[yt-users] error installing mecurial during yt install

Brendan Griffen brendan.f.griffen at gmail.com
Wed Sep 4 06:31:11 PDT 2013


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.

I know how busy you are and how tedious this must be so I appreciate your
help. :)

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
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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