See https://sites.google.com/lbl.gov/cs267-spr2021/hw-1 for details on the assignment.
This is a Git repository. We highly recommend creating your own GitHub repo to track your changes and collaborate with your teammates. Follow these steps to get collaborating:
- Go to https://github.com/new
- Name the repository anything you like, say
cs267-hw1. Make sure it is set to PRIVATE. - Once this is done, run the following commands:
student@cori04:~/hw1> git remote rename origin staff
student@cori04:~/hw1> git remote add origin https://github.com/YOUR_GITHUB_USERNAME/cs267-hw1.git
student@cori04:~/hw1> git push -u origin main
If you prefer to use SSH to connect to GitHub, follow these instructions
Please follow these instructions to ensure your module configuration is correct to run the build system.
This assignment uses CMake to provide a consistent build system for all students. You should not need to modify the provided build in any way (CMakeLists.txt). This document describes the basic process for configuring and building the code.
First, note that this file is in the source directory. You will run CMake commands from the build directory, which you create by running
student@cori04:~/hw1> mkdir build
student@cori04:~/hw1> cd build
From this build directory, it is now possible to configure the build. The basic way to do this is:
student@cori04:~/hw1/build> cmake -DCMAKE_BUILD_TYPE=Release ..
This command tells CMake to generate the build files for HW1 in Release mode.
The syntax -D[VAR]=[VAL] allows you to set a variable.
Only CMAKE_BUILD_TYPE is required, though there are more variables that you might want to change:
CMAKE_BUILD_TYPE-- this is eitherDebugorRelease.CMAKE_C_FLAGS-- this allows you to specify additional compiler flags.MAX_SPEED-- this should be equal to the maximum number of gigaflops-per-second (GF/s) your processor can execute. It is set to 36.8 by default, which matches Cori's processors.TEAM_NO-- when you are ready to submit your assignment, set this to be your two-digit team number.ALL_SIZES-- set toONto test against a large set of matrix sizes.OFFby default.
When you build in Debug mode, optimizations are disabled.
Yet when writing parallel code, it is often the case that problems arise only when optimizations are enabled.
You can recover debugging symbols in Release mode (for use with gdb) by running:
student@cori04:~/hw1/build> cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_FLAGS="-g3" ..
Similarly, you can enable optimizations in Debug mode by running:
student@cori04:~/hw1/build> cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_C_FLAGS="-O2" ..
Once your build is configured, you can actually compile by running make from the build directory.
student@cori04:~/hw1/build> make
This will produce several files:
student@cori04:~/hw1/build> ls
benchmark-blas CMakeCache.txt job-blas Makefile
benchmark-blocked CMakeFiles job-blocked
benchmark-naive cmake_install.cmake job-naive
The executables benchmark-blas, benchmark-blocked, and benchmark-naive are the relevant ones here.
You can freely make configuration changes to the build and re-run make however you choose.
To run your code on the cluster, you can use the generated job-blocked script like so:
student@cori04:~/hw1/build> sbatch job-blocked
Submitted batch job 9637622
The job is now submitted to Cori's job queue. We can now check on the status of our submitted job using a few different commands.
student@cori04:~/hw1/build> squeue -u demmel
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
9637622 debug job-bloc demmel PD 0:00 1 (Priority)
student@cori04:~/hw1/build> sqs
JOBID ST USER NAME NODES REQUESTED USED SUBMIT QOS SCHEDULED_START REASON
9637622 PD demmel job-blocked 1 1:00 0:00 2018-01-19T11:42:17 debug_hsw avail_in_~1.0_hrs Priority
When our job is finished, we'll find new files in our build directory containing the output of our program. For example, we'll find the files job-blas.o9637622 and job-blas.e9637622. The first file contains the standard output of our program, and the second file contains the standard error.
Feel free to modify job-blocked, but note that changes to it will be overwritten by CMake if you reconfigure your
build.
It might therefore be easier to copy it under a new name like my-job and modify it as you desire.
You may find it useful to launch an interactive session when developing your code. This lets you compile and run code interactively on a compute node that you've reserved. In addition, running interactively lets you use the special interactive queue, which means you'll receive your allocation quicker.
Once you're happy with your performance, you can get ready to submit.
First, make sure that your write up is in the same directory as this README and is named cs267GroupNN_hw1.pdf where NN
is your team's two-digit group number.
Then configure the build with your group number:
student@cori04:~/hw1/build> cmake -DGROUP_NO=NN ..
student@cori04:~/hw1/build> make package
This should produce an archive containing the following files:
student@cori04:~/hw1/build> tar tfz cs267GroupNN_hw1.tar.gz
cs267GroupNN_hw1/cs267GroupNN_hw1.pdf
cs267GroupNN_hw1/dgemm-blocked.c
If you prefer to create the archive yourself, make sure that it follows this structure exactly.
We recommend using CLion (free for students)
and WSL (Ubuntu 18.04.3 LTS) for developing on Windows.
CLion provides instructions
for setting up the IDE for use with WSL.
Be sure to install libopenblas-dev from within Ubuntu as well.
The starter code will compiler with MSVC and Visual Studio on Windows, but we do not recommend trying to write first with MSVC and then porting to GCC (the required compiler). MSVC does not implement many useful features in the C language and is fundamentally a C++ compiler.
If you find that certain compiler flags offer a significant speed up to your code, you should add them to your source file using the GCC optimize pragma. For instance if you wanted to specifically enable loop peeling, you could add the following line to the top of your file.
#pragma GCC optimize ("peel-loops")
This works with any -f flag (eg. -fpeel-loops) Note that this applies to all functions. If you want to just tune the optimization of a single function use
__attribute__((optimize("peel-loops")))
void my_func() { ... }
See it in action here: https://godbolt.org/z/RvXfty.
Read more in the GCC documentation here: https://gcc.gnu.org/onlinedocs/gcc/Common-Function-Attributes.html#Common-Function-Attributes