I'm getting a linker error while compiling HYPHY with the MPI make target:
Linking CXX executable HYPHYMPI /opt/mvapich2_18a1/lib/libmpich.a(ibv_param.o):(.bss+0x70): multiple definition of `alpha' CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o:(.bss+0xa0): first defined here /usr/bin/ld: Warning: size of symbol `alpha' changed from 256 in CMakeFiles/HYPHYMPI.dir/src/core/parser2.cpp.o to 4 in /opt/mvapich2_18a1/lib/libmpich.a(ibv_param.o) collect2: ld returned 1 exit status make[3]: *** [HYPHYMPI] Error 1 make[2]: *** [CMakeFiles/HYPHYMPI.dir/all] Error 2 make[1]: *** [CMakeFiles/MPI.dir/rule] Error 2 make: *** [MPI] Error 2
Is there a specific version of MPI that this requires?
The 'alpha' symbol is defined on this line in HYPHY source code file src/core/parser1.cpp:
alpha ("ABCDEFGHIJKLMNOPQRSTUVWXYZ_abcdefghijklmnopqrstuvwxyz"), numeric (".0123456789eE");
which looks reasonable. I'm not sure what is going on in the MPI library.
On Sun, July 15, 2012 3:09 pm, Di Pe wrote:
Hi,
there seems to be an issue with pulling this egg at least since yesterday.
Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.... Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.1_7b95ff194725-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.7-linux-... Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs... Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.7-linux-x86_64-ucs4.eg... Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.... Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.7.egg svgfig 1.1.6 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e svgfig Fetch failed. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: