Abaqus 2016 Installation on Linux: Issues and Solutions

  18 Jan 2017     Abaqus and Linux

Recently, I installed Abaqus 2016 on a few different Linux Distros for workstations in my lab and my PC. Here’s a summary of the issues I encountered and my solutions.

Unsupported Linux Distribution

ABAQUS 2016 officially only has support for SUSE and Red Hat (and CentOS). By default, the installer runs a prerequisites check and an error will return if you runs an unsupported Linux release. I have Fedora 25 for one of my PCs and I successfully installed Abaqus 2016 on it using the following workaround.

The Abaqus installer get the release info using the script located at <installer_dir>/Linux64/1/inst/common/init/Linux.sh. I overrode the command to obtain the OS release using

DSY_OS_Release="CentOS"

I chose CentOS because Fedora is close to Red Hat Linux. I also disabled other system checks by defining environmental variable DSY_Skip_CheckPrereq in the shell before the installation.

export DSY_Skip_CheckPrereq=1

To satisfy the prerequisites of Abaqus, some additional packages must be installed. For example, the libstdc++.so.5 can be installed by

sudo dnf install compat-libstdc++-33

Now you should be able to install Abaqus on your favorite Linux distribution.

Graphical Issues

I failed to start the Abaqus/CAE when the installation done. I got an “X Error” telling me “fmd_GLContext::create(): glXCreateContext() failed”. My Nvidia driver version was 375.26. I found my problem similar to this post. They also gave a suggestion to run Abaqus using

XLIB_SKIP_ARGB_VISUALS=1 abaqus cae -mesa

This works, however, at the price of disabling the hardware acceleration. After some research online, I found this error was related to the indirect GLX rendering. In recent versions, Xorg changed its behavior to disallow indirect GLX by default, probably due to some security concerns.

I tried a few different methods to re-enable the indirect GLX rendering, including modifying the xorg.conf and adding serverargs in startx, but all failed. Finally I found solution in this post to add a wrap for Xorg command. Slightly different in my Fedora 25, my /usr/bin/Xorg is already a wrap, so I simply added the “+iglx” argument in the script:

exec "$basedir"/Xorg "$@" +iglx

Might not be a perfect solution, but hey, now Abaqus can be run natively on my Nvidia GTX 1080!

Fonts Issues

The fonts in my Abaqus/CAE GUI was extremely small and ugly at first. I solved it by installing the 100dpi font in my system:

sudo dnf install xorg-x11-fonts-ISO8859-15-100dpi-7.5-16

I have no idea why this works and I still don’t know how to switch to other fonts. Let me know if you have better ideas about that.


读书笔记:重读《鸟哥的Linux私房菜》【1】

  16 Jan 2017     Book Notes and Linux

引言

从开始用Linux到现在也有四五年了,日常操作早就已经没有什么障碍。但真正遇到问题,常常还是需要网上到处找解决方案。究其原因,自己对Linux的许多基础知识掌握还是很有问题。Linux并非是我的主要操作系统(许多科研需要的CAD/CAE软件还是只支持Windows),我之前玩Linux也只能是断断续续,全凭一时兴起。最近手头上机器多了,好几台服务器都改成了Linux系统,觉得应该利用这个机会,系统的把Linux的知识梳理一下。《鸟哥的Linux私房菜》 是我自己刚接触Linux的时候的入门书,但是内容翔实,我平时日常用都会把它当参考书来用。最近随手翻翻,里面还有好多我不熟悉的内容,此番重读,正好查遗补漏。因为是重读,自然会跳过许多基础的部分,大家有需要可以自行前往鸟哥的网站查看全书。

本篇笔记对应原书第5章

Linux基本权限

Linux基本权限分成r,w,x,赋给owner/group/others三种身份,另外可以用数字4(r),2(w),1(x)来代表。chmod是用来更改权限的命令,需要注意的是递归修改的选项参数是大写的(-R),这对chgrp和chown也是一样的。

另外我一开始经常搞错的是目录权限的意义。对于普通文件而言,r(读取),w(编辑修改),x(执行)的意义非常简单明了。对目录而言,要理解其r,w,x的含义需要对Linux文件系统有更清楚的理解。这里简单对于实际应用来说,

  • r,读取目录内容,可以查询目录下的文件列表(文件名)
  • w,修改目录内容,可以建立新文件/目录,删除、重命名移动已存在文件/目录
  • x,进入目录,所有该目录下指令的前提

举例来说,有一个文件路径为 /dir1/file1,

  • 知道file1存在,需要对/dir1有r权限
  • 读取,修改,执行file1内容,需要对/dir1有x权限(假如已经知道file1文件名,不需要对/dir1有r权限),对file1有相应的r/w/x权限
  • 删除、重命名file1,需要对/dir1有xw权限(注意与file1权限无关!)

一般开放目录给用户访问,需要x和r,而w的权限则权力很大,可以让用户自由删除新建重命名,需要谨慎。

Linux目录配置与FHS

FHS对目录分类主要考量static/variable,shareable/unshareable两个维度。具体可以参考原书以及FHS标准文档。之前我一直搞错的是/usr中usr其实是Unix Software Resource的所写,和user没什么关系。


Publication: Wearable Microfluidic Device for Sweat Monitoring

  25 Nov 2016     Research

Our research on a new type of flexible microfluidic device that can adhere to skin for sweat monitoring was published on latest issue of Science Translational Medicine. The paper was featured as cover story of this issue. Check details by referring to the paper titled “A Soft, Wearable Microfluidic Device for the Capture, Storage, and Colorimetric Sensing of Sweat” on Science Translational Medicine website. Also check the following video describing the operation of the sweat microfluidic device:

The research was widely covered by news & media, including: VOA, CBC, IEEE Spectrum, Northwestern Now, Northwestern Engineering News.