Hi Luigi, That does sound like a good solution. I gave it a quick go myself, but still hit some difficulties. I'd love the details if you wouldn't mind sharing. Elizabeth On 2011-07-15, at 9:28 PM, Luigi Iapichino wrote:

Hi Elisabeth,

I had the same problem, namely I have yt on a machine that does not allow Internet access, outside a number of allowed IPs. My solution was to mount the yt directory remotely on my local (and allowed) PC using sshfs. Afterwards I run the install_script, using alternatively my PC for downloading the needed libraries, and the other machine for compiling. The install_script is not exactly thought for this use, but with some effort and patience it worked; even more important, now I can update my installation with bugfixes and additions, whenever they are available (it's also a bit lengthy, but it works).

If you like this solution, I can provide you the details.

Cheers,

Luigi

On Friday 15 July 2011, Elizabeth Tasker wrote:

...

Hi,

I'm trying to install yt on the xt4 machine in Tokyo, which obnoxiously refuses to let you use wget.

I scp-ed a copy from my desktop to the xt4 and then told the install_script.sh where to find yt so it didn't try and download the packages. I also removed 'done' from each of the packages in src.

Unfortunately, I get:

gcc -fPIC -fPIC -o bzip2. bzip2.o -L. -lbz2 bzip2.o file not recognized: File format not recognized

xt4 does use modules for loading packages, but I don't know if I'm lacking a module or if my self-cleaning is flawed.

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

--

---------------------------------------------------------------

Luigi Iapichino Zentrum fuer Astronomie der Universitaet Heidelberg Institut fuer Theoretische Astrophysik Albert-Ueberle-Str. 2, D-69120 Heidelberg, Germany Tel: +49 6221 548983, Fax: +49 6221 544221 e-mail (NEW!): luigi@uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/ _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi Steffen, Thank you for that suggestion. That, coupled with a few adaptions to distribute.py got me further, but for some reason it is now claiming it can't see the zlib libraries, even though they are in the library path. After install bootstrap. /home/taskerez/yt-test/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info already exists /home/taskerez/yt-test/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate': H5Zdeflate.c:(.text+0x132): undefined reference to `compress2' H5Zdeflate.c:(.text+0x1e5): undefined reference to `inflateInit_' H5Zdeflate.c:(.text+0x1fa): undefined reference to `inflate' H5Zdeflate.c:(.text+0x295): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x2a2): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x3fa): undefined reference to `inflateEnd' collect2: ld returned 1 exit status Still, this might be a system set-up problem, not a yt installation fail. Thanks, Elizabeth On Jul 16, 2011, at 5:37 PM, Steffen Klemer wrote:

Hey Elizabeth,

...

I scp-ed a copy from my desktop to the xt4 and then told the install_script.sh where to find yt so it didn't try and download the packages. I also removed 'done' from each of the packages in src.

You could try to remove everything except the src-Folder. And in src everything except *tar.gz,tgz,zip,tar.bz2, yt-hg and yt-supplemtal and re-run the script. This did it for me in a similar situation.

You could also check in the header of the script whether you want to install your own copy of some libs or not.

bye /Steffen

-- () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

I fixed the issue with installing by loading in some different modules but it still won't run: taskerez@xt05:~> yt-2/bin/iyt Traceback (most recent call last): File "yt-2/bin/iyt", line 7, in <module> execfile(__file__) File "/home/taskerez/yt-libraries/yt-hg/scripts/iyt", line 3, in <module> from yt.mods import * File "/home/taskerez/yt-libraries/yt-hg/yt/mods.py", line 45, in <module> from yt.data_objects.api import \ File "/home/taskerez/yt-libraries/yt-hg/yt/data_objects/api.py", line 34, in <module> from hierarchy import \ File "/home/taskerez/yt-libraries/yt-hg/yt/data_objects/hierarchy.py", line 39, in <module> from yt.utilities.io_handler import io_registry File "/home/taskerez/yt-libraries/yt-hg/yt/utilities/io_handler.py", line 28, in <module> import yt.utilities.amr_utils as au ImportError: /home/taskerez/yt-libraries/yt-hg/yt/utilities/amr_utils.so: invalid ELF header Any ideas what is causing this? On Jul 17, 2011, at 6:53 AM, Steffen Klemer wrote:

Am Sat, 16.07.2011 um 20:37 schrieb Elizabeth Tasker <taskere@mcmaster.ca>:

...

Thank you for that suggestion. That, coupled with a few adaptions to distribute.py got me further, but for some reason it is now claiming it can't see the zlib libraries, even though they are in the library path.

Try to use the zlib-Version from yt (just enable it in the install-script)

/Steffen

-- () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi Steffen, A good thought (since I did copy a lot of things!) but it sadly didn't make any difference. I still get the same error. Elizabeth On Jul 19, 2011, at 7:32 PM, Steffen Klemer wrote:

Hey Elisabeth,

...

ImportError: /home/taskerez/yt-libraries/yt-hg/yt/utilities/amr_utils.so: invalid ELF header

It looks like you copied compiled yt-code to the xt which cannot run there (different architecture compared to your other computer?).

I would try to go to /home/taskerez/yt-libraries/yt-hg/ and run

taskerez@xt05:~> python2.7 setup.py clean taskerez@xt05:~> python2.7 setup.py build

This should rebuild everything on the xt4.

bye /Steffen

-- () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Hi Matt, I think this is basically what I've been doing. Elizabeth On Jul 19, 2011, at 10:41 PM, Matthew Turk wrote:

Elizabeth, Steffen,

(From vacation; sorry about the short reply)

Why not download all the dependencies and copy them over? Going through the install_script.sh, anything listed as get_enzotools something.tar.gz means download from http://yt.enzotools.org/dependencies/something.tar.gz , and the other things you might need are teh hg clone which you can do with hg bundle --all on a remote machine. Put all the archive files in src/ and run the install_script.sh.

-Matt

On Tue, Jul 19, 2011 at 3:52 AM, Elizabeth Tasker <taskere@mcmaster.ca> wrote:

...

Hi Steffen,

A good thought (since I did copy a lot of things!) but it sadly didn't make any difference. I still get the same error.

Elizabeth

On Jul 19, 2011, at 7:32 PM, Steffen Klemer wrote:

...

Hey Elisabeth,

...

ImportError: /home/taskerez/yt-libraries/yt-hg/yt/utilities/amr_utils.so: invalid ELF header

It looks like you copied compiled yt-code to the xt which cannot run there (different architecture compared to your other computer?).

I would try to go to /home/taskerez/yt-libraries/yt-hg/ and run

taskerez@xt05:~> python2.7 setup.py clean taskerez@xt05:~> python2.7 setup.py build

This should rebuild everything on the xt4.

bye /Steffen

-- () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments _______________________________________________ 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

Am Tue, 19.07.2011 um 12:32 schrieb Steffen Klemer <moh@gmx.org>:

taskerez@xt05:~> python2.7 setup.py clean

just saw, that this is not enough - you have to run taskerez@xt05:~> bash clean.sh and afterwards taskerez@xt05:~> python2.7 setup.py develop Sorry :-) lg /Steffen -- () ascii ribbon campaign - against html e-mail /\ www.asciiribbon.org - against proprietary attachments