<div dir="ltr">Hi Matt,<div><br></div><div>Thanks.</div><div><br></div><div>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.</div>
<div><br></div><div>Brendan</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Sep 4, 2013 at 9:33 AM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Brendan,<br>
<div><div class="h5"><br>
On Wed, Sep 4, 2013 at 9:31 AM, Brendan Griffen<br>
<<a href="mailto:brendan.f.griffen@gmail.com">brendan.f.griffen@gmail.com</a>> wrote:<br>
> Hi Matt,<br>
><br>
> I tried to remove the HG flag and reinstall but I get the following:<br>
><br>
> Awesome! Here we go.<br>
><br>
> Using wget<br>
> Using sha512sum<br>
> Downloading xray_emissivity.h5 from <a href="http://yt-project.org" target="_blank">yt-project.org</a><br>
> Cannot find mercurial. Please set INST_HG=1.<br>
> ********************************************<br>
> FAILURE REPORT:<br>
> ********************************************<br>
><br>
><br>
> For information on other options, you may wish to consult the<br>
> documentation at:<br>
><br>
> <a href="http://packages.python.org/distribute/easy_install.html" target="_blank">http://packages.python.org/distribute/easy_install.html</a><br>
><br>
> Please make the appropriate changes for your system and try again.<br>
><br>
> Something went wrong during the installation.<br>
> See the error message above.<br>
><br>
> ********************************************<br>
> ********************************************<br>
> Failure. Check /n/home01/bgriffen/data/lib/yt-x86_64/yt_install.log.<br>
><br>
><br>
> So I thought I could just load the cluster's Mercurial which I did and I got<br>
> the following:<br>
><br>
><br>
> Awesome! Here we go.<br>
><br>
> Using wget<br>
> Using sha512sum<br>
> Downloading xray_emissivity.h5 from <a href="http://yt-project.org" target="_blank">yt-project.org</a><br>
> Setting YT_DIR=/n/home01/bgriffen/data/lib/yt-x86_64/src/yt-hg/<br>
> Installing distribute<br>
> ********************************************<br>
> FAILURE REPORT:<br>
> ********************************************<br>
><br>
><br>
> For information on other options, you may wish to consult the<br>
> documentation at:<br>
><br>
> <a href="http://packages.python.org/distribute/easy_install.html" target="_blank">http://packages.python.org/distribute/easy_install.html</a><br>
><br>
> Please make the appropriate changes for your system and try again.<br>
><br>
> Something went wrong during the installation.<br>
> See the error message above.<br>
><br>
> ********************************************<br>
> ********************************************<br>
> Failure. Check /n/home01/bgriffen/data/lib/yt-x86_64/yt_install.log. The<br>
> last 10 lines are above.<br>
<br>
</div></div>Would it be possible to try to remove this directory:<br>
<br>
/n/home01/bgriffen/data/lib/yt-x86_64/src/yt-hg<br>
<br>
and re-run the install script as it? I suspect there may be a partial<br>
clone issue. If that fails, could you email me (off-list) the<br>
yt_install.log? We can iterate off-list, and then I will write back<br>
with a summary once we've figured out the final issue.<br>
<div class="im"><br>
><br>
> I know how busy you are and how tedious this must be so I appreciate your<br>
> help. :)<br>
<br>
</div>No no, all of this is good information.<br>
<br>
We're currently rethinking our packaging to address these types of<br>
problems -- so all of this is great to know, and I'm sorry it's such a<br>
hassle.<br>
<div class="HOEnZb"><div class="h5"><br>
><br>
> Brendan<br>
><br>
><br>
> On Wed, Sep 4, 2013 at 8:13 AM, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>> wrote:<br>
>><br>
>> Hi Brendan,<br>
>><br>
>> Sorry you're having trouble! My guess is that there is some issue<br>
>> with the way Python and hg are being compiled; it almost looks to me<br>
>> like one was compiled without relocatable symbols, which is odd as I<br>
>> thought Python did not do that by default.<br>
>><br>
>> You can use the system hg by turning INST_HG to 0 in the<br>
>> install_script. This will likely result in not being able to execute<br>
>> "yt update" but that can be worked around.<br>
>><br>
>> Let me know if that works,<br>
>><br>
>> Matt<br>
>><br>
>> On Tue, Sep 3, 2013 at 6:44 PM, Brendan Griffen<br>
>> <<a href="mailto:brendan.f.griffen@gmail.com">brendan.f.griffen@gmail.com</a>> wrote:<br>
>> > Hi,<br>
>> ><br>
>> > I am doing a fresh install so I downloaded the install_script.sh and did<br>
>> > the<br>
>> > usual bash install_script.sh<br>
>> ><br>
>> > I got this error though:<br>
>> ><br>
>> > ....<br>
>> > INST_ZLIB = 1 so I will be installing zlib<br>
>> > INST_BZLIB = 1 so I will be installing bzlib<br>
>> > INST_PNG = 1 so I will be installing libpng<br>
>> > INST_FTYPE = 1 so I will be installing freetype2<br>
>> > INST_SQLITE3 = 1 so I will be installing SQLite3<br>
>> > INST_HG = 1 so I will be installing Mercurial<br>
>> > INST_ENZO = 0 so I won't be checking out Enzo<br>
>> > INST_PYX = 0 so I won't be installing PyX<br>
>> > INST_SCIPY = 1 so I will be installing scipy<br>
>> > INST_0MQ = 1 so I will be installing ZeroMQ<br>
>> > INST_ROCKSTAR = 1 so I will be installing Rockstar<br>
>> > ....<br>
>> ><br>
>> > Downloading xray_emissivity.h5 from <a href="http://yt-project.org" target="_blank">yt-project.org</a><br>
>> > Installing mercurial-2.7<br>
>> > ********************************************<br>
>> > FAILURE REPORT:<br>
>> > ********************************************<br>
>> ><br>
>> > running build<br>
>> > running build_mo<br>
>> > running build_ext<br>
>> > building 'mercurial.base85' extension<br>
>> > gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall<br>
>> > -Wstrict-prototypes -fPIC -I/n/sw/python-2.7.1/include/python2.7 -c<br>
>> > mercurial/base85.c -o build/temp.linux-x86_64-2.7/mercurial/base85.o<br>
>> > gcc -pthread -shared -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/<br>
>> > -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/<br>
>> > build/temp.linux-x86_64-2.7/mercurial/base85.o -L. -lpython2.7 -o<br>
>> > build/lib.linux-x86_64-2.7/mercurial/base85.so<br>
>> > /usr/bin/ld:<br>
>> > /n/home01/bgriffen/data/lib/yt-x86_64/lib//libpython2.7.a(exceptions.o):<br>
>> > relocation R_X86_64_32 against `_Py_NoneStruct' can not be used when<br>
>> > making<br>
>> > a shared object; recompile with -fPIC<br>
>> > /n/home01/bgriffen/data/lib/yt-x86_64/lib//libpython2.7.a: could not<br>
>> > read<br>
>> > symbols: Bad value<br>
>> > collect2: ld returned 1 exit status<br>
>> > error: command 'gcc' failed with exit status 1<br>
>> ><br>
>> > ********************************************<br>
>> > ********************************************<br>
>> ><br>
>> > Can anyone suggest a work-around? Thanks.<br>
>> ><br>
>> > The cluster I'm on also has mecurial installed and I can load that<br>
>> > module if<br>
>> > needs be. I'm not sure if it is critical to getting yt working. Thanks.<br>
>> ><br>
>> > Brendan<br>
>> ><br>
>> > _______________________________________________<br>
>> > yt-users mailing list<br>
>> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> ><br>
>> _______________________________________________<br>
>> yt-users mailing list<br>
>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
><br>
_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
</div></div></blockquote></div><br></div>