16. SSH Keys and Building Code#
ssh -l brownsarahm seawulf.uri.edu
brownsarahm@seawulf.uri.edu's password:
Last login: Tue Oct 31 13:41:16 2023 from 172.20.131.240
[brownsarahm@seawulf ~]$ logout
Connection to seawulf.uri.edu closed.
ssh-keygen -f ~/seawulf -t rsa -b 1024
Generating public/private rsa key pair.
/Users/brownsarahm/seawulf already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /Users/brownsarahm/seawulf.
Your public key has been saved in /Users/brownsarahm/seawulf.pub.
The key fingerprint is:
SHA256:/jDn06CDu24klK2z4dw6acHJuzax9685qHLaGeooX9g brownsarahm@240.131.20.172.s.wireless.uri.edu
The key's randomart image is:
+---[RSA 1024]----+
| |
| |
| o |
| o . |
| + o S |
| o@ .. . |
| .oE& o+..o |
|...+&o* +B. . |
|oo=**X+++=+. |
it asks you for an optional password to lock the key itself.
ssh-copy-id -i ~/seawulf brownsarahm@seawulf.uri.edu
/usr/bin/ssh-copy-id: INFO: Source of key(s) to be installed: "/Users/brownsarahm/seawulf.pub"
/usr/bin/ssh-copy-id: INFO: attempting to log in with the new key(s), to filter out any that are already installed
/usr/bin/ssh-copy-id: INFO: 1 key(s) remain to be installed -- if you are prompted now it is to install the new keys
brownsarahm@seawulf.uri.edu's password:
Number of key(s) added: 1
Now try logging into the machine, with: "ssh 'brownsarahm@seawulf.uri.edu'"
and check to make sure that only the key(s) you wanted were added.
cd
ls -a
. .viminfo
.. .virtual_documents
.CFUserTextEncoding .vscode
.DS_Store .xonshrc
.Rhistory .zsh_history
.Trash .zsh_sessions
.anaconda .zshrc
.anaconda_backup 2023-01-24.md
.atom Applications
.bash_history Creative Cloud Files
.bash_profile Desktop
.bash_profile.pysave DigiCertHighAssuranceEVRootCA.crt
.bash_sessions Documents
.bundle Downloads
.cache Dropbox
.conda Library
.condarc Movies
.config Music
.continuum Pictures
.cups Public
.dropbox PycharmProjects
.gem Untitled.ipynb
.gitconfig Untitled1.ipynb
.ipynb_checkpoints Untitled2.ipynb
.ipython Untitled3.ipynb
.jupyter Untitled4.ipynb
.keras Zotero
.local anaconda3
.matplotlib bash_profile.backup2023-09-06
.mono ca-bundle.crt
.npm configs
.python_history demo.ipynb
.r scikit_learn_data
.rbenv seaborn-data
.ssh seawulf
.tcshrc seawulf.pub
ls .ssh
config known_hosts seawulf seawulf.pub
cd Documents/inclass/systems/
ssh -i ~/.ssh/seawulf brownsarah@seawulf.uri.edu
brownsarah@seawulf.uri.edu's password:
ssh -i ~/seawulf brownsarah@seawulf.uri.edu
brownsarah@seawulf.uri.edu's password:
Permission denied, please try again.
brownsarah@seawulf.uri.edu's password:
Permission denied, please try again.
brownsarah@seawulf.uri.edu's password:
brownsarah@seawulf.uri.edu: Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
ls ~ |grep seawful
ls ~ |grep seawulf
seawulf
seawulf.pub
ssh -i ~/seawulf brownsarahm@seawulf.uri.edu
Last login: Thu Nov 2 12:36:20 2023 from 172.20.131.240
[brownsarahm@seawulf ~]$ interactive
salloc: Granted job allocation 27157
salloc: Waiting for resource configuration
salloc: Nodes n005 are ready for job
[brownsarahm@n005 ~]$ hostname
n005.cluster.com
[brownsarahm@n005 ~]$ mkdir compilec
mkdir: cannot create directory ‘compilec’: File exists
[brownsarahm@n005 ~]$ rm -rf compilec/
[brownsarahm@n005 ~]$ mkdir compilec
[brownsarahm@n005 ~]$ cd compilec/
[brownsarahm@n005 compilec]$ ls
[brownsarahm@n005 compilec]$ nano hello.c
[brownsarahm@n005 compilec]$ cat hello.c
#include <stdio.h>
void main () {
printf("Hello world\n");
}
[brownsarahm@n005 compilec]$ ls
hello.c
[brownsarahm@n005 compilec]$ gcc -E hello.c -o hello.i
[brownsarahm@n005 compilec]$ ls
hello.c hello.i
[brownsarahm@n005 compilec]$ cat hello.i |head
# 1 "hello.c"
# 1 "<built-in>"
# 1 "<command-line>"
# 1 "/usr/include/stdc-predef.h" 1 3 4
# 1 "<command-line>" 2
# 1 "hello.c"
# 1 "/usr/include/stdio.h" 1 3 4
# 27 "/usr/include/stdio.h" 3 4
# 1 "/usr/include/features.h" 1 3 4
# 375 "/usr/include/features.h" 3 4
[brownsarahm@n005 compilec]$ cat hello.i |tail
extern void funlockfile (FILE *__stream) __attribute__ ((__nothrow__ , __leaf__));
# 943 "/usr/include/stdio.h" 3 4
# 2 "hello.c" 2
void main () {
printf("Hello world\n");
}
[brownsarahm@n005 compilec]$ cat hello.i | wc-l
bash: wc-l: command not found
[brownsarahm@n005 compilec]$ cat hello.i | wc -l
842
[brownsarahm@n005 compilec]$ cat hello.c | wc -l
6
[brownsarahm@n005 compilec]$ gcc -S hello.i
[brownsarahm@n005 compilec]$ ls
hello.c hello.i hello.s
[brownsarahm@n005 compilec]$ cat hello.s
.file "hello.c"
.section .rodata
.LC0:
.string "Hello world"
.text
.globl main
.type main, @function
main:
.LFB0:
.cfi_startproc
pushq %rbp
.cfi_def_cfa_offset 16
.cfi_offset 6, -16
movq %rsp, %rbp
.cfi_def_cfa_register 6
movl $.LC0, %edi
call puts
popq %rbp
.cfi_def_cfa 7, 8
ret
.cfi_endproc
.LFE0:
.size main, .-main
.ident "GCC: (GNU) 4.8.5 20150623 (Red Hat 4.8.5-44)"
.section .note.GNU-stack,"",@progbits
[brownsarahm@n005 compilec]$ gcc -c hello.s -o hello.o
[brownsarahm@n005 compilec]$ ls
hello.c hello.i hello.o hello.s
[brownsarahm@n005 compilec]$ cat hello.o
ELF>?@@
UH???]?Hello worldGCC: (GNU) 4.8.5 20150623 (Red Hat 4.8.5-44)zRx
K A?C
?? hello.cmainputs
???????? .symtab.strtab.shstrtab.rela.text.data.bss.rodata.comment.note.GNU-stack.rela.eh_frame @?0
&PP1P
90\.B?W?R@
?
?0a[brownsarahm@n005 compilec]$ gcc -o hello hello.o -lm
[brownsarahm@n005 compilec]$ ls
hello hello.c hello.i hello.o hello.s
[brownsarahm@n005 compilec]$ ./hello
Hello world
[brownsarahm@n005 compilec]$ history
1 ls -hw
2 lshw
3 exit
4 ls
5 pwd
6 whoami
7 wget http://www.hpc-carpentry.org/hpc-shell/files/bash-lesson.tar.gz
8 ls
9 tar -xvf bash-lesson.tar.gz
10 ls
11 cat dmel-all-r6.19.gtf
12 head dmel-all-r6.19.gtf
13 tail dmel-all-r6.19.gtf
14 wc -l dmel-all-r6.19.gtf
15 ls
16 wc -l *.fastw
17 wc -l *.fastq
18 wc -l *.fastq > linecounts.txt
19 cat linecounts.txt
20 grep Act5c dmel-all-r6.19.gtf
21 head dmel-all-r6.19.gtf
22 grep mRNA dmel-all-r6.19.gtf
23 grep mRNA dmel-all-r6.19.gtf | wc -l
24 echo "echo 'script works'" >> demo.sh
25 cat demo.sh
26 ./demo.sh
27 ls -l
28 mkdir results
29 ls -l
30 pwd
31 ls /home/brownsarahm
32 cat /home/brownsarahm/demo.sh
33 bash demo.sh
34 ./ demo.sh
35 ./demo.sh
36 chmod +x demo.sh
37 ls -l
38 ./demo.sh
39 nano demo.sh
40 cat demo.sh
41 ls -l
42 nano my_job.sh
43 sbatch my_job.sh
44 squeue --job 23950
45 interactive
46 wall "hello"
47 exit
48 ls
49 exit
50 cat ~/.ssh/authorized_keys
51 rm ~/.ssh/authorized_keys
52 exit
53 ls -a
54 ls -al
55 exit
56 cat /var/log/auth.log
57 exit
58 ls
59 ls .ssh/
60 rm .ssh/
61 ls
62 rm .ssh/authorized_keys
63 ls
64 exit
65 cat .ssh/authorized_keys
66 exit
67 ls .ssh/
68 cat .ssh/authorized_keys
69 cat /var/log/auth.log
70 exit
71 ls
72 pwd
73 whoami
74 wget http://www.hpc-carpentry.org/hpc-shell/files/bash-lesson.tar.gz
75 ls
76 rm *.fastq
77 tar -xvf bash-lesson.tar.gz
78 cat SRR307023_1.fastq
79 head SRR307023_1.fastq
80 tail SRR307023_1.fastq
81 wc -l SRR307023_1.fastq
82 wc -l *.fastq
83 wc -l dmel-all-r6.19.gtf
84 grep Act5c dmel-all-r6.19.gtf
85 grep mRNA dmel-all-r6.19.gtf
86 echo "echo 'script works'" >> demo.sh
87 cat demo.sh
88 echo "echo 'script works'" > demo.sh
89 cat demo.sh
90 ./demo.sh
91 ls -l
92 chmod +x demo.sh
93 ls -l
94 ./demo.sh
95 exit
96 lshw
97 exit
98 interactive
99 grep Act5C dmel-all-r6.19.gtf
100 grep Act5C dmel-all-r6.19.gtf | wc -l
101 grep Act5C dmel-all-r6.19.gtf | head -n 1
102 exit
103 pwd
104 ls
105 mkdir example
106 cd example/
107 pwd
108 mkdir ex2
109 cd ex2/
110 pwd
111 cd
112 ls -l
113 ls -l --block-size=M
114 exit
115 ls
116 ls -a
117 ls .ssh/
118 ls .ssh/authorized_keys
119 ls
120 ls .ssh/authorized_keys
121 ls .ssh/authorized_keys
122 exit
123 ls
124 lshw
125 cat demo.sh
126 ./demo.sh
127 ls my_job.sh
128 cat my_job.sh
129 exit
130 python3
131 exit
132 pwd
133 lshw
134 interactive
135 interactive -t 0:03:00
136 interactive -c 4
137 interactive
138 exit
139 gcc
140 clear
141 exit
142 mkdir compilec
143 cd compilec/
144 ls
145 nano hello.c
146 cat hello.c
147 ls
148 nano hello.c
149 gcc -E hello.c -o hello.i
150 ls
151 cat hello.i | head
152 cat hello.c
153 cat hello.i | tail
154 cat hello.i | wc -l
155 cat hello.c | wc -l
156 gcc -S hello.i
157 ls
158 cat hello.s
159 cat hello.c
160 gcc -c hello.s -o hello.o
161 ls
162 cat hello.o
163 gcc -o hello hello.o -lm
164 ls
165 ./hello
166 ls -la
167 ls
168 rm hello.i hello.s hello.o hello
169 ls
170 gcc --help
171 gcc -Wall -g -o hello hello.c -lm
172 ls
173 nano main.c
174 nano help.c
175 cat main.c
176 cat help.c
177 gcc -Wall -g -c main.c
178 nano main.c
179 cat main.
180 cat main.c
181 gcc -Wall -g -c main.c
182 gcc -Wall -g -c help.c
183 ls
184 gcc -o demo main.o help.o -lm
185 ls
186 ./demo
187 ./demo 6
188 exit
189 interactive
190 exit
191 ls
192 wget http://www.hpc-carpentry.org/hpc-shell/files/bash-lesson.tar.gz
193 ls
194 man tar
195 tar -xvf bash-lesson.tar.gz
196 cat dmel-all-r6.19.gtf
197 head dmel-all-r6.19.gtf
198 man head
199 head dmel-all-r6.19.gtf -n 5
200 tail dmel-all-r6.19.gtf -n 5
201 wc dmel-all-r6.19.gtf
202 man wc
203 wc -l dmel-all-r6.19.gtf
204 ls
205 wc -l *.fastq
206 wc -l *.fastq > linecounts.txt
207 cat linecounts.txt
208 grep Act5c dmel-all-r6.19.gtf
209 grep mRNA dmel-all-r6.19.gtf
210 grep mRNA dmel-all-r6.19.gtf |wc -l
211 exit
212 pwd
213 ls
214 rm *
215 ls
216 whoami
217 interactive
218 exit
219 nano example-job.sh
220 cat example-job.sh
221 man echo
222 bash example-job.sh
223 ./example-job.sh
224 ls -l
225 chmod +x example-job.sh
226 ls -l | grep example
227 ./example-job.sh
228 cp example-job.sh ex2.sh
229 cp example-job.sh ex3.sh
230 cp example-job.sh ex4.sh
231 ls| grep ex
232 ls -l
233 chmod -x ex*.sh
234 ls -l | grep ex
235 ./example-job.sh
236 chmod +x example-job.sh
237 ./example-job.sh
238 nano example-job.sh
239 cat example-job.sh
240 sbatch example-job.sh
241 squeue -u brownsarahm
242 sbatch example-job.sh
243 squeue -u brownsarahm
244 whoami
245 ls
246 cat slurm-27093.out
247 cat slurm-27107.out
248 nano example-job.sh
249 logout
250 cat ex2.sh
251 chmod +x ex2.sh
252 sbatch -J hello -o name-%j ex2.sh
253 nano ex2.sh
254 sbatch -J hello -o name-%j ex2.sh
255 ls |grap name
256 ls |grep name
257 sbatch ex2.sh
258 sysapprovedbages
259 sysapprovedbadges --help
260 exit
261 logout
262 hostname
263 mkdir compilec
264 rm -rf compilec/
265 mkdir compilec
266 cd compilec/
267 ls
268 nano hello.c
269 cat hello.c
270 ls
271 gcc -E hello.c -o hello.i
272 ls
273 cat hello.i |head
274 cat hello.i |tail
275 cat hello.i | wc-l
276 cat hello.i | wc -l
277 cat hello.c | wc -l
278 gcc -S hello.i
279 ls
280 cat hello.s
281 gcc -c hello.s -o hello.o
282 ls
283 cat hello.o
284 gcc -o hello hello.o -lm
285 ls
286 ./hello
287 history
[brownsarahm@n005 compilec]$ ls -l
total 44
-rwxr-xr-x 1 brownsarahm spring2022-csc392 8360 Nov 2 13:27 hello
-rw-r--r-- 1 brownsarahm spring2022-csc392 64 Nov 2 13:12 hello.c
-rw-r--r-- 1 brownsarahm spring2022-csc392 16865 Nov 2 13:14 hello.i
-rw-r--r-- 1 brownsarahm spring2022-csc392 1496 Nov 2 13:23 hello.o
-rw-r--r-- 1 brownsarahm spring2022-csc392 433 Nov 2 13:19 hello.s
[brownsarahm@n005 compilec]$ ls -la
total 48
drwxr-xr-x 2 brownsarahm spring2022-csc392 98 Nov 2 13:27 .
drwx------ 7 brownsarahm spring2022-csc392 4096 Nov 2 13:11 ..
-rwxr-xr-x 1 brownsarahm spring2022-csc392 8360 Nov 2 13:27 hello
-rw-r--r-- 1 brownsarahm spring2022-csc392 64 Nov 2 13:12 hello.c
-rw-r--r-- 1 brownsarahm spring2022-csc392 16865 Nov 2 13:14 hello.i
-rw-r--r-- 1 brownsarahm spring2022-csc392 1496 Nov 2 13:23 hello.o
-rw-r--r-- 1 brownsarahm spring2022-csc392 433 Nov 2 13:19 hello.s
[brownsarahm@n005 compilec]$ nano hello.c
[brownsarahm@n005 compilec]$ cat hello.
cat: hello.: No such file or directory
[brownsarahm@n005 compilec]$ cat hello.c
#include <stdio.h>
void main () {
printf("Hello world!\n");
}
[brownsarahm@n005 compilec]$ ./hello
Hello world
[brownsarahm@n005 compilec]$ gcc hello.c
[brownsarahm@n005 compilec]$ ./hello
Hello world
[brownsarahm@n005 compilec]$ gcc hello.c -lm
[brownsarahm@n005 compilec]$ ./hello
Hello world
[brownsarahm@n005 compilec]$ ls
a.out hello hello.c hello.i hello.o hello.s
[brownsarahm@n005 compilec]$ ./a.out
Hello world!
[brownsarahm@n005 compilec]$ gcc hello.c -o hello2
[brownsarahm@n005 compilec]$ ./hello2
Hello world!
[brownsarahm@n005 compilec]$ gcc hello.c
[brownsarahm@n005 compilec]$ ls
a.out hello hello2 hello.c hello.i hello.o hello.s
[brownsarahm@n005 compilec]$ nano hello.c
[brownsarahm@n005 compilec]$ gcc hello.c
[brownsarahm@n005 compilec]$ ls
a.out hello hello2 hello.c hello.i hello.o hello.s
[brownsarahm@n005 compilec]$ ./a.out
Hello world! again
[brownsarahm@n005 compilec]$ cat hello.c
#include <stdio.h>
void main () {
printf("Hello world! again\n");
}
[brownsarahm@n005 compilec]$
16.1. Prepare for Next Class#
No separate preparation, focus on badge work and reviewing the notes if you missed class.
Make sure you did the prep for 10-31, we will work from that on 11/2.
16.2. Review today’s class#
create a new ssh key and configure it to your GitHub account
Practice using gcc. Repeat steps we did in class, change the order of parameters; try skipping steps to produce errors, etc. Then in
gcctips.mdsummarize what you learned as a list of tips and reminders on what the parameters do/why/when you would need them (or not). (to reinforce what we learned)
16.3. More Practice#
create a new ssh key and configure it to your GitHub account
Install gcc locally and practice using it. Repeat steps we did in class on your computer and then change the order of parameters; try skipping steps to produce errors, etc. Export the list of variations you tried and summarize what you learned as a list of tips and reminders on what the parameters do/why/when you would need them (or not) in gcctips.md. (to reinforce what we learned)
Write two short programs that do the same thing in different ways and compile them both to assembly (eg using a for vs while loop to sum numbers up to a number). Check the assembly to see if they produce the same thing or if it’s different. Save your code (in code blocks) and notes about your findings in assemblycompare.md
16.4. Experience Report Evidence#
16.5. Questions After Today’s Class#
16.5.1. What else can we create ssh keys for?#
You can use them for GitHub and most developer tools that have authentication provide this option.
16.5.2. Why did we need a .i, .s, .o files?#
When you build your code, your tools often go from source code to executable without saving the file at the intermediate points. We went through and stopped it at the same
16.5.3. How often are SSH keys used by a developer?#
I cannot give a speific number, but they are used for remote systems and can be used for GitHub.
16.5.4. Why did we not need to do the intermediate steps when we changed the program?#
We did not need to stop at the intermediate points the first time, we stopped it after each step to look at it, so that we could learn about all of the steps.
We alwasy have the option to do the whole process at once.
16.5.5. can you use/import other libraies into seawulf and use them in a program made in seawulf?#
Yes. To an extent, there are limits to what you can install, but the basic ones are typically here.
You can see what is there with module available
16.5.6. When compiling using the following line: gcc hello.c -o hello does this remove the .o .s and .i file because it just created the executable file hello?#
It does not remove them, but it does skip writing the file out at those intermediate points.
16.5.7. Are the public and private keys the primes themselves, or are they something derived from the primes?#
The product of the primes is part of the public key along with an exponent integer. The two primes are also used to compute the private key. The primes themselves need to be private, but are actually not needed to be know, so they are generally discarded.
16.5.8. What are the main uses of doing this?#
Understanding the steps of building can help you debug.
16.5.9. Will this ever be seen as a better alternative to write code as opposed?#
Sometimes the terminal is the fastest tool you have available, like today.