Part I – Interacting with Matlab

Transcript Part I – Interacting with Matlab

MATLAB

C E N T E R F O R I N T E G R A T E D R E S E A R C H C O M P U T I N G

http://www.circ.rochester.edu/wiki/index.php/MatlabWorkshop

Outline

Part I – Interacting with Matlab  Running Matlab interactively  Accessing the GUI  Using the terminal for command entry  Using just the terminal  Running Matlab in batch mode  Using PBS job arrays to do embarrassingly parallel computations Part II – Speeding up Matlab Computations  Symmetric Multi-Processing with Matlab  Accelerating Matlab computations with GPUs  Running Matlab in distributed memory environments  Using the Parallel Computing Toolbox  Using the Matlab Distributed Compute Engine Server  Using pMatlab Part III – Mixing Matlab and Fortran/C code  Compiling MEX code from C/Fortran  Turning Matlab routines into C code

Running Matlab Interactively

 To use Matlab's GUI you must connect through suitable environment  Why NX?

 Faster than using X11 forwarding (compresses data)  Has clients for all major operating systems  Saves your session when you are disconnected  You don’t have to restart Matlab if your network connection drops.

 Instructions for obtaining/installing/connecting through NX can be found at: http://www.circ.rochester.edu/wiki/index.php/NX_Cluster

Running Matlab Interactively

 To use GUI you must connect through suitable environment  Why NX?

http://www.circ.rochester.edu/wiki/index.php/NX_Cluster  The link to Matlab on the NX desktop menu bar actually launches a script that submits a job to the blue hive cluster. It does not run Matlab locally, but instead uses X11 forwarding between compute nodes and the NX server.

Running Matlab Interactively

 We could also launch a terminal on the NX desktop and submit an interactive job from there .

Running Matlab Interactively

 We could also launch a terminal on the NX desktop and submit an interactive job from there .

qsub -I -X -q interactive -l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1 module load matlab-R2013a-local matlab -singlecompthread

Running Matlab Interactively

 We could also launch a terminal on the NX desktop and submit an interactive job from there .

qsub -I -X -q interactive -l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1 module load matlab matlab -singlecompthread  Occasionally the Matlab Desktop will respond slowly to commands which can be VERY frustrating. One work around is to use the terminal window as the "desktop" – while still retaining the ability to plot windows / access help etc...

matlab -nodesktop -nosplash

Running Matlab Interactively

 We could also launch a terminal on the NX desktop and submit an interactive job from there .

qsub -I -X -q interactive -l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1 module load matlab matlab -singlecompthread  Occasionally the Matlab Desktop will respond slowly to commands which can be VERY frustrating. One work around is to use the terminal window as the Desktop – while still retaining the ability to plot windows / access help etc...

matlab -nodesktop -nosplash  And finally you may not need to plot anything on the screen – or use any of the GUI features. In that case you can...

matlab -nodisplay

Running Matlab Interactively

 If you are running Matlab without a connected display you can still make plots directly to a file in Matlab H=hilb(1000); Z=fft2(H); f=figure('Visible','off');   imagesc(log(abs(Z)));   print('-dpdf','-r300', 'fig1.pdf')  You may also find it useful to enter many commands into a script file and then execute the script – so you can do something else while Matlab creates several figures etc... This is also a good way to develop a script for batch jobs.

Running Matlab Interactively

 If you are running a machine that has an X-server – you can bypass NX and just use X11 Forwarding. Though if your connection drops – your Matlab session (and your interactive job) will terminate ssh -X [email protected]

qsub -I -X -q interactive –l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1  Also if you do use NX and you finish using Matlab – please terminate your session instead of just disconnecting. This will cleanup any jobs you have running and free up resources for other users.

Outline

Running Matlab in Batch Mode

 To submit a job in batch mode we need to create a batch script #PBS -N Matlab #PBS -q standard . /usr/local/modules/init/bash module load matlab matlab -nodisplay -r "sample_script"

sample_script.pbs

#PBS -l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1  And a Matlab script containing the commands to run H=hilb(1000); Z=fft2(H); imagesc(log(abs(Z))); print('-dpdf','-r300','fig1-batch.pdf');

sample_script.m

 And we should place both files in a folder on /scratch where we will submit the job from.

qsub sample_script.pbs

Outline

Using Job Arrays in Batch Mode

 To use a job array we need to use the “-t” PBS option #PBS -t 0-3 #PBS -N Matlab #PBS -q standard . /usr/local/modules/init/bash module load matlab

sample_script.pbs

#PBS -l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1 matlab -nodisplay -r "sample_function($PBS_ARRAYID)"  And turn our Matlab script into a function that takes arguments. (sample_function.m) function sample_function(n) H=hilb(n); Z=fft2(H); imagesc(log(abs(Z)));

sample_function.m

print('-dpdf','-r300', sprintf('%s%03d%s','fig1-batch_',n,'.pdf'));

Outline

Symmetric Multi-Processing

 By default Matlab uses all cores on a given node for operations that can be threaded – regardless of the submission script. Arrays and matrices   • Basic information: ISFINITE, ISINF, ISNAN, MAX, MIN   • Operators: +, -, .*, ./, .\, .^, *, ^, \ (MLDIVIDE), / (MRDIVIDE)

Symmetric Multi-Processing

 To be sure you only use the resources you request, you should either request an entire node and all of the CPU’s...

qsub -I -X -q interactive -l walltime=1:00:00,nodes=1:ppn=8,vmem=16gb,pvmem=-1 . /usr/local/modules/init/bash module load matlab matlab  Or request a single cpu and specify that Matlab should only use a single thread qsub -I -X -q interactive -l walltime=1:00:00,nodes=1:ppn=1,vmem=4gb,pvmem=-1 . /usr/local/modules/init/bash module load matlab matlab -singleCompThread

Outline

Using GPUs with Matlab

 Matlab can use GPUs to do calculations, provided a GPU is available on the node Matlab is running on. qsub -I -X -q blugpu -l walltime=1:00:00,nodes=1:ppn=1:gpus=1,vmem=16gb,pvmem=-1 . /usr/local/modules/init/bash module load matlab module load cuda matlab  We can query the connected GPUs from within Matlab using gpuDeviceCount() gpuDevice()

Using GPUs with Matlab

 So there is a 2D FFT – but no Hilbert function...

H=hilb(1000); H_=gpuArray(H); Z_=fft2(H_); Z=gather(Z_); imagesc(log(abs(Z))); Distribute data to GPU FFT performed on GPU Gather data from GPU onto CPU  We could do the log and abs functions on the GPU as well. H=hilb(1000); H_=gpuArray(H); Z_=fft2(H_); imagesc(gather(log(abs(Z_)));

Using GPUs with Matlab

 For our example, doing the FFT on the GPU is 7x faster. (4x if you include moving the data to the GPU and back) >> H=hilb(5000); >> tic; A=gather(gpuArray(H)); toc Elapsed time is 0.161166 seconds.

>> tic; A=gather(fft2(gpuArray(H))); toc Elapsed time is 0.348159 seconds.

>> tic; A=fft2(H); toc Elapsed time is 1.210464 seconds.

Using GPUs with Matlab

 Matlab has no built in hilb() function that can run on the GPU – but we can write our own function(kernel) in cuda – and save it to hilbert.cu

__global__ void HilbertKernel( double * const out, size_t const numRows, size_t const numCols) { const int rowIdx = blockIdx.x * blockDim.x + threadIdx.x; const int colIdx = blockIdx.y * blockDim.y + threadIdx.y; if ( rowIdx >= numRows ) return; if ( colIdx >= numCols ) return; size_t linearIdx = rowIdx + colIdx*numRows; out[linearIdx] = 1.0 / (double)(1+rowIdx+colIdx) ; }  And compile it with nvcc to generate a Parallel Thread eXecution file nvcc -ptx hilbert.cu

Using GPUs with Matlab

 We have to initialize the kernel and specify the grid size before executing the kernel.

H_=gpuArray.zeros(1000); hilbert_kernel=parallel.gpu.CUDAKernel('hilbert.ptx','hilbert.cu'); hilbert_kernel.GridSize=size(H_); H_=feval(hilbert_kernel, H_, 1000,1000); Z_=fft2(H_); imagesc(gather(log(abs(Z_))));  The default for matlab kernel’s is 1 thread per block, but we could create fewer blocks that were each 10 x 10 threads.

hilbert_kernel.ThreadBlockSize=[10,10,1]; hilbert_kernel.GridSize=[100,100];  In any event, our speedup is a factor of 50 compared to 1 CPU.

Outline

Parallel Computing Toolbox

 As an alternative you can also use the Parallel Computing Toolbox. This supports parallelism via MPI qsub -I -X -q interactive -l walltime=1:00:00,nodes=1:ppn=8,vmem=16gb,pvmem=-1 . /usr/local/modules/init/bash module load matlab matlab -singleCompThread  You can enable a pool of matlab workers using matlabpool matlabpool(8)  You should create a pool that is the same size as the number of processors you requested in your job submission. Matlab also sells licenses for using a Distributed Computing Server which allows for matlabpools that use more than just the local node.

Parallel Computing Toolbox

matlabpool(4) parfor n=1:100 H=hilb(n); Z=fft2(H); f=figure('Visible','off'); end   imagesc(log(abs(Z))); print('-dpdf','-r300', sprintf('%s%03d%s','fig1-batch_',n,'.pdf')); matlabpool close

Parallel Computing Toolbox

matlabpool(4) spmd for n=drange(1:100) H=hilb(n); Z=fft2(H); f=figure('Visible','off');   imagesc(log(abs(Z))); end end matlabpool close matlabpool(4) spmd for n=labindex:numlabs:100 H=hilb(n); Z=fft2(H); f=figure('Visible','off');   imagesc(log(abs(Z))); end end matlabpool close

Parallel Computing Toolbox

pmode start 4 n=labindex; H=hilb(n); Z=fft2(H); f=figure('Visible','off');   imagesc(log(abs(Z))); print('-dpdf','-r300', sprintf('%s%03d%s','fig1-batch_',n,'.pdf')); pmode lab2client H 3 H3 H3 pmode close

Parallel Computing Toolbox

 You can achieve parallelism in several ways:  parfor loops – execute for loops in parallel  smpd – execute instructions in parallel (using ‘labindex’ or ‘drange’)  pmode – interactive version of smpd  distributed arrays – very similar to gpuArrays Example using gpuArray H=hilb(1000); H_=gpuArray(H); Z_=fft2(H_); Z=gather(Z_); imagesc(log(abs(Z))); Example using distributed arrays matlabpool(8) H=hilb(1000); H_=distributed(H); Z_=fft(fft(H_,[],1),[],2); Z=gather(Z_); imagesc(log(abs(Z))); matlabpool close

Parallel Computing Toolbox

 What about building hilbert matrix in parallel?

matlabpool(4) spmd codist=codistributor1d(1,[250,250,250,250],[1000,1000]); [i_lo, i_hi]=codist.globalIndices(1); H_local=zeros(250,1000); for i=i_lo:i_hi for j=1:1000 end end H_ = codistributed.build(H_local, codist); end H_local(i-i_lo+1,j)=1/(i+j-1); Z_=fft(fft(H_,[],1),[],2); Z=gather(Z_); imagesc(log(abs(Z))); matlabpool close Define partition Get local indices in x-direction Allocate space for local part Initialize local array with Hilbert values.

Assemble codistributed array Now it's distributed like before!

Outline

Using the Matlab Distributed Compute Engine

 To get started, first cd into an empty directory and run  mdce_init This will generate 4 files:  mdce_job.pbs – pbs submission script  mdce_script.m – sample matlab script that uses parallel computing toolbox  mdce_profile.m – matlab function that uses your environment variables to locate the matlab compute cluster for your job  mdce_cleanup is an epilogue script that cleans up the matlab distributed compute server when your job terminates  Then you can submit the sample job with qsub mdce_job.pbs

Using the Matlab Distributed Compute Engine

 Here is the job submission script #!/bin/bash #PBS -N Matlab_mdce #PBS -j oe #PBS -l nodes=2:ppn=8,pvmem=2000mb #PBS -l epilogue=mdce_cleanup #PBS -o matlab.log

. /usr/local/modules/init/bash module load matlab-R2013a-local cd $PBS_O_WORKDIR pbs_mdce_start matlab -nodisplay -r "mdce_script"

mdce_job.pbs

#PBS -l walltime=1:00:00 #PBS -q standard Note that other versions of matlab could take hours to start the matlab cluster!!!

 This script loads the matlab module, starts the cluster with pbs_mdce_start, and runs the matlab script "mdce_script.m"

Using the Matlab Distributed Compute Engine

 And here is the sample matlab script profile=mdce_profile() matlabpool('open', profile) parfor n=1:matlabpool('size') H=hilb(n); Z=fft2(H); imagesc(log(abs(Z))); print('-dpdf','-r300',sprintf('%s%03d%s','fig1-batch',n,'.pdf')); end matlabpool('close')

mdce_script.m

 The mdce_profile() function returns a profile that can be used to connect to the mdce cluster for your job. You can then use matlabpool or pmode, or spmd etc... to startup parallel computations across the matlab cluster.

Using the Matlab Distributed Compute Engine

 For interactive mode, you can use the qMatlab_mdce script. This script will inherit your matlab path from your environment, so be sure to load the matlab-R2013a-local module to speed up the initilization of the cluster.

mkdir /scratch/jcarrol5/matlab_mdce cd /scratch/jcarrol5/matlab_mdce module load matlab-R2013a-local qMatlab_mdce 4 8 16  This will create a matlab cluster which in this case consists of 4 nodes each with 8 workers and 16 GB of memory per. To use the matab cluster, load the profile using the mdce_profile() function and then open the pool of workers with matlabpool – or pmode etc...

profile=mdce_profile() matlabpool('open', profile)

Outline

Using pMatlab

 pMatlab is an alternative method to get distributed matlab functionality without relying on Matlab’s Distributed Computing Server.  It is built on top of MapMPI (an MPI implementation for matlab – written in matlab - that uses file I/O for communication)  It supports various operations on distributed arrays (up to 4D)  Remapping, aggregating, finding non-zero entries, transposing, ghosting  Elementary math functions (trig, exponential, complex, remainder/rounding)  2D Convolutions, FFTs, Discrete Cosine Transform  FFT's need to be properly mapped (cannot be distributed along transform dimension).



It does not have as much functionality as the parallel computing toolbox – but it does support ghosting and more flexible partitioning!

Using pMatlab

 Since pMatlab works by launching other Matlab instances – we need them to startup with pMatlab functionality. To do so we need to add a few lines to our startup.m file in our matlab path. addpath('/usr/local/pMatlab/MatlabMPI/src'); addpath('/usr/local/pMatlab/src'); rehash; pMatlabGlobalsInit;

Running pMatlab in Batch Mode

 To submit a job in batch mode we need to create a batch script #PBS -N Matlab #PBS -q standard . /usr/local/modules/init/bash module load matlab matlab -nodisplay -r "pmatlab_launcher"

sample_script.pbs

#PBS -l walltime=1:00:00,nodes=2:ppn=8,vmem=32gb,pvmem=-1  And a Matlab script to launch the pMatlab script [sreturn, nProcs]=system('cat $PBS_NODEFILE | wc -l'); nProcs=str2num(nProcs); [sreturn, machines]=system('cat $PBS_NODEFILE | uniq'); machines=regexp(machines, '\n', 'split'); machines=machines(1:size(machines,2)-1); eval(pRUN('pmatlab_script',nProcs,machines));

Running pMatlab in Batch Mode

 And finally we have our pmatlab script.

Xmap=map([Np 1],{},0:Np-1); H_=zeros(1000,1000,Xmap); [I1,I2]=global_block_range(H_); H_local=zeros(I1(2)-I1(1)+1,I2(2)-I2(1)+1); for i=I1(1):I1(2) for j=I2(1):I2(2) end end H_local(i-I1(1)+1,j-I2(1)+1)=1/(i+j-1); end H_=put_local(H_,H_local); Z_=fft(fft(H_,[],2),[],1); Z=agg(Z_); if (pMATLAB.my_rank == pMATLAB.leader) f=figure('Visible','off'); imagesc(log(abs(Z))); print('-dpdf','-r300', 'fig1.pdf'); map for distributing array Distributed matrix constructor Indices for local portion of array Allocate and populate local portion of array with Hilbert matrix values X = put_local(X, fft(local(X),[],2)); Z = transpose_grid(X); Z = put_local(Z, fft(local(Z),[],1)); Plot result from 'leader' matlab process

pmatlab_script.m

Using pMatlab

 PBS is unaware of matlab sessions launched from 'pRUN' and therefore cannot properly clean up if something goes wrong (job runs out of walltime etc...) To avoid leaving orphaned Matlab processes on other machines, modify your PBS script #PBS -l epilogue=epilogue_script.sh

to run this epilogue script which must have user-execute permissions #!/bin/bash cd $PBS_O_WORKDIR/MatMPIa echo "running prologue" pwd; for i in `ls pid.*`; do machine=`echo $i | awk -F '.' '{print $2}'`; pid=`echo $i | awk -F '.' '{print $3}'`\; ssh $machine "(kill -9 $pid)" && rm -rf $i; done

epilogue_script.sh

Outline

Compiling Mex Code

 There is a configuration file for mex that you can place in your ~/.matlab/R2012b/ folder – or whatever version of matlab you are using. The file can be downloaded from the CIRC wiki http://www.circ.rochester.edu/wiki/index.php/Mexopts.sh

Compiling Mex Code

 C, C++, or Fortran routines can be called from within Matlab.

#include "fintrf.h" subroutine mexfunction(nlhs, plhs, nrhs, prhs) mwPointer :: plhs(*), prhs(*) integer :: nlhs, nrhs mwPointer :: mxGetPr mwPointer :: mxCreateDoubleMatrix real(8) :: mxGetScalar mwPointer :: pr_out integer :: n n = nint(mxGetScalar(prhs(1))) plhs(1) = mxCreateDoubleMatrix(n,n, 0) pr_out = mxGetPr(plhs(1)) call compute(%VAL(pr_out),n) end subroutine mexfunction subroutine compute(h, n) integer :: n real(8) :: h(n,n) integer :: i,j do i=1,n do j=1,n h(i,j)=1d0/(i+j-1d0) end do end do end subroutine compute mex hilbert.f90

>> H=hilbert(10)

Outline

Turning Matlab code into C

 First we create a log_abs_fft_hilb.m function function result = log_abs_fft_hilb(n) result=log(abs(fft2(hilb(n))));  And then we run >> codegen log_abs_fft_hilb.m –args {uint32(0)}  This will produce a mex file that we can test.

>> A=log_abs_fft_hilb_mex(uint32(16)); >> B=log_abs_fft_hilb(16); >> max(max(abs(A-B))) ans = 8.8818e-16  We could have specified the type of 'n' in our matlab function function result = log_abs_fft_hilb(n) assert(isa(n,'uint32')); result=log(abs(fft2(hilb(n))));

Turning Matlab code into C

 Now we can also export a static library that we can link to: >> codegen log_abs_fft_hilb.m -config coder.config('lib') -args {'uint32(0)'}  This will create a subdirectory codegen/lib/log_abs_fft_hilb that will have the source files '.c and .h' as well as a compiled object files '.o' and a library 'log_abs_fft_hilb.a'  The source files are portable to any platform with a 'C' compiler (ie BlueStreak). We can rebuild the library on BlueStreak by running mpixlc –c *.c

ar rcs log_abs_fft_hilb.a *.o

Turning Matlab code into C

 To use the function, we still need to write a main subroutine that links to it. This requires working with matlab's variable types (which include dynamically resizable arrays) #include "stdio.h" #include "rtwtypes.h" #include "log_abs_fft_hilb_types.h" void main() { uint32_T n=64; emxArray_real_T *result; int32_T i,j; emxInit_real_T(&result, 2); log_abs_fft_hilb(n, result); for(i=0;isize[0];i++) { for(j=0;jsize[1];j++) { } printf("%f ",result->data[i+result->size[0]*j]); printf("\n"); Matlab type definitions Argument to Matlab function Return value of Matlab function Initialize Matlab array to have rank 2 Call matlab function Output result in column major order } emxFree_real_T(&result); Free up memory associated with return array } Exported code was 2x slower.

Turning Matlab code into C

 And here is another example of calling 2D fft's on real data void main() { int32_T q0; int32_T i; int32_T n=8; emxArray_creal_T *result; emxArray_real_T *input; emxInit_creal_T(&result, 2); emxInit_real_T(&input, 2); q0 = input->size[0] * input->size[1]; input->size[0]=n; input->size[1]=n; emxEnsureCapacity((emxArray__common *)input, q0, (int32_T)sizeof(real_T)); my_fft(input, result); for(i=0;isize[0];i++) { for(j=0;jsize[1];j++) { printf("[% 10.4f,% 10.4f] ", result->data[i+result->size[0]*j].re, result->data[i+result->size[0]*j].im); } printf("\n"); } } emxFree_creal_T(&result); emxFree_real_T(&input); for(j=0;jsize[1];j++ { for(i=0;isize[0];i++) { input->data[i+input->size[0]*j]=1.0 / (real_T)(i+j+1); } }

Turning Matlab code into C

 Exported FFT's only work on vectors of length 2 N  Error checking is disabled in exported C code  Mex code will have the same functionality as exported C code, but will also have error checking. It will warn about doing FFT's on arbitrary length vectors, etc...

 Always test your mex code!

Matlab code is not that different from C code

#include #include #include #include void main() { int n=4096; int i,j; double complex temp[n][n], input[n][n]; double result[n][n]; fftw_plan p; p=fftw_plan_dft_2d(n, n, &input[0][0], &temp[0][0], FFTW_FORWARD, FFTW_ESTIMATE); for (i=0;i