CCPNMR v 3.2 crashes

Analysis Version 3
1

I have had problems open projects and spectra in the old 3.1.1 version of CCPNMR and after updating to v 3.2 it seemed to be functioning as intented. But now the program won’t open projects and spectra again. It just crashes and I’m left with this in the terminal:

==> Getting user preferences
==> Language set to “English-UK”
INFO : Folder may be read-only, or may not exist (ProjectArchiver.archives:93)
==> Checking registration on server
==> Done, AnalysisAssign is starting
INFO : application.loadSpectra(’/projects/sbinlab/people/mrp113/data/nmr/men/1Dwater_HSQC/MEN_20090331_del1-9G129RhPRL_gNhsqc.fid/test.ft2’)
INFO : mainWindow.newSpectrumDisplay(‘SP:test’, axisCodes=(‘N’, ‘H’), stripDirection=‘Y’, position=‘right’, relativeTo=None)
Fatal Python error: Segmentation fault

Thread 0x00007f4fda7d9700 (most recent call first):
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/selectors.py”, line 469 in select
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/asyncio/base_events.py”, line 1868 in _run_once
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/asyncio/base_events.py”, line 603 in run_forever
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/site-packages/tornado/platform/asyncio.py”, line 195 in start
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/site-packages/ipykernel/iostream.py”, line 84 in _thread_main
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/threading.py”, line 953 in run
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/threading.py”, line 1016 in _bootstrap_inner
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/threading.py”, line 973 in _bootstrap

Current thread 0x00007f503667c740 (most recent call first):
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/site-packages/OpenGL/platform/baseplatform.py”, line 415 in call
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/ui/gui/lib/OpenGL/CcpnOpenGLArrays.py”, line 277 in drawIndexVBO
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/ui/gui/lib/OpenGL/CcpnOpenGL.py”, line 3476 in drawGrid
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/ui/gui/lib/OpenGL/CcpnOpenGL.py”, line 3245 in _paintGL
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/ui/gui/lib/OpenGL/CcpnOpenGL.py”, line 3145 in paintGL
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/ui/gui/widgets/Application.py”, line 54 in start
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/ui/gui/Gui.py”, line 214 in startUi
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/framework/Framework.py”, line 480 in _startApplication
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/AnalysisAssign/main.py”, line 47 in main
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/src/python/ccpn/AnalysisAssign/main.py”, line 55 in
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/runpy.py”, line 86 in _run_code
File “/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/miniconda/lib/python3.10/runpy.py”, line 196 in _run_module_as_main

Extension modules: PyQt5.QtCore, PyQt5.QtGui, PyQt5.QtWidgets, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.tslib, pandas._libs.lib, pandas._libs.hashing, pandas._libs.ops, pandas._libs.arrays, pandas._libs.index, pandas._libs.join, pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, pandas._libs.internals, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.tslibs.strptime, pandas._libs.groupby, pandas._libs.testing, pandas._libs.parsers, pandas._libs.json, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg._cythonized_array_utils, scipy.linalg._flinalg, scipy.linalg._solve_toeplitz, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_lapack, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, ccpnc.peak.Peak, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.h5r, h5py.utils, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5t, h5py._conv, h5py.h5z, h5py._proxy, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5o, h5py.h5l, h5py._selector, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.signal._sigtools, scipy._lib._uarray._uarray, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal._spline, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.signal._sosfilt, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.signal._spectral, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.stats.ncx2_ufunc, scipy.stats._boost.ncx2_ufunc, scipy.stats.nct_ufunc, scipy.stats._boost.nct_ufunc, scipy.stats.skewnorm_ufunc, scipy.stats._boost.skewnorm_ufunc, scipy.stats.invgauss_ufunc, scipy.stats._boost.invgauss_ufunc, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy.stats._statlib, scipy.stats._mvn, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._rcont.rcont, scipy.signal._peak_finding_utils, PyQt5.QtSvg, PyQt5.QtTest, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt5.QtNetwork, PyQt5.QtPrintSupport, reportlab.lib._rl_accel, reportlab.graphics._renderPM, zmq.backend.cython.context, zmq.backend.cython.message, zmq.backend.cython.socket, zmq.backend.cython._device, zmq.backend.cython._poll, zmq.backend.cython._proxy_steerable, zmq.backend.cython._version, zmq.backend.cython.error, zmq.backend.cython.utils, tornado.speedups, psutil._psutil_linux, psutil._psutil_posix, _pydevd_bundle.pydevd_cython, ccpnc.contour.Contourer2d, _cffi_backend, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 233)
/maps/projects/sbinlab/people/mrp113/ccpnmr3.2.0CentOS7Academic/ccpnmr3.2.0/bin/analysisassign: line 22: 3334914 Segmentation fault (core dumped) “${CCPNMR_TOP_DIR}${CCPN_PYTHON}” -W ignore “${ANALYSIS}” “$@”

I posted a similar problem a couple of months ago but the new version 3.2 seemed to fix it, so I don’t know what the issue is and I really hope you guys can help me.

best regards,
Morten

2

I have the same issue on an Mac M1 Pro (MacOS Ventura 13.5.1)

3

Hi Morten/Lefebrej

Sorry about the problems again, I shall have a look at this.
If I remember correctly, Morten, you are running red-hat8?, which could be the issue,
I suspect that a newer release will be required.
In the meantime, if you could send the spectrum mentioned above to support@ccpn.ac.uk I can check if it’s actually a bug or not. (1Dwater_HSQC/MEN_20090331_del1-9G129RhPRL_gNhsqc.fid/test.ft2)

Similarly for Lefebrej, I think a build on a newer MacOS will solve your problem. I’ll see what I can do.

Cheers
Ed

4

Hello Ed,
I cannot build on an MacOS as I am stuck with my university chosen severs (which runs Red Hat 8). Also I am not able to send the spectrum. However, I copied the file to my local drive and tried it with the same version just for for windows 10, and just works. So i do not believe its the file.

but the funny thing is it worked with red hat for like a week or two and then suddenly the same problem occurred.

The reason why I can’t use windows is that we have to use the red hat 8 servers at my job, so if you could have a look at it, I would really appreciate it.

BR
Morten

5

Hi Morten,

well, I’m currently working on a CentOS8/red hat8 version, which will be ready soon.
In the mean-time, can you try and update again and see if you get the same error.

Can you remember the day you updated and it stopped working?

Many thanks
Ed

6

Hello Ed,

nice to hear from you. I am so glad about the new upcoming CentOS8/Red Hat 8 version. I haven’t updated my own version yet the last 2 weeks, but am about to.

As for the day where it all stop working will have to be an estimate.

But as far as I can figure out it was the 10 of August 2023.

At that point I had been out sick for two weeks before hand, and then it wouldn’t work.

Best Regards,

Morten

7

Hello again,

I’ve finally had time to update and try to display my spectra (I’ve also tried to open projects). It still crashes in the same way. It isn’t an issue to open the spectra in ccpnmr, but when you try to display it, the program crashes.

I’m sending you a file with the error message again as I cannot tell if it is completely identical to the original.

BR

Morten

(Attachment ccprnmr_crash_note.txt is missing)