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 Some eggs are out of date, attempting to fetch...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-x86_64-ucs4.egg
> 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.egg
> 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-x86_64-ucs4.egg
> 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-x86_64-ucs4.egg
> Fetched
> http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg
> Fetched
> http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg
> 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.egg
> 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.egg
> 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.
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