[yt-users] error installing mecurial during yt install

Matthew Turk matthewturk at gmail.com
Wed Sep 4 06:33:53 PDT 2013 

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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