operation not permitted
Optimization terminated abnormally. Falling back to Newton.
17:55:06 - cmdstanpy - INFO - Chain [1] start processing
17:55:06 - cmdstanpy - INFO - Chain [1] done processing
17:55:06 - cmdstanpy - ERROR - Chain [1] error: error during processing Operation not permitted
ERROR: Python: RuntimeError: Error during optimization! Command '/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/stan_model/prophet_model.bin random seed=15412 data file=/tmp/tmp5863norm/6uej5bsv.json init=/tmp/tmp5863norm/1dp0uqpj.json output file=/tmp/tmp5863norm/prophet_model1pgmslsi/prophet_model-20250901175506.csv method=optimize algorithm=newton iter=10000' failed: console log output:

/home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/stan_model/prophet_model.bin: /home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/stan_model/../../../../libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/jska/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/stan_model/../../../../libtbb.so.12)

Python stacktrace:
 [1] optimize
   @ cmdstanpy.model ~/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/cmdstanpy/model.py:659
 [2] fit
   @ prophet.models ~/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/models.py:128
 [3] fit
   @ prophet.forecaster ~/.julia/environments/v1.11/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/prophet/forecaster.py:1232
Stacktrace:
 [1] pythrow()
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/err.jl:89
 [2] errcheck
   @ ~/.julia/packages/PythonCall/avYrV/src/Core/err.jl:10 [inlined]
 [3] pycallargs(f::Py, args::Py)
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/builtins.jl:220
 [4] pycall(::Py, ::Py, ::Vararg{Py}; kwargs::@Kwargs{})
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/builtins.jl:243
 [5] pycall(::Py, ::Py, ::Vararg{Py})
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/builtins.jl:233
 [6] (::Py)(::Py, ::Vararg{Py}; kwargs::@Kwargs{})
   @ PythonCall.Core ~/.julia/packages/PythonCall/avYrV/src/Core/Py.jl:362
 [7] top-level scope
   @ REPL[9]:1
4

It looks like you are on a slightly outdated version of PythonCall, please update to the latest version (0.9.27) and try again, which should fix that CXX ABI error you’re getting.