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问题[environment](ubuntu)

Martin Hope
rchurt
Asked: 2020-07-28 21:00:46 +0800 CST
  • 1

我正在尝试在 Google Colab（Ubuntu 环境）中安装和加载几个 Perl 模块。我正在使用 CPAN 安装它们，然后使用Environment Modules加载它们。我绝对需要使用环境模块来加载它们（例如，我的脚本运行的命令之一是module load Perl），但如果有更好的选择，我不需要使用 CPAN 来安装它们。

首先我用 CPAN 安装了 Perl 模块：

PERL_MM_USE_DEFAULT=1 cpan GD ExtUtils::PkgConfig DBI DBD::mysql DBD::SQLite Capture::Tiny Exporter Log::Message::Simple Getopt::Long \
     List::Util List::MoreUtils IO::File XML::Writer XML::LibXML XML::Parser XML::LibXML::Reader \
     Data::Dumper File::Slurp JSON Storable Scalar::Util Array::Utils Config::IniFiles \
     Statistics::Descriptive GD::Graph::boxplot

然后，跑步perldoc perllocal给了我以下信息：

Tue Jul 28 01:16:13 2020: "Module" App::cpanminus
    *   "installed into: /usr/local/share/perl/5.26.1"

    *   "LINKTYPE: dynamic"

    *   "VERSION: 1.7044"

    *   "EXE_FILES: bin/cpanm"

  Tue Jul 28 01:16:30 2020: "Module" Net::SSLeay
    *   "installed into: /usr/local/share/perl/5.26.1"

    *   "LINKTYPE: dynamic"

    *   "VERSION: 1.88"

    *   "EXE_FILES: "

  Tue Jul 28 01:16:32 2020: "Module" Mozilla::CA
    *   "installed into: /usr/local/share/perl/5.26.1"

    *   "LINKTYPE: dynamic"

    *   "VERSION: 20200520"

    *   "EXE_FILES: "
...

但是，当我运行source /etc/profile.d/modules.sh && module avail列出可用于加载的模块时，我刚刚安装的模块没有显示，我只得到以下信息（不知道为什么相同的东西打印两次）：

------------------------ /usr/share/modules/modulefiles ------------------------
dot  module-git  module-info  modules  null  use.own  

------------------------ /usr/share/modules/modulefiles ------------------------
dot  module-git  module-info  modules  null  use.own

所以我想我需要添加/usr/local/share/perl/5.26.1到modulepath它以找到已安装的模块。但是当我尝试这样做module use --append /usr/local/share/perl/5.26.1然后module avail再次运行时，我得到与上面相同的输出，表明该目录尚未添加。

drivers kernel perl environment
Martin Hope
fizsics
Asked: 2019-12-26 18:16:25 +0800 CST
  • 0

使用environment-modules，我正在尝试使用 intel 编译器和 openmpi 设置自定义环境模块以安装软件。我不熟悉创建自定义模块文件的方法，但我在互联网上提供的少量资源的帮助下构建了两个，尽​​管我似乎无法让它工作。我正在使用运行 ubuntu 18.04 LTS 的 HPC，这是我的 intel 模块文件（../bin 包含“compilervars.csh compilervars.sh”，../lib 包含“ia32 ia32_lin intel64 intel64_lin”）：

#%Module1.0#####################################################################
##")
## intel modulefile
##
proc ModulesHelp { } {
    puts stderr "\tAdds Intel compilers to your environment variables,"

}

module-whatis "adds Intel compilers to your environment variables"

setenv(     "INTELPATH",        "/opt/intel/bin")
prepend_path(   "PATH",         "/opt/intel/bin")
prepend_path(   "LD_LIBRARY_PATH",  "/opt/intel/lib")

接下来对于openmpi，这是我的尝试：

#%Module1.0#####################################################################
##")
## openmpi modulefile
##
proc ModulesHelp { } {
    puts stderr "\tAdds openmpi to your environment variables,"

}

module-whatis "adds openmpi to your environment variables"

setenv(     "INTELPATH",        "/usr/bin")
prepend_path(   "PATH",         "/usr/bin")
prepend_path(   "LD_LIBRARY_PATH",  "/usr/lib/x86_64-linux-gnu/openmpi/lib")

这给出了以下错误（对于英特尔编译器）：

Loading intel
   Module Error: extra characters after close-quote
   In '/usr/local/Modules/modulefiles/intel'
   Please contact <root@localhost>

但是，我不确定我是否正确设置。我找不到 openmpi 的 bin 文件夹，但在 /usr/bin 中找到了 mpicc.openmpi 和 mpirun.openmpi。我也不确定lib。请指导我正确设置环境模块并修复我的两个模块文件。这让我很困惑，因为我对这行工作并不熟悉，因为我在计算科学方面的工作更多。我希望我能尽快让它工作。谢谢！

desktop-environments environment-variables intel mpi environment
Martin Hope
chiehpower
Asked: 2019-12-20 16:37:29 +0800 CST
  • 2

当我需要使用 apt-get 安装某些东西时。

$sudo apt-get install autoconf automake libtool curl make g++ unzip  

Reading package lists... Done
Building dependency tree       
Reading state information... Done
make is already the newest version (4.1-9.1ubuntu1).
unzip is already the newest version (6.0-21ubuntu1).
unzip set to manually installed.
curl is already the newest version (7.58.0-2ubuntu3.8).
g++ is already the newest version (4:7.4.0-1ubuntu2.3).
g++ set to manually installed.
You might want to run 'apt --fix-broken install' to correct these.
The following packages have unmet dependencies:
 autoconf : Depends: m4 (>= 1.4.13)
 automake : Depends: autotools-dev (>= 20020320.1) but it is not going to be installed
 libtool : Depends: autotools-dev but it is not going to be installed
           Recommends: libltdl-dev but it is not going to be installed
 nvidia-cuda-toolkit : Depends: nvidia-cuda-dev (= 9.1.85-3ubuntu1) but it is not going to be installed
E: Unmet dependencies. Try 'apt --fix-broken install' with no packages (or specify a solution).

收到此错误消息后，我尝试修复它。

但是，当我输入“sudo apt --fix-broken install”时，我在下面收到了这个错误。

$sudo apt --fix-broken install                                                                                                                                      

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Correcting dependencies... Done
The following additional packages will be installed:
  nvidia-cuda-dev
Recommended packages:
  libnvcuvid1
The following NEW packages will be installed:
  nvidia-cuda-dev
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
38 not fully installed or removed.
Need to get 0 B/263 MB of archives.
After this operation, 734 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 222357 files and directories currently installed.)
Preparing to unpack .../nvidia-cuda-dev_9.1.85-3ubuntu1_amd64.deb ...
Unpacking nvidia-cuda-dev (9.1.85-3ubuntu1) ...
dpkg: error processing archive /var/cache/apt/archives/nvidia-cuda-dev_9.1.85-3ubuntu1_amd64.deb (--unpack):
 trying to overwrite '/usr/include/cublas.h', which is also in package libcublas-dev 10.2.2.89-1
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
Errors were encountered while processing:
 /var/cache/apt/archives/nvidia-cuda-dev_9.1.85-3ubuntu1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

在这里，关于 nvidia-cuda-dev，我已经多次遇到过这个问题。我安装了 cuda 10.2 版本。但我不知道它为什么要使用版本 9？但是我需要这个版本（10.2），我不想改变它，我害怕我的环境会出错。

$nvcc --version 

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Wed_Oct_23_19:24:38_PDT_2019
Cuda compilation tools, release 10.2, V10.2.89

对不起，我不熟悉这里的环境设置。对这种情况有什么建议吗？

非常感谢！

system-installation nvidia cuda environment
Martin Hope
Alireza M. Kamelabad
Asked: 2019-05-01 09:01:31 +0800 CST
  • 3

我正在使用 Windows 10 在双启动上运行新安装的 Ubuntu 19.04 Disco Dingo。我使用本指南https://docs.anaconda.com/anaconda/install/linux/为 Ubuntu 安装了 Anaconda

完成安装 下次打开终端，好像是这样

(base) username@ubuntu:~$

这意味着我在 Conda 的主要环境中。但是，当 Anaconda 安装完成时，它会说：

if you want conda not to activate automatically when startup, run:
    conda config --set auto_activate_base false

但是当我这样做时，当我离开（基地）时，下次我打开终端并尝试正常打开 Anaconda Navigator 时，anaconda-navigator它会说anaconda-navigator: command not found。

但在它之前不是这样的。有人可以描述我如何删除它(base)并且还能够运行anaconda命令，例如jupyter notebook直接从普通终端打开。

我很感激你的回答。

command-line gnome-terminal anaconda environment 19.04