2.99.57 Version ctest test failed #574
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Not clear if this will be a real problem with using EMAN2 or not. This is an error in libgomp/numpy in your environment, nothing directly related to EMAN2. If you google this issue, you can find some discussion of the underlying problem. Looks like you are running on a Mac? Using the updated conda-forge based installtion instructions, I haven’t seen any issues so far on my own Mac (with EMAN2).
… On Sep 5, 2024, at 4:26 AM, simon28li ***@***.***> wrote:
hi When I was testing version 2.99.57, there was an error in progs. It was an error fragment:
***@***.*** spack-build-xxwzugl]#ctest
Test project /home/stage/root/spack-stage-eman2-2.99.57-xxwzuglpxb35u7p3cmxflnc7c6shtffm/spack-build-xxwzugl
Start 1: py-compile
1/6 Test #1: py-compile ....................... Passed 0.13 sec
Start 2: imports
2/6 Test #2: imports .......................... Passed 0.30 sec
Start 3: test-EMAN2DIR
3/6 Test #3: test-EMAN2DIR .................... Passed 2.47 sec
Start 4: nose-tests
4/6 Test #4: nose-tests ....................... Passed 16.37 sec
Start 5: progs
5/6 Test #5: progs ............................***Failed 30.81 sec
Start 6: test-eer
6/6 Test #6: test-eer ......................... Passed 0.01 sec
83% tests passed, 1 tests failed out of 6
Total Test time (real) = 50.10 sec
The following tests FAILED:
5 - progs (Failed)
Errors while running CTest
Running: e2spt_boxer.py -h
/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/requests/__init__.py:102: RequestsDependencyWarning: urllib3 (1.26.16) or chardet (5.1.0)/charset_normalizer (2.0.12) doesn't match a supported version!
warnings.warn("urllib3 ({}) or chardet ({})/charset_normalizer ({}) doesn't match a supported "
/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/numpy/core/getlimits.py:518: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
return self._float_to_str(self.smallest_subnormal)
/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/numpy/core/getlimits.py:518: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
setattr(self, word, getattr(machar, word).flat[0])
/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
return self._float_to_str(self.smallest_subnormal)
Traceback (most recent call last):
File "/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/sklearn/__check_build/__init__.py", line 45, in <module>
from ._check_build import check_build # noqa
ImportError: /home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/sklearn/__check_build/../../scikit_learn.libs/libgomp-d22c30c5.so.1.0.0: cannot allocate memory in static TLS block
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/eman2-2.99.57-xxwzuglpxb35u7p3cmxflnc7c6shtffm/bin/e2gmm_rigidbody.py", line 24, in <module>
from e2gmm_refine_new import *
File "/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/eman2-2.99.57-xxwzuglpxb35u7p3cmxflnc7c6shtffm/bin/e2gmm_refine_new.py", line 5, in <module>
from sklearn.decomposition import PCA
File "/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/sklearn/__init__.py", line 79, in <module>
from . import (
File "/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/sklearn/__check_build/__init__.py", line 47, in <module>
raise_build_error(e)
File "/home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/sklearn/__check_build/__init__.py", line 31, in raise_build_error
raise ImportError("""%s
ImportError: /home/spack/opt/spack/linux-openeuler20-aarch64/gcc-7.3.0/python-3.8.8-ktpokql7mq2pnofbqca2ujsfpiztrzrv/lib/python3.8/site-packages/sklearn/__check_build/../../scikit_learn.libs/libgomp-d22c30c5.so.1.0.0: cannot allocate memory in static TLS block
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hi When I was testing version 2.99.57, there was an error in progs. It was an error fragment:
The text was updated successfully, but these errors were encountered: