[yt-users] error installing mecurial during yt install

Brendan Griffen brendan.f.griffen at gmail.com
Wed Sep 4 07:05:53 PDT 2013


Hi Matt,

Thanks.

So before you got back to me I just checked what other packages I had
loaded. I found git was loaded and so I removed it from my module list and
re-run the package. It worked mysteriously. I can't think what would cause
a conflict. Thanks for your help.

Brendan


On Wed, Sep 4, 2013 at 9:33 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Brendan,
>
> On Wed, Sep 4, 2013 at 9:31 AM, Brendan Griffen
> <brendan.f.griffen at gmail.com> wrote:
> > Hi Matt,
> >
> > I tried to remove the HG flag and reinstall but I get the following:
> >
> > Awesome!  Here we go.
> >
> > Using wget
> > Using sha512sum
> > Downloading xray_emissivity.h5 from yt-project.org
> > Cannot find mercurial.  Please set INST_HG=1.
> > ********************************************
> >         FAILURE REPORT:
> > ********************************************
> >
> >
> > For information on other options, you may wish to consult the
> > documentation at:
> >
> >   http://packages.python.org/distribute/easy_install.html
> >
> > Please make the appropriate changes for your system and try again.
> >
> > Something went wrong during the installation.
> > See the error message above.
> >
> > ********************************************
> > ********************************************
> > Failure.  Check /n/home01/bgriffen/data/lib/yt-x86_64/yt_install.log.
> >
> >
> > So I thought I could just load the cluster's Mercurial which I did and I
> got
> > the following:
> >
> >
> > Awesome!  Here we go.
> >
> > Using wget
> > Using sha512sum
> > Downloading xray_emissivity.h5 from yt-project.org
> > Setting YT_DIR=/n/home01/bgriffen/data/lib/yt-x86_64/src/yt-hg/
> > Installing distribute
> > ********************************************
> >         FAILURE REPORT:
> > ********************************************
> >
> >
> > For information on other options, you may wish to consult the
> > documentation at:
> >
> >   http://packages.python.org/distribute/easy_install.html
> >
> > Please make the appropriate changes for your system and try again.
> >
> > Something went wrong during the installation.
> > See the error message above.
> >
> > ********************************************
> > ********************************************
> > Failure.  Check /n/home01/bgriffen/data/lib/yt-x86_64/yt_install.log.
>  The
> > last 10 lines are above.
>
> Would it be possible to try to remove this directory:
>
> /n/home01/bgriffen/data/lib/yt-x86_64/src/yt-hg
>
> and re-run the install script as it?  I suspect there may be a partial
> clone issue.  If that fails, could you email me (off-list) the
> yt_install.log?  We can iterate off-list, and then I will write back
> with a summary once we've figured out the final issue.
>
> >
> > I know how busy you are and how tedious this must be so I appreciate your
> > help. :)
>
> No no, all of this is good information.
>
> We're currently rethinking our packaging to address these types of
> problems -- so all of this is great to know, and I'm sorry it's such a
> hassle.
>
> >
> > Brendan
> >
> >
> > On Wed, Sep 4, 2013 at 8:13 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> Hi Brendan,
> >>
> >> Sorry you're having trouble!  My guess is that there is some issue
> >> with the way Python and hg are being compiled; it almost looks to me
> >> like one was compiled without relocatable symbols, which is odd as I
> >> thought Python did not do that by default.
> >>
> >> You can use the system hg by turning INST_HG to 0 in the
> >> install_script.  This will likely result in not being able to execute
> >> "yt update" but that can be worked around.
> >>
> >> Let me know if that works,
> >>
> >> Matt
> >>
> >> On Tue, Sep 3, 2013 at 6:44 PM, Brendan Griffen
> >> <brendan.f.griffen at gmail.com> wrote:
> >> > Hi,
> >> >
> >> > I am doing a fresh install so I downloaded the install_script.sh and
> did
> >> > the
> >> > usual bash install_script.sh
> >> >
> >> > I got this error though:
> >> >
> >> > ....
> >> > INST_ZLIB       = 1 so I will  be installing zlib
> >> > INST_BZLIB      = 1 so I will  be installing bzlib
> >> > INST_PNG        = 1 so I will  be installing libpng
> >> > INST_FTYPE      = 1 so I will  be installing freetype2
> >> > INST_SQLITE3    = 1 so I will  be installing SQLite3
> >> > INST_HG         = 1 so I will  be installing Mercurial
> >> > INST_ENZO       = 0 so I won't be checking out Enzo
> >> > INST_PYX        = 0 so I won't be installing PyX
> >> > INST_SCIPY      = 1 so I will  be installing scipy
> >> > INST_0MQ        = 1 so I will  be installing ZeroMQ
> >> > INST_ROCKSTAR   = 1 so I will  be installing Rockstar
> >> > ....
> >> >
> >> > Downloading xray_emissivity.h5 from yt-project.org
> >> > Installing mercurial-2.7
> >> > ********************************************
> >> >         FAILURE REPORT:
> >> > ********************************************
> >> >
> >> > running build
> >> > running build_mo
> >> > running build_ext
> >> > building 'mercurial.base85' extension
> >> > gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
> >> > -Wstrict-prototypes -fPIC -I/n/sw/python-2.7.1/include/python2.7 -c
> >> > mercurial/base85.c -o build/temp.linux-x86_64-2.7/mercurial/base85.o
> >> > gcc -pthread -shared -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/
> >> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/
> >> > build/temp.linux-x86_64-2.7/mercurial/base85.o -L. -lpython2.7 -o
> >> > build/lib.linux-x86_64-2.7/mercurial/base85.so
> >> > /usr/bin/ld:
> >> >
> /n/home01/bgriffen/data/lib/yt-x86_64/lib//libpython2.7.a(exceptions.o):
> >> > relocation R_X86_64_32 against `_Py_NoneStruct' can not be used when
> >> > making
> >> > a shared object; recompile with -fPIC
> >> > /n/home01/bgriffen/data/lib/yt-x86_64/lib//libpython2.7.a: could not
> >> > read
> >> > symbols: Bad value
> >> > collect2: ld returned 1 exit status
> >> > error: command 'gcc' failed with exit status 1
> >> >
> >> > ********************************************
> >> > ********************************************
> >> >
> >> > Can anyone suggest a work-around? Thanks.
> >> >
> >> > The cluster I'm on also has mecurial installed and I can load that
> >> > module if
> >> > needs be. I'm not sure if it is critical to getting yt working.
> Thanks.
> >> >
> >> > Brendan
> >> >
> >> > _______________________________________________
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> >> >
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