sed, awk and bash it

Edit the files in folder

1. Chop off few words from the 1st line

2. Reads a particular word from the 1st line and then replaces that with some other word.

More particularly 

1. Removes "p tw" from the 1st line.

2. Replace the 3rd word(in line 1) with "0" in all the lines except line 1.

$cat sample

p tw 5 4

1 2

5 2

3 4

1 5

$cat required-sample

5 4

1 2

0 2

3 4

1 0

#!/bin/bash
for file in `ls *.gr`
do
    nodes=`awk 'NR==1{print $3}' $file` #takes the 3rd word which is n or |V|
    sed -i "1s/p tw //" $file             #chops the p and tw from the 1st line
    echo $file - done $nodes
    sed -i '2,$ s/$nodes/0/g' $file     #f   
done

Thanks to Vijay R

Resolving expired GPG key and Github signing

My GPG key during creation had default expiry date which I didn't bother to change it at that time. One fine day it got expired. I was using that same key to sign commits on Github . In all my commits it was showing signed with unverified / expired key. However later from "password and keys" i was able to revoke the expiry. Even then after signing it was showing signed with unverified / expired key.

Here are the steps to resolve:
1. Github setting delete the existing GPG key
2. gpg --list-keys
3. gpg --armour --export  YOUR-KEY-ID
4. Copy it to Github GPG settings as new GPG key
5. Try committing and pushing on github!

All your commits have a verified and have a non-expired signature. :-)

Install Gurobi on Linux and Hello world Gurobi !

Installation

System requirements

Any linux flavour would work

Recent gcc version 

Steps

1. Register Gurobi Optimizer(64b-Linux) Download http://www.gurobi.com/downloads/download-center
2. Register and get an academic licence from the same (note the cmd grbgetkey 36-digit-key )
3. Extract tar file to /opt
4. Generate licence file using the cmd

rajz@warriorwithin :/opt/gurobi751/$ ./linux64/bin/grbgetkey whatever-is-your-key

Note the license file must have got generated!!

6. append at the last line of .bashrc at $HOME/.bashrc using a texteditor

export GUROBI_HOME="/opt/gurobi751/linux64"
export PATH="${PATH}:${GUROBI_HOME}/bin"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${GUROBI_HOME}/lib"
export GRB_LICENSE_FILE="/opt/gurobi751/gurobi.lic"

If any useraccount of the machine wants to use it, then they just have to perform step 6 on their ~/.bashrc

Hello World Gurobi Program!

// coming soon

Installing CUDA on Linux Mint and Hello CUDA Program

CUDA^® is a parallel computing platform and programming model invented by NVIDIA. In case you wanted to write parellel programs that runs on GPU. CUDA will be helpful. 
 Things that are need for CUDA programming.

1. A machine with Nvidia Graphics Card
2. A Supported Linux, Kernel and GCC  [refer here]
3. NVIDIA CUDA Toolkit

My System Specs is the following: 

Dell Inspiron. It has a Nvidia Geforce grapics card.

Installation steps:
WARNING- Read the step completely before starting. I ran into issues with some of these step. Only for expert users or else you may have to endup reinstalling you OS.

1. Go here and download NVIDIA CUDA Toolkit deb/runfile. I am using the deb file. It is about 2GB. So, be careful if you got lesser bandwidth or Internet quota.

2. To check if you have a CUDA compatible GPU, version of kernel and gcc.  
rajz@warriorwithin ~ $ lspci | grep -i nvidia
08:00.0 3D controller: NVIDIA Corporation GM108M [GeForce 840M] (rev a2)
rajz@warriorwithin ~ $ uname -a
Linux warriorwithin 4.4.0-71-generic #92-Ubuntu SMP Fri Mar 24 12:59:01 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
rajz@warriorwithin ~ $ gcc --version
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
3. If nouveau is enabled, then we need to disable it. If the below command prints details which means that it is active. So, just disable it by doing the steps below.

rajz@warriorwithin ~ $ lsmod | grep nouveau

rajz@warriorwithin ~ $ sudo vi /etc/modprobe.d/blacklist-nouveau.conf

blacklist nouveau
options nouveau modeset=0

add above two lines and run the below command.

sudo update-initramfs -u

4. Reboot!!
5.  lsmod | grep nouveau to check if it is active.
6.  Then run the following command based on your file in Step 1. Mine was the following
rajz@warriorwithin ~/install $ dpkg -i cuda-repo-ubuntu1604-8-0-local-ga2_8.0.61-1_amd64.deb
7. Run this sudo apt-get update
8. Run this sudo apt-get install cuda
9. Reboot!!
10. Open  ~/.bashrc file and Add the two lines at the end of file
11. Created a folder under Documents(or wherever you wish) to Install sample files and Run the below
rajz@warriorwithin ~/Documents $ cuda-install-samples-8.0.sh cuda-samples/
12. cd into ~/Documents/cuda-samples/NVIDIA_CUDA-8.0_Samples and do make
13.  Then do the following

14. If it shows up like in the figure. Then it is all fine. 
15. So, far so good. Next up is Hello World CUDA program  


I am unsure if the step 3, 4, 5 are really necessary. But still did it for completeness sake.

ALERT!!!
After Doing these steps. My system went blank after a restart!!!!!
I figured it out that My display is by Intel Graphics Controller.  Where as after NVIDIA Driver installation it set nvidia as my default display or card. So, I was getting a blank screen; Grub loaded. Linux mint Logo appeared. Even login happened. but I can't see any thing. even TTY didn't work. 

Workaround to fix this.
1. During Grub loading. Press 'e'. search a line and prefix nomodeset before quick splash and press enter.
2. It will take you to login. But cinnamon may crash. 
3. Using terminal Uninstall all drivers of nvidia sudo apt-get remove nvidia** 
4. reboot. I reverted the changes I did in step 3,4 of prev installation.
5. Get to know you GPU model from lspci cmd
6. Download http://www.nvidia.com/Download/index.aspx?lang=en-us your driver based on your MODEL, and OS; Mine was this
7. Go to TTY by pressing CTRL+ALT +F1
8. Use cmd to stop display using Card[on Linuxmint] using sudo service mdm stop 
8.1 For ubuntu OS; use sudo service lightdm stop 
9. sudo ./NVIDIA-Linux-x86_64-384.59.run --no-opengl-files
 follow instruction
9.1 I said no only for 32 bit libs; Rest say positively. IMPORTANT.!
10. sudo service mdm start will get you back to GUI mode.
11. Reboot! huh! Hoping that it won't go blank!

Cheers,

Let me know if these steps doesn't work or even if it works! Hope it helps!

References
[1] - www.docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html
[2] - https://askubuntu.com/questions/799184/how-can-i-install-cuda-on-ubuntu-16-04
[3] - https://kislayabhi.github.io/Installing_CUDA_with_Ubuntu/

Installing Gitlab Server

Let me walk through the steps.

1. sudo apt-get install curl openssh-server ca-certificates
2. curl -sS https://packages.gitlab.com/install/repositories/gitlab/gitlab-ce/script.deb.sh | sudo bash 
3. sudo apt-get install gitlab-ce
4. In file /etc/gitlab/gitlab.rb
1. nginx['listen_port'] = 8081
2. external_url 'http://mithun.cse.iitm.ac.in' 
5. sudo gitlab-ctl reconfigure
6. Go to localhost or mithun.cse.iitm.ac.in to set to root's password.

• Note: We tried setting up as gitlab.mithun.cse.iitm.ac.in but wasn't able to as mithun.cse.iitm.ac.in was already running an apache2 webserver from 80 port.
• Note: We decided to run on 8081 instead
• Note: We could have setup as "http://mithun.cse.iitm.ac.in/gitlab" --  I was not in favour of it.

If someone knows how to setup gitlab it as subdomain without affecting the existing webserver. Do let us know. Thank you.

Install custom vimrc file

There are basically only two step. Download and copy it in your home dir and save it as .vimrc. But let me walk thorough.

1. cd ~
2. wget https://raw.githubusercontent.com/pallavagarwal07/_vim/master/_vimrc
3. mv _vimrc .vimrc
4. vim
5. :PlugInstall

If there is error in the 4th step. Check that you have git as well as curl installed already. Do you get error still?, then.

curl -fLo ~/.vim/autoload/plug.vim --create-dirs \
    https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim

And repeat the steps 4 and 5.

Thanks to Pallav

Resolve Linux screen freeze due to external monitor

My Laptop has  Linux mint 18 installed. Here is the thing I wanted to do. There is an extra monitor I wanted use it as a secondary screen (or dual display) and set the monitor's display as my primary screen.

However, the max resolution of the laptop(1366x768 16:9 ) and max resolution of the the monitor(1366x768 16:9 ) are different. So, whenever I connect the VGA cable of the monitor to my laptop(through an HDMI converter), it was just mirroring the screen with a low resolution 1024x768. And when is change the resolution to 1366x768 16:9 (or any other) the screen freezes. And you can not do anything. Either you can hard shutdown or reboot from here. Only the mouse pointer movement is seen but the clicks are not recognized . Keyboad's cap/num lights works but keys don't work. Only thing I can do is long press the power button till it is shutdown. Other option is to go to tty(Ctrl + Alt + F1 ) and login to reboot it. This seems like a bug. But whose OS/Kernal /Cinnamon - don't know the root cause.

These are my atttempts / understanding:

• Updating Linux mint - did NOT work.
• Updating Kernal - did NOT work.
• The secondary monitor is not hot pluggable in Linux mint(or in general Linux or due to HDMI - VGA convertion -- I don't understand it yet). 
• Finally the below steps did work.

Steps to solve the issue.

• Set the secondary monitor to primary in display option.
• Shutdown the machine.
• Make the VGA-HDMI connected to the machine.
• Start the machine.
• Go to the display option, changed the external monitor to max resolution [1366x768 16:9]. 
• Cool. All done and Enjoy the large screen ;-)  

Installing and Using LLVM Clang on Linux

Here are the specs (Hardware and software) of my machine
RAM: 8GB
Proc : Intel Core i7-4510U @ 2.00GHz
Linux mint 18 Cinnamon
word size - 64 bit
Kernel - 4.4.0-21-generic
swap Size - 10GB
HDD :  150GB

There are two ways of installing
1. Install from apt-get
2. Building from src files using tar.gz
Make sure to check this requirements.

GNU Make	3.79, 3.79.1	Makefile/build processor
GCC	>=4.8.0	C/C++ compiler
python	>=2.7	Automated test suite
zlib	>=1.2.3.4	Compression library //it worked without this

1. Install from apt-get

 $ sudo apt-get clang-3.9 llvm-3.9

Reference:  http://apt.llvm.org

2.  Building LLVM 3.9.1 from Source

1. Download two tar file for llvm & clang from here
2. Extract both the files inside some folder // say llvm
3. Rename llvm-3.9.1.src folder as llvm-3.9 //LLVM_SRC
4. Rename cfe-3.9.1.src folder as clang and move inside folder llvm-3.9/tools
5. Create a folder llvm/llvm-build and cd llvm-build // LLVM_OBJ
6. cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE="Release" -DLLVM_ENABLE_ASSERTIONS=On /home/rajz/install/llvm/llvm-3.9
7. // after some time
8. make -j2
9. //after some more time
10. sudo make install
11. opt --version 
12. clang --version 
13. //Done

References: 
1. http://llvm.org/docs/GettingStarted.html
2. https://www.youtube.com/watch?v=4iVc204omI0
3. http://llvm.org/docs/CMake.html

Writing a Sample Pass using LLVM
1. Source folder for LLVM:
    ~/install/llvm/llvm-3.9
2. Build folder for LLVM:
    ~/install/llvm/llvm-build
3. Create a CMakeLists.txt file as below

   add_llvm_loadable_module( LLVMSample
        Sample.cpp
        PLUGIN_TOOL
        opt
        )

4. Create the Sample.cpp as below

#include "llvm/IR/Function.h"
#include "llvm/Pass.h"
#include "llvm/Support/raw_ostream.h"
using namespace llvm;
namespace {
struct Sample : public FunctionPass {
  static char ID;
  Sample() : FunctionPass(ID) {}

  bool runOnFunction(Function &F) override {
    errs() << "Sample: ";
    errs().write_escaped(F.getName()) << '\n';
    return false;
  }
}; // end of struct Sample
} // end of anonymous namespace

char Sample::ID = 0;
static RegisterPass X("sample", "Sample Hello World Pass ",
                              false /* Only looks at CFG */,
                              false /* Analysis Pass */);

5. Sample pass folders at:
    ~/install/llvm/llvm-3.9/lib/Analysis/Sample (contains Sample.cpp and CMakeLists.txt)
    ~/install/llvm/llvm-build/lib/Analysis/Sample (contains only the CMakeLists.txt)
6. Append a line in ~/install/llvm/llvm-3.9/lib/Analysis/CMakeLists.txt

       add_subdirectory(Sample)

7. Created shared library at ~/install/llvm/llvm-build/lib/LLVMSample.so

       $ cd ~/install/llvm/llvm-build
       $ make

8. To run analysis on a test1.c program:
    $ clang -S -O0 -emit-llvm test1.c -o test1.ll
    $ opt -load ~/install/llvm/llvm-build/lib/LLVMSample.so -disable-output -sample test1.ll

Reference
1. http://llvm.org/docs/WritingAnLLVMPass.html
2. AMR, PA TAs