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A brief introduction to the engaging cluster for the NSE and PSFC groups. Assorted recipes and gists.

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engaging_cluster_howto

A brief introduction to the engaging cluster for the NSE and PSFC groups. Assorted recipes and gists.

These slides, related source code and recipes may be found at github repository https://github.com/jcwright77/engaging_cluster_howto.git

The author may be contacted at [email protected].

Abstract

The Massachusetts Green Energy High Performance Computing Center (MGHPCC) in Holyoke, MA is 100 miles from MIT campus connected by formerly dark fiber (100Gb). Completed in November 2012, the 90, 000 square foot, 15 megawatt facility is located on an 8.6 acre former industrial site just a few blocks from City Hall. University partners include B.U., NorthEaster, Harvard, UMass and MIT.

The engaging computer cluster is a large (~500 nodes) multi-departmental compute cluster in the MGHPCC facility. NSE and the PSFC together have 136 nodes in the cluster. We will discuss the MGHPCC and how it came to be, what it provides and what resources are available to members of the NSE and PSFC programs. The presentation will be followed by a live demo of the basic tasks involved in using the new subsystem. Topics covered including how to log in, how to bring up remote applications, using git, compiling, runnning jobs in the batch system.

Administrative questions should be directect to [email protected]

The engaging system and the nse and psfc nodes

- 100+32+4 nodes, 4352 cores Centos 7 , 2x16 cores Intel Xeon 2.1 GHz, 128 GB RAM

  • Nodes available in the sched_any_quicktest partition Centos 6 ,2x8 cores Intel Xeon 2.0 GHz, 64 GB RAM

  • The remaining system nodes run Centos 6 and have 16 cores per node.

Getting an account

First register your kerberos ID with engaging by going to: https://engaging-ood.mit.edu/. You will need your MIT Kerberos credentials to access the cluster. After authenticating, you should be able to SSH to eofe7.mit.edu (the PSFC partition on the Engaging Cluster) with your MIT username and password.

PSFC users may then request access to the PSFC partitions by filling out the form at https://www1.psfc.mit.edu/computers/cluster/index.html .

Logging in.

All logins should be to eofe7.mit.edu

  • ssh (all): ssh is included in linux and osx distributions.

    It is available in the bash shell under Windows 10 Server for Linux (WSL) in Microsoft Store.

    You can do X11 forwarding for remote GUI usage. X11 usage requires XQuartz under OSX or X-Win32 under Windows. Also see MobaXterm that comes with an x-server built in for Windows.

  • SecureCRT (windows): Windows ssh terminal with port forwarding

  • x2go (all): remote desktop access. Not all desktops are supported on engaging, try 'XFCE'

  • putty: ssh terminal program for windows. Requires transformation of your private key to a PPK format using the puttygen program.

  • XWIN32: X11 emulator that also supports ssh connections Uses same ppk format for keys as putty. See IS&T for the license key. Make sure that you get release 53 required for working ssh key support. IS&T is currently providing release 47. You can get the latest release from the vendor.

What is an ssh key?

  • similar to your MIT certificates but you have two parts.

    • public key part : eg id_rsa_user.pub. Linux permissions chmod 700 id_rsa_user.pub in $HOME/.ssh directory

      This is the key that needs to be on the destination machine. engaging signup does this for you.

    • private key part : eg id_rsa_user.Linux permissions chmod 600 id_rsa_user in $HOME/.ssh directory

      This is the key you need on your local machine. On linux in your .ssh directory or specified directly with ssh -i. For gui interfaces on windows, this is the key your provide when setting up a session or preparing a key for putty with puttygen. The private key also includes enough information to generate its matching public key. The converse, of course, computationally prohibitive.

      For the truly interested, ssh keys use public key cryptography. The basic process is that a message is encrypted with your private key and sent along with other details such as key type, public key and username to the sshd server. The server checks for a matching public key in the user's authorized_keys file. This public key is used to decrypt the message and if it matches the expected message (including username among other items) then the connect is accepted. Traffic over the connect is also encrypted with the key pair. The public key is actually like a lock shared with someone else to which you keep the key(the private key). This operations works and is asymmetric because the encryption process uses knowledge of the two primes composing a product whereas the decryption process only requires knowing a value that is coprime to the product, this product is available to both the public and private keys (sorry TMI?).

Working with the file system

  • nfs storage. Long term inexpensive storage, expandable.

    • Group specific, eg:

      /net/eofe-data005/psfclab001/<username> 50 TB available, no quota.

      This volume is automounted so you have to cd into it explicitly to see it.

    • other storage can be used in serial runs : 1TB quota

      /pool001/

  • home directory. Backed up with TSM at MIT.

    /home/<username> 100 GB quota

  • parallel filesystem. Run your parallel codes here. Note the name.

    lustre : /nobackup1/ . 1 PetaByte of storage for engaging, no quota for now, so monitor your usage.

  • file transfers

    • scp ('nix) : scp localfile.txt <username>@eofe7.mit.edu:local/relative/path

    • sftp ('nix) : sftp <username>@eofe7.mit.edu to get prompt.

                `sftp> ?` to get help. `put localfile`

    • sshfs ('nix) : sshfs <username>@eofe7.mit.edu local_empty_dir: Creates a link to remote files in to an local empty folder. After the command, your remote files are accessible for editting or copying to with normal local file operations (eg cp, mv, viewing and editting)

    • winSCP (windows) : specify your key for your engaging connection in SSH > Authentication page of advanced setup. Uses .ppk putty key format. Generate a ppk format key from your private ssh key with PuttyGen.

    • SecureCRT (windows) : Recommended. supports file transfers with a session. type rz <RETURN> to bring up a dialog to upload files. Can also drag-and-drop! Select Z-modem transfer in both cases. sz <args> to transfer files from engaging to your desktop.

Other methods (not recommended at this time)

-   cifs (windows): Not available at this time. possible but not up as a service. brings in
    username and domain mapping issues.

-   x2go (all platforms): Not recommended at this time for file transfers. buggy for file transfers, requires `fuse` group membership on server.

Finding software with Environment Modules

Provide a clean way of managing multiple compiler/MPI combinations, software versions and dependencies. Modules modify search paths and other environmental variables in a user's shell so the executables and libraries associated with a module are found.

  • module avail: list all modules currently available on the system
  • module show: show what environment a module loads
  • module add/unload: add/remove a module from a user's environment
  • module list: list what modules are loaded
  • module purge: remove all loaded modules
  • module use =path=: add a new search path to modules

Module names follow a convention of software/version 

[jcwright@eofe7 ~]$ module use /home/software/psfc/modulefiles #enable psfc specific modules
[jcwright@eofe7 ~]$ module add psfc/config #basic setup for psfc users 
[jcwright@eofe7 ~]$ module avail

---------------------------------- /home/software/psfc/modulefiles/ ------------------------------------
psfc/atlas/gcc-4.8.4/3.10.3      psfc/fftw/2.1.5        psfc/fftw/3.3.5       psfc/totalview/2016.07.22
---------------------------------- /home/software/modulefiles ------------------------------------------
foo/1.0       gcc/4.9.4     gcc/5.4.0     gcc/6.2.0     intel/2017-01 R/3.3.1

...

A research group can create their own set of modules and expose them to users with module use. On engaging, these are located in /home/software/<group>/ eg /home/software/psfc/. This can also be done in a user's own home directory for managing different builds of your own software or local installs.

Running jobs in SLURM gist

  • SLURM

    The Simple Linux Utility for Resource Manager (SLURM) is used on engaging to manage job submissions. If you used the NERSC systems you will be familiar with it.

  • Partitions

    Partitions are what job queues are called in SLURM. The partitions for the NSE and the PSFC are:

    • sched_mit_psfc Has Quality of Servive (QoS), psfc_24h, for 24 hr runs

      sbatch --qos psfc_24h

    • sched_mit_nse

    • sched_mit_emiliob

  • Common slurm commands

    • sbatch :: submit a batch job

    • squeue -u username :: show a users job status

    • scancel :: kill a job

    • scontrol show partition :: list partitions to which you have access

    • scontrol show jobid # :: info on job

    • sinfo -a :: show all partition names, runtimes and available nodes

    • salloc :: request a set of nodes in a partition salloc --gres=gpu:1 -N 1 -n 16 -p sched_any --time=1:00:00 --exclusive You must exit from an salloc session. srun and mpirun within an allocation will use the allocated cores automatically. If logging in to eofe4/5, use partition sched_any_quicktest.

    • srun :: run a program on allocated processors, optionally, also requests the allocation if needed.

    • sacct :: detailed information on usage

    Lots more info

  • Recipes

    • Getting an interactive job, one node

      srun -p sb.q -N 1 -c 1 --pty -t 0-00:05 /bin/bash where sb.q is the partition you want to use. Note quicktest has a 15min limit. -N "num nodes" -c "cpus-per-task"

    srun -p sched_mit_psfc --tasks-per-node=4 -N 4 --pty -t 0-2:05 bash given an interactive job with 4 nodes x 4 cpus per node = 16 cores.

    • Request 16 cores on a node salloc -N 1 -n 16 -p sched_any_quicktest --time=0:15:00 --exclusive

    • Request a specific node, 32 cores, and forward X11 for remote display #x11 forwarding to a specific node, may take a moment to first load srun -w node552 -N 1 -n 32 -p sched_mit_nse --time=1:00:00 --x11=first --pty /bin/bash

    • How much memory is or did my job use sacct -o MaxRSS -j JOBID

Example Script

#!/bin/bash
# submit with sbatch cpi_nse.slurm
# commandline arguments may instead by supplied with #SBATCH <flag> <value>
# commandline arguments override these values

# Number of nodes
#SBATCH -N 32
# Number of processor core (32*32=1024, psfc, mit and emiliob nodes have 32 cores per node)
#SBATCH -n 1024
# specify how long your job needs. Be HONEST, it affects how long the job may wait for its turn.
#SBATCH --time=0:04:00
# which partition or queue the jobs runs in
#SBATCH -p sched_mit_nse

Specify maximum memory needed per cpu. NSE and PSFC nodes have 128 GB = 4 GB/core. default is 4 GB 

#SBATCH --mem-per-cpu=2000 #in MB
#customize the name of the stderr/stdout file. %j is the job number
#SBATCH -o cpi_nse-%j.out

#load default system modules
. /etc/profile.d/modules.sh

#load modules your job depends on. 
#better here than in your $HOME/.bashrc to make debugging and requirements easier to track.
#here we are using gcc under MPI mpich, you may also use intel icc with intel impi
module load mpich/ge/gcc/64/3.1

#I like to echo the running environment
env

#Finally, the command to execute. 
#The job starts in the directory it was submitted from.
#Note that mpirun knows from SLURM how many processor we have
#In this case, we use all processes.

mpirun ./cpi

Other slurm scripts

  • Serial jobs. Specificy one node and one core. No need for mpirun commmand. May specify memory requirement with #SBATCH --mem X to ensure sufficient memory for large jobs.
#!/bin/bash
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mem 10000  #in MB
#SBATCH --time=0:04:00
#SBATCH -p sched_mit_psfc
#SBATCH -o myjob-%j.out

. /etc/profile.d/modules.sh

./pi_serial

How to compile. Sourcecode gist.

  • On engaging there are two main compilers supported, gcc/gfortan (4.9.4, 5.4.0, 6.2.0) and intel 17.

  • to compile, you would load either gcc or intel modules. Optionally load the associated MPI library if compiling parallel programs. Using the mpi compiler command (mpiifort, mpiicc, mpicc, etc) automatically links in the required MPI libraries.

  • fortran

    module load intel
module load impi #for parallel support
ifort -o myprog myprog.f/f90/F90/F
#or if parallel
mpiifort -o my_par_program my_par_prog.f/f90/F90/F

  • C

    module load gcc
module load  mpich/ge/gcc/64/3.1 # for parallel support
gcc -o myprog myprog.c
mpicc -o myprog myprog.c/cc #for parallel compilation

Other trivia

Demos

  • Log in using x2go

    Uses ssh key and passphrase

  • Retrieve demo script and program sources from github, edit and run it.

    Uses git, vim or emacs or gedit, slurm batch system, c and fortran compilers. gist

  • matlab

  • Dropbox

    retrieve and store files from your Dropbox

  • julia

The following are not yet present explicitly in the slide deck.

  • python demo
  • parallel task farm slurm job arrays, multiplexing across nodes (queues)
  • slurm, restarting for long jobs
  • slurm reservations

Log in using x2go

x2go uses your ssh keys to give you a remote desktop on the engaging cluster. This desktop is also persistent so you close a session and return to it later, even on another device. Select desktop choice 'XFCE' when setting up a connection.

Connect using FastX

FastX gives you the remote desktop environment of x2go or nomachine right in your browser. Connect to

https://eofe8.mit.edu  or https://eofe7.mit.edu

Upload your engaging private ssh key into your browswer following the instructions. It is only stored in the local cache. When done, you should be able to start a desktop session in your browser!

Running a serial and then parallel program from github

matlab example

module load mit/matlab
matlab #for gui
matlab -nodesktop -nosplash # for commandline
matlab -nodesktop -nosplash -nodisplay -r "run('/home/user/rest/of/path/mfile.m');" # for a non-interactive process, eg a batch script

julia parallel example

Julia is a parallel interpreted language developed at MIT.

#load julia
module load engaging/julia

#request a node
srun -N 1 -n 32 -p sched_mit_nse --time=1:00:00 --x11=first --pty /bin/bash

#start julia
julia -j 4
julia> nprocs()
5
julia> workers()                           # Identifiers for the worker processes.
4-element Array{Int64,1}:
 2
 3
 4
 5
@everywhere println(@sprintf("ID %d: %f %d", myid(), rand(), p))
ID 1: 0.686332 5
	From worker 4:	ID 4: 0.107924 5
	From worker 5:	ID 5: 0.136019 5
	From worker 2:	ID 2: 0.145561 5
	From worker 3:	ID 3: 0.670885 5

Dropbox example

You can open your dropbox account directly in a web browser on engaging in x2go.

For commandline access, this requires creating a Dropbox app following these instructions. With this program you can download and upload specific files or folders and list contents of folders but it does not auto-sync.

Alternatively, you can install the Dropbox daemon program and run it in your account to synchronize a local folder. Instructions are at the dropbox wiki.

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A brief introduction to the engaging cluster for the NSE and PSFC groups. Assorted recipes and gists.

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