We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture. We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines. We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips. We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64. How do you recommend we proceed? Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages. -- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin
Hi Daniel, We don’t distribute an ARM64 version of ChimeraX for Linux; you would have to build ChimeraX from source. — Zach
On 14 Aug 2024, at 16:16, Daniel Diaz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Can you point me to instructions on how to do that? Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin On Wed, Aug 14, 2024 at 6:28 PM Zach Pearson <zjp@cgl.ucsf.edu> wrote:
Hi Daniel,
We don’t distribute an ARM64 version of ChimeraX for Linux; you would have to build ChimeraX from source.
— Zach
On 14 Aug 2024, at 16:16, Daniel Diaz via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you for the quick response! Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin On Wed, Aug 14, 2024 at 6:31 PM Daniel Diaz <danny.diaz@utexas.edu> wrote:
Can you point me to instructions on how to do that?
Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin
On Wed, Aug 14, 2024 at 6:28 PM Zach Pearson <zjp@cgl.ucsf.edu> wrote:
Hi Daniel,
We don’t distribute an ARM64 version of ChimeraX for Linux; you would have to build ChimeraX from source.
— Zach
On 14 Aug 2024, at 16:16, Daniel Diaz via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
You can find instructions on how to set up an environment and build from source here: https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html in the Developer Guide section. The ChimeraX source code can be found here: https://github.com/RBVI/ChimeraX You can run https://github.com/RBVI/ChimeraX/blob/develop/utils/set_up_ubuntu.sh this script to install prerequisites on your Ubuntu container. If you have to modify the Makefiles to get it working, please consider upstreaming your changes. — Zach
On 14 Aug 2024, at 16:31, Daniel Diaz <danny.diaz@utexas.edu> wrote:
Can you point me to instructions on how to do that?
Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin
On Wed, Aug 14, 2024 at 6:28 PM Zach Pearson <zjp@cgl.ucsf.edu> wrote: Hi Daniel,
We don’t distribute an ARM64 version of ChimeraX for Linux; you would have to build ChimeraX from source.
— Zach
On 14 Aug 2024, at 16:16, Daniel Diaz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Building ChimeraX from source for ARM64/AArch64 is going to be work. ChimeraX depends on lots of third-party packages that might not work on Linux Arm64 yet. And in some cases we build prerequisites by hand. And there are no Linux Arm64 bundles in the ChimeraX toolshed, so I hope you don't depend on any of those. You might able to get the existing x86_64 binaries running under emulation. Ubuntu is based on Debian and Debian supports multiple architectures. See https://unix.stackexchange.com/questions/577953/is-it-possible-to-run-x86-ex... for clues. This would probably be the simplest way to get a complete version of ChimeraX working. Or you might be able to get the flatpak version of ChimeraX running under qemu-user. https://www.reddit.com/r/linux/comments/n6x63p/til_that_flatpak_apps_can_emu... has clues. This tantalizing approach would be a great generic solution if it could be made to work. Since ChimeraX is primarily a desktop application, we have little incentive to try to build an Arm64 version until Lenovo/HP/Dell sell desktops with Arm64 processors (not servers, not chromebooks, maybe graphics-oriented laptops). That's looking like it will happen, but it's still bleeding edge technology. Then we'll need to buy one. Donations are acceptable :-) So while I'd recommend staying away from the shining new arm64 Linux cluster for now, you are more than welcome to try. And we hope you'll share what you try and what works and what doesn't work. Good luck, Greg On 8/14/24 16:43, Zach Pearson via ChimeraX-users wrote:
You can find instructions on how to set up an environment and build from source here: https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html in the Developer Guide section.
The ChimeraX source code can be found here: https://github.com/RBVI/ChimeraX
You can run https://github.com/RBVI/ChimeraX/blob/develop/utils/set_up_ubuntu.sh this script to install prerequisites on your Ubuntu container.
If you have to modify the Makefiles to get it working, please consider upstreaming your changes.
— Zach
On 14 Aug 2024, at 16:31, Daniel Diaz <danny.diaz@utexas.edu> wrote:
Can you point me to instructions on how to do that?
Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin
On Wed, Aug 14, 2024 at 6:28 PM Zach Pearson <zjp@cgl.ucsf.edu> wrote: Hi Daniel,
We don’t distribute an ARM64 version of ChimeraX for Linux; you would have to build ChimeraX from source.
— Zach
On 14 Aug 2024, at 16:16, Daniel Diaz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi! I think using Chimerax for this task is an overkill. Check https://gemmi.readthedocs.io/en/latest/index.html On Thu, Aug 15, 2024 at 2:29 AM Daniel Diaz via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Daniel, I remembered that I have a Raspberry Pi at home that I could use to test Linux arm64 builds. Today I pushed a few changes that should make it possible for you to build ChimeraX inside your Ubuntu 22.04 arm64 docker container. You should be able to run utils/set_up_ubuntu.sh to install dependencies, then run make install. Let me know if you encounter any issues. — Zach
On 14 Aug 2024, at 16:16, Daniel Diaz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture.
We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines.
We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips.
We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64.
How do you recommend we proceed?
Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:
The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages.
-- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Daniel Diaz -
Eugene Pichkur -
Greg Couch -
Zach Pearson