[galaxy-dev] HYPHY MPI linking error
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 Some eggs are out of date, attempting to fetch...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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[galaxy-dev] RPy and R installation problems
When I try to install rpy-1.0.3 against R-2.11.1 or R-2.15.1 I get the
following error about the version number being unobtainable from R
--version.
python setup.py install --prefix=/path/to/shared/python
RHOMES= []
DEBUG= True
Setting RHOMES to ['/argus/app/rhel60/R_2.11.1/lib64/R']
Traceback (most recent call last):
File "setup.py", line 109, in
RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
File "/argus/app/src/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION
raise RuntimeError("Couldn't obtain version number from output\n"
RuntimeError: Couldn't obtain version number from output
of `R --version'.
This is the R --version output:
galaxy[rpy-1.0.3]$ R --version
R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License version 2.
For more information about these matters see
http://www.gnu.org/licenses/.
Although rpy2 builds and installs successfully the linear_regression.py
module can't seem to use it. It is looking for the rpy module not the rpy2
module. If I ln -s rpy2 rpy, it appears to run but gives an name not
defined error in a line like dat= r.list(...
What is the proper procedure for installing the R and rpy dependencies?
What versions are recommended with the current galaxy on mercurial?
On Thu, June 28, 2012 3:51 pm, Susan Hester wrote:
>
> Hi,
>
> I'm trying to register in Galaxy on the public server and under the
> "user" tab "register" is greyed out? How do I register?
>
> Susan Hester, Ph.D.
> Research Biologist
> Systems Biology Branch
> Integrated Systems Toxicology Division (ISTD)
> National Health and Environmental Effects Research Lab
> US Environmental Protection Agency
> 109 T.W. Alexander Dr.
> MD-B143-06
> Research Triangle Park, NC 27711
> hester.susan@epa.gov___
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