VMD環境構築 | On Docker | MacOS | 24/10/3(木) | 失敗ログ

参照先

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LAMMPS環境構築 | MPI並列対応 | Docker | MacOS | 24/9/27, 24/10/2

参照先 DockerでLAMMPSが簡単に動かせる！ LAMMPSのDockerイメージを自分でビルドしてみる 実行環境 MacBook Pro（2018） プロセッサ：2.3 GHz クアッドコアIntel Core i5 グラフィックス...

conohawing-blog.com

2024.09.27

• https://hub.docker.com/layers/afandiadib/vmd/mesa/images/sha256-587314999ff569ca372b74f1c39bb0ec33149d5216c721a8fb89a7587d398af9?context=explore

Docker imageをダウンロード

% pwd
/Users/li/Documents/Research

docker pull afandiadib/vmd:mesa

stdout:

mesa: Pulling from afandiadib/vmd
aeb7866da422: Download complete 
559750659aa4: Download complete 
Digest: sha256:587314999ff569ca372b74f1c39bb0ec33149d5216c721a8fb89a7587d398af9
Status: Downloaded newer image for afandiadib/vmd:mesa
docker.io/afandiadib/vmd:mesa

Docker containerの立ち上げ

docker image ls                    
REPOSITORY       TAG                                        IMAGE ID       CREATED       SIZE
lammps/lammps    stable_29Sep2021_ubuntu20.04_openmpi_py3   4ce3adcff72f   2 years ago   1.85GB
lammps/lammps    latest                                     1aceb06072da   3 years ago   1.85GB
afandiadib/vmd   mesa                                       587314999ff5   5 years ago   1.23GB

% docker container run 587314999ff5
/usr/local/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info)   CPU features: SSE2 AVX AVX2 FMA 
Info) Free system memory: 7365MB (93%)
Info) No CUDA accelerator devices available.
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) Exiting normally.

XQuartzのインストール

• https://www.xquartz.org/

ログアウトボタンを押して，ログアウトした．

以下を実行．

xhost

stdout:

access control enabled, only authorized clients can connect

以下を実行．

xhost +localhost

stdout:

localhost being added to access control list

以下を実行．

xhost

stdout:

access control enabled, only authorized clients can connect
INET:localhost
INET6:localhost

docker image ls
REPOSITORY       TAG                                        IMAGE ID       CREATED       SIZE
lammps/lammps    stable_29Sep2021_ubuntu20.04_openmpi_py3   4ce3adcff72f   2 years ago   1.85GB
lammps/lammps    latest                                     1aceb06072da   3 years ago   1.85GB
afandiadib/vmd   mesa                                       587314999ff5   5 years ago   1.23GB

docker run -e DISPLAY=host.docker.internal:0 -v /tmp/.X11-unix:/tmp/.X11-unix 587314999ff5

ifconfig en0
en0: flags=8863<UP,BROADCAST,SMART,RUNNING,SIMPLEX,MULTICAST> mtu 1500
	options=6460<TSO4,TSO6,CHANNEL_IO,PARTIAL_CSUM,ZEROINVERT_CSUM>
	ether ce:c1:f1:b5:bc:3d
	inet6 fe80::80b:94b3:2b63:fb1f%en0 prefixlen 64 secured scopeid 0x6 
	inet 192.168.222.29 netmask 0xffffff00 broadcast 192.168.222.255
	nd6 options=201<PERFORMNUD,DAD>
	media: autoselect
	status: active

192.168.222.29

docker run -it -e DISPLAY=192.168.222.29 --name 587314999ff5

• https://youtu.be/cNDR6Z24KLM?si=7n2QROBO1g-UKaLz&t=179

% lsof -i :6000

COMMAND   PID USER   FD   TYPE             DEVICE SIZE/OFF NODE NAME
X11.bin 14507   li   10u  IPv6 0xf0cd4e04b36d194e      0t0  TCP *:6000 (LISTEN)
X11.bin 14507   li   11u  IPv4 0xf241a42844896a8a      0t0  TCP *:6000 (LISTEN)

docker image pull activeeon/vmd:latest

latest: Pulling from activeeon/vmd
e0780418928c: Download complete 
10e6159c56c0: Download complete 
552e53b61b22: Download complete 
d63a2a2464d4: Download complete 
ea337d1ec400: Download complete 
6856e9ea7987: Download complete 
09d067531845: Download complete 
a70d879fa598: Download complete 
c4394a92d1f8: Download complete 
Digest: sha256:3c4faa3f376217517e91c5b8cface5f99f77cd1324cf69d3dbc11f01a2e34227
Status: Downloaded newer image for activeeon/vmd:latest
docker.io/activeeon/vmd:latest

% docker image ls
REPOSITORY       TAG                                        IMAGE ID       CREATED       SIZE
lammps/lammps    stable_29Sep2021_ubuntu20.04_openmpi_py3   4ce3adcff72f   2 years ago   1.85GB
lammps/lammps    latest                                     1aceb06072da   3 years ago   1.85GB
activeeon/vmd    latest                                     3c4faa3f3762   3 years ago   1.08GB
afandiadib/vmd   mesa                                       587314999ff5   5 years ago   1.23GB