ubuntu22安装nvidia驱动 GeForce RTX 3050 M 以解Cytoscape3.10找不到libOpenCL.so错， Cytoscape3教程
0. 本机环境
uname -a
#Linux v 6.2.0-39-generic #40~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 16 10:53:04 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
cat /etc/issue
#Ubuntu 22.04.3 LTS \n \l
lspci | grep -i vga
#01:00.0 VGA compatible controller: NVIDIA Corporation GA107M [GeForce RTX 3050 Mobile] (rev a1)
1. 卸载linux自带兼容驱动nouveau
echo 'blacklist nouveau
options nouveau modeset=0' | sudo tee /etc/modprobe.d/blacklist-nouveau.conf
sudo update-initramfs -u
lsmod |grep -i nouveau
#不再有nouveau
2. 重启电脑
重启电脑
sudo reboot
重启电脑后，只剩下集成显卡了，而集成显卡不支持双显示器，因此插外接显示器无用。
3*. 官网下载的NVIDA-Linux*.run驱动自己说不建议使用其
下载 目前较新版本是535.146.02
cd ~/Downloads/
sudo chmod +x ./NVIDIA-Linux-x86_64-535.146.02.run
sudo ./NVIDIA-Linux-x86_64-535.146.02.run
#他会提示说 由于本系统 ubuntu 有做好的驱动 （指 apt安装 ），不建议用本 .run文件
# 若遇到错误： You appear to be running an X server; please exit X before installing. For further details, please see the section INSTALLING THE NVIDIA DRIVER in the README available on the Linux driver download page at www.nvidia.com.
# 增加 --no-x-check 选项
sudo ./NVIDIA-Linux-x86_64-535.146.02.run --no-x-check
这里 选择 卸载 .run 的安装内容，并用apt安装
#获得帮助
./NVIDIA-Linux-x86_64-535.146.02.run --help
#获得更多帮助
./NVIDIA-Linux-x86_64-535.146.02.run -A | grep -i uninstall
#卸载 .run 的安装内容
./NVIDIA-Linux-x86_64-535.146.02.run --uninstall
4. apt安装nvidia驱动
支持GeForce RTX 3050 Mobile的驱动版本
- 第一个支持的驱动版本是510.47.03
- 目前较新版本是535.146.02
ubuntu22已经有nvidia-driver , 因此不需要
添加额外仓库sudo add-apt-repository ppa:graphics-drivers/ppa ; sudo apt update
sudo apt search --names-only nvidia-driver-53*
#确实能搜索到535版本
sudo apt install nvidia-driver-535
内核模块中有nvidia:
lsmod |grep -i nvidia
nvidia_uvm 1765376 0
nvidia_drm 90112 4
nvidia_modeset 1314816 3 nvidia_drm
nvidia 56741888 114 nvidia_uvm,nvidia_modeset
drm_kms_helper 249856 3 drm_display_helper,nvidia_drm,i915
drm 700416 18 drm_kms_helper,drm_display_helper,nvidia,drm_buddy,nvidia_drm,i915,ttm
video 73728 3 asus_wmi,i915,nvidia_modeset
命令
nvidia-smi的输出:
Mon Dec 25 17:04:21 2023
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.129.03 Driver Version: 535.129.03 CUDA Version: 12.2 |
|-----------------------------------------+----------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+======================+======================|
| 0 NVIDIA GeForce RTX 3050 ... Off | 00000000:01:00.0 On | N/A |
| N/A 41C P8 5W / 60W | 57MiB / 4096MiB | 0% Default |
| | | N/A |
+-----------------------------------------+----------------------+----------------------+
+---------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=======================================================================================|
| 0 N/A N/A 1527 G /usr/lib/xorg/Xorg 53MiB |
+---------------------------------------------------------------------------------------+
5. ubuntu22下 Cytoscape3.10能正常使用但启动时报错找不到libOpenCL.so
Cytoscape3.10 所用jdk17环境如下：
env | grep -i java
#JAVA_HOME=/jdk17
which javac && which java
#/jdk17/bin/javac
#/jdk17/bin/java
readlink -f `which javac` && readlink -f `which java`
#/app/zulu17.46.19-ca-jdk17.0.9-linux_x64/bin/javac
#/app/zulu17.46.19-ca-jdk17.0.9-linux_x64/bin/java
Cytoscape3.10启动
/app/cytoscape-unix-3.10.1/cytoscape.sh后能正常使用，但控制台有如下报错：
karaf@Cytoscape 3.10.1()> [LWJGL] Failed to load a library. Possible solutions:
a) Install the library or the driver that provides the library.
b) Ensure that the library is accessible from the system library paths.
[LWJGL] Enable debug mode with -Dorg.lwjgl.util.Debug=true for better diagnostics.
[LWJGL] Enable the SharedLibraryLoader debug mode with -Dorg.lwjgl.util.DebugLoader=true for better diagnostics.
java.lang.UnsatisfiedLinkError: Failed to locate library: libOpenCL.so
at org.lwjgl.system.Library.loadNative(Library.java:346)
at org.lwjgl.system.Library.loadNative(Library.java:236)
at org.lwjgl.system.Library.loadNative(Library.java:217)
at org.lwjgl.system.Library.loadNative(Library.java:431)
at org.lwjgl.system.Library.loadNative(Library.java:402)
at org.lwjgl.opencl.CL.create(CL.java:57)
at org.lwjgl.opencl.CL.(CL.java:45)
at org.cytoscape.cycl.internal.CyCL.initialize(CyCL.java:54)
at org.cytoscape.cycl.internal.CyActivator.lambda$start$0(CyActivator.java:32)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)
No devices found
实际上有opencl库,
ldconfig -p | grep -i opencl：
libnvidia-opencl.so.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libnvidia-opencl.so.1
libnvidia-opencl.so.1 (libc6) => /lib/i386-linux-gnu/libnvidia-opencl.so.1
libOpenCL.so.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libOpenCL.so.1
解决办法是 :
- 按照以上1到4步骤 安装好 nvidia驱动
- 软链接 opencl.so路径 :
sudo ln -s /lib/x86_64-linux-gnu/libOpenCL.so.1.0.0 /lib/x86_64-linux-gnu/libOpenCL.so
Cytoscape3.10启动
/app/cytoscape-unix-3.10.1/cytoscape.sh后（不再报错）说找到nvidia显卡设备了
karaf.base: /app/cytoscape-unix-3.10.1/framework
JAVA_HOME: /jdk17
_
___ _ _| |_ ___ ___ ___ __ _ _ __ ___
/ __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \
| (__| |_| | |_| (_) \__ \ (__| (_| | |_) | __/
\___|\__, |\__|\___/|___/\___|\__,_| .__/ \___|
|___/ |_|
Cytoscape 3.10.1
Hit '' for a list of available commands
and '[cmd] --help' for help on a specific command.
Hit '' or 'osgi:shutdown' to shutdown Cytoscape.
karaf@Cytoscape 3.10.1()> Found 1 platforms #找到1平台
Got 1 platforms
Got 1 devices
Platform: NVIDIA CUDA
Device: OpenCL 3.0 CUDA NVIDIA GeForce RTX 3050 Laptop GPU #即 找到了 nvidia显卡
The cl_program [0x7F4B88B75B60] was built successfully
BUILD LOG:
----
-----
Program built
Top device after init = OpenCL 3.0 CUDA NVIDIA GeForce RTX 3050 Laptop GPU
UserAgent = Cytoscape v3.10.1 Java 17.0.9 Linux 6.2.0-39-generic
latestVersion = 3.10.1
6. cytoscape3.10教程
6.1 Cytoscape界面操作
- 导入 起点_终点_边字段们，边字段们 是可选的，起点、终点 都是节点，
- 导入属性字段, 属性 即 节点的属性
- 根据某属性字段的值调整节点颜色，该属性字段是枚举 即 离散, 视频中枚举字段名是type字段
- 根据某属性字段的值调整节点尺寸，该属性字段是连续的，视频中的连续字段名是Genenum
- 根据某边字段的值调整边的颜色，该字段是边字段，视频中的字段名是PCC
此文内容和上面视频差不多，导入属性字段 较 清楚
6.2 Cytoscape脚本
Cytoscape脚本,
脚本例子New_wrapper_api_sample.ipynb
脚本例子目录 py2cytoscape/examples/