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A common nuisance among programmers and especially non-expert users is the assembly of an environment to run a computer program. This is a crucial step that may require upgrading an operating system and downloading and installing the latest release of software, a compiler, or a supporting library. Assembly of the environment may involve permission from IT and a substantial amount of troubleshooting, which may lead to a long delay before analysis can begin. Additionally, inconsistent machine state between computers (including operating systems, libraries, and compilers) can lead to inconsistent results from the same computation.

In recent years, the ENIGMA Consortium has conducted collaborative meta-analyses of schizophrenia ( van Erp et al., 2016) and bipolar disorder ( Hibar et al., 2017), in which subcortical brain volumes and cortical thicknesses were compared between patients and controls, respectively. In these studies, many univariate linear regression models were created in parallel to examine group differences for different regions of the brain. ENIGMA distributes analysis software to many sites and aggregates the results to conduct a meta-analysis. The upcoming version of COINSTAC will facilitate such studies by allowing researchers to specify models that contain combinations of selected dependent and independent variables. Table 1 elaborates on this point by showing an example in which a researcher selects a group of dependent variables (right and left cerebellum cortexes) and a group of independent variables (age and isControl). One model is computed separately for each combination of dependent and independent variables. The advantage of COINSTAC is that dissemination of software and aggregation of results will be handled by our software, eliminating many manual steps. In addition, as mentioned earlier, COINSTAC enables us to run multishot regression (hence converting a meta-analysis into a mega-analysis). Finally, COINSTAC opens up the possibility of running multivariate analysis (such as SVM ( Sarwate et al., 2014) or IVA), as well as incorporating differentially private analyses, which would significantly extend the current ENIGMA approach, while also preserving the powerful decentralized model.

[ summary | part a | part b | part c | part d | part e | how to submit | grading ] Summary. For homework #0, you will fetch a source distribution that we have prepared. Next, you will trivially modify a simple hello world C application, use "make" to compile it, and run it to learn the magic code. You will also run a tool that checks your code for memory leaks and another that checks for potential style problems. Finally, you will package up and submit your code. As you can probably tell, the real goal of this homework is to make sure that all of the course infrastructure is working for you. Part A -- Fetch the code Overview For this quarter, you'll fetch code from the course web site. The code is packaged as a "gzip'ed tar archive" so you'll need to un-gzip and un-tar it to produce your working directory. Once you've done that, you'll have the homework files and can edit them locally until ready to turn them in. We'll use the course drop box for turn-in. You may want to use some source control system to help manage your files, and to provide a crude form of backup for them. Popular options are git and subversion. For details on how to access a repository once you've set it up on your CSE account, see the Version Control Systems section at the bottom of the Computing Resources for Undergrads page. Fetch the code Create a directory to contain your cse333 projects. Click (or right-click if needed) on this hw0.tar.gz link to download the compressed archive containing the starter code and store it in that directory. Expand the tar file First, have a look at what is about to happen: bash% tar tzf hw0.tar.gzclint.pyhw0/hw0/hello_world.chw0/Makefilebash%The files listed will be created when we expand the tar file.The paths are relative to the current working directory.So, subdirectory hw0 and the files it contains will be created in the current working directory.bash% # expand the tar filebash% tar xzf hw0.tar.gzbash% cd hw0 Part B -- edit, compile, and run hello_world In the hw0 directory, type make. This command will use the instructions in file Makefile to compile the hello_world application using the gcc compiler. Run hello_world by typing the command ./hello_world. You should see one line of output that looks like:bash% ./hello_worldThe magic code is: bash% for some . Now, edit hello_world.c using your favorite Unix-based editor (mine is emacs), and change the printf so that it instead says: bash% ./hello_worldThe magic word is: bash% Execute make to rebuild, and then re-run hello_world to make sure it does what you expect. Part C -- experience the gdb debugger You're unlikely to have any run time bugs in this homework, but let's use the debugger so that you know what it can do. Here is a session that launches the debugger, sets a breakpoint on source line 27 of hello_world.c, prints the values of a couple of variables and an expression, prints a "backtrace" of the stack (showing the sequence of procedure calls that led to executing line 27 of hello_world.c), and then continues execution. Type the italicized lines. bash$ gdb ./hello_world GNU gdb (GDB) Fedora (7.4.50.20120120-54.fc17)Copyright (C) 2012 Free Software Foundation, Inc.License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it.There is NO WARRANTY, to the extent permitted by law. Type "show copying"and "show warranty" for details.This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: ... Reading symbols from /home/auser/cse333/hw0/hello_world...done.(gdb) b 27Breakpoint 1 at 0x400511: file hello_world.c, line 27.(gdb) rStarting program: /home/auser/cse333/hw0/hello_world Breakpoint 1, main (argc=1, argv=0x7fffffffe0c8) at hello_world.c:2727 printf("The magic code is: %X\n", a + b);(gdb) p argv[0]$1 = 0x7fffffffe394 "/home/auser/cse333/hw0/hello_world"(gdb) p a$2 = -889262067(gdb) p /x a$3 = 0xcafef00d(gdb) p a+b$4 = -559038737(gdb) bt#0 main (argc=1, argv=0x7fffffffe0c8) at hello_world.c:27(gdb) cContinuing.The magic code is: [Inferior 1 (process 6760) exited normally](gdb) qbash$Notes: For gdb to be useful, you must give the -g switchto gcc when compiling. The make file we distributed does that. If you have already modified your file for part B you will see the new output message after "Continuing." Part D -- verify you have no leaks Throughout the quarter, we'll also be testing whether your code has any memory leaks. We'll be using Valgrind to do this. Try out Valgrind for yourself, to make sure you can run it: bash% valgrind --leak-check=full ./hello_world Note that Valgrind prints out that no memory leaks were found. Part E -- check for style issues Another requirement during the quarter is that your code must be written in good style. Although there are many opinions about what constitutes "good style", in this course we will generally follow the Google C++ Style Guide for both C and C++ code. The distribution file for this assignment included a Python script clint.py to check C source files for style issues. Try it yourself to be sure you can run it: bash% ../clint.py hello_world.c No style-checking tool is perfect, but you should try to clean up any problems that clint detects. Turn in When you're ready to turn in your assignment, do the following: Create a README.TXT file in directory hw0 that contains your name, student number, and UW email address. As well, write a sentence that reveals the magic word you learned from Part B. Execute the following commands:bash$ lshello_world hello_world.c hello_world.o Makefile README.TXTbash$ make clean/bin/rm -f *.o *~ hello_worldbash$ lshello_world.c Makefile README.TXTbash$ cd ..bash$ tar czf hw0_.tar.gz hw0 # substitute your CSE user namebash$ Verify that what you're turning in is what you expect to be turning in:$ tar tzf hw0_ 2b1af7f3a8