¶ Internal pages
¶ Hardware
- A total of 20 computers named
thunderbird1-thunderbird9,thunderbird11 - 15,thunderbird16(kolmogorov), andthunderbird21 - 25 - 1,9,11,13,14,15 have Nvidia Titan Black GPUs with 6GB of GPU RAM
- 21-25 have Nvidia Titan V GPUs with 12GB of GPU RAM
- 1-9 have 6 core intel core i7-3930K processors [12 threads with hyper-threading] and 64GB of RAM
- 11-15 have 6 core intel core i7-5820K processors [12 threads with hyper-threading] and 64GB of RAM
- 16 has two Tesla K40 GPUs, each with 12GB of RAM
- 21,25 have 6 core intel core i7-8700K processors [12 threads with hyper-threading] and 64GB of RAM
- 22,23,24 have 10 core intel core i9-7900X processors [20 threads with hyper-threading] and 128GB of RAM
¶ Usage
Anyone with a department unix log in should be able to access and use these machines.
They have basic developer tools (gcc, lapack, fftw, gsl etc) installed and have matlab.
You directly log into a particular thunderbird computer and run your jobs (e.g. using ssh -X to run matlab with a graphical user interface).
Try not too hog the resource. If you want to use more than half the machines you should renice your jobs.
The NFS disks staff, stud, and (gnostic) jdc are mounted.
¶ Ssh access
For this purpose you will need ssh access to hoodoo.otago.ac.nz, see the network administrator.
To get passwordless ssh access from outside the building, follow these steps.
I will assume your hoodoo username is myid, with machine name mysys.
- Working in your root folder, make a public/private ssh key pair (here called
mykey) and save them in the.sshdirectory:
ssh-keygen -t rsa -f .ssh/mykey
add a passphrase when prompted.
- Change permissions of private and public key
chmod 600 .ssh/mykey
chmod 600 .ssh/mykey.pub
- Copy the public key to hoodoo: (this step not needed for ssh inside the building)
scp .ssh/mykey.pub hoodoo.otago.ac.nz:
and ssh into hoodoo as usual ssh myid@hoodoo.otago.ac.nz
- Copy the public key to authorized keys file:
cat mykey.pub >> .ssh/authorized_keys
- Copy the public key to thunderdbird1 (and hence all thunderbirds)
scp mykey.pub thunderbird1:
ssh thunderbird1
cat mykey.pub >> .ssh/authorized_keys
Now go back to mysys, and add the following lines to the top of your .ssh/config file, with appropriate replacements for myid and mykey
Host thunderbird?
User myid
IdentityFile ~/.ssh/mykey
Host d*
Hostname thunderbir%h
ProxyCommand ssh -oClearAllForwardings=yes myid@hoodoo.otago.ac.nz nc %h %p
IdentityFile ~/.ssh/mykey
Host d? Thunderbird?
User myid
IdentityFile ~/.ssh/mykey
ForwardX11 yes
ForwardX11Trusted yes
From your local machine mysis you should now be able to do e.g. ssh d1 to get to thunderbird1, and scp myfile d1: to copy a file to your user account root directory on thunderbird1, without needing to enter your password.
If you want to be able to do passwordless ssh between thunderbirds, you will need to repeat the key generation process on one of the thunderbirds, say d21, creating key21, key21.pub, and cat .ssh/key21.pub >> .ssh/authorized_keys and add this to the .ssh/config on that machine
Host *
IdentityFile ~/.ssh/key21
ForwardX11 yes
ForwardX11Trusted yes
Then once you ssh once for setup into d21 and from there to the other d* you will get internode access.
¶ Julia on thunderbirds
-
The default version will go out of date quickly, so use the cross-platform julia installation tool juliaup
-
If you want multithreading on by default add this to your
.bashrc
export JULIA_NUM_THREADS=auto