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Michael_S_1
Beginner
688 Views

Illegal Instruction (core dumped) on CentOS 7

I am running on an HPC cluster which contains 4 different Intel CPU generations, the oldest of which is Nehalem (which has SSE4.2).  Whenever I run `help("modules")` in either the python2 or python3 distribution on our two older architectures (family 6, model 44 and 45), I get an illegal instruction exception and python crashes.  It seems to be whenever it is doing the deprecation check on matplotlib. It runs fine on all of our newer (AVX and up, through Haswell) machines. attached is a screenshot of the error occurring and the cpuinfo output for each architecture.

 

OS is CentOS 7, 3.10.0-229.el7.x86_64 #1 SMP Fri Mar 6 11:36:42 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

 

 

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4 Replies
David_L_Intel1
Employee
688 Views

Hi Michael, thanks for the extended info on the issue you are running into.  I've let the engineering team know about it–they are looking into the issue now.

Thanks,

David

Denis_N_Intel
Employee
688 Views

Hi Michael,

I'm trying to reproduce issue you reported. Unfortunately it seems that matplotlib isn't enough in my configurations.

Could you send what 'help("modules")' prints when it finishes successfully. 

And if you installed Python with conda's help then send us 'conda list' output too, please.

Denis

 

Michael_S_1
Beginner
688 Views

[jschnaitter@ec48 ~]$ python
Python 2.7.12 |Intel Corporation| (default, Feb 12 2017, 04:02:31) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution
>>> help("modules")

Please wait a moment while I gather a list of all available modules...

/apps/python/intel-python-2.7/lib/python2.7/site-packages/IPython/kernel/__init__.py:13: ShimWarning: The `IPython.kernel` package has been deprecated. You should import from ipykernel or jupyter_client instead.
  "You should import from ipykernel or jupyter_client instead.", ShimWarning)
/apps/python/intel-python-2.7/lib/python2.7/site-packages/matplotlib/cbook.py:137: MatplotlibDeprecationWarning: The matplotlib.delaunay module was deprecated in version 1.4. Use matplotlib.tri.Triangulation instead.
  warnings.warn(message, mplDeprecation, stacklevel=1)
/apps/python/intel-python-2.7/lib/python2.7/pkgutil.py:110: FutureWarning: The pandas.rpy module is deprecated and will be removed in a future version. We refer to external packages like rpy2. 
See here for a guide on how to port your code to rpy2: http://pandas.pydata.org/pandas-docs/stable/r_interface.html
  __import__(name)
/apps/python/intel-python-2.7/lib/python2.7/site-packages/skimage/filter/__init__.py:6: skimage_deprecation: The `skimage.filter` module has been renamed to `skimage.filters`.  This placeholder module will be removed in v0.13.
  warn(skimage_deprecation('The `skimage.filter` module has been renamed '
/apps/python/intel-python-2.7/lib/python2.7/site-packages/skimage/viewer/__init__.py:6: UserWarning: Viewer requires Qt
  warn('Viewer requires Qt')
/apps/python/intel-python-2.7/lib/python2.7/site-packages/theano/sandbox/gpuarray/__init__.py:10: UserWarning: theano.sandbox.gpuarray has been moved to theano.gpuarray. Please update your code and pickles. If the warning persists, clear theano's cache ('$theano/bin/theano-cache clear').
  warnings.warn(message)
BaseHTTPServer      cPickle             jupyter_client      sets
Bastion             cProfile            jupyter_console     setuptools
CDROM               cStringIO           jupyter_core        sgmllib
CGIHTTPServer       caffe               keyword             sha
Canvas              cairo               lib2to3             shelve
ConfigParser        calendar            linecache           shlex
Cookie              cgi                 linuxaudiodev       shutil
Cython              cgitb               llvmlite            signal
DLFCN               chunk               locale              simplegeneric
Dialog              cmath               logging             singledispatch
DocXMLRPCServer     cmd                 macpath             singledispatch_helpers
FileDialog          code                macurl2path         site
FixTk               codecs              mailbox             six
HTMLParser          codeop              mailcap             skimage
IN                  collections         markupbase          sklearn
IPython             colorsys            markupsafe          smtpd
MimeWriter          command             marshal             smtplib
PIL                 commands            math                sndhdr
Queue               compileall          matplotlib          socket
ScrolledText        compiler            md5                 spwd
SimpleDialog        concurrent          mhlib               sqlite3
SimpleHTTPServer    conda               mimetools           sre
SimpleXMLRPCServer  conda_env           mimetypes           sre_compile
SocketServer        configparser        mimify              sre_constants
StringIO            contextlib          mistune             sre_parse
TBB                 cookielib           mmap                ssl
TYPES               copy                modulefinder        stat
Tix                 copy_reg            mpi4py              statvfs
Tkconstants         crypt               mpl_toolkits        storemagic
Tkdnd               csv                 mpmath              string
Tkinter             ctypes              multifile           stringold
UserDict            curses              multiprocessing     stringprep
UserList            cycler              mutex               strop
UserString          cython              nbconvert           struct
_LWPCookieJar       cythonmagic         nbformat            subprocess
_MozillaCookieJar   daal                netrc               sunau
_TBB                datetime            networkx            sunaudio
__builtin__         dateutil            new                 symbol
__future__          dbhash              nis                 sympy
_abcoll             dbm                 nntplib             sympyprinting
_ast                decimal             nose                symtable
_bisect             decorator           notebook            sys
_bsddb              difflib             ntpath              sysconfig
_codecs             dircache            nturl2path          syslog
_codecs_cn          dis                 numba               tables
_codecs_hk          distarray           numbers             tabnanny
_codecs_iso2022     distutils           numexpr             tarfile
_codecs_jp          doctest             numpy               telnetlib
_codecs_kr          dumbdbm             opcode              tempfile
_codecs_tw          dummy_thread        operator            terminado
_collections        dummy_threading     optparse            termios
_csv                easy_install        os                  test
_ctypes             email               os2emxpath          test_path
_ctypes_test        encodings           ossaudiodev         test_pycosat
_curses             entrypoints         pandas              tests
_curses_panel       enum                parser              textwrap
_elementtree        errno               path                theano
_functools          examples            pathlib2            this
_hashlib            exceptions          pdb                 thread
_heapq              extern              pexpect             threading
_hotshot            fcntl               pickle              time
_io                 filecmp             pickleshare         timeit
_json               fileinput           pickletools         tkColorChooser
_locale             fnmatch             pip                 tkCommonDialog
_lsprof             formatter           pipes               tkFileDialog
_multibytecodec     fpformat            pkg_resources       tkFont
_multiprocessing    fractions           pkgutil             tkMessageBox
_osx_support        ftplib              platform            tkSimpleDialog
_pyio               funcsigs            plistlib            toaiff
_random             functools           popen2              token
_socket             functools32         poplib              tokenize
_sqlite3            future_builtins     posix               tornado
_sre                gc                  posixfile           trace
_ssl                gdbm                posixpath           traceback
_strptime           genericpath         pprint              traitlets
_struct             getopt              profile             ttk
_symtable           getpass             prompt_toolkit      tty
_sysconfigdata      gettext             pstats              turtle
_testcapi           gflags              pty                 types
_threading_local    glob                ptyprocess          unicodedata
_tkinter            grp                 pwd                 unittest
_vendor             gzip                py_compile          urllib
_warnings           h5py                pyclbr              urllib2
_weakref            hashlib             pycosat             urlparse
_weakrefset         heapq               pydoc               user
_yaml               hmac                pydoc_data          uu
abc                 hotshot             pyexpat             uuid
aifc                htmlentitydefs      pygments            warnings
antigravity         htmllib             pylab               wave
anydbm              httplib             pyparsing           wcwidth
argparse            idlelib             pytz                weakref
array               ihooks              pyximport           webbrowser
ast                 imaplib             quopri              wheel
asynchat            imghdr              random              whichdb
asyncore            imp                 re                  widgetsnbextension
atexit              importlib           repr                wsgiref
audiodev            imputil             requests            xdrlib
audioop             inspect             resource            xml
autoreload          io                  rexec               xmllib
backports           ipykernel           rfc822              xmlrpclib
backports_abc       ipyparallel         rlcompleter         xxsubtype
base64              ipython_genutils    rmagic              yaml
bdb                 ipywidgets          robotparser         zipfile
binascii            itertools           ruamel_yaml         zipimport
binhex              jinja2              runpy               zlib
bisect              json                sched               zmq
bsddb               jsonschema          scipy               
bz2                 jupyter             select              

Enter any module name to get more help.  Or, type "modules spam" to search
for modules whose descriptions contain the word "spam".

 

 

this is the output when run on our newest machines, with E5-2683v4 chips.

 

and it was installed from the downloaded archive from the portal, not with conda.

Michael_S_1
Beginner
688 Views

Any updates on this?

Reply