libstdc++

[Stijn Franssen-van Rijsingen]

Hi Raven-team,

I am trying to install raven but I running into a problem with libstdc++.

The way i understand I need version 3.4.30, but my OS (RHEL 9) only comes with 3.4.29.

In order to install raven i cloned the most recent version, established the conda environment (./scripts/establish_conda_env.sh --install) and build raven (./build_raven).

Then when I try to run the tests, i get the error shown below.

Could you help me with this?

Kind regards,

Stijn Franssen

PS I've added some info about the libstdc++ files included in my OS at the bottom of this message.

Running RAVEN tests ...
rook: loading init file "/home/executables/raven/developer_tools/rook.ini"
rook: ... loaded setting "add_non_default_run_types = qsub"
rook: ... loaded setting "test_dir = tests, doc/workshop"
rook: found 123 test dirs under "tests" ...
rook: found 13 test dirs under "doc/workshop" ...
rook: loading init file "/home/executables/raven/developer_tools/rook.ini"
rook: ... loaded setting "add_non_default_run_types = qsub"
rook: ... loaded setting "test_dir = tests, doc/workshop"
Failed loading NetCDFDiffer.py with exception: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-310-x86_64-linux-gnu.so)
Traceback (most recent call last):
  File "/home/executables/raven/rook/main.py", line 245, in get_testers_and_differs
    module = __import__(filename[:-3]) #[:-3] to remove .py
  File "/home/executables/raven/scripts/TestHarness/testers/NetCDFDiffer.py", line 23, in <module>
    from UnorderedCSVDiffer import UnorderedCSVDiffer, UnorderedCSV
  File "/home/executables/raven/scripts/TestHarness/testers/UnorderedCSVDiffer.py", line 35, in <module>
    from ravenframework.utils import mathUtils
  File "/home/executables/raven/ravenframework/utils/mathUtils.py", line 24, in <module>
    from scipy import interpolate, stats
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/__init__.py", line 211, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/__init__.py", line 467, in <module>
    from ._stats_py import *
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/_stats_py.py", line 46, in <module>
    from . import distributions
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/distributions.py", line 8, in <module>
    from ._distn_infrastructure import (rv_discrete, rv_continuous, rv_frozen)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/_distn_infrastructure.py", line 24, in <module>
    from scipy import optimize
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/__init__.py", line 211, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/__init__.py", line 413, in <module>
    from ._linprog import linprog, linprog_verbose_callback
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_linprog.py", line 21, in <module>
    from ._linprog_highs import _linprog_highs
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_linprog_highs.py", line 20, in <module>
    from ._highs._highs_wrapper import _highs_wrapper
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-310-x86_64-linux-gnu.so)
Failed loading RavenFramework.py with exception: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-310-x86_64-linux-gnu.so)
Traceback (most recent call last):
  File "/home/executables/raven/rook/main.py", line 245, in get_testers_and_differs
    module = __import__(filename[:-3]) #[:-3] to remove .py
  File "/home/executables/raven/scripts/TestHarness/testers/RavenFramework.py", line 24, in <module>
    import UnorderedCSVDiffer
  File "/home/executables/raven/scripts/TestHarness/testers/UnorderedCSVDiffer.py", line 35, in <module>
    from ravenframework.utils import mathUtils
  File "/home/executables/raven/ravenframework/utils/mathUtils.py", line 24, in <module>
    from scipy import interpolate, stats
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/__init__.py", line 211, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/__init__.py", line 467, in <module>
    from ._stats_py import *
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/_stats_py.py", line 46, in <module>
    from . import distributions
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/distributions.py", line 8, in <module>
    from ._distn_infrastructure import (rv_discrete, rv_continuous, rv_frozen)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/_distn_infrastructure.py", line 24, in <module>
    from scipy import optimize
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/__init__.py", line 211, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/__init__.py", line 413, in <module>
    from ._linprog import linprog, linprog_verbose_callback
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_linprog.py", line 21, in <module>
    from ._linprog_highs import _linprog_highs
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_linprog_highs.py", line 20, in <module>
    from ._highs._highs_wrapper import _highs_wrapper
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-310-x86_64-linux-gnu.so)
Failed loading UnorderedCSVDiffer.py with exception: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-310-x86_64-linux-gnu.so)
Traceback (most recent call last):
  File "/home/executables/raven/rook/main.py", line 245, in get_testers_and_differs
    module = __import__(filename[:-3]) #[:-3] to remove .py
  File "/home/executables/raven/scripts/TestHarness/testers/UnorderedCSVDiffer.py", line 35, in <module>
    from ravenframework.utils import mathUtils
  File "/home/executables/raven/ravenframework/utils/mathUtils.py", line 24, in <module>
    from scipy import interpolate, stats
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/__init__.py", line 211, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/__init__.py", line 467, in <module>
    from ._stats_py import *
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/_stats_py.py", line 46, in <module>
    from . import distributions
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/distributions.py", line 8, in <module>
    from ._distn_infrastructure import (rv_discrete, rv_continuous, rv_frozen)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/stats/_distn_infrastructure.py", line 24, in <module>
    from scipy import optimize
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/__init__.py", line 211, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/__init__.py", line 413, in <module>
    from ._linprog import linprog, linprog_verbose_callback
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_linprog.py", line 21, in <module>
    from ._linprog_highs import _linprog_highs
  File "/home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_linprog_highs.py", line 20, in <module>
    from ._highs._highs_wrapper import _highs_wrapper
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/franssen/.conda/envs/raven_libraries/lib/python3.10/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-310-x86_64-linux-gnu.so)
Traceback (most recent call last):
  File "/home/executables/raven/rook/main.py", line 425, in <module>
    param_handler = tester_params[node.attrib['type']]
KeyError: 'RavenFramework'

Finding the libstdc++ that I have installed.

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_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_3.4.29
GLIBCXX_DEBUG_MESSAGE_LENGTH

Trying to find the package which I have installed.

dnf list installed "libstdc++-*"
Not root, Subscription Management repositories not updated
Installed Packages
libstdc++-devel.x86_64                     11.4.1-2.1.el9                      @rhel-9-for-x86_64-appstream-rpms

[Joshua J. Cogliati]

This sometimes happens if the system library is older than the conda library. This can be overridden by using a LD_LIBRARY_PATH something like:

export LD_LIBRARY_PATH=/home/franssen/.conda/envs/raven_libraries/lib

(Note, if you have a LD_LIBRARY_PATH already defined, then you probably would instead need to use:
export LD_LIBRARY_PATH="/home/franssen/.conda/envs/raven_libraries/lib:$LD_LIBRARY_PATH"

so that it inserts the path instead of creating it.

)

and then running the tests

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[Stijn Franssen-van Rijsingen]

Hi Jrin,

Thank you for your quick response.

This solved my problem, the tests are running fine now.

Kind regards,

Stijn Franssen