一、编译安装R-4.2.1
1、升级gcc
R语言及很多它的包，要从源码编译安装，所以要先升级gcc到最新版，这是升级好的，最新的是11版。
root@VM-0-14-ubuntu:~# apt list --installed | grep gcc
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
gcc/bionic-security,bionic-updates,now 4:7.4.0-1ubuntu2.3 amd64 [已安装]
gcc-11/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安装]
gcc-11-base/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
gcc-7/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安装，自动]
gcc-7-base/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安装，自动]
gcc-7-multilib/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安装，自动]
gcc-8-base/bionic-security,bionic-updates,now 8.4.0-1ubuntu1~18.04 amd64 [已安装]
gcc-multilib/bionic-security,bionic-updates,now 4:7.4.0-1ubuntu2.3 amd64 [已安装]
lib32gcc-7-dev/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安装，自动]
lib32gcc-s1/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
lib32gcc1/bionic,now 1:11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
libgcc-11-dev/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
libgcc-7-dev/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安装，自动]
libgcc-s1/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
libgcc1/bionic-security,bionic-updates,now 1:8.4.0-1ubuntu1~18.04 amd64 [已安装，可升级至：1:11.1.0-1ubuntu1~18.04.1]
libx32gcc-7-dev/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安装，自动]
libx32gcc-s1/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
libx32gcc1/bionic,now 1:11.1.0-1ubuntu1~18.04.1 amd64 [已安装，自动]
root@VM-0-14-ubuntu:~#
参阅资料，依次执行下面的命令升级。
root@VM-0-14-ubuntu:~# add-apt-repository ppa:ubuntu-toolchain-r/test
root@VM-0-14-ubuntu:~# apt update
root@VM-0-14-ubuntu:~# apt install gcc-11 g++-11
root@VM-0-14-ubuntu:~# updatedb
root@VM-0-14-ubuntu:~# ldconfig
root@VM-0-14-ubuntu:~# locate gcc | grep -E "/usr/bin/gcc-"
root@VM-0-14-ubuntu:~# update-alternatives --remove-all gcc
root@VM-0-14-ubuntu:~# update-alternatives --remove-all g++
root@VM-0-14-ubuntu:~# update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 1
root@VM-0-14-ubuntu:~# update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 10
root@VM-0-14-ubuntu:~# update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-7 1
root@VM-0-14-ubuntu:~# update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 10
装好验证：
root@VM-0-14-ubuntu:~# gcc --version
gcc (Ubuntu 11.1.0-1ubuntu1~18.04.1) 11.1.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
root@VM-0-14-ubuntu:~# g++ --version
g++ (Ubuntu 11.1.0-1ubuntu1~18.04.1) 11.1.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
2、安装虚拟屏幕以在编译时支持X11图形界面
详细介绍见我的另一篇文章《在Rstudio Linux Server上使用X window OpenGL图形系统》，以及该参考资料1，参考资料2。
# apt install xvfb x11vnc
# Xvfb :2 -screen 0 1280x960x24 2>/dev/null &
# export DISPLAY=:2
配置开机自动启动这两个服务，该镜像已经激活了ubuntu18的rc-local.service。
root@VM-0-14-ubuntu:~# vi /etc/rc.local
加入启动Xvfb的命令。
# Startup Xvfb and assign DISPLAY :2 to virtual X11 Server.
/usr/bin/Xvfb :2 -screen 0 1280x960x24 2>/dev/null &
export DISPLAY=:2
参考这篇资料，为x11vnc配置一个开机启动服务：
root@VM-0-14-ubuntu:/etc# cd /lib/systemd/system
root@VM-0-14-ubuntu:/lib/systemd/system# vi x11vnc.service
[Unit]
Description=Start x11vnc at startup.
After=multi-user.target
[Service]
Type=simple
ExecStart=/usr/bin/x11vnc -listen 0.0.0.0 -rfbport 5900 -noipv6 -passwd password -display :2 -forever
[Install]
WantedBy=multi-user.target
激活服务并重启系统：
root@VM-0-14-ubuntu:/lib/systemd/system# systemctl enable x11vnc.service
root@VM-0-14-ubuntu:/lib/systemd/system# systemctl daemon-reload
root@VM-0-14-ubuntu:/lib/systemd/system# reboot now
root@VM-0-14-ubuntu:~# ps -ef|grep Xvfb
root 2150 1 0 07:55 ? 00:00:00 /usr/bin/Xvfb :2 -screen 0 1280x960x24
root 9678 7329 0 08:38 pts/0 00:00:00 grep --color=auto Xvfb
root@VM-0-14-ubuntu:~# ps -ef|grep x11vnc
root 2171 1 0 07:55 ? 00:00:00 /usr/bin/x11vnc -listen 0.0.0.0 -rfbport 5900 -noipv6 -display :2 -forever
root 9724 7329 0 08:39 pts/0 00:00:00 grep --color=auto x11vnc
3、安装编译R的依赖包
参阅资料1，参阅资料2，参阅资料3。
# apt-get install libpng-dev
# apt-get install libjpeg-dev
# apt-get install libtiff-dev
# apt-get install libcairo-dev
# sudo apt-get install libicu-dev
# apt-get install liblzma-dev libblas
# apt-get install libbz2-dev
# apt-get install libreadline-dev
# apt install libssl-dev libcurl4-openssl-dev libxml2-dev
4、编译安装R-4.2.1
从源码编译R-4.2.1需要libicu58，该软件包用于软件包的国际化支持。装好Python部分后，系统中装了好几个版本的libicu：libicu60.2(ubuntu18.04)，libicu58(Anaconda3)，libicu56(CUDA 11)。参考下面的资料，从源码重新编译安装libicu58，把ubuntu18中libicu的版本降下来。参考资料1，参考资料2，参考资料3，参考资料4。
root@VM-0-14-ubuntu:~# apt list --installed | grep libicu
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
libicu-dev/bionic-security,bionic-updates,now 60.2-3ubuntu3.2 amd64 [已安装，自动]
libicu-le-hb-dev/bionic,now 1.0.3+git161113-4 amd64 [已安装，自动]
libicu-le-hb0/bionic,now 1.0.3+git161113-4 amd64 [已安装，自动]
libicu60/bionic-security,bionic-updates,now 60.2-3ubuntu3.2 amd64 [已安装]
libiculx60/bionic-security,bionic-updates,now 60.2-3ubuntu3.2 amd64 [已安装，自动]
root@VM-0-14-ubuntu:~# find / -name libicu*
/usr/lib/x86_64-linux-gnu/libicui18n.so.60
......
/usr/local/cuda-11.2/nsight-compute-2020.3.1/host/linux-desktop-glibc_2_11_3-x64/libicui18n.so.56
/usr/local/cuda-11.2/nsight-compute-2020.3.1/host/linux-desktop-glibc_2_11_3-x64/libicuuc.so.56
/usr/local/cuda-11.2/nsight-compute-2020.3.1/host/linux-desktop-glibc_2_11_3-x64/libicudata.so.56
/usr/local/cuda-11.2/nsight-systems-2020.4.3/host-linux-x64/libicui18n.so.56
/usr/local/cuda-11.2/nsight-systems-2020.4.3/host-linux-x64/libicuuc.so.56
/usr/local/cuda-11.2/nsight-systems-2020.4.3/host-linux-x64/libicudata.so.56
/usr/local/anaconda3/pkgs/icu-58.2-he6710b0_3/lib/libicuio.so.58
......
/usr/local/anaconda3/lib/libicuio.so.58
......
/usr/local/anaconda3/envs/gpu/lib/libicuio.so.58
......
/usr/share/lintian/overrides/libicu60
/usr/share/doc/libicu-le-hb-dev
/usr/share/doc/libicu-le-hb0
/usr/share/doc/libiculx60
/usr/share/doc/libicu-dev
/usr/share/doc/libicu60
......
用系统默认的libicu60.2编译R时会报错：
gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/anaconda3/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -c Rmain.c -o Rmain.o
gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -L/usr/local/lib -o R.bin Rmain.o -lR -lRblas
../../lib/libR.so：对‘u_versionToString_58’未定义的引用
../../lib/libR.so：对‘u_getVersion_58’未定义的引用
../../lib/libR.so：对‘uloc_setDefault_58’未定义的引用
../../lib/libR.so：对‘ucol_setStrength_58’未定义的引用
../../lib/libR.so：对‘ucol_open_58’未定义的引用
../../lib/libR.so：对‘ucol_close_58’未定义的引用
../../lib/libR.so：对‘ucol_strcollIter_58’未定义的引用
../../lib/libR.so：对‘ucol_setAttribute_58’未定义的引用
../../lib/libR.so：对‘uiter_setUTF8_58’未定义的引用
../../lib/libR.so：对‘ucol_getLocaleByType_58’未定义的引用
先重新编译安装libicu58：
# cd /home/ubuntu
# wget https://github.com/unicode-org/icu/releases/download/release-58-3/icu4c-58_3-src.tgz
# tar -xzvf icu4c-58_3-src.tgz
# cd icu/source
# ./configure
# # 编译需要xlocale.h
# ln -s /usr/include/locale.h /usr/include/xlocale.h
# make
# make install
编译安装R-4.2.1：
# cd /home/ubuntu
# wget https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/base/R-4/R-4.2.1.tar.gz
# tar -zxvf R-4.2.1.tar.gz
# cd R-4.2.1
# ./configure --prefix=/usr/lib64/R-4.2.1 --enable-R-shlib --with-pcre1 --with-cairo --with-libpng
# make -j4
# make install
# cd /usr/lib64/R-4.2.1/bin
# DISPLAY=:2 ./R
把R加入PATH搜索：
# vi /etc/environment
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib64/R-4.2.1/bin"
source 或logout/login使环境变量生效。
root@VM-0-14-ubuntu:/home/ubuntu/R-4.2.1# R
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R是自由软件，不带任何担保。
在某些条件下你可以将其自由散布。
用'license()'或'licence()'来看散布的详细条件。
R是个合作计划，有许多人为之做出了贡献.
用'contributors()'来看合作者的详细情况
用'citation()'会告诉你如何在出版物中正确地引用R或R程序包。
用'demo()'来看一些示范程序，用'help()'来阅读在线帮助文件，或
用'help.start()'通过HTML浏览器来看帮助文件。
用'q()'退出R.
> capabilities()
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE FALSE TRUE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE TRUE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE FALSE TRUE FALSE TRUE
libcurl
TRUE
>
5、指定R软件包C++14、C++17的编译器。
后面从源码安装的一些R软件包指定了C++要14或17版以上，需要为R指定它们的编译器。
# cd /root
# mkdir ~/.R
# vi ~/.R/Makevars
CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=g++
CXX17FLAGS=-O3 -march=native -mtune=native -fPIC
CXX17=g++
6、为R进程指定X window屏幕。
root@VM-0-14-ubuntu:/usr/lib64/R-4.2.1/lib/R/etc# vi Renviron
增加下面一行：
# Added by Jean for Xvfb 2022/11/10
DISPLAY=:2
二、安装Rstudio server
1、确保软件的版本符合要求：
RStudio Server requires Debian version 10 (or higher) or Ubuntu version 18 (or higher). RStudio requires a previous installation of R version 3.3.0 or higher.
下载：
# cd /home/ubuntu
# apt-get install gdebi-core
# wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.07.2-576-amd64.deb
2、执行安装，会下载安装依赖的几个软件包，然后安装程序要启动Rstudio Server可能会出错，因为还没有在配置文件中指定要用的R。
root@VM-0-14-ubuntu:/home/ubuntu# gdebi rstudio-server-2022.07.2-576-amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading state information... Done
需要安装以下软件包： libclang-6.0-dev libclang-common-6.0-dev libclang-dev libclang1-6.0 libllvm6.0 libpq5
RStudio Server
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.
您是否想安装这个软件包？[y/N]:y
......
正在选中未选择的软件包 rstudio-server。
(正在读取数据库 ... 系统当前共安装有 134749 个文件和目录。)
正准备解包 rstudio-server-2022.07.2-576-amd64.deb ...
正在解包 rstudio-server (2022.07.2+576) ...
正在设置 rstudio-server (2022.07.2+576) ...
Created symlink /etc/systemd/system/multi-user.target.wants/rstudio-server.service → /lib/systemd/system/rstudio-server.service.
TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to '/var/log/rstudio/rstudio-server/rserver.log'.
● rstudio-server.service - RStudio Server
Loaded: loaded (/lib/systemd/system/rstudio-server.service; enabled; vendor preset: enabled)
Active: activating (auto-restart) (Result: exit-code) since Wed 2022-11-09 16:01:25 CST; 34ms ago
Process: 6716 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS)
Main PID: 6725 (code=exited, status=1/FAILURE)
root@VM-0-14-ubuntu:/home/ubuntu#
3、配置Rstudio Server。
A、增加用户组rusers，加入用户ubuntu，后面将配置只有rusers用户组才能登录。Rstudio Server默认uid 1000以下的用户（系统用户）不能登录，要查询用户ubuntu的id，后面修改一下uid的限制：
root@VM-0-14-ubuntu:/home/ubuntu# groupadd rusers
root@VM-0-14-ubuntu:/home/ubuntu# usermod -a -G rusers ubuntu
root@VM-0-14-ubuntu:/home/ubuntu# grep rusers /etc/group
rusers:x:1001:ubuntu
root@VM-0-14-ubuntu:/home/ubuntu# id ubuntu
uid=500(ubuntu) gid=500(ubuntu) 组=500(ubuntu),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),114(sambashare),1001(rusers)
B、服务器配置。
root@VM-0-14-ubuntu:/home/ubuntu# vi /etc/rstudio/rserver.conf
# Server Configuration File
www-port=8787
rsession-which-r=/usr/lib64/R-4.2.1/bin/R
auth-required-user-group=rusers
auth-minimum-user-id=500
C、session配置。
root@VM-0-14-ubuntu:/home/ubuntu# vi /etc/rstudio/rsession.conf
# R Session Configuration File
session-timeout-minutes=0
D、为作图配置Rstudio(Browser Client)全局选项，否则作图会出错，因为服务器上没有物理的X11图形设备。这里是正常的作图，显示在Rstudio Plots窗口中，不用Xvfb虚拟屏幕。
Tools menu is the Global Options... command that lets you set the graphics backend (under the General section, Graphics tab). Changing the graphics device backend to "Cairo".
或者配置服务器的全局选项，参阅：参考资料。
root@VM-0-14-ubuntu:/home/ubuntu# vi /etc/rstudio/rstudio-prefs.json
#"enum": ["default", "cairo", "cairo-png", "quartz", "windows", "ragg"],
#options(RStudioGD.backend = "ragg")
#set it in (say) your R installation's Rprofile.site
{
graphics_backend: "cairo"
}
E、指定所有R进程的图形设备都用cairo，否则后面运行Shiny App时会报错：“无法打开链结到X11显示，无法打开PNG设备”，因为ubuntu上它默认的图形设备是Xlib，会连接到X11，参阅资料1，参阅资料2。
root@VM-0-14-ubuntu:/usr/lib64/R-4.2.1/lib/R/etc# vi Rprofile.site
options(bitmapType='cairo')
4、管理Rstudio Server。
先让服务器成为系统守护进程，开机自启动。
#systemctl enable rstudio-server.service
管理服务：
#systemctl start rstudio-server.service
#systemctl stop rstudio-server.service
#systemctl status rstudio-server
5、查看日志。
root@VM-0-14-ubuntu:/home/ubuntu# vi /var/log/rstudio/rstudio-server/rserver.log
2022-11-09T08:01:24.931865Z [rserver] ERROR Path to R not specified, and no module binary specified; Invalid R module (); LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:812
2022-11-09T08:19:30.050217Z [rserver] WARNING User ubuntu could not be authenticated because they did not meet the minimum required user id (1000). The minimum user id is controlled by the auth-minimum-user-id rserver.conf option.; LOGGED FROM: bool rstudio::server::auth::validateUser(const string&, const string&, unsigned int, bool) src/cpp/server/auth/ServerValidateUser.cpp:94
2022-11-09T08:42:58.588563Z [rserver] ERROR Failed to validate sign-in with invalid CSRF form; LOGGED FROM: bool rstudio::server::auth::common::validateSignIn(const rstudio::core::http::Request&, rstudio::core::http::Response*) src/cpp/server/auth/ServerAuthCommon.cpp:133
6、登录系统测试。
访问网址http://106.52.33.185:8787，输入用户名ubuntu/password登录，运行一段简单的作图程序测试。现在是没有https加密的，先用着，后面再与Shiny Server一起配Nginx反向代理https加密。
Rstudio Server初步装好
三、安装Shiny等常用软件包。
1、安装shiny及rmarkdown包，用于Rstudio IDE中开发测试。
>install.packages("shiny")
>install.packages("rmarkdown")
会从源码下载安装一大堆依赖的包。
运行一个简单的Shiny App测试，~/Rscripts/ShinyDev/shinyAppExample/app.R。
library(shiny)
# Define UI for app that draws a histogram ----
ui <- fluidPage(
# App title ----
titlePanel("Hello Shiny!"),
# Sidebar layout with input and output definitions ----
sidebarLayout(
# Sidebar panel for inputs ----
sidebarPanel(
# Input: Slider for the number of bins ----
sliderInput(inputId = "bins",
label = "Number of bins:",
min = 1,
max = 50,
value = 30)
),
# Main panel for displaying outputs ----
mainPanel(
# Output: Histogram ----
plotOutput(outputId = "distPlot")
)
)
)
# Define server logic required to draw a histogram ----
server <- function(input, output) {
# Histogram of the Old Faithful Geyser Data ----
# with requested number of bins
# This expression that generates a histogram is wrapped in a call
# to renderPlot to indicate that:
#
# 1. It is "reactive" and therefore should be automatically
# re-executed when inputs (input$bins) change
# 2. Its output type is a plot
output$distPlot <- renderPlot({
x <- faithful$waiting
bins <- seq(min(x), max(x), length.out = input$bins + 1)
hist(x, breaks = bins, col = "#75AADB", border = "white",
xlab = "Waiting time to next eruption (in mins)",
main = "Histogram of waiting times")
})
}
# Create Shiny app ----
shinyApp(ui = ui, server = server)
Rstudio-installation-2.PNG
2、安装reticulate、tensorflow、keras连接Python深度学习环境。
深度学习框架Tensorflow GPU只有Python版，Rstudio通过reticulate包连接Python调用它们，R语言的tensorflow与keras包提供了对Python版相应包的封装，参阅资料1，参阅资料2。
A、安装软件包。用root在终端上启动R，安装到R的系统library目录下。
>install.packages("reticulate")
>install.packages("tensorflow")
>install.packages("keras")
>install.packages("dplyr")
上面的命令会自动安装它们依赖的其它R包。
B、设置RETICULATE_PYTHON环境变量，所有R进程都使用Anaconda3的Python，注意用的是虚拟环境"gpu"的python。
root@VM-0-14-ubuntu:~# conda activate gpu
(gpu) root@VM-0-14-ubuntu:~# cd /usr/lib64/R-4.2.1/lib/R/etc
(gpu) root@VM-0-14-ubuntu:/usr/lib64/R-4.2.1/lib/R/etc# vi Renviron
增加下面的环境变量。
# Added for python by Jean 2022/02/27
RETICULATE_PYTHON='/usr/local/anaconda3/envs/gpu/bin/python'
重启当前的Rstudio Session以使环境变量生效，运行一个matplotlib程序画个简单的图测试一下。
import numpy as np
import matplotlib.pyplot as plt
Xc = np.array([-1, 2, 3, 4])
Yc = np.array([-2, 3, 4, 5])
plt.plot(Xc,Yc)
plt.title("中文测试")
plt.show()
在Rstudio中运行Python程序
C、测试keras和tensorflow-gpu，testKeras.R。
library(reticulate)
library(keras)
library(dplyr)
py_discover_config()
py_config()
mnist <- dataset_mnist()
# keras的数据文件默认放在/home/ubuntu/.keras/datasets/mnist.npz
str(mnist)
train_images <- mnist$train$x
train_label <- mnist$train$y
test_images <- mnist$test$x
test_label <- mnist$test$y
dim(train_images)
dim(test_images)
dim(train_label)
dim(test_label)
str(train_images)
glimpse(train_images)
str(test_images)
# 设计神经网络结构,由2个完全连接层处理，一个有512个神经元，一个有10个神经元， 28*28=784 -> 512 ->10
# 用线性堆栈层构建模型
network <- keras_model_sequential() %>%
layer_dense(units = 512, activation = "relu", input_shape = c(28 * 28)) %>%
layer_dense(units = 10, activation = "softmax") # 第二层没有输入格式参数，接受第一层的输出，512维向量。
# 设计算法的损失函数，优化算法和度量准则
network %>% compile(
optimizer = "rmsprop", # 优化器，选择的梯度下降算法
loss = "categorical_crossentropy", # 损失函数
metrics = c("accuracy") # 观察指标
)
# 数据预处理， 每张图由二维数组变为1维数组，输入是1维数组（1维张量），标准化至[0,1]，完全连接层要求二维张量
train_images <- array_reshape(train_images, c(60000, 28 * 28))
train_images <- train_images / 255
test_images <- array_reshape(test_images, c(10000, 28 * 28))
test_images <- test_images / 255
# 目标变量因子化，变为类变量
train_labels <- to_categorical(train_label)
test_labels <- to_categorical(test_label)
dim(train_images)
dim(test_images)
dim(train_labels)
dim(test_labels)
# 训练数据集上拟合模型
network %>% fit(train_images, train_labels, epochs = 5, batch_size = 128)
# 60000/128 =469，GPU版并行处理，每批128个样本，共469批，书中 60000/60000是CPU版串行训练，每次迭代要9~10s
# 测试数据集测试模型
metrics <- network %>% evaluate(test_images, test_labels, batch_size = 128)
metrics
# 10000/313=32，GPU并行处理同上。evaluate()如果没有给出 batch_size参数，默认是32。
# 测试样本的前10个样本的类别预测
# 参阅 https://blog.csdn.net/yiyihuazi/article/details/122323349
# keras 2.6删除了predict_classes()函数
#network %>% predict_classes(test_images[1:10, ])
predicts<- network %>% predict(test_images[1:10, ])
result<- rep(0,10)
for(i in 1:length(predicts[,1])){
result[i]<- which.max(predicts[i,])-1
}
cat(result)
# [1] 7 2 1 0 4 1 4 9 5 9
# 画出这10个样本，看看识别的效果，因为test_images经过reshape，要引用原来载入的数据。
# 第9个数字识别为5，有疑问。
opar <- par(no.readonly = TRUE)
par(mfrow=c(2,5),mai=c(0.1,0.1,0.3,0.1))
for(i in 1:10){
digit<- mnist$test$x[i,,]
plot(as.raster(digit, max=255))
}
par(opar)
手写数字识别训练
手写数字识别预测
四、安装Shiny Server
1、安装。
Before installing Shiny Server, you must install R and the Shiny R package.
前面已经安装好了，直接装Shiny Server。
(gpu) root@VM-0-14-ubuntu:/home/ubuntu# wget https://download3.rstudio.org/ubuntu-18.04/x86_64/shiny-server-1.5.19.995-amd64.deb
(gpu) root@VM-0-14-ubuntu:/home/ubuntu# gdebi shiny-server-1.5.19.995-amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading state information... Done
Shiny Server
Shiny Server is a server program from RStudio, Inc. that makes Shiny applications available over the web. Shiny is a web application framework for the R statistical computation language.
您是否想安装这个软件包？[y/N]:y
正在选中未选择的软件包 shiny-server。
(正在读取数据库 ... 系统当前共安装有 138801 个文件和目录。)
正准备解包 shiny-server-1.5.19.995-amd64.deb ...
正在解包 shiny-server (1.5.19.995) ...
正在设置 shiny-server (1.5.19.995) ...
Creating user shiny
Adding LANG to /etc/systemd/system/shiny-server.service, setting to zh_CN.UTF-8
Created symlink /etc/systemd/system/multi-user.target.wants/shiny-server.service → /etc/systemd/system/shiny-server.service.
● shiny-server.service - ShinyServer
Loaded: loaded (/etc/systemd/system/shiny-server.service; enabled; vendor preset: enabled)
Active: active (running) since Thu 2022-11-10 10:44:54 CST; 7ms ago
Main PID: 32193 (shiny-server)
Tasks: 1 (limit: 4915)
CGroup: /system.slice/shiny-server.service
└─32193 /opt/shiny-server/ext/node/bin/shiny-server /opt/shiny-server/lib/main.js
11月 10 10:44:54 VM-0-14-ubuntu systemd[1]: Started ShinyServer.
This will install Shiny Server into /opt/shiny-server/, with the main executable in /opt/shiny-server/bin/shiny-server, and also create a new shiny user.
2、指定使用的R版本。
因为我的R没有装在默认的位置，shiny server在尝试运行Shiny App时没有找到R命令，需要设置Shiny Server使用的R版本，参阅资料1，参阅资料2，r_path参数只有在专业版中才有。于是参考该帖子建立一个软连接解决，不用改配置。
# ln -s /usr/lib64/R-4.2.1/bin/R /usr/bin/R
3、管理Shiny Server：
# systemctl start shiny-server
# systemctl stop shiny-server
# systemctl restart shiny-server
# systemctl status shiny-server
重启Shiny Server，访问http://106.52.33.185:3838，安装完成。现在它没有加密连接，先用着。Rstudio Server与Shiny Server的开源免费版都不支持加密连接，后面再通过Nginx反向代理加密。
验证Shiny Server安装
4、配置Shiny Server为用户发布模式，允许用户自行发布App。
这样用户只要把APP拷贝到Ta的home目录下的~/ShinyApps目录下即可，比如ubuntu把/home/ubuntu/Rscripts/ShinyDev/shinyAppExample拷贝成/home/ubuntu/ShinyApps/shinyAppExample就发布了APP。具体可参阅Shiny Server Administrator’s Guide。
root@VM-0-14-ubuntu:/etc/shiny-server# vi shiny-server.conf
# Define a top-level server which will listen on a port
server {
# Instruct this server to listen on port 3838
listen 3838;
# Define the location available at the base URL
location /{
# Define the user we should use when spawning R Shiny processes
run_as shiny;
# Run this location in 'site_dir' mode, which hosts the entire directory
# tree at '/srv/shiny-server'
site_dir /srv/shiny-server;
# Define where we should put the log files for this location
log_dir /var/log/shiny-server;
# Should we list the contents of a (non-Shiny-App) directory when the user
# visits the corresponding URL?
directory_index on;
}
# Should make a directory named ShinyApps at user home directory
location /users {
run_as :HOME_USER:;
user_dirs;
}
}
5、在用户home目录下建立ShinyApps目录，测试好的App拷贝到该目录下，每个App一个子目录。
1）单文件发布，在子目录下命名为app.R，DESCRIPTION文件可选。
2）双文件发布，在子目录下命名为ui.R与server.R，global.R可选。
(base) ubuntu@VM-0-14-ubuntu:~$ cd ShinyApps
(base) ubuntu@VM-0-14-ubuntu:~/ShinyApps$ cp -R /home/ubuntu/Rscripts/ShinyDev/shinyAppExample shinyAppExample
(base) ubuntu@VM-0-14-ubuntu:~/ShinyApps$ ls
shinyAppExample
6、通过 http://ip:port/users/UserName/AppDirectory访问App。比如：
http://106.52.33.185:3838/users/ubuntu/shinyAppExample
访问用户自行发布的Shiny App
五、安装Nginx并配置反向代理
1、安装Nginx，参阅资料。
(gpu) root@VM-0-14-ubuntu:/var/log/shiny-server# apt install nginx
正在读取软件包列表... 完成
正在分析软件包的依赖关系树
正在读取状态信息... 完成
将会同时安装下列软件：
libnginx-mod-http-geoip libnginx-mod-http-image-filter libnginx-mod-http-xslt-filter libnginx-mod-mail libnginx-mod-stream
nginx-common nginx-core
建议安装：
fcgiwrap nginx-doc ssl-cert
下列【新】软件包将被安装：
libnginx-mod-http-geoip libnginx-mod-http-image-filter libnginx-mod-http-xslt-filter libnginx-mod-mail libnginx-mod-stream
nginx nginx-common nginx-core
升级了 0 个软件包，新安装了 8 个软件包，要卸载 0 个软件包，有 26 个软件包未被升级。
需要下载 599 kB 的归档。
解压缩后会消耗 2,120 kB 的额外空间。
您希望继续执行吗？ [Y/n] y
......
正在处理用于 systemd (237-3ubuntu10.56) 的触发器 ...
(gpu) root@VM-0-14-ubuntu:/var/log/shiny-server# systemctl status nginx
● nginx.service - A high performance web server and a reverse proxy server
Loaded: loaded (/lib/systemd/system/nginx.service; enabled; vendor preset: enabled)
Active: active (running) since Thu 2022-11-10 16:23:05 CST; 30s ago
Docs: man:nginx(8)
Main PID: 21512 (nginx)
Tasks: 9 (limit: 4915)
CGroup: /system.slice/nginx.service
├─21512 nginx: master process /usr/sbin/nginx -g daemon on; master_process on;
├─21514 nginx: worker process
├─21516 nginx: worker process
├─21518 nginx: worker process
├─21520 nginx: worker process
├─21522 nginx: worker process
├─21523 nginx: worker process
├─21524 nginx: worker process
└─21525 nginx: worker process
11月 10 16:23:05 VM-0-14-ubuntu systemd[1]: Starting A high performance web server and a reverse proxy server...
11月 10 16:23:05 VM-0-14-ubuntu systemd[1]: Started A high performance web server and a reverse proxy server.
2、管理Nginx：
#systemctl start nginx
#systemctl stop nginx
#systemctl status nginx
#systemctl restart nginx
3、配置SSL代理Rstduio Server与Shiny Server。
A、Nginx的服务器证书要把自签CA的证书打包在一起形成完整的证书链，否则手机上访问SSL会有问题。有关自签证书的生成，请参阅我的另一篇文章《GPU Linux虚拟主机GN7型安装配置文档》。
root@VM-0-14-ubuntu:~# cd /root/cert
root@VM-0-14-ubuntu:~/cert# cat ./demoCA/cacert.pem >> server.crt
B、修改Rstudio Server配置。
为了从同一个https端口分别反向代理Rstudio与Shiny Server，Nginx给它们加上了不同的前缀，Rstudio Server加的是/rstudio，Shiny Server加的是/shiny。可以关闭防火墙的8787端口，或在Rstudio Server的配置中限制8787端口只能从本机访问。
root@VM-0-14-ubuntu:/etc/rstudio# vi rserver.conf
# Server Configuration File
www-port=8787
rsession-which-r=/usr/lib64/R-4.2.1/bin/R
auth-required-user-group=rusers
auth-minimum-user-id=500
# Added by Jean for Nginx reverse proxy 2022/11/10
www-address=127.0.0.1
C、修改Nginx配置。
(gpu) root@VM-0-14-ubuntu:/etc/nginx# vi nginx.conf
默认的80端口定义了一个非加密的http服务器，提供静态的主页等。增加了一个SSL服务器的定义，指定了它使用的自签服务器证书与密钥，在443号默认端口侦听。然后一个location /rstudio定义是对Rstudio Server的反向代理，一个location /shiny定义是对Shiny Server的反向代理。
user www-data;
worker_processes auto;
pid /run/nginx.pid;
include /etc/nginx/modules-enabled/*.conf;
events {
worker_connections 768;
# multi_accept on;
}
http {
##
# Basic Settings
##
sendfile on;
tcp_nopush on;
tcp_nodelay on;
keepalive_timeout 65;
types_hash_max_size 2048;
# server_tokens off;
# server_names_hash_bucket_size 64;
# server_name_in_redirect off;
include /etc/nginx/mime.types;
default_type application/octet-stream;
##
# SSL Settings
##
ssl_protocols TLSv1 TLSv1.1 TLSv1.2; # Dropping SSLv3, ref: POODLE
ssl_prefer_server_ciphers on;
##
# Logging Settings
##
access_log /var/log/nginx/access.log;
error_log /var/log/nginx/error.log;
##
# Gzip Settings
##
gzip on;
# gzip_vary on;
# gzip_proxied any;
# gzip_comp_level 6;
# gzip_buffers 16 8k;
# gzip_http_version 1.1;
# gzip_types text/plain text/css application/json application/javascript text/xml application/xml application/xml+rss text/javascript;
##
# Virtual Host Configs
##
include /etc/nginx/conf.d/*.conf;
include /etc/nginx/sites-enabled/*;
# Support proxying of web-socket connections
map $http_upgrade $connection_upgrade {
default upgrade;
'' close;
}
# Server on http:80
server {
listen 80;
server_name 106.52.33.185;
location / {
root /usr/share/nginx/html;
index index.html;
autoindex on;
}
}
# Server with SSL enabled
server {
listen 443 ssl http2;
listen [::]:443 ssl http2;
server_name 106.52.33.185;
# Change to point to your certs
ssl_certificate /root/cert/server.crt;
ssl_certificate_key /root/cert/server.key;
ssl_protocols TLSv1.2 TLSv1.1 TLSv1;
# Reverse proxy for Rstudio Server
rewrite ^/rstudio$ $scheme://$http_host/rstudio/ permanent;
location /rstudio/ {
# Needed only for prefix of /rstudio
rewrite ^/rstudio/(.*)$ /$1 break;
# Use http here when ssl-enabled=0 is set in rserver.conf
proxy_pass http://localhost:8787;
proxy_redirect http://localhost:8787/ $scheme://$http_host/rstudio/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
# In some cases, such as when streaming job statuses from the launcher, the default response buffering in nginx
# can be too slow for delivering real-time updates, especially when configured to use SSL.
# disabling response buffering
proxy_buffering off;
}
# Reverse proxy for Shiny server
rewrite ^/shiny$ $scheme://$http_host/shiny/ permanent;
location /shiny/ {
rewrite ^/shiny/(.*)$ /$1 break;
proxy_pass http://localhost:3838;
proxy_redirect / $scheme://$http_host/shiny/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
proxy_buffering off;
}
}
}
4、通过https加密协议访问Rstudio Server与Shiny Server。
重启各个服务。
#systemctl restart rstudio-server.service
#systemctl restart shiny-server
#systemctl restart nginx
A、访问Rstudio Server
https://106.52.33.185/rstudio/
通过https加密协议访问Rstudio Server
B、访问Shiny Server。原来的URL中间加上/shiny即可。
https://106.52.33.185/shiny/users/ubuntu/shinyAppExample/
通过https加密协议访问Shiny Server
C、Nginx的非加密静态网页。
http://106.52.33.185
Nginx的非加密通道可以提供一些不包含敏感信息的静态网页
六、配置R使用OpenGL图形系统
1、Ubuntu安装OpenGL开发环境。
参考资料。
root@VM-0-14-ubuntu:/home/ubuntu# apt-get install libglu1-mesa-dev
root@VM-0-14-ubuntu:/home/ubuntu# apt-get install freeglut3-dev
root@VM-0-14-ubuntu:/home/ubuntu# export DISPLAY=:2
root@VM-0-14-ubuntu:/home/ubuntu# glxinfo | grep "OpenGL version"
OpenGL version string: 3.1 Mesa 20.0.8
编一个OpenGL测试程序。
# cd /home/ubuntu
# vi test.cc
#include <GL/gl.h>
#include <GL/glut.h>
#include <stdlib.h>
void init(void)
{
glClearColor(0.0, 0.0, 0.0, 0.0);
glMatrixMode(GL_PROJECTION);
glOrtho(-5,5,-5,5,5,15);
glMatrixMode(GL_MODELVIEW);
gluLookAt(0,0,10,0,0,0,0,1,0);
return;
}
void display(void)
{
glClear(GL_COLOR_BUFFER_BIT);
glColor3f(1.0, 0, 0);
glutWireTeapot(3);
glFlush();
return;
}
int main(int argc, char* argv[])
{
glutInit(&argc, argv);
glutInitDisplayMode(GLUT_RGB|GLUT_SINGLE);
glutInitWindowPosition(0,0);
glutInitWindowSize(300, 300);
glutCreateWindow("OpenGL 3D View");
init();
glutDisplayFunc(display);
glutMainLoop();
return 0;
}
编译测试：
root@VM-0-14-ubuntu:/home/ubuntu# gcc -o test test.cc -lGL -lGLU -lglut
root@VM-0-14-ubuntu:/home/ubuntu# ./test
VNC viewer连接远端虚拟桌面：
OpenGL开发环境测试
2、R语言使用OpenGL例子。
A、安装gdal，参考资料：
root@VM-0-14-ubuntu:/home/ubuntu# apt-get install libgdal-dev libproj-dev gdal-bin -y
root@VM-0-14-ubuntu:/home/ubuntu# ogrinfo --version
GDAL 2.2.3, released 2017/11/20
B、安装R软件包：
>install.packages(c("rgdal","rgl","rayshader"，"rayrender","ambient"))
C、Rstudio中测试rgl包，最后运行rgl.close()关闭X window窗口。
library(rgl)
open3d()
x <- sort(rnorm(1000))
y <- rnorm(1000)
z <- rnorm(1000) + atan2(x,y)
plot3d(x, y, z, col=rainbow(1000))
rgl.postscript("foo.pdf", fmt="pdf")
sessionInfo()
#rgl.close()
VNC Viewer查看：
测试rgl包正确运行
D、测试rayshader包。
library(rgl)
library(rayshader)
library(rayrender)
library(ambient)
loadzip = tempfile()
download.file("https://tylermw.com/data/dem_01.tif.zip", loadzip)
localtif = raster::raster(unzip(loadzip, "dem_01.tif"))
unlink(loadzip)
elmat = raster_to_matrix(localtif)
montshadow = ray_shade(montereybay, zscale = 50, lambert = FALSE)
montamb = ambient_shade(montereybay, zscale = 50)
montereybay %>%
sphere_shade(zscale = 10, texture = "imhof1") %>%
add_shadow(montshadow, 0.5) %>%
add_shadow(montamb,0) %>%
plot_3d(montereybay, zscale = 50, fov = 0, theta = -100, phi = 30, windowsize = c(1000, 800), zoom = 0.6,
water = TRUE, waterdepth = 0, waterlinecolor = "white", waterlinealpha = 0.5,
wateralpha = 0.5, watercolor = "lightblue")
render_label(montereybay, x = 350, y = 160, z = 1000, zscale = 50,
text = "Moss Landing", textsize = 2, linewidth = 5)
render_label(montereybay, x = 220, y = 70, z = 7000, zscale = 50,
text = "Santa Cruz", textcolor = "darkred", linecolor = "darkred",
textsize = 2, linewidth = 5)
render_label(montereybay, x = 300, y = 270, z = 4000, zscale = 50,
text = "Monterey", dashed = TRUE, textsize = 2, linewidth = 5)
render_label(montereybay, x = 50, y = 270, z = 1000, zscale = 50, textcolor = "white", linecolor = "white",
text = "Monterey Canyon", relativez = FALSE, textsize = 2, linewidth = 5)
Sys.sleep(0.2)
render_snapshot('demo.png')
#rgl.close()
VNC Viewer查看：
测试rayshader包正确运行，远程桌面打开了OpenGL 3D X Window作图
