hpc201-2014-10-15 - Advanced Research Computing at UM

Report
Advanced High Performance
Computing Workshop
HPC 201
Charles J Antonelli
Mark Champe
Seth Meyer
LSAIT ARS
October, 2014
Roadmap
Flux review
Globus Connect
Advanced PBS
Array & dependent scheduling
Tools
GPUs on Flux
Scientific applications
R, Python, MATLAB
Parallel programming
Debugging & profiling
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Flux review
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The Flux cluster
…
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A Flux node
48 GB - 1 TB RAM
8 GPUs (GPU Flux)
12-40 Intel cores
Local disk
Each GPU contains 2,688 GPU cores
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Programming Models
Two basic parallel programming models
Message-passing
The application consists of several processes running on different nodes and
communicating with each other over the network
Used when the data are too large to fit on a single node, and simple synchronization is
adequate
"Coarse parallelism" or "SPMD"
Implemented using MPI (Message Passing Interface) libraries
Multi-threaded
The application consists of a single process containing several parallel threads
that communicate with each other using synchronization primitives
Used when the data can fit into a single process, and the communications overhead of
the message-passing model is intolerable
"Fine-grained parallelism" or "shared-memory parallelism"
Implemented using OpenMP (Open Multi-Processing) compilers and libraries
Both
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Using Flux
Three basic requirements:
A Flux login account
A Flux allocation
An MToken (or a Software Token)
Logging in to Flux
ssh flux-login.engin.umich.edu
Campus wired or MWireless
Otherwise:
VPN
ssh login.itd.umich.edu first
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Cluster batch workflow
You create a batch script and submit it to PBS
PBS schedules your job, and it enters the flux queue
When its turn arrives, your job will execute the batch script
Your script has access to all Flux applications and data
When your script completes, anything it sent to standard output and
error are saved in files stored in your submission directory
You can ask that email be sent to you when your jobs starts, ends, or
aborts
You can check on the status of your job at any time,
or delete it if it's not doing what you want
A short time after your job completes, it disappears from PBS
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Loosely-coupled batch script
#PBS -N yourjobname
#PBS -V
#PBS -A youralloc_flux
#PBS -l qos=flux
#PBS -q flux
#PBS -l procs=12,pmem=1gb,walltime=00:05:00
#PBS -M youremailaddress
#PBS -m abe
#PBS -j oe
#Your Code Goes Below:
cat $PBS_NODEFILE
cd $PBS_O_WORKDIR
mpirun ./c_ex01
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Tightly-coupled batch script
#PBS -N yourjobname
#PBS -V
#PBS -A youralloc_flux
#PBS -l qos=flux
#PBS -q flux
#PBS -l nodes=1:ppn=12,mem=4gb,walltime=00:05:00
#PBS -M youremailaddress
#PBS -m abe
#PBS -j oe
#Your Code Goes Below:
cd $PBS_O_WORKDIR
matlab -nodisplay -r script
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GPU batch script
#PBS -N yourjobname
#PBS -V
#PBS -A youralloc_flux
#PBS -l qos=flux
#PBS -q flux
#PBS -l nodes=1:gpus=1,walltime=00:05:00
#PBS -M youremailaddress
#PBS -m abe
#PBS -j oe
#Your Code Goes Below:
cat $PBS_NODEFILE
cd $PBS_O_WORKDIR
matlab -nodisplay -r gpuscript
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Copying data
From Linux or Mac OS X, use scp or sftp
Non-interactive (scp)
scp localfile [email protected]:remotefile
scp -r localdir [email protected]:remotedir
scp [email protected]:remotefile localfile
Use "." as destination to copy to your Flux home directory:
scp localfile [email protected]:.
... or to your Flux scratch directory:
scp localfile [email protected]:/scratch/allocname/uniqname
Interactive (sftp)
sftp [email protected]
From Windows, use WinSCP
U-M Blue Disc: http://www.itcs.umich.edu/bluedisc/
LSA IT ARS / cja © 2014
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Version ca-0.96 - 8 Oct 2014
Globus Online
Features
High-speed data transfer, much faster than SCP or SFTP
Reliable & persistent
Minimal client software: Mac OS X, Linux, Windows
GridFTP Endpoints
Gateways through which data flow
Exist for XSEDE, OSG, …
UMich: umich#flux, umich#nyx
Add your own client endpoint!
Add your own server endpoint: contact [email protected]
More information
http://cac.engin.umich.edu/resources/login-nodes/globus-gridftp
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Advanced PBS
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Job Arrays
• Submit copies of identical jobs
• Invoked via qsub -t:
qsub -t array-spec pbsbatch.txt
Where array-spec can be
m-n
a,b,c
m-n%slotlimit
e.g.
qsub -t 1-50%10
Fifty jobs, numbered 1 through 50,
only ten can run simultaneously
• $PBS_ARRAYID records array identifier
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Dependent scheduling
• Submit job to become eligible for execution at a given time
• Invoked via qsub -a:
qsub -a [[[[CC]YY]MM]DD]hhmm[.SS] …
qsub -a 201412312359 j1.pbs
j1.pbs becomes eligible one minute before New Year's Day 2015
qsub -a 1800 j2.pbs
j2.pbs becomes eligible at six PM today (or tomorrow, if submitted after six PM)
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Dependent scheduling
• Submit job to run after specified job(s)
• Invoked via qsub -W:
qsub -W depend=type:jobid[:jobid]…
Where depend can be
after
afterany
afterok
afternotok
Schedule this job after jobids have started
Schedule this job after jobids have finished
Schedule this job after jobids have finished with no errors
Schedule this job after jobids have finished with errors
qsub first.pbs
# assume receives jobid 12345
qsub -W afterany:12345 second.pbs
Schedule second.pbs after first.pbs completes
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Dependent scheduling
• Submit job to run before specified job(s)
• Requires dependent jobs to be scheduled first
• Invoked via qsub -W:
qsub -W depend=type:jobid[:jobid]…
Where depend can be
before
beforeany
beforeok
beforenotok
on:N
jobids scheduled after this job starts
jobids scheduled after this job completes
jobids scheduled after this job completes with no errors
jobids scheduled after this job completes with errors
wait for N job completions
qsub -W on:1 second.pbs
# assume receives jobid 12345
qsub -W beforeany:12345 first.pbs
Schedule second.pbs after first.pbs completes
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Troubleshooting
showq [-r][-i][-b][-w user=uniq]
# running/idle/blocked jobs
qstat -f jobno
# full info incl gpu
qstat -n jobno
# nodes/cores where job running
diagnose -p
# job prio and components
pbsnodes
# nodes, states, properties
pbsnodes -l
# list nodes marked down
checkjob [-v] jobno
# why job jobno not running
mdiag -a
# allocs & users (flux)
freenodes
# aggregate node/core busy/free
mdiag -u uniq
# allocs for uniq (flux)
mdiag -a alloc_flux
# cores active, alloc (flux)
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Scientific applications
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Scientific Applications
R (incl snow and multicore)
R with GPU (GpuLm, dist)
SAS, Stata
Python, SciPy, NumPy, BioPy
MATLAB with GPU
CUDA Overview
CUDA C (matrix multiply)
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Python
Python software available on Flux
EPD
The Enthought Python Distribution provides scientists with a
comprehensive set of tools to perform rigorous data analysis and
visualization.
https://www.enthought.com/products/epd/
biopython
Python tools for computational molecular biology
http://biopython.org/wiki/Main_Page
numpy
Fundamental package for scientific computing
http://www.numpy.org/
scipy
Python-based ecosystem of open-source software for mathematics,
science, and engineering
http://www.scipy.org/
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Debugging & profiling
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Debugging with GDB
Command-line debugger
Start programs or attach to running programs
Display source program lines
Display and change variables or memory
Plant breakpoints, watchpoints
Examine stack frames
Excellent tutorial documentation
http://www.gnu.org/s/gdb/documentation/
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Compiling for GDB
Debugging is easier if you ask the compiler to generate extra
source-level debugging information
Add -g flag to your compilation
icc -g serialprogram.c -o serialprogram
or
mpicc -g mpiprogram.c -o mpiprogram
GDB will work without symbols
Need to be fluent in machine instructions and hexadecimal
Be careful using -O with -g
Some compilers won't optimize code when debugging
Most will, but you sometimes won't recognize the resulting source
code at optimization level -O2 and higher
Use -O0 -g to suppress optimization
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Running GDB
Two ways to invoke GDB:
Debugging a serial program:
gdb ./serialprogram
Debugging an MPI program:
mpirun -np N xterm -e gdb ./mpiprogram
This gives you N separate GDB sessions, each debugging one
rank of the program
Remember to use the -X or -Y option to ssh when connecting
to Flux, or you can't start xterms there
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Useful GDB commands
gdb exec
gdb exec core
l [m,n]
disas
disas func
b func
b line#
b *0xaddr
ib
d bp#
r [args]
bt
c
step
next
stepi
p var
p *var
p &var
p arr[idx]
x 0xaddr
x *0xaddr
x/20x 0xaddr
ir
i r ebp
set var = expression
q
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start gdb on executable exec
start gdb on executable exec with core file core
list source
disassemble function enclosing current instruction
disassemble function func
set breakpoint at entry to func
set breakpoint at source line#
set breakpoint at address addr
show breakpoints
delete beakpoint bp#
run program with optional args
show stack backtrace
continue execution from breakpoint
single-step one source line
single-step, don't step into function
single-step one instruction
display contents of variable var
display value pointed to by var
display address of var
display element idx of array arr
display hex word at addr
display hex word pointed to by addr
display 20 words in hex starting at addr
display registers
display register ebp
set variable var to expression
quit gdb
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Debugging with DDT
Allinea's Distributed Debugging Tool is a
comprehensive graphical debugger designed for the
complex task of debugging parallel code
Advantages include
Provides GUI interface to debugging
Similar capabilities as, e.g., Eclipse or Visual Studio
Supports parallel debugging of MPI programs
Scales much better than GDB
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Running DDT
Compile with -g:
mpicc -g mpiprogram.c -o mpiprogram
Load the DDT module:
module load ddt
Start DDT:
ddt mpiprogram
This starts a DDT session, debugging all ranks concurrently
Remember to use the -X or -Y option to ssh when connecting to Flux, or
you can't start ddt there
http://arc.research.umich.edu/flux-and-other-hpc-resources/flux/software-library/
http://content.allinea.com/downloads/userguide.pdf
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Application Profiling with MAP
Allinea's MAP Tool is a statistical application profiler
designed for the complex task of profiling parallel
code
Advantages include
Provides GUI interface to profiling
Observe cumulative results, drill down for details
Supports parallel profiling of MPI programs
Handles most of the details under the covers
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Running MAP
Compile with -g:
mpicc -g mpiprogram.c -o mpiprogram
Load the MAP module:
module load ddt
Start MAP:
ddt mpiprogram
This starts a MAP session
Runs your program, gathers profile data, displays summary statistics
Remember to use the -X or -Y option to ssh when connecting to
Flux, or you can't start ddt there
http://content.allinea.com/downloads/userguide.pdf
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Resources
http://arc.research.umich.edu/flux-and-other-hpc-resources/flux/software-library/
U-M Advanced Research Computing Flux pages
http://arc.research.umich.edu/resources-services/flux/
U-M Advanced Research Computing Flux pages
http://cac.engin.umich.edu/
CAEN HPC Flux pages
http://www.youtube.com/user/UMCoECAC
CAEN HPC YouTube channel
For assistance: [email protected]
Read by a team of people including unit support staff
Cannot help with programming questions, but can help with
operational Flux and basic usage questions
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References
1.
Supported Flux software, http://arc.research.umich.edu/flux-and-other-hpcresources/flux/software-library/, (accessed June 2014)
2. Free Software Foundation, Inc., "GDB User Manual,"
http://www.gnu.org/s/gdb/documentation/ (accessed June 2014).
3. Intel C and C++ Compiler 14 User and Reference Guide, https://software.intel.com/enus/compiler_14.0_ug_c (accessed June 2014).
4. Intel Fortran Compiler 14 User and Reference Guide,https://software.intel.com/enus/compiler_14.0_ug_f(accessed June 2014).
5. Torque Administrator's Guide, http://docs.adaptivecomputing.com/torque/4-28/torqueAdminGuide-4.2.8.pdf (accessed June 2014).
6. Submitting GPGPU Jobs, https://sites.google.com/a/umich.edu/engincac/resources/systems/flux/gpgpus (accessed June 2014).
7. http://content.allinea.com/downloads/userguide.pdf (accessed October 2014)
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