facusapienza21 commented 2 years ago

Following #99, even when both PyMC3 and Theano-PyMC seem to be installed, when trying to execute code based on PyMC I always see the same error. Here there is a minimum example extracted from Getting started with PyMC3:

import numpy as np
import pymc3 as pm

# True parameter values
alpha, sigma = 1, 1
beta = [1, 2.5]

# Size of dataset
size = 100

# Predictor variable
X1 = np.random.randn(size)
X2 = np.random.randn(size) * 0.2

# Simulate outcome variable
Y = alpha + beta[0] * X1 + beta[1] * X2 + np.random.randn(size) * sigma

basic_model = pm.Model()

with basic_model:

    # Priors for unknown model parameters
    alpha = pm.Normal("alpha", mu=0, sigma=10)
    beta = pm.Normal("beta", mu=0, sigma=10, shape=2)
    sigma = pm.HalfNormal("sigma", sigma=1)

    # Expected value of outcome
    mu = alpha + beta[0] * X1 + beta[1] * X2

    # Likelihood (sampling distribution) of observations
    Y_obs = pm.Normal("Y_obs", mu=mu, sigma=sigma, observed=Y)

A similar error was reported here, where they mention something about the installation of Theano. However, the version of theano installed in the Hub seems to be the rigth one.

@abbyazari @consideRatio

consideRatio commented 2 years ago

Error message

Running the code leads to two segments, first some kind of summary, then a python traceback.

1. Error summary

You can find the C code in this temporary file: /tmp/theano_compilation_error_pw8rhar_
library inux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: is not found.

Looking in the tmp file, I find C (C++?) code looking like this that ends with a more detailed error message:

===============================
1       #include <Python.h>
2       #include <iostream>
3       #include "theano_mod_helper.h"
4       #include <math.h>
5       #include <numpy/arrayobject.h>

...

586         return m;
587     }
588
===============================
Problem occurred during compilation with the command line below:
/srv/conda/envs/notebook/bin/g++ -shared -g -O3 -fno-math-errno -Wno-unused-label -Wno-unused-variable -Wno-write-strings -Wno-c++11-narrowing -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -I/srv/conda/envs/notebook/lib/python3.9/site-packages/numpy/core/include -I/srv/conda/envs/notebook/include/python3.9 -I/srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/c_code -L/srv/conda/envs/notebook/lib -fvisibility=hidden -o /home/jovyan/.theano/compiledir_Linux-5.4-amzn2.x86_64-x86_64-with-glibc2.31-x86_64-3.9.9-64/tmpwnsmohb_/m31975b6dadb59d49af3f2b36405378825884299512ee0ed9081be33fa591d30d.so /home/jovyan/.theano/compiledir_Linux-5.4-amzn2.x86_64-x86_64-with-glibc2.31-x86_64-3.9.9-64/tmpwnsmohb_/mod.cpp -lpython3.9/srv/conda/envs/notebook/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find /usr/lib64/libc_nonshared.a
collect2: error: ld returned 1 exit status

2. Python traceback

Click to expand

```python-traceback --------------------------------------------------------------------------- Exception Traceback (most recent call last) Input In [1], in 18 basic_model = pm.Model() 20 with basic_model: 21 22 # Priors for unknown model parameters ---> 23 alpha = pm.Normal("alpha", mu=0, sigma=10) 24 beta = pm.Normal("beta", mu=0, sigma=10, shape=2) 25 sigma = pm.HalfNormal("sigma", sigma=1) File /srv/conda/envs/notebook/lib/python3.9/site-packages/pymc3/distributions/distribution.py:121, in Distribution.__new__(cls, name, *args, **kwargs) 119 dist = cls.dist(*args, **kwargs, shape=shape) 120 else: --> 121 dist = cls.dist(*args, **kwargs) 122 return model.Var(name, dist, data, total_size, dims=dims) File /srv/conda/envs/notebook/lib/python3.9/site-packages/pymc3/distributions/distribution.py:130, in Distribution.dist(cls, *args, **kwargs) 127 @classmethod 128 def dist(cls, *args, **kwargs): 129 dist = object.__new__(cls) --> 130 dist.__init__(*args, **kwargs) 131 return dist File /srv/conda/envs/notebook/lib/python3.9/site-packages/pymc3/distributions/continuous.py:488, in Normal.__init__(self, mu, sigma, tau, sd, **kwargs) 485 self.tau = tt.as_tensor_variable(tau) 487 self.mean = self.median = self.mode = self.mu = mu = tt.as_tensor_variable(floatX(mu)) --> 488 self.variance = 1.0 / self.tau 490 assert_negative_support(sigma, "sigma", "Normal") 491 assert_negative_support(tau, "tau", "Normal") File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/tensor/var.py:176, in _tensor_py_operators.__rtruediv__(self, other) 175 def __rtruediv__(self, other): --> 176 return theano.tensor.basic.true_div(other, self) File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/graph/op.py:253, in Op.__call__(self, *inputs, **kwargs) 250 node = self.make_node(*inputs, **kwargs) 252 if config.compute_test_value != "off": --> 253 compute_test_value(node) 255 if self.default_output is not None: 256 rval = node.outputs[self.default_output] File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/graph/op.py:126, in compute_test_value(node) 123 compute_map[o] = [False] 125 # Create a thunk that performs the computation --> 126 thunk = node.op.make_thunk(node, storage_map, compute_map, no_recycling=[]) 127 thunk.inputs = [storage_map[v] for v in node.inputs] 128 thunk.outputs = [storage_map[v] for v in node.outputs] File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/graph/op.py:634, in COp.make_thunk(self, node, storage_map, compute_map, no_recycling, impl) 630 self.prepare_node( 631 node, storage_map=storage_map, compute_map=compute_map, impl="c" 632 ) 633 try: --> 634 return self.make_c_thunk(node, storage_map, compute_map, no_recycling) 635 except (NotImplementedError, MethodNotDefined): 636 # We requested the c code, so don't catch the error. 637 if impl == "c": File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/graph/op.py:600, in COp.make_c_thunk(self, node, storage_map, compute_map, no_recycling) 598 print(f"Disabling C code for {self} due to unsupported float16") 599 raise NotImplementedError("float16") --> 600 outputs = cl.make_thunk( 601 input_storage=node_input_storage, output_storage=node_output_storage 602 ) 603 thunk, node_input_filters, node_output_filters = outputs 605 def rval(): File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/basic.py:1203, in CLinker.make_thunk(self, input_storage, output_storage, storage_map) 1175 """ 1176 Compiles this linker's fgraph and returns a function to perform the 1177 computations, as well as lists of storage cells for both the inputs (...) 1200 first_output = ostor[0].data 1201 """ 1202 init_tasks, tasks = self.get_init_tasks() -> 1203 cthunk, module, in_storage, out_storage, error_storage = self.__compile__( 1204 input_storage, output_storage, storage_map 1205 ) 1207 res = _CThunk(cthunk, init_tasks, tasks, error_storage, module) 1208 res.nodes = self.node_order File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/basic.py:1138, in CLinker.__compile__(self, input_storage, output_storage, storage_map) 1136 input_storage = tuple(input_storage) 1137 output_storage = tuple(output_storage) -> 1138 thunk, module = self.cthunk_factory( 1139 error_storage, 1140 input_storage, 1141 output_storage, 1142 storage_map, 1143 ) 1144 return ( 1145 thunk, 1146 module, (...) 1155 error_storage, 1156 ) File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/basic.py:1634, in CLinker.cthunk_factory(self, error_storage, in_storage, out_storage, storage_map) 1632 for node in self.node_order: 1633 node.op.prepare_node(node, storage_map, None, "c") -> 1634 module = get_module_cache().module_from_key(key=key, lnk=self) 1636 vars = self.inputs + self.outputs + self.orphans 1637 # List of indices that should be ignored when passing the arguments 1638 # (basically, everything that the previous call to uniq eliminated) File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/cmodule.py:1191, in ModuleCache.module_from_key(self, key, lnk) 1189 try: 1190 location = dlimport_workdir(self.dirname) -> 1191 module = lnk.compile_cmodule(location) 1192 name = module.__file__ 1193 assert name.startswith(location) File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/basic.py:1543, in CLinker.compile_cmodule(self, location) 1541 try: 1542 _logger.debug(f"LOCATION {location}") -> 1543 module = c_compiler.compile_str( 1544 module_name=mod.code_hash, 1545 src_code=src_code, 1546 location=location, 1547 include_dirs=self.header_dirs(), 1548 lib_dirs=self.lib_dirs(), 1549 libs=libs, 1550 preargs=preargs, 1551 ) 1552 except Exception as e: 1553 e.args += (str(self.fgraph),) File /srv/conda/envs/notebook/lib/python3.9/site-packages/theano/link/c/cmodule.py:2546, in GCC_compiler.compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols) 2542 # We replace '\n' by '. ' in the error message because when Python 2543 # prints the exception, having '\n' in the text makes it more 2544 # difficult to read. 2545 compile_stderr = compile_stderr.replace("\n", ". ") -> 2546 raise Exception( 2547 f"Compilation failed (return status={status}): {compile_stderr}" 2548 ) 2549 elif config.cmodule__compilation_warning and compile_stderr: 2550 # Print errors just below the command line. 2551 print(compile_stderr) Exception: ('Compilation failed (return status=1): /srv/conda/envs/notebook/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find /usr/lib64/libc_nonshared.a. collect2: error: ld returned 1 exit status. ', 'FunctionGraph(Elemwise{true_div,no_inplace}(TensorConstant{1.0}, TensorConstant{0.01}))') ```

Conclusion

The failure relates to pymc3 relies on theano, and theano relies on compiling C++ code, and that C++ code relies on the linker ld to have access to a relevant library that it fails to find. I'm not confident on how to solve this, but perhaps:

by installing some C library or similar, via a apt-get install command
by setting LD_LIBRARY_PATH to be something of relevance

Next steps

To google a bit more and see if we can install something to avoid this C++ code compilation failure, for example libc6-dev as described here and try doing that.
Ask for help by people with better C experience.

consideRatio commented 2 years ago

Result

Installing libc6-dev didn't help. The failure is related to g++ compilation of code as invoked by pymc3-theano. The failure is for the ld program to find a specific file: /usr/lib64/libc_nonshared.a. This file is available at /usr/lib/x86_64-linux-gnu/libc_nonshared.a, but I've also failed to influence to make it detected. The issue is very similar to whats reported here by someone more knowledgeable about C++: https://github.com/awslabs/aws-lambda-cpp/issues/96

@abbyazari @fperez - do you have ideas on how to go about this? I've been down trying to debug these situations in the past and typically fail.

Note that I couldn't make LD_LIBRARY_PATH or LIBRARY_PATH influence the ld executable to find the libc_nonshared.a file. I also don't understand why or what makes it look for the file in the wrong folder. I think the LD_LIBRARY_PATH and such envs are relevant based on https://stackoverflow.com/a/4250666/2220152 and past experience. I'm not confident the ld executable had those environment variables set though, because there is a lot of environment variable manipulation related to these ones... I ran into a rabbit hole about this in the past when sudo was involved. Currently we are not using sudo though - this is done as the jovyan non-sudo user.

I think I'm stuck at this point trying to figure this out =/

fperez commented 2 years ago

Thanks for the input and hard work, @consideRatio! These issues are a royal pain, and my most recent attempts at similar ones have not been super successful... I used to do a lot of this kind of work but most of my knowledge is a bit old and pre-conda days. I think we're experiencing some nasty interactions between system compilers/configuration and conda tools...

I'll try to make a local docker build where I can run these kinds of manual linux experiments purely by hand, but I would suggest pinging folks on the 2i2c slack - perhaps someone else on the team has experienced similar problems and can make a suggestion...

abbyazari commented 2 years ago

@consideRatio thank you for working on this and tracking it down! I have not run into this type of issue myself yet, I would second @fperez and see if the 2i2c folks have seen this before, I'll do some digging myself too.

abbyazari commented 2 years ago

Small update @consideRatio / @facusapienza21. @fperez has created a new environment that is working with pymc3. To access the directions are here:

create in your $HOME directory on the hub a file called .condarc, in .condarc put: envs_dirs: - ~/shared/envs - ~/shared-readwrite/envs

When running pymc3 notebooks then change the kernel to be the pymc3 kernel. More updates pending from @fperez on the exact nature of the pymc3 environment.

fperez commented 2 years ago

The embarrassing part is that I don't recall what I did! We can check which packages are installed in that env and do a comparison, as I think the solution is in one of the installed tools...

I still think there was a problem I wasn't quite able to solve with local compilation, and perhaps that's why I thought I hadn't quite fixed the pymc issue. But it seems for now that env works for pymc, so we can use that and keep iterating on this question.

consideRatio commented 2 years ago

I could reproduce successfully using pymc3 with the example @facusapienza21 provides at the top post of this issue. Comparing the included content, I don't see much of importance be changed. I think these could be relatively interesting parts...

-libclang                  11.1.0          default_ha53f305_1    conda-forge
+libclang                  13.0.0          default_hc23dcda_0    conda-forge

-abseil-cpp                20210324.2           h9c3ff4c_0    conda-forge
-arrow-cpp                 6.0.1           py39h01fd06f_8_cpu    conda-forge
-compilers                 1.3.0                ha770c72_0    conda-forge
-cython                    0.29.27          py39he80948d_0    conda-forge

 gcc                       9.4.0                h192d537_4    conda-forge
 gcc_impl_linux-64         9.4.0               h03d3576_12    conda-forge
 gcc_linux-64              9.4.0                h391b98a_4    conda-forge
 mkl                       2021.4.0           h8d4b97c_729    conda-forge
 mkl-service               2.4.0            py39h7e14d7c_0    conda-forge

I know that I've added compilers before in an attempt to help make regreg installable (Related: https://github.com/pangeo-data/jupyter-earth/issues/66).

Perhaps uninstalling compilers is relevant? Perhaps trying to update to a modern libclang which probably has been installed by another dependency though - like arrow-cpp or abseil-cpp I suspect.

Click to see full diff between default conda env (notebook) and pymc3 env

```diff (notebook) jovyan@jupyter-consideratio:~$ mamba list > env-notebook.txt (notebook) jovyan@jupyter-consideratio:~$ conda activate /home/jovyan/shared/envs/pymc3 (pymc3) jovyan@jupyter-consideratio:~$ mamba list > env-pymc3.txt (pymc3) jovyan@jupyter-consideratio:~$ git diff --no-index env-notebook.txt env-pymc3.txt diff --git a/env-notebook.txt b/env-pymc3.txt index 634dc39..82cea98 100644 --- a/env-notebook.txt +++ b/env-pymc3.txt @@ -1,169 +1,51 @@ -# packages in environment at /srv/conda/envs/notebook: +# packages in environment at /home/jovyan/shared/envs/pymc3: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge -abseil-cpp 20210324.2 h9c3ff4c_0 conda-forge absl-py 1.0.0 pyhd8ed1ab_0 conda-forge -adal 1.2.7 pyhd8ed1ab_0 conda-forge -adlfs 2021.10.0 pyhd8ed1ab_0 conda-forge -affine 2.3.0 py_0 conda-forge -aiobotocore 2.0.1 pyhd8ed1ab_0 conda-forge -aiohttp 3.8.1 py39h3811e60_0 conda-forge -aioitertools 0.8.0 pyhd8ed1ab_0 conda-forge -aiosignal 1.2.0 pyhd8ed1ab_0 conda-forge -alabaster 0.7.12 py_0 conda-forge -alembic 1.7.5 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge -altair 4.2.0 pyhd8ed1ab_1 conda-forge -anyio 3.5.0 py39hf3d152e_0 conda-forge -aom 3.2.0 h9c3ff4c_2 conda-forge -aplus 0.11.0 py_1 conda-forge -appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py39h3811e60_1 conda-forge -arrow-cpp 6.0.1 py39h01fd06f_8_cpu conda-forge -arviz 0.11.2 pyhd8ed1ab_0 conda-forge -asciitree 0.3.3 py_2 conda-forge -asgiref 3.5.0 pyhd8ed1ab_0 conda-forge -asn1crypto 1.4.0 pyh9f0ad1d_0 conda-forge -astroid 2.9.3 py39hf3d152e_0 conda-forge -astropy 5.0.1 py39hce5d2b2_0 conda-forge +arviz 0.11.4 pyhd8ed1ab_0 conda-forge asttokens 2.0.5 pyhd8ed1ab_0 conda-forge -async-timeout 4.0.2 pyhd8ed1ab_0 conda-forge -async_generator 1.10 py_0 conda-forge -atk-1.0 2.36.0 h3371d22_4 conda-forge -attrs 20.3.0 pyhd3deb0d_0 conda-forge -av 8.0.3 py39h7b1e1d3_0 conda-forge -aws-c-cal 0.5.11 h95a6274_0 conda-forge -aws-c-common 0.6.2 h7f98852_0 conda-forge -aws-c-event-stream 0.2.7 h3541f99_13 conda-forge -aws-c-io 0.10.5 hfb6a706_0 conda-forge -aws-checksums 0.1.11 ha31a3da_7 conda-forge -aws-sdk-cpp 1.8.186 hb4091e7_3 conda-forge -awscli 1.21.8 py39hf3d152e_2 conda-forge -azure-core 1.21.1 pyhd8ed1ab_0 conda-forge -azure-datalake-store 0.0.51 pyh9f0ad1d_0 conda-forge -azure-identity 1.7.1 pyhd8ed1ab_0 conda-forge -azure-storage-blob 12.9.0 pyhd8ed1ab_0 conda-forge -babel 2.9.1 pyh44b312d_0 conda-forge +attrs 21.4.0 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge -beautifulsoup4 4.10.0 pyha770c72_0 conda-forge +bambi 0.7.1 pyhd8ed1ab_0 conda-forge binutils 2.36.1 hdd6e379_2 conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge binutils_linux-64 2.36 hf3e587d_4 conda-forge -black 22.1.0 pyhd8ed1ab_0 conda-forge -blake3 0.2.1 py39h860a657_0 conda-forge +black 21.12b0 pyhd8ed1ab_0 conda-forge bleach 4.1.0 pyhd8ed1ab_0 conda-forge -blinker 1.4 py_1 conda-forge -blosc 1.21.0 h9c3ff4c_0 conda-forge bokeh 2.4.2 py39hf3d152e_0 conda-forge -boost-cpp 1.74.0 h312852a_4 conda-forge -boto3 1.19.8 pyhd8ed1ab_0 conda-forge -botocore 1.22.8 pyhd8ed1ab_0 conda-forge -bottleneck 1.3.2 py39hce5d2b2_5 conda-forge -bounded-pool-executor 0.0.3 pyhd8ed1ab_0 conda-forge -bqplot 0.12.32 pyhd8ed1ab_0 conda-forge -branca 0.4.2 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h7f98852_6 conda-forge brotli-bin 1.0.9 h7f98852_6 conda-forge -brotlipy 0.7.0 py39h3811e60_1003 conda-forge -brunsli 0.1 h9c3ff4c_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge -c-blosc2 2.0.4 h5f21a17_1 conda-forge c-compiler 1.3.0 h7f98852_0 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge -cached-property 1.5.2 hd8ed1ab_1 conda-forge -cached_property 1.5.2 pyha770c72_1 conda-forge 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pyhd8ed1ab_0 conda-forge -xmltodict 0.12.0 py_0 conda-forge -xorg-fixesproto 5.0 h7f98852_1002 conda-forge -xorg-inputproto 2.3.2 h7f98852_1002 conda-forge -xorg-kbproto 1.0.7 h7f98852_1002 conda-forge -xorg-libice 1.0.10 h7f98852_0 conda-forge -xorg-libsm 1.2.3 hd9c2040_1000 conda-forge -xorg-libx11 1.7.2 h7f98852_0 conda-forge +xarray 0.20.2 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge -xorg-libxext 1.3.4 h7f98852_1 conda-forge -xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge -xorg-libxi 1.7.10 h7f98852_0 conda-forge -xorg-libxrender 0.9.10 h7f98852_1003 conda-forge -xorg-renderproto 0.11.1 h7f98852_1002 conda-forge -xorg-xextproto 7.3.0 h7f98852_1002 conda-forge -xorg-xproto 7.0.31 h7f98852_1007 conda-forge -xpublish 0.1.0 py_0 conda-forge -xrft 0.4.1 pyhd8ed1ab_0 conda-forge -xskillscore 0.0.24 pyhd8ed1ab_0 conda-forge -xyzservices 2022.1.1 pyhd8ed1ab_0 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h7f98852_2 conda-forge -yarl 1.7.2 py39h3811e60_1 conda-forge -zarr 2.10.3 pyhd8ed1ab_0 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge -zfp 0.5.5 h9c3ff4c_8 conda-forge -zict 2.0.0 py_0 conda-forge zipp 3.7.0 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h36c2ea0_1013 conda-forge zstd 1.5.2 ha95c52a_0 conda-forge ```

consideRatio commented 1 year ago

Closing as resolved by relying on the functional environment with pymc3 in shared/envs/pymc3 on the shared network file system.

pangeo-data / jupyter-earth

Running PyMC3 #104

Error message

1. Error summary

2. Python traceback

Conclusion

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Result