[yt-users] error installing mecurial during yt install

Matthew Turk matthewturk at gmail.com
Wed Sep 4 07:13:18 PDT 2013 

On Wed, Sep 4, 2013 at 10:05 AM, Brendan Griffen
<brendan.f.griffen at gmail.com> wrote:
> 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.

Wow!  Me neither, but happy to see it's working.  To my best
recollection, the hg/git conflict has always been a cold war, but
perhaps the cluster you're on is the first breakout of hostilities.
We better keep an eye on it.

Glad to see that everything has resolved itself.  One note is that now
that you are using the system hg, to update yt you can't (necessarily)
use "yt update".  You will have to do:

cd /n/home01/bgriffen/data/lib/yt-x86_64/src/yt-hg
hg pull
hg up
python2.7 setup.py develop

to update your yt installation.  To update dependencies ("yt update
--all"), you'll have to get a new copy of the install script and
re-run it over top of the old one -- this will only update the
necessary bits, not the ones that are all up to date already.  But
this is all just for the future, not for now.

Let us know if you run into any other issues!

-Matt

>
> 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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