Hyak and you pt 2. Github and Pitchfork.

We’re logged in and have a build node with internet access, so lets get some programs on here!

Pitchfork is a nice installer for PacBio related software, and since I plan to run PBJelly on Hyak, we’re going to need it.

First, we clone the GitHub repo via git clone git@github.com:PacificBiosciences/pitchfork.git pitchfork

which nets us an error stating:

Cloning into '/usr/lusers/seanb80/programs/pitchfork'...
Warning: Permanently added the RSA host key for IP address '' to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

I know the repo exists, since I used it yesterday, so it’s an access thing. After a bit of googling, I realize that I forgot I had to add an SSH key for my GitHub account on the GitHub website. Oops.

ssh-keygen -t rsa -b 4096 -C "seanb80@uw.edu"

to make the key pairs

ssh-add -k ~/.ssh/id_rsa2

to add the code to the list of active key pairs

cat /usr/lusers/seanb80/.ssh/id_rsa2.pub

to show the public key, which I copy in to GitHub via the directions found here starting at step 2.

We try the clone again and receive

Cloning into '/usr/lusers/seanb80/programs/pitchfork'...
remote: Counting objects: 9046, done.
remote: Total 9046 (delta 0), reused 0 (delta 0), pack-reused 9045
Receiving objects: 100% (9046/9046), 1.01 MiB | 0 bytes/s, done.
Resolving deltas: 100% (4769/4769), done.

[seanb80@n2185 pitchfork]$ ls
bin  LICENSE  Makefile	mk  ports  README.md  settings.mk  settings.mk.example

We installed something!

Then we switch to the legacy blasr version via git checkout legacy_blasr

and try make init

which gets us the error

[seanb80@n2185 pitchfork]$ make init
make -f mk/init.mk init
make[1]: Entering directory `/gscratch/home/seanb80/programs/pitchfork'
/gscratch/home/seanb80/programs/pitchfork/bin/checkCC gcc
[ERROR] gcc version needs to be newer than or equal to 4.9
make[1]: *** [sanity] Error 1
make[1]: Leaving directory `/gscratch/home/seanb80/programs/pitchfork'
/gscratch/home/seanb80/programs/pitchfork/bin/checkCC gcc
[ERROR] gcc version needs to be newer than or equal to 4.9
make: *** [sanity] Error 1

What version of GCC are we running?

[seanb80@n2185 pitchfork]$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)

Hm… Time to test out the yum package manager

[seanb80@n2185 pitchfork]$ yum install devtoolset-3-gcc-c++
Loaded plugins: fastestmirror
Repodata is over 2 weeks old. Install yum-cron? Or run: yum makecache fast
You need to be root to perform this command.

[seanb80@n2185 pitchfork]$ sudo yum install devtoolset-3-gcc-c++
bash: sudo: command not found

Hah. We don’t even have access to sudo on a build node. That’s an issue!

Found a workaround here