cuda install； ubuntu22安装nvidia驱动以解Cytoscape3.10找不到libOpenCL.so错， Cytoscape3教程

ziix

已于 2024-05-26 15:04:00 修改

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文章标签： python cuda安装 cytoscape安装 cytoscape

于 2023-12-25 17:02:06 首次发布

本文链接：https://blog.csdn.net/hfcaoguilin/article/details/135203694

版权

笔记本 shinelon E479 (NVIDIA GM108M [GeForce 940M] rev a2 )

0. 本机环境

sudo cat /sys/class/dmi/id/board_name 
# E479

sudo dmidecode -t baseboard

uname -a
#Linux SHL 6.5.0-35-generic #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May  7 09:00:52 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

cat /etc/issue
#Ubuntu 22.04.3 LTS \n \l

lspci  | grep -i nvidia
#01:00.0 3D controller: NVIDIA Corporation GM108M [GeForce 940M] (rev a2)

4. apt安装nvidia驱动 then reboot

ubuntu-drivers devices
"""
== /sys/devices/pci0000:00/0000:00:01.0/0000:01:00.0 ==
modalias : pci:v000010DEd00001347sv00001B6Csd00005038bc03sc02i00
vendor   : NVIDIA Corporation
model    : GM108M [GeForce 940M]
driver   : nvidia-driver-390 - distro non-free
driver   : nvidia-driver-535 - distro non-free recommended 推荐
driver   : nvidia-driver-535-server - distro non-free
driver   : nvidia-driver-470 - distro non-free
driver   : nvidia-driver-470-server - distro non-free
driver   : nvidia-driver-418-server - distro non-free
driver   : nvidia-driver-450-server - distro non-free
driver   : nvidia-driver-545 - distro non-free
driver   : xserver-xorg-video-nouveau - distro free builtin
"""

sudo apt-get install nvidia-driver-535
sudo reboot

重启后

内核模块中有nvidia

lsmod |grep -i nvidia

"""
nvidia_uvm           1802240  0
nvidia_drm             94208  2
nvidia_modeset       1314816  2 nvidia_drm
nvidia              56815616  82 nvidia_uvm,nvidia_modeset
drm_kms_helper        274432  3 drm_display_helper,nvidia_drm,i915
drm                   765952  15 drm_kms_helper,drm_display_helper,nvidia,drm_buddy,nvidia_drm,i915,ttm
video                  73728  2 i915,nvidia_modeset
"""

驱动版本 NVIDIA-SMI 535.171.04

nvidia-smi

+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.171.04             Driver Version: 535.171.04   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 940M            Off | 00000000:01:00.0 Off |                  N/A |
| N/A   47C    P8              N/A / 200W |      3MiB /  2048MiB |      0%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+
                                                                                         
+---------------------------------------------------------------------------------------+
| Processes:                                                                            |
|  GPU   GI   CI        PID   Type   Process name                            GPU Memory |
|        ID   ID                                                             Usage      |
|=======================================================================================|
|    0   N/A  N/A       979      G   /usr/lib/xorg/Xorg                            2MiB |

到此时 nvidia驱动已经安装完毕

sudo prime-select --help
#Usage: /usr/bin/prime-select nvidia|intel|on-demand|query

sudo prime-select query
#on-demand

此时(安装完nvida驱动后），可以禁止Wayland（恢复x11协议）

此步骤不用做，这台是服务器，不是工作机，因此不关心x11或wayland

cuda toolkit

ref1, ref2

assert : cuda version <= driver version

assert : cudaToolkit version cuda_12.2.2_535.104.05_linux.run <= driver version : NVIDIA-SMI 535.171.04

链接点击步骤：

wget https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux.run
#sudo sh cuda_12.2.2_535.104.05_linux.run

cuda env setting:


echo 'export CUDA_HOME=/app2/nvidia_cuda_12.2.2_535.104.05_linux
export PATH=$PATH:$CUDA_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64' | tee -a ~/.bashrc 

source ~/.bashrc

#cat /etc/ld.so.conf
#include /etc/ld.so.conf.d/*.conf

#echo   "/app2/nvidia_cuda_12.2.2_535.104.05_linux/lib64/" | sudo tee -a /etc/ld.so.conf

install cuda : skip driver install

uninstall: sudo /app2/nvidia_cuda_12.2.2_535.104.05_linux/bin/cuda-uninstaller

sh cuda_12.2.2_535.104.05_linux.run --toolkitpath=/app1/nvidia_cuda_12.2.2_535.104.05_linux  --toolkit --no-drm --silent
echo $?  #0

which nvcc #/app2/nvidia_cuda_12.2.2_535.104.05_linux/bin/nvcc

nvcc -V

"""
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Aug_15_22:02:13_PDT_2023
Cuda compilation tools, release 12.2, V12.2.140
Build cuda_12.2.r12.2/compiler.33191640_0
"""

mechrev 2022 jiguang_z (GeForce RTX 3050 Mobile)

nvidia driver

ref1

0. 本机环境

uname -a
#Linux mchrv 6.5.0-15-generic #15~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

cat /etc/issue
#Ubuntu 22.04.3 LTS \n \l


lspci  | grep -i vga
#00:02.0 VGA compatible controller: Intel Corporation Alder Lake-P GT1 [UHD Graphics] (rev 0c)
#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
#after reboot 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

4. apt安装nvidia驱动 then reboot

ubuntu-drivers devices
"""
== /sys/devices/pci0000:00/0000:00:01.0/0000:01:00.0 ==
modalias : pci:v000010DEd000025A2sv00001D05sd00001178bc03sc00i00
vendor   : NVIDIA Corporation
model    : GA107M [GeForce RTX 3050 Mobile]
driver   : nvidia-driver-470 - distro non-free
driver   : nvidia-driver-525 - distro non-free
driver   : nvidia-driver-545-open - distro non-free
driver   : nvidia-driver-535-server-open - distro non-free
driver   : nvidia-driver-535-server - distro non-free
driver   : nvidia-driver-535 - distro non-free recommended
driver   : nvidia-driver-535-open - distro non-free
driver   : nvidia-driver-525-server - distro non-free
driver   : nvidia-driver-525-open - distro non-free
driver   : nvidia-driver-470-server - distro non-free
driver   : nvidia-driver-545 - distro non-free
driver   : xserver-xorg-video-nouveau - distro free builtin
"""

sudo apt-get install nvidia-driver-535

sudo reboot

内核模块中有nvidia: lsmod |grep -i nvidia

nvidia_uvm           1777664  0
nvidia_drm             90112  8
nvidia_modeset       1314816  10 nvidia_drm
nvidia              56786944  524 nvidia_uvm,nvidia_modeset
drm_kms_helper        270336  3 drm_display_helper,nvidia_drm,i915
drm                   761856  15 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: (driver version : NVIDIA-SMI 535.154.05 )

Sat Feb  3 20:44:02 2024       
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.154.05             Driver Version: 535.154.05   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    P0              11W /  60W |    831MiB /  4096MiB |      4%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+
                                                                                         
+---------------------------------------------------------------------------------------+
| Processes:                                                                            |
|  GPU   GI   CI        PID   Type   Process name                            GPU Memory |
|        ID   ID                                                             Usage      |
|=======================================================================================|
|    0   N/A  N/A      1159      G   /usr/lib/xorg/Xorg                          210MiB |
|    0   N/A  N/A      1641      G   /usr/bin/gnome-shell                        115MiB |
|    0   N/A  N/A      2017      G   ...irefox/2987/usr/lib/firefox/firefox      444MiB |
|    0   N/A  N/A      3995      G   gnome-control-center                         19MiB |
+---------------------------------------------------------------------------------------+

到此时 nvidia驱动已经安装完毕

sudo prime-select --help
#Usage: /usr/bin/prime-select nvidia|intel|on-demand|query

sudo prime-select query
on-demand

此时(安装完nvida驱动后），可以禁止Wayland（恢复x11协议）

#去掉 '#WaylandEnable=false' 前面的井号， 即 禁止Wayland
sed -i 's/#WaylandEnable=false/WaylandEnable=false/g'  /etc/gdm3/custom.conf 

# 禁止Wayland 后 的样子 
grep WaylandEnable  /etc/gdm3/custom.conf 
#此行内容为'WaylandEnable=false'

sudo systemctl restart gdbm3

如果在自带驱动nouveau的状况下，禁止Wayland后则会外接屏幕白屏，猜测是bug( nouveau 依赖于Wayland?)

禁止Wayland ，即用回x11 的好处是， xdotool等基于x11协议的工具能正常使用

启用Wayland ，则基于x11 协议的工具 xdotool等不能正常工作

Wayland 是x11的进化，但Wayland不兼容x11协议， Wayland比x11更讲究安全性，但这里不需要考虑安全性。

禁止Wayland 以正常化x11协议，常常是为了 sxhkd+xdotool （键盘替代鼠标，效率工具）

sudo prime-select nvidia or sudo prime-select intel

ldconfig -p | grep -i cuda:

	libicudata.so.70 (libc6,x86-64) => /lib/x86_64-linux-gnu/libicudata.so.70
	libicudata.so.70 (ELF) => /lib/i386-linux-gnu/libicudata.so.70
	libcudadebugger.so.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libcudadebugger.so.1
	libcuda.so.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libcuda.so.1
	libcuda.so.1 (libc6) => /lib/i386-linux-gnu/libcuda.so.1
	libcuda.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libcuda.so
	libcuda.so (libc6) => /lib/i386-linux-gnu/libcuda.so

cuda toolkit

ref1, ref2

assert : cuda version <= driver version

assert : cudaToolkit version cuda_12.2.2_535.104.05_linux.run <= driver version : NVIDIA-SMI 535.154.05

cuda-toolkit-archive
在这里插入图片描述
 cuda-12-2-2-download-archive
cuda-12-2-2-download-archive?target_os=Linux&target_arch=x86_64&Distribution=Ubuntu&target_version=22.04&target_type=runfile_local

wget https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_535.104.05_linux.run

在这里插入图片描述

ls -lh cuda_12.2.2_535.104.05_linux.run 
#-rw-rw-r--  4.1G  2月  3 21:15 cuda_12.2.2_535.104.05_linux.run
ls -l cuda_12.2.2_535.104.05_linux.run 
# -rw-rw-r--  4344134690  2月  3 21:15 cuda_12.2.2_535.104.05_linux.run

cuda env setting:


echo 'export CUDA_HOME=/app1/nvidia_cuda_12.2.2_535.104.05_linux
export PATH=$PATH:$CUDA_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64' | tee -a ~/.bashrc 

source ~/.bashrc

#cat /etc/ld.so.conf
#include /etc/ld.so.conf.d/*.conf

#echo   "/app1/nvidia_cuda_12.2.2_535.104.05_linux/lib64/" | sudo tee -a /etc/ld.so.conf

install cuda : skip driver install

uninstall: sudo /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin/cuda-uninstaller

sh cuda_12.2.2_535.104.05_linux.run --toolkitpath=/app1/nvidia_cuda_12.2.2_535.104.05_linux  --toolkit --no-drm --silent
echo $?  #0

which nvcc: /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin/nvcc

nvcc -V:

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Aug_15_22:02:13_PDT_2023
Cuda compilation tools, release 12.2, V12.2.140
Build cuda_12.2.r12.2/compiler.33191640_0

install cuda : error

uninstall: sudo /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin/cuda-uninstaller

sudo sh cuda_12.2.2_535.104.05_linux.run --installpath=/app1/nvidia_cuda_12.2.2_535.104.05_linux
or
sh cuda_12.2.2_535.104.05_linux.run --toolkitpath=/app1/nvidia_cuda_12.2.2_535.104.05_linux --toolkit

get error :

===========
= Summary =
===========

Driver:   Not Selected
Toolkit:  Installed in /app1/nvidia_cuda_12.2.2_535.104.05_linux/

Please make sure that
 -   PATH includes /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin
 -   LD_LIBRARY_PATH includes /app1/nvidia_cuda_12.2.2_535.104.05_linux/lib64, or, add /app1/nvidia_cuda_12.2.2_535.104.05_linux/lib64 to /etc/ld.so.conf and run ldconfig as root

To uninstall the CUDA Toolkit, run cuda-uninstaller in /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin
***WARNING: Incomplete installation! This installation did not install the CUDA Driver. A driver of version at least 535.00 is required for CUDA 12.2 functionality to work.
To install the driver using this installer, run the following command, replacing <CudaInstaller> with the name of this run file:
    sudo <CudaInstaller>.run --silent --driver

Logfile is /tmp/cuda-installer.log

choose “Continue”
在这里插入图片描述 input “accept”

uncheck “Driver”, uncheck “535.104.05”

test cuda:

1. nvcc

nvcc -V,

2. deviceQuery

/app1/nvidia_cuda_12.2.2_535.104.05_linux/extras/demo_suite/deviceQuery :

/app1/nvidia_cuda_12.2.2_535.104.05_linux/extras/demo_suite/deviceQuery Starting...

 CUDA Device Query (Runtime API) version (CUDART static linking)

Detected 1 CUDA Capable device(s)

Device 0: "NVIDIA GeForce RTX 3050 Laptop GPU"
  CUDA Driver Version / Runtime Version          12.2 / 12.2
  CUDA Capability Major/Minor version number:    8.6
  Total amount of global memory:                 3902 MBytes (4091478016 bytes)
  (16) Multiprocessors, (128) CUDA Cores/MP:     2048 CUDA Cores
  GPU Max Clock rate:                            1500 MHz (1.50 GHz)
  Memory Clock rate:                             6001 Mhz
  Memory Bus Width:                              128-bit
  L2 Cache Size:                                 1572864 bytes
  Maximum Texture Dimension Size (x,y,z)         1D=(131072), 2D=(131072, 65536), 3D=(16384, 16384, 16384)
  Maximum Layered 1D Texture Size, (num) layers  1D=(32768), 2048 layers
  Maximum Layered 2D Texture Size, (num) layers  2D=(32768, 32768), 2048 layers
  Total amount of constant memory:               65536 bytes
  Total amount of shared memory per block:       49152 bytes
  Total number of registers available per block: 65536
  Warp size:                                     32
  Maximum number of threads per multiprocessor:  1536
  Maximum number of threads per block:           1024
  Max dimension size of a thread block (x,y,z): (1024, 1024, 64)
  Max dimension size of a grid size    (x,y,z): (2147483647, 65535, 65535)
  Maximum memory pitch:                          2147483647 bytes
  Texture alignment:                             512 bytes
  Concurrent copy and kernel execution:          Yes with 2 copy engine(s)
  Run time limit on kernels:                     Yes
  Integrated GPU sharing Host Memory:            No
  Support host page-locked memory mapping:       Yes
  Alignment requirement for Surfaces:            Yes
  Device has ECC support:                        Disabled
  Device supports Unified Addressing (UVA):      Yes
  Device supports Compute Preemption:            Yes
  Supports Cooperative Kernel Launch:            Yes
  Supports MultiDevice Co-op Kernel Launch:      Yes
  Device PCI Domain ID / Bus ID / location ID:   0 / 1 / 0
  Compute Mode:
     < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) >

deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 12.2, CUDA Runtime Version = 12.2, NumDevs = 1, Device0 = NVIDIA GeForce RTX 3050 Laptop GPU
Result = PASS

3. cupti_query

cd /app1/nvidia_cuda_12.2.2_535.104.05_linux/extras/CUPTI/samples/cupti_query/
make
ls
#cupti_query  cupti_query.cpp  cupti_query.o  Makefile

file /app1/nvidia_cuda_12.2.2_535.104.05_linux/extras/CUPTI/lib64/libcupti.so.12

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/app1/nvidia_cuda_12.2.2_535.104.05_linux/extras/CUPTI/lib64/

./cupti_query
"""Assuming default device id 0
CUDA Device Id  : 0
CUDA Device Name: NVIDIA GeForce RTX 3050 Laptop GPU

cupti_query.cpp:450: Error: Function cuptiDeviceEnumEventDomains(dev, &size, (CUpti_EventDomainID *)&domainId) failed with error: CUPTI_ERROR_LEGACY_PROFILER_NOT_SUPPORTED.
"""

if not add extras/CUPTI/lib64/````to LD_LIBRARY_PATH, run ``./cupti_queryget error:
./cupti_query: error while loading shared libraries: libcupti.so.12: cannot open shared object file: No such file or directory

other

if not set PATH , LD_LIBRARY_PATH then executesudo sh cuda_12.2.2_535.104.05_linux.run --installpath=/app1/nvidia_cuda_12.2.2_535.104.05_linuxget error:

===========
= Summary =
===========

Driver:   Not Selected
Toolkit:  Installed in /app1/nvidia_cuda_12.2.2_535.104.05_linux/

Please make sure that
 -   PATH includes /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin
 -   LD_LIBRARY_PATH includes /app1/nvidia_cuda_12.2.2_535.104.05_linux/lib64, or, add /app1/nvidia_cuda_12.2.2_535.104.05_linux/lib64 to /etc/ld.so.conf and run ldconfig as root

To uninstall the CUDA Toolkit, run cuda-uninstaller in /app1/nvidia_cuda_12.2.2_535.104.05_linux/bin
***WARNING: Incomplete installation! This installation did not install the CUDA Driver. A driver of version at least 535.00 is required for CUDA 12.2 functionality to work.
To install the driver using this installer, run the following command, replacing <CudaInstaller> with the name of this run file:
    sudo <CudaInstaller>.run --silent --driver

Logfile is /var/log/cuda-installer.log

sudo sh ./cuda_12.2.2_535.104.05_linux.run --help:

Options:
  --silent
    Performs an installation with no further user-input and minimal
    command-line output based on the options provided below. Silent
    installations are useful for scripting the installation of CUDA.
    Using this option implies acceptance of the EULA. If running with
    non-root permissions, additional customizations may be necessary
    with other command-line options.

  --driver
    Install the CUDA Driver.

  --kernelobjects
    Install the CUDA Kernel Objects.
  
  --kopath=<path>
    Install the CUDA Kernel Objects to <path>.

  --toolkit
    Install the CUDA Toolkit.

  --toolkitpath=<path>
    Install the CUDA Toolkit to the <path> directory. If this flag is not
    provided, the default path of /usr/local/cuda-12.2 is used.

  --installpath=<path>
    Install everything to the <path> directory. This flag overrides the
    --toolkitpath flag if it is set.

  --extract=<path>
    Extracts driver runfile and the raw files of the toolkit to <path>.

    This is especially useful when one wants to install the driver using one or
    more of the command-line options provided by the driver installer which
    are not exposed in this installer.

  --override
    Ignores compiler version checks which would prevent installation.

  --no-opengl-libs
    Prevents the driver installation from installing NVIDIA's GL libraries.
    Useful for systems where the display is driven by a non-NVIDIA GPU.
    In such systems, NVIDIA's GL libraries could prevent X from loading
    properly.

  --no-man-page
    Do not install the man pages under /usr/share/man.

  --kernel-module-build-directory=<kernel|kernel-open>
    Tells the driver installation to use legacy or open flavor of kernel source
    when building the NVIDIA kernel module. The kernel-open flavor is only
    supported on Turing GPUs and newer.

  -m=kernel
    Tells the driver installation to use legacy flavor of kernel source when
    building the NVIDIA kernel module.
    Shorthand for --kernel-module-build-directory=kernel

  -m=kernel-open
    Tells the driver installation to use open flavor of kernel source when
    building the NVIDIA kernel module. The kernel-open flavor is only supported
    on Turing GPUs and newer.
    Shorthand for --kernel-module-build-directory=kernel-open

  --kernel-source-path=<path>
    Tells the driver installation to use <path> as the kernel source directory
    when building the NVIDIA kernel module. Required for systems where the
    kernel source is installed to a non-standard location.

  --kernel-output-path=<path>
    Tells the driver installation to use <path> as the kernel output directory
    when building the NVIDIA kernel module. Required for systems where the
    kernel obects are loaded from a non-standard location.

  --run-nvidia-xconfig
    Tells the driver installation to run nvidia-xconfig to update the system
    X configuration file so that the NVIDIA X driver is used. The pre-existing
    X configuration file will be backed up.

    This option should not be used on systems that require a custom
    X configuration, or on systems where a non-NVIDIA GPU is rendering the
    display.

  --no-drm
    Do not install the nvidia-drm kernel module. This kernel module provides 
    several features, including X11 autoconfiguration, support for PRIME, and 
    DRM-KMS. The latter is used to support modesetting on windowing systems 
    that run independently of X11. The '--no-drm' option should only be used 
    to work around failures to build or install the nvidia-drm kernel module 
    on systems that do not need these features.

  --tmpdir=<path>
    Performs any temporary actions within <path> instead of /tmp. Useful in
    cases where /tmp cannot be used (doesn't exist, is full, is mounted with
    'noexec', etc.).

  --help
    Prints this help message.

cuDNN(cuda Deep Nueral Network?)

cudnn
在这里插入图片描述
 nvidia login

another ASUS (Geforce 610M)

在这里插入图片描述

cat /etc/issue
#Ubuntu 22.04.3 LTS \n \l
#compiled by gcc12

#wget https://cn.download.nvidia.cn/XFree86/Linux-x86_64/390.157/NVIDIA-Linux-x86_64-390.157.run
sudo apt search --names-only nvida-driver-390*
sudo apt install nvida-driver-390 #error , detail see :

sudo bash NVIDIA-Linux-x86_64-390.157.run --no-x-check  #error detail:

在这里插入图片描述

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
#after reboot 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

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.<clinit>(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 '<tab>' for a list of available commands
   and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' 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/

ziix

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cuda install； ubuntu22安装nvidia驱动以解Cytoscape3.10找不到libOpenCL.so错， Cytoscape3教程

cuda install； ubuntu22安装nvidia驱动以解Cytoscape3.10找不到libOpenCL.so错， Cytoscape3教程
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