{"id":1511,"date":"2024-05-04T17:17:46","date_gmt":"2024-05-04T17:17:46","guid":{"rendered":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1511"},"modified":"2024-05-08T15:16:15","modified_gmt":"2024-05-08T15:16:15","slug":"ubuntu22-for-minion-mk1b-%e5%ae%89%e8%a3%9d%e7%ad%86%e8%a8%98","status":"publish","type":"post","link":"https:\/\/megagenome.nchu.edu.tw\/wordpress\/?p=1511","title":{"rendered":"Ubuntu22 for MinION mk1B (\u5b89\u88dd\u7b46\u8a18)"},"content":{"rendered":"\n

\u6211\u5011\u628a\u820a\u7684\u96fb\u8166\u5de5\u4f5c\u7ad9SSD\u5316\u4e4b\u5f8c\uff0c\u60f3\u8981\u7528\u4f86\u8dd1Nanopore\u5b9a\u5e8f(\u914d\u5408mk1B)\u3002\u4ee5\u4e0b\u5167\u5bb9\u662f\u5b89\u88dd\u904e\u7a0b\u7684\u7b46\u8a18\u3002\u6211\u5011\u8981\u5b89\u88dd\u7684\u662fUbuntu 22 (Jammy Jellyfish)\u9084\u6709MinKNOW\uff0c\u8aaa\u7c21\u55ae\u662f\u883b\u9593\u55ae\u7684\uff0c\u4f46\u662f\u4e2d\u9593\u4e5f\u6709\u9047\u5230\u4e00\u4e9b\u4e9b\u5c0f\u72c0\u6cc1\u3002<\/p>\n\n\n\n\n\n\n\n

\u4e0b\u8f09Ubuntu22<\/h2>\n\n\n\n

https:\/\/ubuntu.com\/download\/desktop<\/a><\/p>\n\n\n\n

\u73fe\u5728\u7db2\u7ad9\u4e0a\u6700\u65b0\u7684\u7248\u672c\u662fUbuntu 24\uff0c\u4f46\u662f\u76ee\u524dMinKNOW\u652f\u63f4\u7684\u7248\u672c\u523022(\u6211\u5011\u8a66\u904e\u4e86\u7528Ubuntu 24\uff0c\u4f46\u662fMinKNOW\u4e0d\u884c\u7528)\uff0c\u6240\u4ee5\u7e3d\u800c\u8a00\u4e4b\u5fc5\u9808\u88dd\u7a0d\u5fae\u820a\u4e00\u9ede\u7684\u7248\u672c\u3002\u6240\u4ee5\u6211\u5011\u5f9e’check out our alternative downloads<\/a>‘ \u7684\u5730\u65b9\u53bb\u4e0b\u8f09Ubuntu 22 (Jammy Jellyfish)\u4f86\u88dd\u624d\u884c\u3002\u53f0\u7063\u7684\u570b\u7db2\u4e2d\u5fc3\u4e5f\u53ef\u4ee5\u4e0b\u8f09\uff1ahttps:\/\/free.nchc.org.tw\/ubuntu-cd\/<\/a> (\u901a\u5e38\u4e0b\u8f09\u901f\u5ea6\u6bd4\u8f03\u5feb)<\/p>\n\n\n\n

\n

\u820a\u7684\u4e0d\u4e00\u5b9a\u4e0d\u597d\uff0c\u80fd\u628a\u4e8b\u60c5\u505a\u597d\u5c31\u597d<\/p>\n<\/blockquote>\n\n\n\n

\"\"<\/a><\/figure>\n\n\n\n

\u9019\u4e0b\u8f09\u4e0b\u4f86\u662f\u4e00\u500b\u8d85\u904e6GB\u7684disk image\uff0c\u6709\u6d41\u91cf\u9650\u5236\u7684\u8a71\u8981\u6ce8\u610f\u3002\u6240\u8b02\u7684disk image\u662f\u4e00\u500b\u5b8c\u6574\u4fdd\u5b58\u4e86\u7cfb\u7d71\u5b89\u88dd\u789f\u7684\u5167\u5bb9\u8207\u7d50\u69cb\u7684\u6a94\u6848\uff0c\u5728\u9019\u88e1\u5b83\u53ef\u4ee5\u62ff\u4f86\u88fd\u4f5c\u53ef\u4ee5\u7528\u4f86\u5e6b\u96fb\u8166\u958b\u6a5f\u4e26\u9032\u884c\u7cfb\u7d71\u5b89\u88dd\u7684\u958b\u6a5f\u78c1\u789f(\u9019\u88e1\u6307\u7684\u901a\u5e38\u662fUSB\u96a8\u8eab\u789f\u3001\u5149\u789f\u4e4b\u985e\u7684)\u3002\u6240\u4ee5\u4e0b\u8f09\u5b8c\u6210\u4e4b\u5f8c\uff0c\u6211\u5011\u5fc5\u9808\u7528\u5b83\u5efa\u7acb\u5b89\u88dd\u5a92\u9ad4\u3002<\/p>\n\n\n\n

\u5efa\u7acbUbuntu\u5b89\u88dd\u5a92\u9ad4<\/h2>\n\n\n\n
\"\"<\/a><\/figure>\n\n\n\n

\u5f9e\u524d\u53ef\u4ee5\u628a\u4e0b\u8f09\u7684image file\u71d2\u5230\u5149\u789f\uff0c\u4f46\u662f\u6211\u5efa\u8b70\u4f60\u9084\u662f\u7528USB flash drive\u5c31\u597d\u5594<\/a>\uff0c\u7528\u9019\u500b\u5f88\u65b9\u4fbf\uff1a<\/p>\n\n\n\n

https:\/\/etcher.balena.io\/#download-etcher<\/a><\/p>\n\n\n\n

\u5b89\u88ddUbuntu<\/h2>\n\n\n\n

\u7528\u505a\u597d\u7684USB flash drive\u958b\u6a5f\uff0c\u9078\u64c7\u958b\u59cb\u5b89\u88ddUbuntu\uff0c\u9078\u64c7\u8a9e\u8a00\u6642\u5340\u9375\u76e4\u4ec0\u9ebc\u7684\u90fd\u7167\u820a\uff0c\u6211\u5011\u662f\u9078\u6700\u5c0f\u5b89\u88dd\u3002\u5efa\u7acb\u4f7f\u7528\u8005\uff0c\u8a2d\u5b9a\u597d\u7db2\u8def\u300222\u9019\u500b\u7248\u672c\u7684Ubuntu\u684c\u9762\u662f\u4e00\u96bb\u6c34\u6bcd\u5462\uff01<\/p>\n\n\n\n

\u5b89\u88ddCUDA driver<\/h2>\n\n\n\n

\u73fe\u5728\u7684basecaller\uff0c\u4e5f\u5c31\u662f\u628a\u5b9a\u5e8f\u7684RAW data\u89e3\u8b80\u6210\u6838\u9178\u5e8f\u5217\u7684\u9019\u500b\u6b65\u9a5f\u7528\u7684\u8edf\u9ad4\uff0c\u4e3b\u8981\u662f\u9760\u6a5f\u5668\u5b78\u7fd2\u7684\u6280\u8853\u4f86\u9032\u884c\u7684\u3002\u6240\u4ee5\u6211\u5011\u9700\u8981\u8db3\u5920\u5f37\u5927\u7684GPU\u4f86\u8dd1\u9019\u4e9b\u6a21\u578b\u3002\u6211\u5011\u7684\u986f\u5361\u662fQuadro RTX-4000\uff0c\u73fe\u5728\u6211\u5011\u88dd\u597d\u7cfb\u7d71\u4e4b\u5f8c\uff0c\u5fc5\u9808\u8981\u518d\u53e6\u5916\u5b89\u88ddCUDA tool kit\u4f86\u91cb\u653e\u5b83\u7684\u80fd\u529b…<\/p>\n\n\n\n

\u5b89\u88dd\u7684\u65b9\u6cd5\u9019\u500b\u7db2\u7ad9\u6709\u8aaa\u660e\uff1ahttps:\/\/docs.nvidia.com\/cuda\/cuda-installation-guide-linux<\/a><\/p>\n\n\n\n

\"\"<\/a><\/figure>\n\n\n\n

\u7167\u8457\u8aaa\u660e\uff0c\u6211\u5011\u4e0b\u8f09\u4e86NVIDIA-Linux-x86_64-550.78.run\uff0c\u4f46\u662f\u60f3\u5728\u9019\u88e1\u76f4\u63a5\u5b89\u88dd\uff0c\u6703\u9047\u5230\u4e00\u500b\u554f\u984c\uff0c\u56e0\u70ba\u73fe\u5728\u6211\u5011\u662f\u958b\u8457X Windows(\u5c31\u662fUbuntu Desktop\u73fe\u5728\u7684GUI)\u5728\u9019\u88e1\u641e\uff0c\u6240\u4ee5\u5982\u679c\u4f60\u5728Terminal\u5e95\u4e0b\u7528 sudo sh NVIDIA-Linux-x86_64-550.78.run\u53bb\u57f7\u884c\u5b89\u88dd\uff0c\u4ed6\u6703\u5361\u5728\u4e00\u500b\u5730\u65b9\uff0c\u8aaa\u4f60\u5fc5\u9808\u5148\u95dc\u6389\u9019\u4e9bGUI\u7684\u6771\u897f\u3002<\/p>\n\n\n\n

\u9019\u500b\u6709\u5f88\u591a\u505a\u6cd5\uff0c\u6211\u5011\u7684\u505a\u6cd5\u662f\uff0c\u5728Ubuntu\u9019\u908a\u5148\u88ddSSH\uff0c\u7136\u5f8c\u5f9e\u9060\u7aef\u9032\u4f86\u505a\u5b89\u88dd\u3002\u53cd\u6b63SSH\u5f88\u65b9\u4fbf\u7d42\u7a76\u8981\u88dd\u7684\uff0c\u5c0d\u5427\uff1f<\/p>\n\n\n\n

\u5b89\u88ddSSH\u7684\u65b9\u6cd5\uff1a<\/p>\n\n\n\n

sudo apt-get install openssh-server<\/code><\/pre>\n\n\n\n
\u7a0d\u7b49\u5b83\u5b89\u88dd\u597d\uff0c\u7136\u5f8c\u6aa2\u67e5\u4e00\u4e0bSSH\u8a2d\u5b9a\uff1a<\/p>\n\n\n\n
cd \/etc\/ssh\/<\/p>\n\n\n\n
vi sshd_config \u628a\u88e1\u9762\u9700\u8981\u95dc\u7684\u9580\u95dc\u4e00\u4e0b<\/p>\n\n\n\n
sudo \/etc\/init.d\/ssh restart \u91cd\u555fSSH\u5c31\u53ef\u4ee5\u505a\u9060\u7aef\u767b\u5165\u4e86\u3002<\/p>\n\n\n\n
\u66ab\u6642\u95dc\u6389gdm<\/h2>\n\n\n\n
\u8a71\u8aaa\u5f9e\u982d\uff0c\u6211\u5011\u8981\u95dc\u6389\u7684\u6771\u897f\u53eb\u505agdm\uff0cgdm\u662fX Windows System(\u53c8\u7a31X11)\u7684\u986f\u793a\u7ba1\u7406\u5668(display manager)\u7a0b\u5f0f\u3002X11\u5c31\u662f\u6211\u5011\u5728Ubuntu(\u9084\u6709\u5176\u4ed6\u7684Linux)\u4e0a\u9762\u7684\u9019\u500b\u53ef\u4ee5\u7528\u6ed1\u9f20\u6e38\u6a19\u9ede\u8457\u4f7f\u7528\u7684\u9019\u500bGUI\u7684\u6771\u897f\u3002\u6211\u5011\u73fe\u5728\u8981\u5b89\u88ddNvidia\u7e6a\u5716\u5361\u7684\u7a0b\u5f0f\uff0c\u70ba\u4ec0\u9ebc\u8981\u66ab\u6642\u95dc\u6389gdm\u5462\uff1f\u5c31\u597d\u50cf\u4f60\u8981\u63db\u5730\u6bef\uff0c\u5fc5\u9808\u5148\u628a\u8eba\u5728\u4e0a\u9762\u7761\u89ba\u7684\u6a58\u8272\u8c93\u8d95\u8d70(\u54c8)….<\/p>\n\n\n\n
Linux\u7cfb\u7d71\u4e0d\u4e00\u6a23\u7684\u8a71\uff0c\u4e5f\u53ef\u80fd\u88dd\u7684\u662f\u4e0d\u540c\u7684display manager\uff0c\u8b6c\u5982\u8aaalightdm\uff0c\u53cd\u6b63\u4e0d\u7ba1\u4ec0\u9ebc\u8c93\uff0c\u5148\u53eb\u4ed6\u8d77\u4f86\u4e00\u4e0b\u5c31\u5c0d\u4e86….<\/p>\n\n\n\n
Ubuntu\u684c\u9762GUI\u9019\u908a\u53ef\u4ee5\u5c07\u4f7f\u7528\u8005\u767b\u51fa\u4e86\u3002\u7136\u5f8c\u6211\u5011\u53bb\u627e\u53e6\u4e00\u53f0\u96fb\u8166\uff0c\u56e0\u70ba\u525b\u525b\u5df2\u7d93\u88dd\u4e86SSH Server\uff0c\u6211\u5011\u53ef\u4ee5\u7528SSH\u9023\u7dda\u9032\u4f86\uff0c\u63a5\u8457\u7528\u4ee5\u4e0b\u6307\u4ee4\u95dc\u6389\u9019\u500bUbuntu\u4e0a\u9762\u7684gdm (\u5982\u679c\u662flightdm\u61c9\u8a72\u4e5f\u662f\u770b\u8457\u8fa6)\uff1a<\/p>\n\n\n\n
sudo service gdm stop<\/code><\/pre>\n\n\n\n
\u9019\u6642\u5019Ubuntu\u90a3\u908a\u87a2\u5e55\u6703\u9ed1\u6389\uff0c\u5225\u6015\uff0c\u9019\u5c31\u662f\u6211\u5011\u8981\u7684\u3002\u73fe\u5728\u8c93\u5df2\u7d93\u8d70\u958b\uff0c\u6211\u5011\u89ba\u5f97\u61c9\u8a72\u53ef\u4ee5\u900f\u904eSSH\u5f9e\u9060\u7aef\u4f86\u88ddNVIDIA-Linux-x86_64-550.78.run\u4e86\uff01<\/p>\n\n\n\n
sudo sh NVIDIA-Linux-x86_64-550.78.run<\/code><\/pre>\n\n\n\n
\u4f46\u662f\u4e0d\u884c\uff0c\u4f60\u9084\u9700\u8981gcc-12(\u5b89\u88ddgcc-12)<\/h2>\n\n\n\n
\u679c\u7136\u4e8b\u60c5\u6c92\u6709\u90a3\u9ebc\u7c21\u55ae\uff0csudo sh NVIDIA-Linux-x86_64-550.78.run\u4e0b\u53bb\uff0c\u4ed6\u85cd\u85cd\u7684\u756b\u9762\u88dd\u5230\u4e00\u534a\u5c31\u8df3\u51fa\u932f\u8aa4\u4e86\uff0c\u6aa2\u67e5log\u6a94\uff0c\u5b83\u8aaa\u6211\u5011\u7684\u7248\u672c\u662fgcc 11\uff0c\u4f46\u662f\u4ed6\u8981gcc 12\uff0c\u6240\u4ee5\u898b\u62db\u62c6\u62db\u5427\uff1a<\/p>\n\n\n\n
\u6aa2\u67e5\/var\/log\/nvidia-installer.log\uff0c\u7d00\u9304\u88e1\u9762\u8aaa\uff1a<\/p>\n\n\n\n
The major and minor number of the compiler used to\ncompile the kernel:\n\nx86_64-linux-gnu-gcc-12 (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38\n\ndoes not match the compiler used here:\n\ncc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0\nCopyright (C) 2021 Free Software Foundation, Inc.\nThis is free software; see the source for copying conditions.  There is NO\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.<\/code><\/pre>\n\n\n\n
\u6240\u4ee5\u6211\u5011\u9700\u8981\u5b89\u88ddgcc-12\uff0c\u9019\u6a23\u88dd\uff1a<\/p>\n\n\n\n
sudo apt-get install gcc-12<\/code><\/pre>\n\n\n\n
\u6aa2\u67e5\u4e00\u4e0b\u7248\u672c\uff0c\u73fe\u5728gcc\u662f11.4.0\uff0c\u800c\u6211\u5011\u4e5f\u525b\u525b\u88dd\u597d\u4e86gcc-12(12.3.0)<\/p>\n\n\n\n
$ gcc --version\ngcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0\nCopyright (C) 2021 Free Software Foundation, Inc.\nThis is free software; see the source for copying conditions.  There is NO\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n\n$ gcc-12 --version\ngcc-12 (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0\nCopyright (C) 2022 Free Software Foundation, Inc.\nThis is free software; see the source for copying conditions.  There is NO\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.<\/code><\/pre>\n\n\n\n
\u6539\u4e00\u4e0b\uff0c\u4ee5\u5f8c\u7528gcc-12\u5427\uff01\u5728\/usr\/bin\u5e95\u4e0b\u7684gcc\u5176\u5be6\u662f\u4e00\u500blink\uff0c\u6211\u5011\u628a\u5b83\u6307\u5411\u525b\u525b\u88dd\u7684gcc-12\uff0c\u9019\u6a23\u4ee5\u5f8c\u8ab0\u8981gcc\u5c31\u6703\u88ab\u5f15\u5c0e\u5230gcc-12\u53bb\u4e86\uff01<\/p>\n\n\n\n
\/usr\/bin$ sudo ln -f \/usr\/bin\/gcc-12 gcc<\/code><\/pre>\n\n\n\n
\u6211\u5011\u65e2\u7136\u89e3\u6c7a\u4e86gcc\u7684\u7248\u672c\uff0c\u5c31\u8d95\u5feb\u518d\u91cd\u8dd1\u4e00\u6b21\u5b89\u88dd\u5427\uff1a<\/p>\n\n\n\n
sudo sh NVIDIA-Linux-x86_64-550.78.run<\/code><\/pre>\n\n\n\n
\u9019\u4e0b\u53ef\u4ee5\u6b63\u5e38\u5b89\u88dd\u4e86\uff01\u53ea\u8981\u56de\u7b54\u554f\u984c\u7e7c\u7e8c\u7e7c\u7e8c\u4e0b\u4e00\u6b65…\uff0c\u5168\u90e8\u5b8c\u6210\u4e4b\u5f8c\uff0c\u7528sudo reboot now\u91cd\u65b0\u958b\u6a5f\u3002<\/p>\n\n\n\n
\u56de\u5230Ubuntu Desktop\u524d\u9762\uff0c\u91cd\u65b0\u958b\u6a5f\u4e4b\u5f8c\u767b\u5165\u756b\u9762\u4f3c\u4e4e\u53c8\u51fa\u73fe\u4e86\uff0c\u9032\u53bb\u770b\u770b\u662f\u5426\u4e00\u5207\u6b63\u5e38\u56c9\uff01<\/p>\n\n\n\n
\u6aa2\u67e5\u986f\u793a\u5361\u72c0\u614b<\/h2>\n\n\n\n
\u4f60\u53ef\u4ee5\u7528nvidia-smi\u6307\u4ee4\u6aa2\u67e5\u986f\u5361\u662f\u4e0d\u662f\u4e56\u4e56\u7684\u5537\uff01\u9019\u88e1\u986f\u793a\u6211\u5011\u7684Quadro RTX 4000\u9084\u6709P620\u7684\u6eab\u5ea6\u3001\u80fd\u8017\u3001\u8a18\u61b6\u9ad4\u4f7f\u7528\u7b49\u72c0\u6cc1\u3002<\/p>\n\n\n\n
$ nvidia-smi\nSat May  4 12:47:13 2024       \n+-----------------------------------------------------------------------------------------+\n| NVIDIA-SMI 550.78                 Driver Version: 550.78         CUDA Version: 12.4     |\n|-----------------------------------------+------------------------+----------------------+\n| GPU  Name                 Persistence-M | Bus-Id          Disp.A | Volatile Uncorr. ECC |\n| Fan  Temp   Perf          Pwr:Usage\/Cap |           Memory-Usage | GPU-Util  Compute M. |\n|                                         |                        |               MIG M. |\n|=========================================+========================+======================|\n|   0  Quadro RTX 4000                Off |   00000000:01:00.0 Off |                  N\/A |\n| 30%   47C    P8              8W \/  125W |       6MiB \/   8192MiB |      0%      Default |\n|                                         |                        |                  N\/A |\n+-----------------------------------------+------------------------+----------------------+\n|   1  Quadro P620                    Off |   00000000:02:00.0  On |                  N\/A |\n| 38%   44C    P8             N\/A \/  N\/A  |      34MiB \/   2048MiB |      0%      Default |\n|                                         |                        |                  N\/A |\n+-----------------------------------------+------------------------+----------------------+\n                                                                                         \n+-----------------------------------------------------------------------------------------+\n| Processes:                                                                              |\n|  GPU   GI   CI        PID   Type   Process name                              GPU Memory |\n|        ID   ID                                                               Usage      |\n|=========================================================================================|\n|    0   N\/A  N\/A       921      G   \/usr\/lib\/xorg\/Xorg                              4MiB |\n|    1   N\/A  N\/A       921      G   \/usr\/lib\/xorg\/Xorg                             25MiB |\n|    1   N\/A  N\/A      1088      G   \/usr\/bin\/gnome-shell                            5MiB |\n+-----------------------------------------------------------------------------------------+<\/code><\/pre>\n\n\n\n
\u5b89\u88ddMinKNOW<\/h2>\n\n\n\n
MinKNOW\u662fNanopore\u5b9a\u5e8f\u7684\u63a7\u5236\u7a0b\u5f0f\uff0c\u5f9e\u5b98\u7db2\u53ef\u4ee5\u627e\u5230MinKNOW\u5728Linux\u4e0a\u7684\u5b89\u88dd\u65b9\u6cd5\uff1a<\/p>\n\n\n\n
\"\"<\/a><\/figure>\n\n\n\n
https:\/\/community.nanoporetech.com\/docs\/prepare\/library_prep_protocols\/experiment-companion-minknow\/v\/mke_1013_v1_revdc_11apr2016\/installing-minknow-on-linu<\/a><\/p>\n\n\n\n
\u4f9d\u7167\u4ee5\u4e0a\u7db2\u7ad9\u7684\u8aaa\u660e\u9032\u884c\u5b89\u88dd\u56c9\uff0c\u6211\u5011\u662fUbuntu22\uff0c\u6240\u4ee5\u7167\u4ed6\u6307\u793a\u7684\uff0c\u7b2c\u4e00\u6b65\uff0c\u5148\u7528\u4ee5\u4e0b\u6307\u4ee4\u5148\u628arepo\u5f04\u597d\uff1a<\/p>\n\n\n\n
sudo apt update\nsudo apt install wget\nwget -O- https:\/\/cdn.oxfordnanoportal.com\/apt\/ont-repo.pub | sudo apt-key add -\necho \"deb http:\/\/cdn.oxfordnanoportal.com\/apt jammy-stable non-free\" | sudo tee \/etc\/apt\/sources.list.d\/nanoporetech.sources.list <\/code><\/pre>\n\n\n\n
\u7136\u5f8c\u6211\u5011\u9078GPU\u7248\u672c\u4f86\u88dd\uff1a<\/p>\n\n\n\n
sudo apt update\nsudo apt install ont-standalone-minknow-gpu-release<\/code><\/pre>\n\n\n\n
\"\"<\/a><\/figure>\n\n\n\n
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\u7e3d\u7d50<\/h2>\n\n\n\n
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