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            <h1 id="seo-header">复旦高性能计算 (一) Linux无root权限安装软件：以R为示例</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="第一步-ssh登录到终端"><a href="#第一步-ssh登录到终端" class="headerlink" title="第一步 ssh登录到终端"></a>第一步 ssh登录到终端</h2><p>推荐使用 <code>[FinalShell](https://www.hostbuf.com/)</code> 或 <a target="_blank" rel="noopener" href="https://mobaxterm.mobatek.net/"><code>MobaXterm</code></a></p>
<p>或者 <code>PowerShell</code> 也可以用，下面是 <code>PowerShell</code> 优化SSH连接体验的方法</p>
<ul>
<li>打开 C:\Users 找到自己的 home，比如我是C:\Users\11248</li>
<li>新建 C:\Users\11248\.ssh 目录，或打开已有的这个目录</li>
<li>新建 config 配置文件，并且没有后缀名</li>
<li>记事本打开 C:\Users\11248\.ssh\ config</li>
<li>添加内容 <code>ServerAliveInterval 60</code> 并保存</li>
</ul>
<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/09/image.png"><img src="https://img-cdn.limour.top/blog_wp/2021/09/image.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<ul>
<li>按下 <code>win+R</code> 快捷键</li>
<li>输入 <code>powershell</code> 确定</li>
<li>输入 <code>ssh userName@server</code> 回车，如 <code>pi@192.168.1.2</code> 或 <code>pi@raspberrypi</code></li>
</ul>
<h2 id="第二步-建立相关文件夹"><a href="#第二步-建立相关文件夹" class="headerlink" title="第二步 建立相关文件夹"></a>第二步 建立相关文件夹</h2><ul>
<li>bin: <code>mkdir ~/zlliu/bin</code></li>
<li>lib: <code>mkdir ~/zlliu/lib</code></li>
<li>include: <code>mkdir ~/zlliu/include</code></li>
<li>源码存放位置<code>libsource</code>：<code>mkdir ~/zlliu/libsource</code></li>
<li>软件存放位置<code>dev</code>：<code>mkdir ~/zlliu/dev</code></li>
</ul>
<h2 id="第三步-安装编译器"><a href="#第三步-安装编译器" class="headerlink" title="第三步 安装编译器"></a>第三步 安装编译器</h2><ul>
<li>下载 <a target="_blank" rel="noopener" href="https://mirrors.ustc.edu.cn/gnu/gcc/gcc-11.1.0/gcc-11.1.0.tar.gz">https://mirrors.ustc.edu.cn/gnu/gcc/gcc-11.1.0/gcc-11.1.0.tar.gz</a> 并通过ssh上传到 <code>libsource</code> 目录</li>
<li>打开 <code>libsource</code> 目录：<code>cd ~/zlliu/libsource</code></li>
<li>解压 <code>[gcc-11.1.0.tar.gz](https://mirrors.ustc.edu.cn/gnu/gcc/gcc-11.1.0/gcc-11.1.0.tar.gz)</code>：<code>tar -zvxf gcc-11.1.0.tar.gz</code></li>
<li>进入 <code>gcc-11.1.0</code> 目录，创建 <code>gcc-build</code> 目录：<code>cd gcc-11.1.0 &amp;&amp; mkdir gcc-build</code></li>
<li>安装依赖库：<code>./contrib/download_prerequisites</code></li>
<li>编译前配置：<code>cd gcc-build &amp;&amp; ../configure --prefix=$HOME/zlliu/dev/gcc11 --enable-checking=release --enable-languages=c,c++,fortran,d,go,lto,objc,obj-c++ --disable-multilib</code></li>
<li>编译并安装：<code>make -j8 &amp;&amp; make install</code></li>
<li>创建动态链接1：<code>ln -s /home/rqzhang/zlliu/dev/gcc11/lib64/lib* ~/zlliu/lib/</code></li>
<li>创建动态链接2：<code>ln -s /home/rqzhang/zlliu/dev/gcc11/bin/* ~/zlliu/bin/</code></li>
<li>创建动态链接3：<code>ln -s /home/rqzhang/zlliu/dev/gcc11/include/* ~/zlliu/include/</code></li>
<li>修改 <code>~/.bash_profile</code> 文件，添加如下内容：<br><a target="_blank" rel="noopener" href="https://www.cnblogs.com/lidabo/p/6068448.html">Makefile编译选项CC与CXX&#x2F;CPPFLAGS、CFLAGS与CXXFLAGS&#x2F;LDFLAGS</a></li>
</ul>
<figure class="highlight routeros"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs routeros"><span class="hljs-built_in">export</span> <span class="hljs-attribute">PATH</span>=<span class="hljs-variable">$HOME</span>/zlliu/bin:$HOME/zlliu/lib:$HOME/zlliu/include:$PATH:$HOME/.local/bin:$HOME/bin<br><br><span class="hljs-built_in">export</span> <span class="hljs-attribute">LD_LIBRARY_PATH</span>=<span class="hljs-variable">$HOME</span>/zlliu/lib/<br><span class="hljs-built_in">export</span> <span class="hljs-attribute">LIBRARY_PATH</span>=<span class="hljs-variable">$HOME</span>/zlliu/lib/ <br><span class="hljs-built_in">export</span> <span class="hljs-attribute">CPLUS_INCLUDE_PATH</span>=<span class="hljs-variable">$HOME</span>/zlliu/include/<br><span class="hljs-built_in">export</span> <span class="hljs-attribute">C_INCLUDE_PATH</span>=<span class="hljs-variable">$HOME</span>/zlliu/include/<br><span class="hljs-built_in">export</span> <span class="hljs-attribute">BOOST_ROOT</span>=<span class="hljs-variable">$HOME</span>/zlliu/dev/boost<br><br><span class="hljs-built_in">export</span> <span class="hljs-attribute">CC</span>=<span class="hljs-variable">$HOME</span>/zlliu/bin/gcc<br><span class="hljs-built_in">export</span> <span class="hljs-attribute">CXX</span>=<span class="hljs-variable">$HOME</span>/zlliu/bin/g++<br><span class="hljs-built_in">export</span> <span class="hljs-attribute">FC</span>=<span class="hljs-variable">$HOME</span>/zlliu/bin/gfortran<br><br><span class="hljs-built_in">export</span> <span class="hljs-attribute">CXXFLAGS</span>=<span class="hljs-string">&quot;-ggdb -pipe -Wall -pedantic -I/home/rqzhang/zlliu/include&quot;</span> <br><span class="hljs-built_in">export</span> <span class="hljs-attribute">CPPFLAGS</span>=<span class="hljs-string">&#x27;-I/home/rqzhang/zlliu/include&#x27;</span><br><span class="hljs-built_in">export</span> <span class="hljs-attribute">LDFLAGS</span>=<span class="hljs-string">&#x27;-L/home/rqzhang/zlliu/lib -Wl,-R/home/rqzhang/zlliu/lib&#x27;</span><br></code></pre></td></tr></table></figure>

<ul>
<li>激活配置：<code>source .bash_profile</code></li>
<li>测试是否成功：<code>gcc --version</code></li>
</ul>
<h2 id="第四步-编译安装R"><a href="#第四步-编译安装R" class="headerlink" title="第四步 编译安装R"></a>第四步 编译安装R</h2><ul>
<li>下载R语言安装文件：<a target="_blank" rel="noopener" href="https://mirrors.tuna.tsinghua.edu.cn/CRAN/">https://mirrors.tuna.tsinghua.edu.cn/CRAN/</a></li>
<li>上传解压进入并创建r-build目录</li>
<li>编译配置：<code>../`configure` </code> <code>--prefix=$HOME/zlliu/dev/r4 --enable-R-shlib --with-x=no</code> <code>--with-cairo</code></li>
<li>编译并安装：<code>make -j8 &amp;&amp; make install</code></li>
<li>创建动态链接1：<code>ln -s /home/rqzhang/zlliu/dev/r4/bin/* ~/zlliu/bin/</code></li>
<li>创建动态链接2：<code>ln -s /home/rqzhang/zlliu/dev/`r4`/lib64/R/lib/lib* ~/zlliu/lib/</code></li>
<li>测试是否成功：<code>R --version</code></li>
</ul>
<h2 id="第五步-依次解决编译过程中的依赖缺失报错"><a href="#第五步-依次解决编译过程中的依赖缺失报错" class="headerlink" title="第五步 依次解决编译过程中的依赖缺失报错"></a>第五步 依次解决编译过程中的依赖缺失报错</h2><ul>
<li>修改 <strong><code>config.site</code></strong> 文件<br><code>nano -K ../**config.site**</code><br><code>CPPFLAGS=&#39;-I/es01/paratera/sce2622/include&#39;   LDFLAGS=&#39;-L/es01/paratera/sce2622/lib&#39;</code></li>
<li>configure: error: –with-readline&#x3D;yes (default) and headers&#x2F;libs are not available<br>下载源码：<a target="_blank" rel="noopener" href="https://ftp.gnu.org/gnu/readline/?C=M;O=D">https://ftp.gnu.org/gnu/readline/?C=M;O=D</a><br><code>tar -zxvf readline-master.tar.gz   ./configure --prefix=$HOME/dev/readline</code><br><code>make -j8 &amp;&amp; make install</code><br><code>ln -s /es01/paratera/sce2622/dev/readline/lib/lib* ~/lib/   ln -s /es01/paratera/sce2622/dev/readline/include/* ~/include/</code><br>下载源码：<a target="_blank" rel="noopener" href="https://ftp.gnu.org/gnu/termcap/">https://ftp.gnu.org/gnu/termcap/</a><br>安装同上</li>
<li>configure: error: bzip2 library and headers are required<br>下载源码：<a target="_blank" rel="noopener" href="https://sourceforge.net/projects/bzip2/files/">https://sourceforge.net/projects/bzip2/files/</a><br><code>make &amp;&amp; make install PREFIX=$HOME/dev/bzip2</code><br><code>ln -s /es01/paratera/sce2622/dev/bzip2/lib/lib* ~/lib/   ln -s /es01/paratera/sce2622/dev/bzip2/bin/* ~/bin/   ln -s /es01/paratera/sce2622/dev/bzip2/include/* ~/include/</code></li>
<li>configure: error: “liblzma library and headers are required”<br>下载源码：<a target="_blank" rel="noopener" href="https://tukaani.org/xz/">https://tukaani.org/xz/</a><br>安装同上</li>
<li>configure: error: PCRE2 library and headers are required, or use –with-pcre1 and PCRE &gt;&#x3D; 8.32 with UTF-8 support<br>下载源码：<a target="_blank" rel="noopener" href="http://www.pcre.org/">http://www.pcre.org/</a><br>安装同上</li>
<li>configure: error: libcurl &gt;&#x3D; 7.28.0 library and headers are required with support for https<br>确保有 openssl<br>下载源码：<a target="_blank" rel="noopener" href="https://curl.haxx.se/download.html">https://curl.haxx.se/download.html</a><br><code>whereis openssl</code><br><code>./configure --with-ssl --prefix=$HOME/dev/curl</code><br>安装同上</li>
<li>编译安装新版make<br>下载源码：<a target="_blank" rel="noopener" href="https://ftp.gnu.org/gnu/make/">https://ftp.gnu.org/gnu/make/</a><br>安装同上</li>
<li>编译安装binutils<br>下载源码：<a target="_blank" rel="noopener" href="https://ftp.gnu.org/gnu/binutils/">https://ftp.gnu.org/gnu/binutils/</a><br>安装同上</li>
<li>libbz2.a(blocksort.o): warning: relocation against <code>memset@@GLIBC_2.2.5&#39; in read-only section</code>.text’<br>修改bzip2-1.0.6的Makefile文件 <br>CC&#x3D;gcc —&gt; CC&#x3D;gcc -fPIC<br>LDFLAGS&#x3D; -L&#x2F;es01&#x2F;paratera&#x2F;sce2622&#x2F;lib -Wl,-R&#x2F;es01&#x2F;paratera&#x2F;sce2622&#x2F;lib<br>重编译 bzip2</li>
<li>libtermcap.a(tparam.o): relocation R_X86_64_32 against `.rodata’ can not be used when making a shared object; recompile with -fPIC<br>处理同上</li>
</ul>
<h2 id="第七步-删除无效软连接"><a href="#第七步-删除无效软连接" class="headerlink" title="第七步 删除无效软连接"></a>第七步 删除无效软连接</h2><figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-meta">#! /bin/bash</span><br><br><span class="hljs-built_in">read</span> path<br><br><span class="hljs-keyword">if</span> [ -z <span class="hljs-variable">$path</span> ] <br><span class="hljs-keyword">then</span><br>    <span class="hljs-built_in">echo</span> <span class="hljs-string">&quot;please enter scan path&quot;</span><br>    <span class="hljs-built_in">exit</span> <br><span class="hljs-keyword">fi</span> <br><span class="hljs-keyword">for</span> file <span class="hljs-keyword">in</span> $(find <span class="hljs-variable">$path</span> -<span class="hljs-built_in">type</span> l) <br><span class="hljs-keyword">do</span><br>    <span class="hljs-keyword">if</span> [ ! -e <span class="hljs-variable">$file</span> ]<br>    <span class="hljs-keyword">then</span><br>        <span class="hljs-built_in">echo</span> <span class="hljs-string">&quot;rm <span class="hljs-variable">$file</span>&quot;</span><br>        <span class="hljs-built_in">rm</span> -f <span class="hljs-variable">$file</span><br>    <span class="hljs-keyword">fi</span> <br><span class="hljs-keyword">done</span> <br></code></pre></td></tr></table></figure>
                
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