Hi Brendan, On Wed, Sep 4, 2013 at 9:31 AM, Brendan Griffen 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 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 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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On Wed, Sep 4, 2013 at 10:05 AM, Brendan Griffen 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 wrote:

...

Hi Brendan,

On Wed, Sep 4, 2013 at 9:31 AM, Brendan Griffen 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 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 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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

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

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

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