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