2.3 install issues #389
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Unfortunately, due to a pure python dependency of To have For this to work the |
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Hi Ben,
sorry you are having problems. While we will look at this channel, general EMAN2 discussion is in a Google Group, not on Github, so you will only get responses from a handful of developers here, not the general user community. We do use Github as a repository for the source, but we eschew it for other purposes.
The site: https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda <https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda>
does actually have a link at the top of the page you can follow to the the binary install instructions. I realize it may be easy to miss, and we should probably try to find a strategy to convert this to an auto-redirect (I'm not sure the Wiki has this capability).
These instructions used to be on a single page, but we switched to having version specific instructions, as the Anaconda installer seems to evolve with time. If you go to
http://eman2.org
you will find also the instructions there, which have a pointer to the correct download.
Installing the EMAN2 binaries in a Docker instance is somewhat pointless with the new Anaconda based install scheme, as Anaconda itself is somewhat similar to docker at this point. ie - it isn't a real virtual environment, but it includes basically all library dependencies, and the sole change required to use it is a change to PATH. So, while you certainly can put it in docker, it sort of like having 2 layers of virtualization (not really, just sort of). It also means you need to insure that your Docker instance properly supports CUDA and OpenGL (I realize this is quite doable).
Anyway, the installer was working fine when I checked a few days ago, but occasionally something gets changed in Anaconda itself which breaks downstream tools. Such things are usually transitory, and are quite annoying, but it is hard to completely avoid them.
I'm going to forward this to Tunay for his attention.
…--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke@bcm.edu <mailto:sludtke@bcm.edu>> Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem <http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core (cryoem.bcm.edu <http://cryoem.bcm.edu/>)
Co-Director CIBR Center (www.bcm.edu/research/cibr <http://www.bcm.edu/research/cibr>)
On May 10, 2019, at 11:58 AM, Ben Evans ***@***.***> wrote:
We have several researchers clamoring for this new and improved version of EMAN2, but I am having a heck of a time getting it to run. To troubleshoot, I have started my install attempts in a docker container. The install feels like it could use some work. I can try to run parts of EMAN2 after an install and figure out which things are missing here and there, but that feels inefficient if there are folks who have this running for them.
I'm hopeful that someone more familiar with what is needed could give it a once-over and update things so all needed packages are properly installed (preferably once?). It would also be really nice if the site that the installer points to for documentation (https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda <https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda>) had some. If there is some way in which I can contribute I am open to suggestions.
Here is the dockerfile:
FROM ubuntu:18.04
RUN apt-get update && \
apt-get -y install build-essential \
libgl1-mesa-dev \
libglu1-mesa \
libglu1-mesa-dev \
libsm-dev \
libxrender-dev \
mesa-common-dev \
mesa-utils \
wget
RUN cd /tmp && \
wget --quiet https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh && \
bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2
ENV PATH="/opt/EMAN2/bin:$PATH"
And the log from a build attempt:
$ docker build -t eman2:2.3-testing .
Sending build context to Docker daemon 2.56kB
Step 1/4 : FROM ubuntu:18.04
---> d131e0fa2585
Step 2/4 : RUN apt-get update && apt-get -y install build-essential libgl1-mesa-dev libglu1-mesa libglu1-mesa-dev libsm-dev libxrender-dev mesa-common-dev mesa-utils wget
---> Running in b96d2a72e160
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu ca-certificates cpp cpp-7
dirmngr dpkg-dev fakeroot g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gnupg
gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf
gpgsm libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libasan4 libasn1-8-heimdal libassuan0 libatomic1
libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libdpkg-perl
libdrm-amdgpu1 libdrm-common libdrm-dev libdrm-intel1 libdrm-nouveau2
libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libexpat1
libfakeroot libfile-fcntllock-perl libgbm1 libgcc-7-dev libgcc1
libgdbm-compat4 libgdbm5 libgl1 libgl1-mesa-dri libglapi-mesa libgles1
libgles2 libglvnd-core-dev libglvnd-dev libglvnd0 libglx-mesa0 libglx0
libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libisl19 libitm1
libkrb5-26-heimdal libksba8 libldap-2.4-2 libldap-common libllvm7
liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libmpx2 libnpth0 libopengl0
libpciaccess0 libperl5.26 libpsl5 libpthread-stubs0-dev libquadmath0
libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules
libsasl2-modules-db libsensors4 libsm6 libsqlite3-0 libssl1.1
libstdc++-7-dev libstdc++6 libtsan0 libubsan0 libwayland-client0
libwayland-server0 libwind0-heimdal libx11-6 libx11-data libx11-dev
libx11-doc libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev
libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev
libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev
libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1
libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxfixes-dev libxfixes3 libxrender1 libxshmfence-dev libxshmfence1
libxxf86vm-dev libxxf86vm1 linux-libc-dev make manpages manpages-dev
multiarch-support netbase openssl patch perl perl-modules-5.26
pinentry-curses publicsuffix readline-common x11-common x11proto-core-dev
x11proto-damage-dev x11proto-dev x11proto-fixes-dev x11proto-xext-dev
x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev xz-utils
Suggested packages:
binutils-doc cpp-doc gcc-7-locales dbus-user-session libpam-systemd
pinentry-gnome3 tor debian-keyring g++-multilib g++-7-multilib gcc-7-doc
libstdc++6-7-dbg gcc-multilib autoconf automake libtool flex bison gdb
gcc-doc gcc-7-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan4-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
libmpx2-dbg libquadmath0-dbg parcimonie xloadimage scdaemon glibc-doc git
bzr gdbm-l10n libice-doc pciutils libsasl2-modules-gssapi-mit
| libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp
libsasl2-modules-sql lm-sensors libsm-doc libstdc++-7-doc libxcb-doc
libxext-doc make-doc man-browser ed diffutils-doc perl-doc
libterm-readline-gnu-perl | libterm-readline-perl-perl pinentry-doc
readline-doc
The following NEW packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu build-essential
ca-certificates cpp cpp-7 dirmngr dpkg-dev fakeroot g++ g++-7 gcc gcc-7
gcc-7-base gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client
gpg-wks-server gpgconf gpgsm libalgorithm-diff-perl
libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan4 libasn1-8-heimdal
libassuan0 libatomic1 libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0
libcilkrts5 libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-dev
libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0
libegl1 libelf1 libexpat1 libfakeroot libfile-fcntllock-perl libgbm1
libgcc-7-dev libgdbm-compat4 libgdbm5 libgl1 libgl1-mesa-dev libgl1-mesa-dri
libglapi-mesa libgles1 libgles2 libglu1-mesa libglu1-mesa-dev
libglvnd-core-dev libglvnd-dev libglvnd0 libglx-mesa0 libglx0 libgomp1
libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libisl19 libitm1
libkrb5-26-heimdal libksba8 libldap-2.4-2 libldap-common libllvm7
liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libmpx2 libnpth0 libopengl0
libpciaccess0 libperl5.26 libpsl5 libpthread-stubs0-dev libquadmath0
libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules
libsasl2-modules-db libsensors4 libsm-dev libsm6 libsqlite3-0 libssl1.1
libstdc++-7-dev libtsan0 libubsan0 libwayland-client0 libwayland-server0
libwind0-heimdal libx11-6 libx11-data libx11-dev libx11-doc libx11-xcb-dev
libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0
libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev
libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0
libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev
libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev
libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
libxfixes-dev libxfixes3 libxrender-dev libxrender1 libxshmfence-dev
libxshmfence1 libxxf86vm-dev libxxf86vm1 linux-libc-dev make manpages
manpages-dev mesa-common-dev mesa-utils multiarch-support netbase openssl
patch perl perl-modules-5.26 pinentry-curses publicsuffix readline-common
wget x11-common x11proto-core-dev x11proto-damage-dev x11proto-dev
x11proto-fixes-dev x11proto-xext-dev x11proto-xf86vidmode-dev
xorg-sgml-doctools xtrans-dev xz-utils
The following packages will be upgraded:
gcc-8-base libgcc1 libstdc++6
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Get:86 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB]
Get:87 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB]
Get:88 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libldap-common all 2.4.45+dfsg-1ubuntu1.2 [16.7 kB]
Get:89 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libldap-2.4-2 amd64 2.4.45+dfsg-1ubuntu1.2 [155 kB]
Get:90 http://archive.ubuntu.com/ubuntu bionic/main amd64 libnpth0 amd64 1.5-3 [7668 B]
Get:91 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 dirmngr amd64 2.2.4-1ubuntu1.2 [316 kB]
Get:92 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfakeroot amd64 1.22-2ubuntu1 [25.9 kB]
Get:93 http://archive.ubuntu.com/ubuntu bionic/main amd64 fakeroot amd64 1.22-2ubuntu1 [62.3 kB]
Get:94 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg-l10n all 2.2.4-1ubuntu1.2 [49.6 kB]
Get:95 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg-utils amd64 2.2.4-1ubuntu1.2 [127 kB]
Get:96 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg amd64 2.2.4-1ubuntu1.2 [467 kB]
Get:97 http://archive.ubuntu.com/ubuntu bionic/main amd64 pinentry-curses amd64 1.1.0-1 [35.8 kB]
Get:98 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-agent amd64 2.2.4-1ubuntu1.2 [227 kB]
Get:99 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-wks-client amd64 2.2.4-1ubuntu1.2 [91.9 kB]
Get:100 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-wks-server amd64 2.2.4-1ubuntu1.2 [84.9 kB]
Get:101 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpgsm amd64 2.2.4-1ubuntu1.2 [215 kB]
Get:102 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg amd64 2.2.4-1ubuntu1.2 [249 kB]
Get:103 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-diff-perl all 1.19.03-1 [47.6 kB]
Get:104 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-diff-xs-perl amd64 0.04-5 [11.1 kB]
Get:105 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]
Get:106 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-amdgpu1 amd64 2.4.95-1~18.04.1 [17.4 kB]
Get:107 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpciaccess0 amd64 0.14-1 [17.9 kB]
Get:108 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-intel1 amd64 2.4.95-1~18.04.1 [59.9 kB]
Get:109 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-radeon1 amd64 2.4.95-1~18.04.1 [21.7 kB]
Get:110 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-nouveau2 amd64 2.4.95-1~18.04.1 [16.5 kB]
Get:111 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-dev amd64 2.4.95-1~18.04.1 [121 kB]
Get:112 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libwayland-server0 amd64 1.16.0-1ubuntu1.1~18.04.1 [29.8 kB]
Get:113 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgbm1 amd64 18.2.8-0ubuntu0~18.04.2 [24.2 kB]
Get:114 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglapi-mesa amd64 18.2.8-0ubuntu0~18.04.2 [23.4 kB]
Get:115 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libwayland-client0 amd64 1.16.0-1ubuntu1.1~18.04.1 [23.8 kB]
Get:116 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb1 amd64 2:1.6.4-3ubuntu0.2 [9376 B]
Get:117 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri2-0 amd64 1.13-2~ubuntu18.04 [6920 B]
Get:118 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri3-0 amd64 1.13-2~ubuntu18.04 [6568 B]
Get:119 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-present0 amd64 1.13-2~ubuntu18.04 [5552 B]
Get:120 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-sync1 amd64 1.13-2~ubuntu18.04 [8808 B]
Get:121 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-xfixes0 amd64 1.13-2~ubuntu18.04 [9352 B]
Get:122 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence1 amd64 1.3-1 [5028 B]
Get:123 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libegl-mesa0 amd64 18.2.8-0ubuntu0~18.04.2 [87.5 kB]
Get:124 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-fcntllock-perl amd64 0.22-3build2 [33.2 kB]
Get:125 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libllvm7 amd64 1:7-3~ubuntu0.18.04.1 [15.9 MB]
Get:126 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsensors4 amd64 1:3.4.0-4 [28.8 kB]
Get:127 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dri amd64 18.2.8-0ubuntu0~18.04.2 [6587 kB]
Get:128 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd0 amd64 1.0.0-2ubuntu2.2 [46.6 kB]
Get:129 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgles1 amd64 1.0.0-2ubuntu2.2 [11.2 kB]
Get:130 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-glx0 amd64 1.13-2~ubuntu18.04 [22.1 kB]
Get:131 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage1 amd64 1:1.1.4-3 [6934 B]
Get:132 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes3 amd64 1:5.0.3-1 [10.8 kB]
Get:133 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx-mesa0 amd64 18.2.8-0ubuntu0~18.04.2 [135 kB]
Get:134 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx0 amd64 1.0.0-2ubuntu2.2 [28.1 kB]
Get:135 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1 amd64 1.0.0-2ubuntu2.2 [84.8 kB]
Get:136 http://archive.ubuntu.com/ubuntu bionic/main amd64 libglu1-mesa amd64 9.0.0-2.1build1 [168 kB]
Get:137 http://archive.ubuntu.com/ubuntu bionic/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB]
Get:138 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-dev all 2018.4-4 [251 kB]
Get:139 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-core-dev all 2018.4-4 [2620 B]
Get:140 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxau-dev amd64 1:1.0.8-1 [11.1 kB]
Get:141 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [25.1 kB]
Get:142 http://archive.ubuntu.com/ubuntu bionic/main amd64 xtrans-dev all 1.3.5-1 [70.5 kB]
Get:143 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpthread-stubs0-dev amd64 0.3-4 [4068 B]
Get:144 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb1-dev amd64 1.13-2~ubuntu18.04 [80.0 kB]
Get:145 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-dev amd64 2:1.6.4-3ubuntu0.2 [640 kB]
Get:146 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 mesa-common-dev amd64 18.2.8-0ubuntu0~18.04.2 [559 kB]
Get:147 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd-core-dev amd64 1.0.0-2ubuntu2.2 [12.9 kB]
Get:148 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libegl1 amd64 1.0.0-2ubuntu2.2 [31.9 kB]
Get:149 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgles2 amd64 1.0.0-2ubuntu2.2 [17.4 kB]
Get:150 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libopengl0 amd64 1.0.0-2ubuntu2.2 [31.3 kB]
Get:151 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd-dev amd64 1.0.0-2ubuntu2.2 [3408 B]
Get:152 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb-dev amd64 2:1.6.4-3ubuntu0.2 [9756 B]
Get:153 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri3-dev amd64 1.13-2~ubuntu18.04 [7384 B]
Get:154 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-randr0 amd64 1.13-2~ubuntu18.04 [16.4 kB]
Get:155 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-render0 amd64 1.13-2~ubuntu18.04 [14.7 kB]
Get:156 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-render0-dev amd64 1.13-2~ubuntu18.04 [18.4 kB]
Get:157 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-randr0-dev amd64 1.13-2~ubuntu18.04 [20.4 kB]
Get:158 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-shape0 amd64 1.13-2~ubuntu18.04 [5972 B]
Get:159 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-shape0-dev amd64 1.13-2~ubuntu18.04 [7144 B]
Get:160 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-xfixes0-dev amd64 1.13-2~ubuntu18.04 [11.7 kB]
Get:161 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-sync-dev amd64 1.13-2~ubuntu18.04 [10.6 kB]
Get:162 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-present-dev amd64 1.13-2~ubuntu18.04 [6972 B]
Get:163 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence-dev amd64 1.3-1 [3692 B]
Get:164 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri2-0-dev amd64 1.13-2~ubuntu18.04 [8472 B]
Get:165 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-glx0-dev amd64 1.13-2~ubuntu18.04 [27.9 kB]
Get:166 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-fixes-dev all 1:2018.4-4 [2620 B]
Get:167 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes-dev amd64 1:5.0.3-1 [11.0 kB]
Get:168 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-damage-dev all 1:2018.4-4 [2620 B]
Get:169 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage-dev amd64 1:1.1.4-3 [5028 B]
Get:170 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-xext-dev all 2018.4-4 [2620 B]
Get:171 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxext-dev amd64 2:1.3.3-1 [82.1 kB]
Get:172 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-xf86vidmode-dev all 2018.4-4 [2632 B]
Get:173 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13.3 kB]
Get:174 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dev amd64 18.2.8-0ubuntu0~18.04.2 [4428 B]
Get:175 http://archive.ubuntu.com/ubuntu bionic/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1build1 [206 kB]
Get:176 http://archive.ubuntu.com/ubuntu bionic/main amd64 libice-dev amd64 2:1.0.9-2 [46.8 kB]
Get:177 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [48.7 kB]
Get:178 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsm-dev amd64 2:1.2.2-1 [16.2 kB]
Get:179 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-doc all 2:1.6.4-3ubuntu0.2 [2065 kB]
Get:180 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB]
Get:181 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrender-dev amd64 1:0.9.10-1 [24.9 kB]
Get:182 http://archive.ubuntu.com/ubuntu bionic/main amd64 manpages-dev all 4.15-1 [2217 kB]
Get:183 http://archive.ubuntu.com/ubuntu bionic/universe amd64 mesa-utils amd64 8.4.0-1 [34.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 81.0 MB in 7s (12.0 MB/s)
Selecting previously unselected package liblocale-gettext-perl.
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Unpacking multiarch-support (2.27-3ubuntu1) ...
Setting up multiarch-support (2.27-3ubuntu1) ...
Selecting previously unselected package libxau6:amd64.
(Reading database ... 4057 files and directories currently installed.)
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Unpacking libxau6:amd64 (1:1.0.8-1) ...
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Unpacking libbsd0:amd64 (0.8.7-1) ...
Selecting previously unselected package libxdmcp6:amd64.
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Unpacking libxdmcp6:amd64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:amd64.
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Unpacking libxcb1:amd64 (1.13-2~ubuntu18.04) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../04-libx11-data_2%3a1.6.4-3ubuntu0.2_all.deb ...
Unpacking libx11-data (2:1.6.4-3ubuntu0.2) ...
Selecting previously unselected package libx11-6:amd64.
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Unpacking libx11-6:amd64 (2:1.6.4-3ubuntu0.2) ...
Selecting previously unselected package libxext6:amd64.
Preparing to unpack .../06-libxext6_2%3a1.3.3-1_amd64.deb ...
Unpacking libxext6:amd64 (2:1.3.3-1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../07-x11-common_1%3a7.7+19ubuntu7.1_all.deb ...
dpkg-query: no packages found matching nux-tools
Unpacking x11-common (1:7.7+19ubuntu7.1) ...
Selecting previously unselected package libice6:amd64.
Preparing to unpack .../08-libice6_2%3a1.0.9-2_amd64.deb ...
Unpacking libice6:amd64 (2:1.0.9-2) ...
Selecting previously unselected package libsm6:amd64.
Preparing to unpack .../09-libsm6_2%3a1.2.2-1_amd64.deb ...
Unpacking libsm6:amd64 (2:1.2.2-1) ...
Selecting previously unselected package libxxf86vm1:amd64.
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Unpacking libxxf86vm1:amd64 (1:1.1.4-1) ...
Selecting previously unselected package perl-modules-5.26.
Preparing to unpack .../11-perl-modules-5.26_5.26.1-6ubuntu0.3_all.deb ...
Unpacking perl-modules-5.26 (5.26.1-6ubuntu0.3) ...
Selecting previously unselected package libgdbm5:amd64.
Preparing to unpack .../12-libgdbm5_1.14.1-6_amd64.deb ...
Unpacking libgdbm5:amd64 (1.14.1-6) ...
Selecting previously unselected package libgdbm-compat4:amd64.
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Unpacking libgdbm-compat4:amd64 (1.14.1-6) ...
Selecting previously unselected package libperl5.26:amd64.
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Unpacking libperl5.26:amd64 (5.26.1-6ubuntu0.3) ...
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Unpacking perl (5.26.1-6ubuntu0.3) ...
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Unpacking gcc-8-base:amd64 (8.3.0-6ubuntu1~18.04) over (8.2.0-1ubuntu2~18.04) ...
Setting up gcc-8-base:amd64 (8.3.0-6ubuntu1~18.04) ...
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Preparing to unpack .../libstdc++6_8.3.0-6ubuntu1~18.04_amd64.deb ...
Unpacking libstdc++6:amd64 (8.3.0-6ubuntu1~18.04) over (8.2.0-1ubuntu2~18.04) ...
Setting up libstdc++6:amd64 (8.3.0-6ubuntu1~18.04) ...
(Reading database ... 6304 files and directories currently installed.)
Preparing to unpack .../libgcc1_1%3a8.3.0-6ubuntu1~18.04_amd64.deb ...
Unpacking libgcc1:amd64 (1:8.3.0-6ubuntu1~18.04) over (1:8.2.0-1ubuntu2~18.04) ...
Setting up libgcc1:amd64 (1:8.3.0-6ubuntu1~18.04) ...
Selecting previously unselected package libssl1.1:amd64.
(Reading database ... 6304 files and directories currently installed.)
Preparing to unpack .../000-libssl1.1_1.1.0g-2ubuntu4.3_amd64.deb ...
Unpacking libssl1.1:amd64 (1.1.0g-2ubuntu4.3) ...
Selecting previously unselected package openssl.
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Unpacking openssl (1.1.0g-2ubuntu4.3) ...
Selecting previously unselected package ca-certificates.
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Unpacking ca-certificates (20180409) ...
Selecting previously unselected package libelf1:amd64.
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Unpacking libelf1:amd64 (0.170-0.4) ...
Selecting previously unselected package libexpat1:amd64.
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Unpacking libexpat1:amd64 (2.2.5-3) ...
Selecting previously unselected package readline-common.
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Unpacking readline-common (7.0-3) ...
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Unpacking libreadline7:amd64 (7.0-3) ...
Selecting previously unselected package libsqlite3-0:amd64.
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Unpacking libsqlite3-0:amd64 (3.22.0-1) ...
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Unpacking netbase (5.4) ...
Selecting previously unselected package xz-utils.
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Unpacking xz-utils (5.2.2-1.3) ...
Selecting previously unselected package libdrm-common.
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Unpacking libdrm-common (2.4.95-1~18.04.1) ...
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Unpacking libdrm2:amd64 (2.4.95-1~18.04.1) ...
Selecting previously unselected package libedit2:amd64.
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Unpacking libedit2:amd64 (3.1-20170329-1) ...
Selecting previously unselected package libpsl5:amd64.
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Unpacking libpsl5:amd64 (0.19.1-5build1) ...
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Unpacking publicsuffix (20180223.1310-1) ...
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Unpacking wget (1.19.4-1ubuntu2.2) ...
Selecting previously unselected package binutils-common:amd64.
Preparing to unpack .../017-binutils-common_2.30-21ubuntu1~18.04.1_amd64.deb ...
Unpacking binutils-common:amd64 (2.30-21ubuntu1~18.04.1) ...
Selecting previously unselected package libbinutils:amd64.
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Unpacking libbinutils:amd64 (2.30-21ubuntu1~18.04.1) ...
Selecting previously unselected package binutils-x86-64-linux-gnu.
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Unpacking binutils-x86-64-linux-gnu (2.30-21ubuntu1~18.04.1) ...
Selecting previously unselected package binutils.
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Unpacking binutils (2.30-21ubuntu1~18.04.1) ...
Selecting previously unselected package libc-dev-bin.
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Unpacking libc-dev-bin (2.27-3ubuntu1) ...
Selecting previously unselected package linux-libc-dev:amd64.
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Unpacking linux-libc-dev:amd64 (4.15.0-48.51) ...
Selecting previously unselected package libc6-dev:amd64.
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Ahh, I see, I missed the "-t" he had in there.
Ben, we consider the "tests" to be for developer use only at this point. Please just don't even try and run them. They will produce errors even if they work in general, but this indicates a deficiency in the test, not a problem with the system.
…--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke@bcm.edu <mailto:sludtke@bcm.edu>> Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem <http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core (cryoem.bcm.edu <http://cryoem.bcm.edu/>)
Co-Director CIBR Center (www.bcm.edu/research/cibr <http://www.bcm.edu/research/cibr>)
On May 10, 2019, at 12:23 PM, shadow_walker ***@***.***> wrote:
Unfortunately, due to a pure python dependency of conda-build and the way the installer is made, running conda-build will not run out-of-the-box. Running the installer with -t option does run conda-build to run the package tests. The workaround here would be not to run the tests during installation. And, I don't know if it is possible to run the tests once installation is complete.
bash ./eman2.3.linux64.sh -b -p /opt/EMAN2
To have conda-build available to users, add a conda-install command.
bash ./eman2.3.linux64.sh -b -p /opt/EMAN2 && conda install --force-reinstall pytz -y
For this to work the PATH needs to have been updated. So, ENV line may have to go before the installation line.
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@sludtke42 While I appreciate and usually recommend using conda to manage a good number of installs, I've had trouble getting EMAN2 (this and previous versions) working on my machine and our HPC clusters. My goal in using a container is to ensure exactly the same base environment. The installer that gets distributed appears to rely on things about the host OS that are not explicitly stated, which makes troubleshooting installs feel like guesswork for those less familiar with the development history of the EMAN2 suite. As for CUDA/cuDNN, it looks like conda is dragging in those runtimes, so having an OS version would if anything be undesirable. Just poking in the proper drivers with singularity or nvidia docker feels like the right way to handle that. Also, having some idea of the range of OpenGL versions that work well with EMAN2 would be really helpful. If the |
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Hi Ben,
I have nothing against containers, and we have been discussing including a Docker instance as another option for the binary distributions. I'm just saying that since we switched to Anaconda, most of the special tricks you had to deal with for EMAN2/SPARX/SPHIRE installs, and issues with library conflicts no longer exist. Anaconda has now started recompiling almost everything themselves, with their own specific C compiler, so an Anaconda install is now close to being a container itself.
If you have EMAN2.3 installed somewhere, if it's the first thing in the PATH, it should work on virtually any computer, and if it isn't in the PATH it shouldn't interfere with anything else on the machine. In practice, of course, there may still be odd OS-version-specific conflicts, but these are very far between nowadays. Yes, while we do pull in cuda and tensorflow via Anaconda, this still relies on specific NVidia driver versions, etc. so the possibility for problems still exists.
Anyway, if you read the installation instructions it gives you a list of things to check after the install. The most likely failure is with the GUI and corresponding OpenGL calls, so alas, testing must be done manually, by displaying something.
…--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke@bcm.edu <mailto:sludtke@bcm.edu>> Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (www.bcm.edu/biochem <http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core (cryoem.bcm.edu <http://cryoem.bcm.edu/>)
Co-Director CIBR Center (www.bcm.edu/research/cibr <http://www.bcm.edu/research/cibr>)
On May 10, 2019, at 1:44 PM, Ben Evans ***@***.***> wrote:
@sludtke42 <https://github.com/sludtke42> While I appreciate and usually recommend using conda to manage a good number of installs, I've had trouble getting EMAN2 (this and previous versions) working on my machine and our HPC clusters. My goal in using a container is to ensure exactly the same base environment. The installer that gets distributed appears to rely on things about the host OS that are not explicitly stated, which makes troubleshooting installs feel like guesswork for those less familiar with the development history of the EMAN2 suite.
As for CUDA/cuDNN, it looks like conda is dragging in those runtimes, so having an OS version would if anything be undesirable. Just poking in the proper drivers with singularity or nvidia docker feels like the right way to handle that. Also, having some idea of the range of OpenGL versions that work well with EMAN2 would be really helpful.
If the -t is not a good way to test an install, are there a standard set of tests that can be run post-install to convince oneself that the installation is usable?
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@brevans , closed this assuming there was no more feedback. If that's not the case, please, let us know. |
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We have several researchers clamoring for this new and improved version of EMAN2, but I am having a heck of a time getting it to run. To troubleshoot, I have started my install attempts in a docker container. The install feels like it could use some work. I can try to run parts of EMAN2 after an install and figure out which things are missing here and there, but that feels inefficient if there are folks who have this running for them.
I'm hopeful that someone more familiar with what is needed could give it a once-over and update things so all needed packages are properly installed (preferably once?). It would also be really nice if the site that the installer points to for documentation (https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda) had some. If there is some way in which I can contribute I am open to suggestions.
Here is the dockerfile:
And the log from a build attempt:
The text was updated successfully, but these errors were encountered: