CS87: Wed lab

Week 8

XSEDE Resources

XSEDE at Swarthmore
XSEDE homepage

Andy Danner's XSEDE Documentation. This is a good reference for using some XSEDE resources in a way that is most compatable with our types of use. I recommend starting with the first list item on connecting to XSEDE for the first time. Using gsissh and installing ssh keys is the smoothest and most linux-y way to set things up. Note that the TACC resources require that you register with TACC in addition to XSEDE. See details in the "Running on Longhorn" link.

Nick Felt wrote a script that you can use that preforms these set-up steps for you. You can copy the script from here, set it to executable, and run it:

 cp ~newhall/public/cs87/xsede_setup.sh
 chmod 755 xsede_setup.sh
 ./xsede_setup.sh

Here is detailed directions of what to follow in Andy's pages and in what order:

You need xsede and longhorn accounts

Follow steps of Andy's http://svn.cs.swarthmore.edu/gis_mpi/wiki/XsedeOverview

(1) See the XsedeAccount page for details ..

    (a) follow the gsissh login steps 
    (b) follow the XsedeSSH link for creating and installing ssh keys
    (c) then follow the rest of the ssh keys ssh-add stuff
    (d) then try:  ssh tg-longhorn
        this will be the regular way to connect from now on

(2) Trying out some stuff on longhorn

    (a) Configuring longhorn for gpu/mpi use
        (svn.cs.swarthmore.edu/gis_mpi/wiki/Longhorn/Build)

        (i) chsh
            password:
            /bin/bash
        (ii) add entries to .profile_user
        (iii) source .profile_user

(3) Try out some of Andy's tg-demos
    
    (a) git clone user@cs.swarthmore.edu:/home/adanner/public/repos/tg-demos
        (http://svn.cs.swarthmore.edu/gis_mpi/wiki/XsedeOverview)

    (b) buid the tg-demos using cmake

(4) Running on Longhorn link

    look at http://svn.cs.swarthmore.edu/gis_mpi/wiki/Longhorn/Tutorial

    (a) mpi-hello

        (i) cd jobscripts

        (ii) edit jobscripts/.sge_request and replace adanner email address 
             with your address. 

        mkdir ~/logs     Make a logs folder in your home directory.

        qsub longhorn-mpi-hello
        qstat

    (b) longhorn user's guide (https://www.xsede.org/web/guest/tacc-longhorn)

         running batch jobs on Longhorn:

          qsub subfile 

          qstat fields explained (search for "Batch query"): 
           https://www.xsede.org/web/guest/tacc-lonestar#running

           qdel jobID

Week 6

MPI programming resources:

Running OpenMPI on our system: this is probably a good place to start
MPI programming links and tutorials

Week 5

CUDA programming resources:

Nvidia's Cuda Developer Documentation
a local copy of the CUDA C Programming Guide
CUDA Quick Reference by Barry Wilkinson
Cuda by Example book. There is a sample chapter, Chapter 4, available off this page.
We also have a copy of this in the main lab that you can use while you are working in there.

We have copies of the CUDA-SDK examples installed on our system that you can try out and examine the code:

source files are here: /usr/local/CUDA_SDK/C/src/
the binaries are here: /usr/local/CUDA_SDK/C/bin/linux/release/

To query the device on the machine you are running, run:
```
/usr/local/stow/cuda-4.0-sdk/CUDA_SDK/C/bin/linux/release/deviceQuery
```
from this you can see the number of cores, the size of GPU memory, the max number of CUDA threads per block, max number of dimentions of blocks, the max threads per dimention, ... For this project, using a 2D 500x500 blocks, each with a single thread, is a size that is supported on all CS lab machines.
CURAND Library documentation

Weeks 3 and 4

Unix utilities that will help you with lab 3:

Example Pthreads program from last week:

cp -r ~newhall/public/cs87/pthreads_example .

Example Pthreads program with signals:

cp -r ~newhall/public/cs87/pthreads_signals_example .

Staring points of TCP/IP client server programs:

cp -r ~newhall/public/cs87/socket_startingpt .

Socket programming links and tutorials. Beej's Guide is a good place to start. The Steven's "Unix Network Programming" book in the main lab is also a very good resource.

Week 2

Unix utilities that will help you with lab assignments

man, apropos
Example Pthreads program:
Create a cs87/pthreads subdirectory and copy over my simple pthreads example:
```
cp ~newhall/public/cs87/pthreads_example/* .
```
C programming tools: gdb and valgrind
Create a cs87/gdb subdirectory, and copy over my gdb example programs into it:
```
/home/newhall/public/gdb_examples
```
Create a cs87/valgrind subdirectory and copy over my valgrind example programs into it:
```
/home/newhall/public/purify_valgrind_examples
```
using gdb to debug pthreads programs
tools for running experiements screen, script, dos2unix, bash scripts, ...

(the above links are also available off my Unix and CS help pages)

Week 1

Setting up a git repository for lab 1:

First, we will set up a git repository for you and your lab 1 partner's joint work. We will losely follow these general directions for setting up and using git on our system: git

C code organization, makefiles, man, appropos, gdb, valgrind:

Next, we will go over some C code organization and Unix utilities that will help you with the first lab assignment.

Create a cs87 subdirectory and then copy over the following into your cs87 subdirectory:
```
cp -r ~newhall/public/cs87/lab1 .
```
We will take a look at this code, which shows some examples of where C differs from C++, and an example of dividing a C program into multiple modules (.c files), using .h files, using static and extern definitions, and writing and using a makefile to build an executable.
man, apropos
C programming tools: gdb and valgrind
Create a cs87/gdb subdirectory, and copy over my gdb example programs into it:
```
/home/newhall/public/gdb_examples
```
Create a cs87/valgrind subdirectory and copy over my valgrind example programs into it:
```
/home/newhall/public/purify_valgrind_examples
```

(the above links are also available off my Unix and CS help pages)

CS87 Wednesday labs

Setting up a git repository for lab 1:

C code organization, makefiles, man, appropos, gdb, valgrind: