problem installing yt on kraken
Greetings, I'm trying to install yt on kraken using the install_script. I have done a 'module swap PrgEnv-pgi PrgEnv-gnu' to switch to gnu compilers. I have also done 'module unload mercurial' and 'module unload python' to remove the system mercurial and python2.6 installs. Finally, I have added --enable-shared to the Python configure line in the install script, since I will try to build enzo with inline yt enabled. The build is failing on numpy with the following error: C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/lustre/scratch/britton/yt-embedded/include/python2.6 -Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c' gcc -pthread -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.6 -lm -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_sort.so /usr/bin/ld: cannot find -lpython2.6 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lpython2.6 collect2: ld returned 1 exit status Because I can see the error is that it can't find the python library, I tried adding /lustre/scratch/britton/yt-embedded/lib/python2.6/config/:/lustre/scratch/britton/yt-embedded/lib to my $LD_LIBRARY_PATH, and restarting the install, but I get the same error. I have also added the appropriate paths to PATH and PYTHONPATH and that has not helped either. Does anyone have any ideas? Britton
Stephen is the expert for YT on Kraken, something about the scratch disk cannot see the home directories when running jobs and requires static linked libraries. There is a working version of YT, just have to set these environment variables: export PATH=.:/lustre/scratch/proj/yt_common/trunk/bin:$PATH export PYTHONPATH=/lustre/scratch/proj/yt_common/trunk/bin/python export LD_LIBRARY_PATH=/lustre/scratch/proj/yt_common/trunk/lib:$LD_LIBRARY_PATH export MPLCONFIGDIR=/lustre/scratch/<user name> If you need the latest version from the install script, probably best to ask Stephen. The old documentation shows some brief install steps for the different machines (a section devoted to Kraken), but I'm not sure if Kraken is taken into account in the new script with its strange requirements. From G.S.
Greetings,
I'm trying to install yt on kraken using the install_script. I have done a 'module swap PrgEnv-pgi PrgEnv-gnu' to switch to gnu compilers. I have also done 'module unload mercurial' and 'module unload python' to remove the system mercurial and python2.6 installs. Finally, I have added --enable-shared to the Python configure line in the install script, since I will try to build enzo with inline yt enabled.
The build is failing on numpy with the following error: C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/lustre/scratch/britton/yt-embedded/include/python2.6 -Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c' gcc -pthread -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o -L. -Lbuild/temp.linux-x86_64-2.6 -lm -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_sort.so /usr/bin/ld: cannot find -lpython2.6 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lpython2.6 collect2: ld returned 1 exit status
Because I can see the error is that it can't find the python library, I tried adding /lustre/scratch/britton/yt-embedded/lib/python2.6/config/:/lustre/scratch/britton/yt-embedded/lib to my $LD_LIBRARY_PATH, and restarting the install, but I get the same error. I have also added the appropriate paths to PATH and PYTHONPATH and that has not helped either.
Does anyone have any ideas?
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Britton Smith
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gso@physics.ucsd.edu