Cython discrepancy in yt install from source
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt ******************************************** FAILURE REPORT: ********************************************
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
******************************************** ********************************************
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt
FAILURE REPORT:
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt
FAILURE REPORT:
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site- packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt
FAILURE REPORT:
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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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Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt
FAILURE REPORT:
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site- packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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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Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/27dafcdaf068829c78f34c4c7211f...
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt
FAILURE REPORT:
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packag es/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
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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Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/ 27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Dear yt-users,
I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?
Here is a piece of the failure report I got:
Installing GitPython-2.1.3 Installing sympy-1.0 Building Rockstar Installing yt
FAILURE REPORT:
File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packag es/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command cmd_obj.ensure_finalized() File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized self.finalize_options() File "setup.py", line 308, in finalize_options cython.__version__) RuntimeError: Building yt from source requires Cython 0.24 or newer but Cython 0.23.5 is installed. Please update Cython using the appropriate package manager for your python environment.
Cheers, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.
If that's not the problem I'm not sure what the issue is.
You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:
http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda
On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/27dafcdaf068829c78f34c4c7211f...
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.
Nathan
On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
> Dear yt-users, > > I am trying to compile yt with rockstar enabled, so I am having yt > install itself from source. The code downloads Cython 0.23.5, but later > then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this > failed (I probably did it wrong). What do I need to change to make the > install_script.sh work with Cython? > > Here is a piece of the failure report I got: > > Installing GitPython-2.1.3 > Installing sympy-1.0 > Building Rockstar > Installing yt > ******************************************** > FAILURE REPORT: > ******************************************** > > File > "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", > line 132, in add_defaults > File > "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line > 299, in get_finalized_command > cmd_obj.ensure_finalized() > File > "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line > 107, in ensure_finalized > self.finalize_options() > File "setup.py", line 308, in finalize_options > cython.__version__) > RuntimeError: Building yt from source requires Cython 0.24 or newer > but > Cython 0.23.5 is installed. Please update Cython using the > appropriate > package manager for your python environment. > > ******************************************** > ******************************************** > > Cheers, > Carla Bernhardt > PhD Student > ZAH Institut für Theoretische Astrophysik > Universität Heidelberg > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
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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
I did delete the previous partial installations of yt before each attempt at installation. I previously tried installing rockstar manually for a conda-based environment, but I don't remember what went wrong, so I will try that again and let you know. Either way, thank you for your insights.
Cheers, Carla
2017-06-20 14:59 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.
If that's not the problem I'm not sure what the issue is.
You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:
http://yt-project.org/docs/dev/installing.html# installing-yt-using-anaconda
On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/ 27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got this strange error https://pastebin.com/EWXsbzCx that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.
Cheers, Carla
2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
> Hi Carla, > > I think we need to update the install script for the case with > INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get > rockstar setup, we made it so you can use rockstar with a conda-based > install a while back. > > Nathan > > On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < > carla.j.bernhardt@gmail.com> wrote: > >> Dear yt-users, >> >> I am trying to compile yt with rockstar enabled, so I am having yt >> install itself from source. The code downloads Cython 0.23.5, but later >> then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this >> failed (I probably did it wrong). What do I need to change to make the >> install_script.sh work with Cython? >> >> Here is a piece of the failure report I got: >> >> Installing GitPython-2.1.3 >> Installing sympy-1.0 >> Building Rockstar >> Installing yt >> ******************************************** >> FAILURE REPORT: >> ******************************************** >> >> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site- >> packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", >> line 132, in add_defaults >> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", >> line 299, in get_finalized_command >> cmd_obj.ensure_finalized() >> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", >> line 107, in ensure_finalized >> self.finalize_options() >> File "setup.py", line 308, in finalize_options >> cython.__version__) >> RuntimeError: Building yt from source requires Cython 0.24 or newer >> but >> Cython 0.23.5 is installed. Please update Cython using the >> appropriate >> package manager for your python environment. >> >> ******************************************** >> ******************************************** >> >> Cheers, >> Carla Bernhardt >> PhD Student >> ZAH Institut für Theoretische Astrophysik >> Universität Heidelberg >> >> _______________________________________________ >> 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
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
Also if this is a cluster, make sure you have any modules unloaded. I think your HDF5 issue might be because h5py is picking up a system HDF5 installation.
On Tue, Jun 20, 2017 at 8:05 AM Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
I did delete the previous partial installations of yt before each attempt at installation. I previously tried installing rockstar manually for a conda-based environment, but I don't remember what went wrong, so I will try that again and let you know. Either way, thank you for your insights.
Cheers, Carla
2017-06-20 14:59 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.
If that's not the problem I'm not sure what the issue is.
You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:
http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda
On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/27dafcdaf068829c78f34c4c7211f...
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
No, I haven't seen that error before.
I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.
By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:
https://github.com/yt-project/yt/issues/1289
Nathan
On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
> Hi Nathan, > > I did try running with rockstar install enabled, INST_CONDA=1 and > INST_YT_SOURCE=1 and I got this strange error > https://pastebin.com/EWXsbzCx that I don't have the file > "libisl.so.10". Any suggestions on that? I wasn't able to find anything > helpful about this online. I just want to get a working version of yt going > with rockstar enabled, it doesn't have to be from source. > > Cheers, > Carla > > 2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com: > >> Hi Carla, >> >> I think we need to update the install script for the case with >> INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get >> rockstar setup, we made it so you can use rockstar with a conda-based >> install a while back. >> >> Nathan >> >> On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < >> carla.j.bernhardt@gmail.com> wrote: >> >>> Dear yt-users, >>> >>> I am trying to compile yt with rockstar enabled, so I am having yt >>> install itself from source. The code downloads Cython 0.23.5, but later >>> then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this >>> failed (I probably did it wrong). What do I need to change to make the >>> install_script.sh work with Cython? >>> >>> Here is a piece of the failure report I got: >>> >>> Installing GitPython-2.1.3 >>> Installing sympy-1.0 >>> Building Rockstar >>> Installing yt >>> ******************************************** >>> FAILURE REPORT: >>> ******************************************** >>> >>> File >>> "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", >>> line 132, in add_defaults >>> File >>> "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line >>> 299, in get_finalized_command >>> cmd_obj.ensure_finalized() >>> File >>> "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line >>> 107, in ensure_finalized >>> self.finalize_options() >>> File "setup.py", line 308, in finalize_options >>> cython.__version__) >>> RuntimeError: Building yt from source requires Cython 0.24 or >>> newer but >>> Cython 0.23.5 is installed. Please update Cython using the >>> appropriate >>> package manager for your python environment. >>> >>> ******************************************** >>> ******************************************** >>> >>> Cheers, >>> Carla Bernhardt >>> PhD Student >>> ZAH Institut für Theoretische Astrophysik >>> Universität Heidelberg >>> >>> _______________________________________________ >>> 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
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
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I did forget to take off the modules (yes, that solves the h5py problem!), but I just tried again without any modules and I got the print_line error again (which I really don't understand): ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T).
Cheers, Carla
2017-06-20 15:08 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Also if this is a cluster, make sure you have any modules unloaded. I think your HDF5 issue might be because h5py is picking up a system HDF5 installation.
On Tue, Jun 20, 2017 at 8:05 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
I did delete the previous partial installations of yt before each attempt at installation. I previously tried installing rockstar manually for a conda-based environment, but I don't remember what went wrong, so I will try that again and let you know. Either way, thank you for your insights.
Cheers, Carla
2017-06-20 14:59 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.
If that's not the problem I'm not sure what the issue is.
You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:
http://yt-project.org/docs/dev/installing.html# installing-yt-using-anaconda
On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/ 27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.
Cheers, Carla
2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
> No, I haven't seen that error before. > > I'll be heading into the office shortly and will update the install > script when I get in. If you can't wait on me, you could try updating it > yourself to download the latest cython release from e.g. pypi. > > By the way, do you happen to be using the latest version of MacOS? > In that case building rockstar from source will not work: > > https://github.com/yt-project/yt/issues/1289 > > Nathan > > On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < > carla.j.bernhardt@gmail.com> wrote: > >> Hi Nathan, >> >> I did try running with rockstar install enabled, INST_CONDA=1 and >> INST_YT_SOURCE=1 and I got this strange error >> https://pastebin.com/EWXsbzCx that I don't have the file >> "libisl.so.10". Any suggestions on that? I wasn't able to find anything >> helpful about this online. I just want to get a working version of yt going >> with rockstar enabled, it doesn't have to be from source. >> >> Cheers, >> Carla >> >> 2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com: >> >>> Hi Carla, >>> >>> I think we need to update the install script for the case with >>> INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get >>> rockstar setup, we made it so you can use rockstar with a conda-based >>> install a while back. >>> >>> Nathan >>> >>> On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < >>> carla.j.bernhardt@gmail.com> wrote: >>> >>>> Dear yt-users, >>>> >>>> I am trying to compile yt with rockstar enabled, so I am having >>>> yt install itself from source. The code downloads Cython 0.23.5, but later >>>> then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this >>>> failed (I probably did it wrong). What do I need to change to make the >>>> install_script.sh work with Cython? >>>> >>>> Here is a piece of the failure report I got: >>>> >>>> Installing GitPython-2.1.3 >>>> Installing sympy-1.0 >>>> Building Rockstar >>>> Installing yt >>>> ******************************************** >>>> FAILURE REPORT: >>>> ******************************************** >>>> >>>> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site- >>>> packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", >>>> line 132, in add_defaults >>>> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", >>>> line 299, in get_finalized_command >>>> cmd_obj.ensure_finalized() >>>> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", >>>> line 107, in ensure_finalized >>>> self.finalize_options() >>>> File "setup.py", line 308, in finalize_options >>>> cython.__version__) >>>> RuntimeError: Building yt from source requires Cython 0.24 or >>>> newer but >>>> Cython 0.23.5 is installed. Please update Cython using the >>>> appropriate >>>> package manager for your python environment. >>>> >>>> ******************************************** >>>> ******************************************** >>>> >>>> Cheers, >>>> Carla Bernhardt >>>> PhD Student >>>> ZAH Institut für Theoretische Astrophysik >>>> Universität Heidelberg >>>> >>>> _______________________________________________ >>>> 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 > >
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
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
Hi Carla,
I think setuptools likely needs to be updated in the install script as well. I've gone ahead and done that:
https://github.com/yt-project/yt/pull/1458
For the INST_CONDA=0 portion of the install script, keeping everything up-to-date is a perpetually losing battle. I'd really like it if we could just get rid of that option, since we don't really have the resources to ensure it's always up-to-date and working on a variety of platforms.
Nathan
On Tue, Jun 20, 2017 at 9:49 AM Carla Bernhardt carla.j.bernhardt@gmail.com wrote:
I did forget to take off the modules (yes, that solves the h5py problem!), but I just tried again without any modules and I got the print_line error again (which I really don't understand): ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T).
Cheers, Carla
2017-06-20 15:08 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Also if this is a cluster, make sure you have any modules unloaded. I think your HDF5 issue might be because h5py is picking up a system HDF5 installation.
On Tue, Jun 20, 2017 at 8:05 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
I did delete the previous partial installations of yt before each attempt at installation. I previously tried installing rockstar manually for a conda-based environment, but I don't remember what went wrong, so I will try that again and let you know. Either way, thank you for your insights.
Cheers, Carla
2017-06-20 14:59 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.
If that's not the problem I'm not sure what the issue is.
You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:
http://yt-project.org/docs/dev/installing.html# installing-yt-using-anaconda
On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Done:
https://github.com/yt-project/yt/pull/1458/files
You should be able to get an updated install script by downloading it from my fork:
$ wget https://raw.githubusercontent.com/ngoldbaum/yt/ 27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh
-Nathan
On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
> Hi Nathan, > > I don't mind waiting, I think you will do a better job updating the > script. I tried before, but the installation still failed. I am not using > MacOS, I am on a server using Redhat. > > Cheers, > Carla > > 2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com: > >> No, I haven't seen that error before. >> >> I'll be heading into the office shortly and will update the install >> script when I get in. If you can't wait on me, you could try updating it >> yourself to download the latest cython release from e.g. pypi. >> >> By the way, do you happen to be using the latest version of MacOS? >> In that case building rockstar from source will not work: >> >> https://github.com/yt-project/yt/issues/1289 >> >> Nathan >> >> On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < >> carla.j.bernhardt@gmail.com> wrote: >> >>> Hi Nathan, >>> >>> I did try running with rockstar install enabled, INST_CONDA=1 and >>> INST_YT_SOURCE=1 and I got this strange error >>> https://pastebin.com/EWXsbzCx that I don't have the file >>> "libisl.so.10". Any suggestions on that? I wasn't able to find anything >>> helpful about this online. I just want to get a working version of yt going >>> with rockstar enabled, it doesn't have to be from source. >>> >>> Cheers, >>> Carla >>> >>> 2017-06-19 15:17 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com >>> : >>> >>>> Hi Carla, >>>> >>>> I think we need to update the install script for the case with >>>> INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get >>>> rockstar setup, we made it so you can use rockstar with a conda-based >>>> install a while back. >>>> >>>> Nathan >>>> >>>> On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < >>>> carla.j.bernhardt@gmail.com> wrote: >>>> >>>>> Dear yt-users, >>>>> >>>>> I am trying to compile yt with rockstar enabled, so I am having >>>>> yt install itself from source. The code downloads Cython 0.23.5, but later >>>>> then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this >>>>> failed (I probably did it wrong). What do I need to change to make the >>>>> install_script.sh work with Cython? >>>>> >>>>> Here is a piece of the failure report I got: >>>>> >>>>> Installing GitPython-2.1.3 >>>>> Installing sympy-1.0 >>>>> Building Rockstar >>>>> Installing yt >>>>> ******************************************** >>>>> FAILURE REPORT: >>>>> ******************************************** >>>>> >>>>> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site- >>>>> packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", >>>>> line 132, in add_defaults >>>>> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", >>>>> line 299, in get_finalized_command >>>>> cmd_obj.ensure_finalized() >>>>> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", >>>>> line 107, in ensure_finalized >>>>> self.finalize_options() >>>>> File "setup.py", line 308, in finalize_options >>>>> cython.__version__) >>>>> RuntimeError: Building yt from source requires Cython 0.24 or >>>>> newer but >>>>> Cython 0.23.5 is installed. Please update Cython using the >>>>> appropriate >>>>> package manager for your python environment. >>>>> >>>>> ******************************************** >>>>> ******************************************** >>>>> >>>>> Cheers, >>>>> Carla Bernhardt >>>>> PhD Student >>>>> ZAH Institut für Theoretische Astrophysik >>>>> Universität Heidelberg >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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Hi Nathan,
I finally got yt installed successfully with rockstar using INST_CONDA=1 and INST_YT_SOURCE=1. Thanks for your help. I must have just not disabled the modules before.
Cheers, Carla
2017-06-20 17:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Hi Carla,
I think setuptools likely needs to be updated in the install script as well. I've gone ahead and done that:
https://github.com/yt-project/yt/pull/1458
For the INST_CONDA=0 portion of the install script, keeping everything up-to-date is a perpetually losing battle. I'd really like it if we could just get rid of that option, since we don't really have the resources to ensure it's always up-to-date and working on a variety of platforms.
Nathan
On Tue, Jun 20, 2017 at 9:49 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
I did forget to take off the modules (yes, that solves the h5py problem!), but I just tried again without any modules and I got the print_line error again (which I really don't understand): ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T).
Cheers, Carla
2017-06-20 15:08 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Also if this is a cluster, make sure you have any modules unloaded. I think your HDF5 issue might be because h5py is picking up a system HDF5 installation.
On Tue, Jun 20, 2017 at 8:05 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
I did delete the previous partial installations of yt before each attempt at installation. I previously tried installing rockstar manually for a conda-based environment, but I don't remember what went wrong, so I will try that again and let you know. Either way, thank you for your insights.
Cheers, Carla
2017-06-20 14:59 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.
If that's not the problem I'm not sure what the issue is.
You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:
http://yt-project.org/docs/dev/installing.html#installing- yt-using-anaconda
On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt < carla.j.bernhardt@gmail.com> wrote:
Hi Nathan,
Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: ValueError: HDF5 version string must be in X.Y.Z format (more of the error here https://pastebin.com/ci3QMtRL). So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error: ImportError: cannot import name 'print_line' (more of the error here https://pastebin.com/61haGr3T). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (same result https://pastebin.com/xgXyzBQx). Any suggestions?
Cheers, Carla
2017-06-19 16:45 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com:
> Done: > > https://github.com/yt-project/yt/pull/1458/files > > You should be able to get an updated install script by downloading > it from my fork: > > $ wget https://raw.githubusercontent.com/ngoldbaum/yt/27dafcda > f068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh > > -Nathan > > On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt < > carla.j.bernhardt@gmail.com> wrote: > >> Hi Nathan, >> >> I don't mind waiting, I think you will do a better job updating the >> script. I tried before, but the installation still failed. I am not using >> MacOS, I am on a server using Redhat. >> >> Cheers, >> Carla >> >> 2017-06-19 15:43 GMT+02:00 Nathan Goldbaum nathan12343@gmail.com: >> >>> No, I haven't seen that error before. >>> >>> I'll be heading into the office shortly and will update the >>> install script when I get in. If you can't wait on me, you could try >>> updating it yourself to download the latest cython release from e.g. pypi. >>> >>> By the way, do you happen to be using the latest version of MacOS? >>> In that case building rockstar from source will not work: >>> >>> https://github.com/yt-project/yt/issues/1289 >>> >>> Nathan >>> >>> On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt < >>> carla.j.bernhardt@gmail.com> wrote: >>> >>>> Hi Nathan, >>>> >>>> I did try running with rockstar install enabled, INST_CONDA=1 and >>>> INST_YT_SOURCE=1 and I got this strange error >>>> https://pastebin.com/EWXsbzCx that I don't have the file >>>> "libisl.so.10". Any suggestions on that? I wasn't able to find anything >>>> helpful about this online. I just want to get a working version of yt going >>>> with rockstar enabled, it doesn't have to be from source. >>>> >>>> Cheers, >>>> Carla >>>> >>>> 2017-06-19 15:17 GMT+02:00 Nathan Goldbaum <nathan12343@gmail.com >>>> >: >>>> >>>>> Hi Carla, >>>>> >>>>> I think we need to update the install script for the case with >>>>> INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get >>>>> rockstar setup, we made it so you can use rockstar with a conda-based >>>>> install a while back. >>>>> >>>>> Nathan >>>>> >>>>> On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt < >>>>> carla.j.bernhardt@gmail.com> wrote: >>>>> >>>>>> Dear yt-users, >>>>>> >>>>>> I am trying to compile yt with rockstar enabled, so I am having >>>>>> yt install itself from source. The code downloads Cython 0.23.5, but later >>>>>> then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this >>>>>> failed (I probably did it wrong). What do I need to change to make the >>>>>> install_script.sh work with Cython? >>>>>> >>>>>> Here is a piece of the failure report I got: >>>>>> >>>>>> Installing GitPython-2.1.3 >>>>>> Installing sympy-1.0 >>>>>> Building Rockstar >>>>>> Installing yt >>>>>> ******************************************** >>>>>> FAILURE REPORT: >>>>>> ******************************************** >>>>>> >>>>>> File "/home/hd/hd_hd/hd_ri129/yt-x8 >>>>>> 6_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5. >>>>>> egg/setuptools/command/sdist.py", line 132, in add_defaults >>>>>> File "/home/hd/hd_hd/hd_ri129/yt-x8 >>>>>> 6_64/lib/python3.5/distutils/cmd.py", line 299, in >>>>>> get_finalized_command >>>>>> cmd_obj.ensure_finalized() >>>>>> File "/home/hd/hd_hd/hd_ri129/yt-x8 >>>>>> 6_64/lib/python3.5/distutils/cmd.py", line 107, in >>>>>> ensure_finalized >>>>>> self.finalize_options() >>>>>> File "setup.py", line 308, in finalize_options >>>>>> cython.__version__) >>>>>> RuntimeError: Building yt from source requires Cython 0.24 or >>>>>> newer but >>>>>> Cython 0.23.5 is installed. Please update Cython using the >>>>>> appropriate >>>>>> package manager for your python environment. >>>>>> >>>>>> ******************************************** >>>>>> ******************************************** >>>>>> >>>>>> Cheers, >>>>>> Carla Bernhardt >>>>>> PhD Student >>>>>> ZAH Institut für Theoretische Astrophysik >>>>>> Universität Heidelberg >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>> >>> >> >> _______________________________________________ >> 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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Carla Bernhardt -
Nathan Goldbaum