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.

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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 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi JC, I don't know why python works with the intel compiler, but I suspect if you tried to do very much with it, it would eventually have trouble finding a shared library. It is telling you right on the command line what compiler it was built with:

[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

Load that module, and yt should work. j

Thanks guys, it worked perfectly. Cheers, Jean-Claude Matthew Turk a écrit :

Hi JC,

I agree with Jeff and John -- what seems likely to me is that the last time you rebuilt the amr_utils.so module, the intel compiler was loaded. This can happen when, for instance, you run "yt instinfo -u". To fix this, I would suggest you load the gnu module and do:

# module load gnu first! cd /global/home/jcpassy/yt-x86_64/src/yt-trunk-svn/ python2.6 setup.py build_ext -i -f

That should rebuild all your yt C modules, this time with GNU.

-Matt

On Wed, May 5, 2010 at 3:33 PM, j s oishi wrote:

...

Hi JC,

I don't know why python works with the intel compiler, but I suspect if you tried to do very much with it, it would eventually have trouble finding a shared library.

It is telling you right on the command line what compiler it was built with:

...

[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

Load that module, and yt should work.

j _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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