I listed the commands I executed - just git clone and python3 setup.py build. I cannot use pip, on BW it first tries to uninstall the system-wide distribution of yt, so their Python expert suggested I try setup.py. On 1/7/19 12:24 PM, Nathan Goldbaum wrote:
Hi Nick,
This "setup.py build" thing is new to me. It's not a setup.py command we've ever supported or documented for use with yt. I wonder why the blue waters staff told you to use it.
That said, I'm not able to reproduce the failure you're seeing (python3 setup.py build runs without error after making a fresh clone of the yt repo).
What branch and changeset are you building yt from?
What were the rest of the steps in the installation instructions you were trying to follow?
I bet if you do "pip install ." inside of your checkout of the repository, things will "just work". However since I'm not able to reproduce the failure you're seeing you may run into the same issue with "pip install". If that happens answering the questions above will allow me to do additional debugging steps on my local machine.
-Nathan
On Mon, Jan 7, 2019 at 12:03 PM Nick Gnedin <ngnedin@gmail.com <mailto:ngnedin@gmail.com>> wrote:
Folks,
I am getting an error trying to install the latest version of yt using setup.py (I have to use this method per BlueWaters staff instructions):
----------------------------- >git clone https://ngnedin@github.com/yt-project/yt.git <https://urldefense.proofpoint.com/v2/url?u=https-3A__ngnedin-40github.com_yt-2Dproject_yt.git&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=Pc6JtSRT1-838ckp3d6CNT14gEDzmp_nRldYAbQIM_I&s=g6wRdY0vpPwRXDrRCHpGZMcqG5BkhosRJoR0_o2jQEc&e=> ... Checking out files: 100% (1258/1258), done.
>cd yt yt >python3 setup.py build ... [48/48] Cythonizing yt/utilities/lib/write_array.pyx reading manifest template 'MANIFEST.in' no previously-included directories found matching 'doc/source/reference/api/generated' no previously-included directories found matching 'doc/build' writing manifest file 'yt.egg-info/SOURCES.txt' error: can't copy 'yt/analysis_modules': doesn't exist or not a regular file
yt > --------------------
Thank you,
Nick _______________________________________________ yt-users mailing list -- yt-users@python.org <mailto:yt-users@python.org> To unsubscribe send an email to yt-users-leave@python.org <mailto:yt-users-leave@python.org>
I was asking to see what the next steps were to see what sort of installation you were trying to set up. I understand that it fails for you at the "setup.py build" stage but my alternate build command suggestion would be for you will depend on what the subsequent steps would be. For pip, have you tried installing yt in your home directory by passing by pasing --local? That should be sufficient for it not to try to mess with the systemwide installation. Does the same error happen with "python setup.py install"? What python version are you using? What packages are already installed in your python environment? Again, it would be good to know what branch and changeset of yt you are trying to build. I'd assume just the master branch. Is there a "yt/analysis_modules" folder in your checkout of yt? There should be... It would also be helpful to see the full console output (e.g. by copy-pasting into a pastebin service like bpaste.net) from trying to build yt, there might be hints earlier in the output that were elided in the snippet you shared in your first e-mail. On Mon, Jan 7, 2019 at 1:27 PM Nick Gnedin <ngnedin@gmail.com> wrote:
I listed the commands I executed - just git clone and python3 setup.py build.
I cannot use pip, on BW it first tries to uninstall the system-wide distribution of yt, so their Python expert suggested I try setup.py.
On 1/7/19 12:24 PM, Nathan Goldbaum wrote:
Hi Nick,
This "setup.py build" thing is new to me. It's not a setup.py command we've ever supported or documented for use with yt. I wonder why the blue waters staff told you to use it.
That said, I'm not able to reproduce the failure you're seeing (python3 setup.py build runs without error after making a fresh clone of the yt repo).
What branch and changeset are you building yt from?
What were the rest of the steps in the installation instructions you were trying to follow?
I bet if you do "pip install ." inside of your checkout of the repository, things will "just work". However since I'm not able to reproduce the failure you're seeing you may run into the same issue with "pip install". If that happens answering the questions above will allow me to do additional debugging steps on my local machine.
-Nathan
On Mon, Jan 7, 2019 at 12:03 PM Nick Gnedin <ngnedin@gmail.com <mailto:ngnedin@gmail.com>> wrote:
Folks,
I am getting an error trying to install the latest version of yt using setup.py (I have to use this method per BlueWaters staff instructions):
----------------------------- >git clone https://ngnedin@github.com/yt-project/yt.git < https://urldefense.proofpoint.com/v2/url?u=https-3A__ngnedin-40github.com_yt-2Dproject_yt.git&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=Pc6JtSRT1-838ckp3d6CNT14gEDzmp_nRldYAbQIM_I&s=g6wRdY0vpPwRXDrRCHpGZMcqG5BkhosRJoR0_o2jQEc&e=
... Checking out files: 100% (1258/1258), done.
>cd yt yt >python3 setup.py build ... [48/48] Cythonizing yt/utilities/lib/write_array.pyx reading manifest template 'MANIFEST.in' no previously-included directories found matching 'doc/source/reference/api/generated' no previously-included directories found matching 'doc/build' writing manifest file 'yt.egg-info/SOURCES.txt' error: can't copy 'yt/analysis_modules': doesn't exist or not a regular file
yt > --------------------
Thank you,
Nick _______________________________________________ yt-users mailing list -- yt-users@python.org <mailto:yt-users@python.org> To unsubscribe send an email to yt-users-leave@python.org <mailto:yt-users-leave@python.org>
Hi Nick, This doesn't specifically answer your question, but I was able to get my own install of yt going on Blue Waters in a simpler way. Here's everything I did; maybe this will work for you. module swap PrgEnv-cray PrgEnv-gnu module load bwpy git clone <some repo> cd <repo directory> pip install --user -e . Don't forget the "." on the end of the pip command. The --user flag allows you to install packages to locally, but using the system's python/pip. This should work in general for packages you want to install with pip. The installation files are stored in a .local directory in your home dir. One last thought, the analysis_modules directory was removed from the yt-4.0 branch recently. It's possible that we missed something and there is still an installation process that's looking for it. However, if you're not using the yt-4.0 branch, this is probably unrelated. Britton On Mon, Jan 7, 2019 at 11:39 AM Nathan Goldbaum <nathan12343@gmail.com> wrote:
I was asking to see what the next steps were to see what sort of installation you were trying to set up. I understand that it fails for you at the "setup.py build" stage but my alternate build command suggestion would be for you will depend on what the subsequent steps would be.
For pip, have you tried installing yt in your home directory by passing by pasing --local? That should be sufficient for it not to try to mess with the systemwide installation.
Does the same error happen with "python setup.py install"? What python version are you using? What packages are already installed in your python environment?
Again, it would be good to know what branch and changeset of yt you are trying to build. I'd assume just the master branch.
Is there a "yt/analysis_modules" folder in your checkout of yt? There should be...
It would also be helpful to see the full console output (e.g. by copy-pasting into a pastebin service like bpaste.net) from trying to build yt, there might be hints earlier in the output that were elided in the snippet you shared in your first e-mail.
On Mon, Jan 7, 2019 at 1:27 PM Nick Gnedin <ngnedin@gmail.com> wrote:
I listed the commands I executed - just git clone and python3 setup.py build.
I cannot use pip, on BW it first tries to uninstall the system-wide distribution of yt, so their Python expert suggested I try setup.py.
On 1/7/19 12:24 PM, Nathan Goldbaum wrote:
Hi Nick,
This "setup.py build" thing is new to me. It's not a setup.py command we've ever supported or documented for use with yt. I wonder why the blue waters staff told you to use it.
That said, I'm not able to reproduce the failure you're seeing (python3 setup.py build runs without error after making a fresh clone of the yt repo).
What branch and changeset are you building yt from?
What were the rest of the steps in the installation instructions you were trying to follow?
I bet if you do "pip install ." inside of your checkout of the repository, things will "just work". However since I'm not able to reproduce the failure you're seeing you may run into the same issue with "pip install". If that happens answering the questions above will allow me to do additional debugging steps on my local machine.
-Nathan
On Mon, Jan 7, 2019 at 12:03 PM Nick Gnedin <ngnedin@gmail.com <mailto:ngnedin@gmail.com>> wrote:
Folks,
I am getting an error trying to install the latest version of yt using setup.py (I have to use this method per BlueWaters staff instructions):
----------------------------- >git clone https://ngnedin@github.com/yt-project/yt.git < https://urldefense.proofpoint.com/v2/url?u=https-3A__ngnedin-40github.com_yt-2Dproject_yt.git&d=DwMFaQ&c=gRgGjJ3BkIsb5y6s49QqsA&r=7jSLZBQB_2gqGQ3elA922w&m=Pc6JtSRT1-838ckp3d6CNT14gEDzmp_nRldYAbQIM_I&s=g6wRdY0vpPwRXDrRCHpGZMcqG5BkhosRJoR0_o2jQEc&e=
... Checking out files: 100% (1258/1258), done.
>cd yt yt >python3 setup.py build ... [48/48] Cythonizing yt/utilities/lib/write_array.pyx reading manifest template 'MANIFEST.in' no previously-included directories found matching 'doc/source/reference/api/generated' no previously-included directories found matching 'doc/build' writing manifest file 'yt.egg-info/SOURCES.txt' error: can't copy 'yt/analysis_modules': doesn't exist or not a regular file
yt > --------------------
Thank you,
Nick _______________________________________________ yt-users mailing list -- yt-users@python.org <mailto:yt-users@python.org> To unsubscribe send an email to yt-users-leave@python.org <mailto:yt-users-leave@python.org>
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
participants (3)
-
Britton Smith -
Nathan Goldbaum -
Nick Gnedin