wsl2 gui issues

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gerrit wilkens

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Nov 17, 2023, 11:10:35 AM11/17/23
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Hi all,

I am trying to run Eman2 on WSL and a Xserver (vcxsrv). Everything seem to work, the output from e2version.py is like this:

EMAN 2.99.54 ( GITHUB: 2023-11-16 23:40 - commit: 510750f9d )

Your EMAN2 is running on: Linux-5.15.133.1-microsoft-standard-WSL2-x86_64-with-glibc2.35 5.15.133.1-microsoft-standard-WSL2

Your Python version is: 3.11.6

E2projectmanager.py also opens and looks fine. However, after importing my micrographs when I try to launch Interactive particle picking, everything crashes (see below). Anyone who can help?

Thank you!

Gerrit Wilkens

Centre de Biologie Structurale, Montpellier

Postdoc

#########

QStandardPaths: wrong permissions on runtime directory /run/user/1000/, 0755 instead of 0700

NOT Writing notes, ppid=-2

Using GPU...

Using project voltage of  120.0 kV

Using project Cs of  2.0 mm

WARNING: Strongly recommend using a box size 1.5 - 2.0x the maximum dimension of the particle! This may be pushed to ~1.25x in some cases, but results may be suboptimal.

Your box size is 1.40x the particle size. Recommend a size of at least 750

QStandardPaths: wrong permissions on runtime directory /run/user/1000/, 0755 instead of 0700

Traceback (most recent call last):

  File "/home/gerrit/miniconda3/envs/eman2/bin/e2boxer.py", line 3279, in <module>

    main()

  File "/home/gerrit/miniconda3/envs/eman2/bin/e2boxer.py", line 318, in main

    gui=GUIBoxer(args,options.voltage,options.apix,options.cs,options.ac,options.boxsize,options.ptclsize,options.threads)

        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/gerrit/miniconda3/envs/eman2/bin/e2boxer.py", line 1949, in __init__

    self.wbgrefs.set_data(self.bgrefs)

  File "/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/eman2_gui/emimagemx.py", line 893, in set_data

    self.resize(min(x,mx),min(y,my))

  File "/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/eman2_gui/emapplication.py", line 110, in resize

    QtOpenGL.QGLWidget.resize(self, w, h)

TypeError: arguments did not match any overloaded call:

  resize(self, a0: QSize): argument 2 has unexpected type 'float'

  resize(self, w: int, h: int): argument 2 has unexpected type 'float'

Ludtke, Steven J.

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Nov 17, 2023, 2:34:52 PM11/17/23
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The recent new version of PyQt introduced a couple of new bugs into existing programs. A few patches for these bugs were just committed to Github yesterday. We may not have caught everything yet. Please report any bugs like this that you run into. They are hard to detect with routine testing.

I just committed a fix for the problem you encountered, so if you have installed from source (which seems likely given your version), you just need to cd to the source folder and run "git pull", then cd to the build folder and "make install". If you find more issues like this, as I said, just post them here. They are easily fixed.

---
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center


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gerrit wilkens

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Nov 17, 2023, 5:22:12 PM11/17/23
to EMAN2
Thank you for the quick fix! Everything is working now as far as I can tell.

Gerrit

gerrit wilkens

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Nov 19, 2023, 5:32:32 PM11/19/23
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Dear Steven, 
I just run into another bug when trying reference free 2d class averaging:

Building initial averages

/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.

  setattr(self, word, getattr(machar, word).flat[0])

/home/gerrit/miniconda3/envs/eman2/lib/python3.11/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)

/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.

  setattr(self, word, getattr(machar, word).flat[0])

/home/gerrit/miniconda3/envs/eman2/lib/python3.11/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)

Traceback (most recent call last):

  File "/home/gerrit/miniconda3/envs/eman2/bin/e2msa.py", line 331, in <module>

    main()

  File "/home/gerrit/miniconda3/envs/eman2/bin/e2msa.py", line 155, in main

    msa.fit(data)

  File "/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/sklearn/base.py", line 1152, in wrapper

    return fit_method(estimator, *args, **kwargs)

           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/sklearn/decomposition/_pca.py", line 434, in fit

    self._fit(X)

  File "/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/sklearn/decomposition/_pca.py", line 510, in _fit

    return self._fit_full(X, n_components)

           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  File "/home/gerrit/miniconda3/envs/eman2/lib/python3.11/site-packages/sklearn/decomposition/_pca.py", line 524, in _fit_full

    raise ValueError(

ValueError: n_components=12 must be between 0 and min(n_samples, n_features)=7 with svd_solver='full'

Error running:

e2msa.py r2d_00/input_fp.hdf r2d_00/input_fp_basis.hdf --normalize --nbasis=12

Ludtke, Steven J.

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Nov 19, 2023, 6:33:09 PM11/19/23
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This is an error with your inputs to the program. We'd need to see the e2refine2d_bispec command line to help you debug the issue. You can get it from the "command" tab in e2projectmanager, or from .eman2log.txt


---
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

Ludtke, Steven J.

unread,
Nov 19, 2023, 6:33:09 PM11/19/23
to em...@googlegroups.com
This is an error with your inputs to the program. We'd need to see the e2refine2d_bispec command line to help you debug the issue. You can get it from the "command" tab in e2projectmanager, or from .eman2log.txt

---
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

On Nov 19, 2023, at 4:32 PM, gerrit wilkens <gerwi...@gmail.com> wrote:

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