Midterm 4770
What is MPI?
Message passing interface. Standardized message passing library.
What is Block-based PFS?
Objects are created as fixed-width blocks. (file can be split up)
What is Object-based PFS?
Objects are created as variable length regions of the file. A file has a constant number of objects
Lines starting with _____ will be interpreted by the PBS scheduler
#PBS
Use the ____ flag to name the pbs job
#PBS -N
Use the ______ flag to configure PBS to merge output and error logs
#PBS -j oe
Use the ____ flag to specify the desired resources
#PBS -l
What is a shared file?
(N-to-1), single file is created, and all application tasks write to that file
What is a file-per-process?
(N-to-N), each application task creates a separate file and writes only to that file
Which filesystems on Palmetto are parallel?
/scratch1
Which filesystems on Palmetto are general purpose?
/scratch2, /scratch3
What is the envvar of the index of job launched as part of a PBS job array
PBS_ARRAY_INDEX
What is the envvar for the name of the file containing list of compute nodes allocated for the job?
PBS_NODEFILE
What is the environment variable indicating the directory from which qsub was called?
PBS_O_WORKDIR
MPI4PY uses ____ to facilitate sending and receiving of complex data
Pickle
What is a GPU?
Processor on graphics card designed to support graphic rendering (numerical manipulation)
Pros and Cons of FPGA?
Pros: Power efficient, low heat. Cons: expensive and difficult to program
What is parallel efficiency?
Ratio of performance improvement per individual unit of computing resource
Amdahl's Law
S(p) = p/((p-1)f + 1) f is fraction of program that isn't parallelizable
Equation for Speedup
S(p) = seq_run_time/par_run_time, where p is num processors
What is MPI size? And what statement?
The number of MPI processes in the communicator group. size = comm.Get_size()
What is theoretical max?
The point where adding more compute resources doesn't help speedup or efficiency
What module should you load for MPI in jupyterhub?
openmpi/1.10.3
How do you delete a job?
qdel <jobID> only done from head node
How do you view the status of your job from any node?
qstat -anu <username>
What command is used to submit a job to palmetto?
qsub
What flag is used to start an interactive job in palmetto?
qsub -I
In a scatter, the data is divided according to ____
rank
What is the call for MPI broadcast?
recv_buffer = comm.bcast(data, root=<rprocess>)
What is the call to MPI scatter?
recv_data = comm.scatter(data_array, root=<rprocess>)
What PBS tag is used to specify the number of chunks?
select
What are the two MPI commands for point-to-point communication?
send and receive
What command is run to login to palmetto?
What statement for MPI reduce?
sum = comm.reduce(rank, op=MPI.SUM, root=0)
What is MPI Rank? And what statement is used?
unique ID for individual processes within a communicator group. rank = comm.Get_rank()
What PBS tag is used to specify the amount of time to run the script?
walltime
What is the address of the file management node?
xfer01-ext.palmetto.clemson.edu
Which processes call MPI reduce?
All of them
Who calls Numpy MPI scatter?
All processes
Who calls Bcast?
All processes after the root value is set
What does a distributed file system do?
Allows transparent access to files stored on a remote disk
What are the benefits of file-per-process?
Avoids lock contention Can create massive amount of small files
How do the MPI function names differ for Numpy variables?
Begin with a capital letter
What is the issue with a shared file?
Can create lock contention and reduce performance
What is the issue with file-per-process?
Can't support app restart on different number of tasks
What is the difference between DFS and PFS regarding workloads?
DFS is geared for loosely coupled, distributed apps (big data), PFS targets HPC applications that require coordinated I/O access with massive bandwidth requirements
What is the difference between DFS and PFS regarding symmetry?
DFS runs on architecture where storage is with the application, PFS separates storage from compute system
What is the difference between DFS and PFS regarding data distribution?
DFS stores entire file on a node, PFS splits the file across many nodes
What is the difference between DFS and PFS regarding fault-tolerance?
DFS takes on fault tolerance responsibilities, PFS runs on enterprise shared storage (no fault-tolerance but rely on hardware quality)
Efficiency equation
E = 1/((p-1)f + 1) * 100% E is the ratio of speedup over the number of processors
What does a parallel file system do?
Enable parallel access to files
(T/F) MPI processes are launched as they are needed during program execution
False, all launched at the beginning of execution
(T/F) Only the process broadcasting should call comm.bcast
False, all processes, the source is specified in the function call
(T/F) A resource request (qsub) can be done from any node?
False, only login001
(T/F) All MPI processes share memory space
False, they have their own and have access to the same source codes
TOP500 ranks supercomputers based on their ____ score
LINPACK
What statement should be used to initialize the communicator?
comm = MPI.COMM_WORLD
What is the call for Numpy MPI broadcast?
comm.Bcast(values, root=<rootrank>)
What is the call to Numpy MPI gather?
comm.Gather(smallarray, bigarray, root=<rootrank>)
What is the call for Numpy MPI receive?
comm.Recv(values, source=<srcrank>, tag=MPI.ANY_TAG, status=status)
What is the call to Numpy MPI reduce?
comm.Reduce(localval, reducedval, op=<MPI.OP>, root=<rootrank>)
What is the call for Numpy MPI scatter?
comm.Scatter(bigarray, localarray, root=<rootrank>)
What is the call for a Numpy MPI send?
comm.Send(values, dest=<destrank>, tag=<tag>)
How is MPI send called?
comm.send(data, dest_rank)
How is MPI receive called?
data = comm.recv(source_rank)
GRAPH500 ranks systems based on benchmarks designed for ______ computing
data-intensive
GREEN500 ranks supercomputers with an emphasis on ______
energy usage (LINPACK/ power consumption)
What is FPGA?
field programmable gate array. Dynamically reconfigurable circuit board
What is an MPI communicator used for?
groups for point-to-point and collective communications
The ____ node is the only gateway to access Palmetto nodes from outside
login
What PBS tag is used to specify the amount of ram per chunk?
mem
Processes handle their own ____, data is passed between processes via _____
memory, messages
Processes communicate via ____
messages
What is the package to enable mpi in Python?
mpi4py
What PBS tag is used to specify the number of mpi processors per chunk?
mpiprocs
What call is made to execute an MPI program with 4 processes?
mpirun -np 4 <executable>
How do you get the name of the host for an MPI process?
name = MPI.Get_processor_name()
What PBS tag is used to specify the number of cpus per chunk?
ncpus
What are the two aspects of a parallel PROBLEM?
1. Can be broken into discrete pieces of work that can be solved simultaneously 2. Can be solved in less time with multiple compute resources than a single compute resource
What is one aspect of a parallel EXECUTION FRAMEWORK?
1. Can execute multiple program instructions concurrently at any moment in time
What are the aspects of a parallel COMPUTE RESOURCE?
1. Might be a single computer with multiple processors 2. Might be an arbitrary number of computers connected by a network 3. May be a GPU
What are the limiting factors of distributed computing?
1. Non-parallelizable code 2. Communication overhead
How is data distributed in PFS?
1. Original file is converted into a sequence of offsets 2. Offsets are mapped to objects 3. Objects are distributed across PFS servers
What are the 4 models in Flynn's taxonomy?
1. SISD 2. SIMD 3. MISD 4. MIMD
What character is used to separate tags on a PBS job
:
What character is used to set the value of tags on a PBS job?
=
What is a Distributed Computing System?
A collection of individual computing devices that can communicate with each other
What is HPCC?
High Performance Computing Challenge. Runs a ****ton of different tests.
What is parallel speedup?
How much faster the program becomes once some computing resources are added
What is TestDFSIO?
I/O performance of mapreduce/hadoop dfs
What is the benefit of a shared file?
Increased usability: only one file is needed
What is the issue with round robin object placement on PFS?
Scalability. Two dimensional distribution and limits number of server per file
What is SHOC? and what is it used for?
Scalable Heterogeneous Computing, used for non-traditional systems (GPUs)
What are the two file access mechanisms in PFS?
Shared file (N-to-1) File-per-Process (N-to-N)
(T/F) All processes make the call to MPI scatter
True
(T/F) MPI broadcast is a blocking call for all processes
True
(T/F) The number of MPI processes is user-specified
True
What is a PBS script?
a bash script that can be submitted to palmetto to run when resources are available for a certain amount of time
Who calls Numpy MPI gather?
all processes
What statement for MPI gather?
all_data = comm.gather(data, root=<rprocess>)
