[yt-users] undefined symbol: _intel_fast_memcpy

John Wise jwise at astro.princeton.edu
Wed May 5 15:33:46 PDT 2010


I think you can look in yt_install.log to see the compiler the script used when compiling yt.

I know how to force an installation to use a particular compiler by setting the environment variable CC and CXX.
Something like "env CC=gcc CXX=g++ python setup.py install" would work for a simple python install.  You can put the "env CC=gcc CXX=g++" in front of most installations.

John


On 5 May 2010, at 18:24, Jean-Claude Passy wrote:

> Hi Jeff,
> 
> sorry I am little bit lost. Python seems to work fine even if the intel module is loaded:
> 
> ###########################################################
> [11:37:45] seawolf1:$ module load intel/11.0.074
> [11:37:49] seawolf1:$ which python2.6
> ~/yt-x86_64/bin/python2.6
> [11:37:59] seawolf1:$ python2.6
> Python 2.6.3 (r263:75183, Apr 14 2010, 08:48:56) 
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> 
> ###########################################################
> 
> How do I know which compiler I used to build yt ? I can't find it in the install script.
> Thanks,
> 
> JC
> 
> j s oishi a écrit :
>> 
>> JC,
>> 
>> You cannot use yt (or python) with the intel module loaded. What
>> compiler did you build yt with? It was probably gcc, and you must load
>> that module at runtime in order to use yt. You can switch with
>> 
>> $ module swap <name-of-intel> <name-of-gcc>
>> 
>> j
>> 
>> On Wed, May 5, 2010 at 9:40 AM, Jean-Claude Passy <jcpassy at gmail.com> wrote:
>>   
>>> Dear all,
>>> 
>>> an error occurred when I try to launch yt:
>>> 
>>> [ 9:30:33] seawolf2:$ iyt
>>> Traceback (most recent call last):
>>>  File "/global/home/jcpassy/yt-x86_64/bin/iyt", line 7, in <module>
>>>   execfile(__file__)
>>>  File "/global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/scripts/iyt", line 3,
>>> in <module>
>>>   from yt.mods import *
>>>  File "/global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/mods.py", line 32,
>>> in <module>
>>>   import yt.lagos as lagos
>>>  File
>>> "/global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/lagos/__init__.py", line
>>> 58, in <module>
>>>   import yt.amr_utils as amr_utils
>>> ImportError:
>>> /global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/yt/amr_utils.so: undefined
>>> symbol: _intel_fast_memcpy
>>> 
>>> 
>>> I am loading the intel module at start (see my bashrc).
>>> Any help much appreciated.
>>> 
>>> Thanks,
>>> 
>>> Jean-Claude
>>> 
>>> # .bashrc
>>> # user functions and aliases
>>> # Environment stuff goes in .profile
>>> #
>>> #  Read a common system Bashrc file first
>>>   if [  -f /global/system/common/Bashrc ] ;
>>>   then
>>>        . /global/system/common/Bashrc
>>>   fi
>>> 
>>> # set bash variable to keep 50 command in history
>>> HSTSIZE=100
>>> 
>>> #  Include any personal modifications below
>>> #  modification can include the aliases functions etc.
>>> 
>>> # PS1
>>> export PS1="[\$(date +%k:%M:%S)] \h:\$ "
>>> 
>>> # Path
>>> export
>>> PATH=/global/home/jcpassy/orcinus_jc/hdf5-1.8.4/bin:/global/home/jcpassy/orcinus_jc/openmpi-1.4.1/bin:/global/home/jcpassy/yt-x86_64/bin/:/global/home/jcpassy/hg/bin:${PATH}
>>> export
>>> PYTHONPATH=/global/home/jcpassy/yt-x86_64/lib/python2.6/site-packages/:/global/home/jcpassy/hg/lib64/python2.4/site-packages:${PYTHONPATH}
>>> export
>>> LD_LIBRARY_PATH=/global/home/jcpassy/orcinus_jc/hdf5-1.8.4/lib:/global/home/jcpassy/orcinus_jc/openmpi-1.4.1/lib:/global/home/jcpassy/yt-x86_64/lib/:${LD_LIBRARY_PATH}
>>> export
>>>  LD_LIBRARY_PATH=/global/home/jcpassy/orcinus_jc/szip-2.1/lib:${LD_LIBRARY_PATH}
>>> 
>>> # Linux aliases
>>> alias rm='rm -f'
>>> alias rmjc='rm *~ *#'
>>> alias lsd='ls -d'
>>> alias ed='emacs -nw'
>>> alias ls2='ls -s -h -CF -G'
>>> alias df='df -h'
>>> alias dus='du -s -h'
>>> 
>>> alias tarcvzf='tar -cvzf'
>>> alias tarzxvf='tar -zxvf'
>>> 
>>> # Loading modules
>>> module load intel/11.0.074
>>> 
>>> # Some small programs
>>> alias calc_orbit='/global/home/jcpassy/TOOLS/orbit/calc_orbit.exe'
>>> alias clean_enzo='/global/home/jcpassy/TOOLS/enzo/clean_enzo_output.exe'
>>> alias print_units='/global/home/jcpassy/TOOLS/units/print_units.exe'
>>> 
>>> 
>>> #From falk
>>> 
>>> alias qjc='qstat -u jcpassy'
>>> alias mjobs='showq -u jcpassy'
>>> alias qjobs='showq -i | more'
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>> 
>>> 
>>>     
>> 
>> 
>> 
>>   
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