一崇猫、編譯安裝R-4.2.1
1诅福、升級gcc
??R語言及很多它的包匾委，要從源碼編譯安裝，所以要先升級gcc到最新版氓润，這是升級好的赂乐，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 [已安裝]
gcc-11/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安裝]
gcc-11-base/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安裝咖气，自動]
gcc-7/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安裝挨措，自動]
gcc-7-base/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安裝，自動]
gcc-7-multilib/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安裝崩溪，自動]
gcc-8-base/bionic-security,bionic-updates,now 8.4.0-1ubuntu1~18.04 amd64 [已安裝]
gcc-multilib/bionic-security,bionic-updates,now 4:7.4.0-1ubuntu2.3 amd64 [已安裝]
lib32gcc-7-dev/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安裝浅役，自動]
lib32gcc-s1/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安裝，自動]
lib32gcc1/bionic,now 1:11.1.0-1ubuntu1~18.04.1 amd64 [已安裝伶唯，自動]
libgcc-11-dev/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安裝觉既，自動]
libgcc-7-dev/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安裝，自動]
libgcc-s1/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安裝抵怎，自動]
libgcc1/bionic-security,bionic-updates,now 1:8.4.0-1ubuntu1~18.04 amd64 [已安裝奋救，可升級至：1:11.1.0-1ubuntu1~18.04.1]
libx32gcc-7-dev/bionic-security,bionic-updates,now 7.5.0-3ubuntu1~18.04 amd64 [已安裝榄审，自動]
libx32gcc-s1/bionic,now 11.1.0-1ubuntu1~18.04.1 amd64 [已安裝航厚，自動]
libx32gcc1/bionic,now 1:11.1.0-1ubuntu1~18.04.1 amd64 [已安裝，自動]
root@VM-0-14-ubuntu:~#
??參閱資料炕吸，依次執(zhí)行下面的命令升級姿染。
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
??裝好驗證：
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背亥、安裝虛擬屏幕以在編譯時支持X11圖形界面
??詳細(xì)介紹見我的另一篇文章《在Rstudio Linux Server上使用X window OpenGL圖形系統(tǒng)》，以及該參考資料1悬赏，參考資料2狡汉。
# apt install xvfb x11vnc
# Xvfb :2 -screen 0 1280x960x24 2>/dev/null &
# export DISPLAY=:2
??配置開機(jī)自動啟動這兩個服務(wù)，該鏡像已經(jīng)激活了ubuntu18的rc-local.service闽颇。
root@VM-0-14-ubuntu:~# vi /etc/rc.local
??加入啟動Xvfb的命令盾戴。
# Startup Xvfb and assign DISPLAY :2 to virtual X11 Server.
/usr/bin/Xvfb :2 -screen 0 1280x960x24 2>/dev/null &
export DISPLAY=:2
??參考這篇資料，為x11vnc配置一個開機(jī)啟動服務(wù)：
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
??激活服務(wù)并重啟系統(tǒng)：
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兵多、安裝編譯R的依賴包
??參閱資料1尖啡，參閱資料2，參閱資料3剩膘。
# 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衅斩、編譯安裝R-4.2.1
??從源碼編譯R-4.2.1需要libicu58，該軟件包用于軟件包的國際化支持怠褐。裝好Python部分后畏梆，系統(tǒng)中裝了好幾個版本的libicu：libicu60.2(ubuntu18.04)，libicu58(Anaconda3)，libicu56(CUDA 11)奠涌。參考下面的資料宪巨，從源碼重新編譯安裝libicu58，把ubuntu18中l(wèi)ibicu的版本降下來铣猩。參考資料1揖铜，參考資料2，參考資料3达皿，參考資料4天吓。
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 [已安裝，自動]
libicu-le-hb-dev/bionic,now 1.0.3+git161113-4 amd64 [已安裝峦椰，自動]
libicu-le-hb0/bionic,now 1.0.3+git161113-4 amd64 [已安裝龄寞，自動]
libicu60/bionic-security,bionic-updates,now 60.2-3ubuntu3.2 amd64 [已安裝]
libiculx60/bionic-security,bionic-updates,now 60.2-3ubuntu3.2 amd64 [已安裝，自動]
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
......
??用系統(tǒng)默認(rèn)的libicu60.2編譯R時會報錯：
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：對‘u_versionToString_58’未定義的引用
../../lib/libR.so：對‘u_getVersion_58’未定義的引用
../../lib/libR.so：對‘uloc_setDefault_58’未定義的引用
../../lib/libR.so：對‘ucol_setStrength_58’未定義的引用
../../lib/libR.so：對‘ucol_open_58’未定義的引用
../../lib/libR.so：對‘ucol_close_58’未定義的引用
../../lib/libR.so：對‘ucol_strcollIter_58’未定義的引用
../../lib/libR.so：對‘ucol_setAttribute_58’未定義的引用
../../lib/libR.so：對‘uiter_setUTF8_58’未定義的引用
../../lib/libR.so：對‘ucol_getLocaleByType_58’未定義的引用
??先重新編譯安裝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
# # 編譯需要xlocale.h
# ln -s /usr/include/locale.h /usr/include/xlocale.h
# make
# make install
??編譯安裝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使環(huán)境變量生效汤功。
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是自由軟件物邑，不帶任何擔(dān)保。
在某些條件下你可以將其自由散布滔金。
用'license()'或'licence()'來看散布的詳細(xì)條件色解。
R是個合作計劃，有許多人為之做出了貢獻(xiàn).
用'contributors()'來看合作者的詳細(xì)情況
用'citation()'會告訴你如何在出版物中正確地引用R或R程序包餐茵。
用'demo()'來看一些示范程序科阎，用'help()'來閱讀在線幫助文件，或
用'help.start()'通過HTML瀏覽器來看幫助文件忿族。
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锣笨、指定R軟件包C++14、C++17的編譯器道批。
??后面從源碼安裝的一些R軟件包指定了C++要14或17版以上错英，需要為R指定它們的編譯器。
# 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隆豹、為R進(jìn)程指定X window屏幕椭岩。
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、安裝Rstudio server
1璃赡、確保軟件的版本符合要求：
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.
下載：
# 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簿煌、執(zhí)行安裝，會下載安裝依賴的幾個軟件包鉴吹，然后安裝程序要啟動Rstudio Server可能會出錯，因為還沒有在配置文件中指定要用的R惩琉。
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
需要安裝以下軟件包： 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.
您是否想安裝這個軟件包豆励？[y/N]:y
......
正在選中未選擇的軟件包 rstudio-server。
(正在讀取數(shù)據(jù)庫 ... 系統(tǒng)當(dāng)前共安裝有 134749 個文件和目錄。)
正準(zhǔn)備解包 rstudio-server-2022.07.2-576-amd64.deb ...
正在解包 rstudio-server (2022.07.2+576) ...
正在設(shè)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良蒸、配置Rstudio Server技扼。
A、增加用戶組rusers嫩痰，加入用戶ubuntu剿吻，后面將配置只有rusers用戶組才能登錄。Rstudio Server默認(rèn)uid 1000以下的用戶（系統(tǒng)用戶）不能登錄串纺，要查詢用戶ubuntu的id丽旅，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) 組=500(ubuntu),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),114(sambashare),1001(rusers)
B、服務(wù)器配置纺棺。
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榄笙、session配置。
root@VM-0-14-ubuntu:/home/ubuntu# vi /etc/rstudio/rsession.conf
# R Session Configuration File
session-timeout-minutes=0
D祷蝌、為作圖配置Rstudio(Browser Client)全局選項茅撞，否則作圖會出錯，因為服務(wù)器上沒有物理的X11圖形設(shè)備巨朦。這里是正常的作圖米丘，顯示在Rstudio Plots窗口中，不用Xvfb虛擬屏幕糊啡。
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".
或者配置服務(wù)器的全局選項拄查，參閱：參考資料。
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悔橄、指定所有R進(jìn)程的圖形設(shè)備都用cairo靶累，否則后面運(yùn)行Shiny App時會報錯：“無法打開鏈結(jié)到X11顯示，無法打開PNG設(shè)備”癣疟，因為ubuntu上它默認(rèn)的圖形設(shè)備是Xlib挣柬，會連接到X11，參閱資料1睛挚，參閱資料2邪蛔。
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扎狱。
先讓服務(wù)器成為系統(tǒng)守護(hù)進(jìn)程侧到，開機(jī)自啟動。
#systemctl enable rstudio-server.service
管理服務(wù)：
#systemctl start rstudio-server.service
#systemctl stop rstudio-server.service
#systemctl status rstudio-server
5淤击、查看日志匠抗。
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、登錄系統(tǒng)測試污抬。
訪問網(wǎng)址http://106.52.33.185:8787汞贸，輸入用戶名ubuntu/password登錄绳军，運(yùn)行一段簡單的作圖程序測試。現(xiàn)在是沒有https加密的矢腻，先用著门驾，后面再與Shiny Server一起配Nginx反向代理https加密。
Rstudio Server初步裝好
三多柑、安裝Shiny等常用軟件包奶是。
1、安裝shiny及rmarkdown包竣灌，用于Rstudio IDE中開發(fā)測試聂沙。
>install.packages("shiny")
>install.packages("rmarkdown")
會從源碼下載安裝一大堆依賴的包。
運(yùn)行一個簡單的Shiny App測試帐偎，~/Rscripts/ShinyDev/shinyAppExample/app.R逐纬。
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、安裝reticulate削樊、tensorflow豁生、keras連接Python深度學(xué)習(xí)環(huán)境。
深度學(xué)習(xí)框架Tensorflow GPU只有Python版漫贞，Rstudio通過reticulate包連接Python調(diào)用它們甸箱，R語言的tensorflow與keras包提供了對Python版相應(yīng)包的封裝，參閱資料1迅脐，參閱資料2芍殖。
A、安裝軟件包谴蔑。用root在終端上啟動R豌骏，安裝到R的系統(tǒng)library目錄下。
>install.packages("reticulate")
>install.packages("tensorflow")
>install.packages("keras")
>install.packages("dplyr")
上面的命令會自動安裝它們依賴的其它R包隐锭。
B窃躲、設(shè)置RETICULATE_PYTHON環(huán)境變量，所有R進(jìn)程都使用Anaconda3的Python钦睡，注意用的是虛擬環(huán)境"gpu"的python蒂窒。
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
增加下面的環(huán)境變量。
# Added for python by Jean 2022/02/27
RETICULATE_PYTHON='/usr/local/anaconda3/envs/gpu/bin/python'
重啟當(dāng)前的Rstudio Session以使環(huán)境變量生效荞怒，運(yùn)行一個matplotlib程序畫個簡單的圖測試一下洒琢。
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("中文測試")
plt.show()
在Rstudio中運(yùn)行Python程序
C、測試keras和tensorflow-gpu褐桌，testKeras.R衰抑。
library(reticulate)
library(keras)
library(dplyr)
py_discover_config()
py_config()
mnist <- dataset_mnist()
# keras的數(shù)據(jù)文件默認(rèn)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)
# 設(shè)計神經(jīng)網(wǎng)絡(luò)結(jié)構(gòu),由2個完全連接層處理，一個有512個神經(jīng)元荧嵌，一個有10個神經(jīng)元停士， 28*28=784 -> 512 ->10
# 用線性堆棧層構(gòu)建模型
network <- keras_model_sequential() %>%
layer_dense(units = 512, activation = "relu", input_shape = c(28 * 28)) %>%
layer_dense(units = 10, activation = "softmax") # 第二層沒有輸入格式參數(shù)挖帘，接受第一層的輸出，512維向量恋技。
# 設(shè)計算法的損失函數(shù)，優(yōu)化算法和度量準(zhǔn)則
network %>% compile(
optimizer = "rmsprop", # 優(yōu)化器逻族，選擇的梯度下降算法
loss = "categorical_crossentropy", # 損失函數(shù)
metrics = c("accuracy") # 觀察指標(biāo)
)
# 數(shù)據(jù)預(yù)處理蜻底， 每張圖由二維數(shù)組變?yōu)?維數(shù)組，輸入是1維數(shù)組（1維張量）聘鳞，標(biāo)準(zhǔn)化至[0,1]薄辅，完全連接層要求二維張量
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
# 目標(biāo)變量因子化，變?yōu)轭愖兞?train_labels <- to_categorical(train_label)
test_labels <- to_categorical(test_label)
dim(train_images)
dim(test_images)
dim(train_labels)
dim(test_labels)
# 訓(xùn)練數(shù)據(jù)集上擬合模型
network %>% fit(train_images, train_labels, epochs = 5, batch_size = 128)
# 60000/128 =469抠璃，GPU版并行處理站楚，每批128個樣本，共469批搏嗡，書中 60000/60000是CPU版串行訓(xùn)練窿春，每次迭代要9~10s
# 測試數(shù)據(jù)集測試模型
metrics <- network %>% evaluate(test_images, test_labels, batch_size = 128)
metrics
# 10000/313=32，GPU并行處理同上采盒。evaluate()如果沒有給出 batch_size參數(shù)旧乞，默認(rèn)是32。
# 測試樣本的前10個樣本的類別預(yù)測
# 參閱 https://blog.csdn.net/yiyihuazi/article/details/122323349
# keras 2.6刪除了predict_classes()函數(shù)
#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
# 畫出這10個樣本磅氨，看看識別的效果尺栖，因為test_images經(jīng)過reshape，要引用原來載入的數(shù)據(jù)烦租。
# 第9個數(shù)字識別為5延赌，有疑問。
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)
手寫數(shù)字識別訓(xùn)練
手寫數(shù)字識別預(yù)測
四叉橱、安裝Shiny Server
1挫以、安裝。
Before installing Shiny Server, you must install R and the Shiny R package.
前面已經(jīng)安裝好了赏迟，直接裝Shiny Server屡贺。
(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.
您是否想安裝這個軟件包？[y/N]:y
正在選中未選擇的軟件包 shiny-server锌杀。
(正在讀取數(shù)據(jù)庫 ... 系統(tǒng)當(dāng)前共安裝有 138801 個文件和目錄甩栈。)
正準(zhǔn)備解包 shiny-server-1.5.19.995-amd64.deb ...
正在解包 shiny-server (1.5.19.995) ...
正在設(shè)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版本糕再。
因為我的R沒有裝在默認(rèn)的位置量没，shiny server在嘗試運(yùn)行Shiny App時沒有找到R命令，需要設(shè)置Shiny Server使用的R版本突想，參閱資料1殴蹄，參閱資料2究抓，r_path參數(shù)只有在專業(yè)版中才有。于是參考該帖子建立一個軟連接解決袭灯，不用改配置刺下。
# 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
重啟Shiny Server稽荧，訪問http://106.52.33.185:3838橘茉，安裝完成。現(xiàn)在它沒有加密連接姨丈，先用著畅卓。Rstudio Server與Shiny Server的開源免費版都不支持加密連接，后面再通過Nginx反向代理加密蟋恬。
驗證Shiny Server安裝
4翁潘、配置Shiny Server為用戶發(fā)布模式，允許用戶自行發(fā)布App歼争。
這樣用戶只要把APP拷貝到Ta的home目錄下的~/ShinyApps目錄下即可拜马，比如ubuntu把/home/ubuntu/Rscripts/ShinyDev/shinyAppExample拷貝成/home/ubuntu/ShinyApps/shinyAppExample就發(fā)布了APP。具體可參閱Shiny Server Administrator’s Guide矾飞。
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;
}
}
5一膨、在用戶home目錄下建立ShinyApps目錄，測試好的App拷貝到該目錄下洒沦，每個App一個子目錄豹绪。
1）單文件發(fā)布，在子目錄下命名為app.R申眼，DESCRIPTION文件可選瞒津。
2）雙文件發(fā)布，在子目錄下命名為ui.R與server.R括尸，global.R可選巷蚪。
(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、通過 http://ip:port/users/UserName/AppDirectory訪問App濒翻。比如：
http://106.52.33.185:3838/users/ubuntu/shinyAppExample
訪問用戶自行發(fā)布的Shiny App
五屁柏、安裝Nginx并配置反向代理
1、安裝Nginx有送，參閱資料淌喻。
(gpu) root@VM-0-14-ubuntu:/var/log/shiny-server# apt install nginx
正在讀取軟件包列表... 完成
正在分析軟件包的依賴關(guān)系樹
正在讀取狀態(tài)信息... 完成
將會同時安裝下列軟件：
libnginx-mod-http-geoip libnginx-mod-http-image-filter libnginx-mod-http-xslt-filter libnginx-mod-mail libnginx-mod-stream
nginx-common nginx-core
建議安裝：
fcgiwrap nginx-doc ssl-cert
下列【新】軟件包將被安裝：
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
升級了 0 個軟件包，新安裝了 8 個軟件包雀摘，要卸載 0 個軟件包裸删，有 26 個軟件包未被升級。
需要下載 599 kB 的歸檔阵赠。
解壓縮后會消耗 2,120 kB 的額外空間涯塔。
您希望繼續(xù)執(zhí)行嗎肌稻？ [Y/n] y
......
正在處理用于 systemd (237-3ubuntu10.56) 的觸發(fā)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匕荸、配置SSL代理Rstduio Server與Shiny Server爹谭。
A、Nginx的服務(wù)器證書要把自簽CA的證書打包在一起形成完整的證書鏈每聪，否則手機(jī)上訪問SSL會有問題旦棉。有關(guān)自簽證書的生成，請參閱我的另一篇文章《GPU Linux虛擬主機(jī)GN7型安裝配置文檔》药薯。
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配置救斑。
為了從同一個https端口分別反向代理Rstudio與Shiny Server童本，Nginx給它們加上了不同的前綴，Rstudio Server加的是/rstudio脸候，Shiny Server加的是/shiny穷娱。可以關(guān)閉防火墻的8787端口运沦，或在Rstudio Server的配置中限制8787端口只能從本機(jī)訪問泵额。
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配置携添。
(gpu) root@VM-0-14-ubuntu:/etc/nginx# vi nginx.conf
默認(rèn)的80端口定義了一個非加密的http服務(wù)器嫁盲，提供靜態(tài)的主頁等。增加了一個SSL服務(wù)器的定義烈掠，指定了它使用的自簽服務(wù)器證書與密鑰羞秤，在443號默認(rèn)端口偵聽。然后一個location /rstudio定義是對Rstudio Server的反向代理左敌，一個location /shiny定義是對Shiny Server的反向代理瘾蛋。
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、通過https加密協(xié)議訪問Rstudio Server與Shiny Server矫限。
重啟各個服務(wù)哺哼。
#systemctl restart rstudio-server.service
#systemctl restart shiny-server
#systemctl restart nginx
A、訪問Rstudio Server
https://106.52.33.185/rstudio/
通過https加密協(xié)議訪問Rstudio Server
B叼风、訪問Shiny Server取董。原來的URL中間加上/shiny即可。
https://106.52.33.185/shiny/users/ubuntu/shinyAppExample/
通過https加密協(xié)議訪問Shiny Server
C咬扇、Nginx的非加密靜態(tài)網(wǎng)頁甲葬。
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靜態(tài)網(wǎng)頁
六、配置R使用OpenGL圖形系統(tǒng)
1懈贺、Ubuntu安裝OpenGL開發(fā)環(huán)境经窖。
參考資料坡垫。
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
編一個OpenGL測試程序。
# 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;
}
編譯測試：
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連接遠(yuǎn)端虛擬桌面：
OpenGL開發(fā)環(huán)境測試
2画侣、R語言使用OpenGL例子冰悠。
A、安裝gdal配乱，參考資料：
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溉卓、安裝R軟件包：
>install.packages(c("rgdal","rgl","rayshader"，"rayrender","ambient"))
C搬泥、Rstudio中測試rgl包桑寨，最后運(yùn)行rgl.close()關(guān)閉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：
測試rgl包正確運(yùn)行
D忿檩、測試rayshader包尉尾。
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：
測試rayshader包正確運(yùn)行，遠(yuǎn)程桌面打開了OpenGL 3D X Window作圖
