Julia parallel processing on PBS multiple nodes - julia

I am looking for a way to run simple parallel processes (one function run multiple times with different arguments, no communication between process) across multiple nodes in a PBS cluster.
Currently I am able to run it on a single node setting the number of threads with an environment variable in the PBS script, and using a for loop with #thread.threads
I have found references to clustermanager.jl, but no clear working example on how to use it on PBS.
For example: does addprocs_pbs in the file take care also of the script part, or do I still need to run a pbs script as usual, and this function is called inside the julia file?
This is the code structure I am using now. Ideally, it would stay more or less the same but parallel process could run across multiple nodes.
using JLD
include("path/to/library/with/function.jl")
seed = 342;
n = 18; # number of simulations
changing_parameter = [1,2,3,4];
input_file = "some file"
CSV.read(string(input_files_folder,input_file));
# I should also parallelise this external for loop
# it currently runs 18 simulations per run, and saves the results each time
for P in changing_parameter
Random.seed!(seed);
seeds = rand(1:100000,n)
results = []
Threads.#threads for i = 1:n
push!(results,function(some_fixed_parameters, P=P, seed=seeds[i]);)
end
# get the results
# save the results
JLD.save(filename,to_save,compress=true)
end

For distributed computing you normally need to use multiprocessing rather than multi-threading (although it is OK to have multi-threaded parallel processes if you need).
Hence, what you need to do is to use the ClustersManagers library to use the cluster manager to allocate processes for your Julia cluster.
I have been using Julia with Cray clusters using SLURM so not exactly PBS, however I since your question remain unanswered here is my working code. You will use addprocs_pbs that looks to have a very similar structure.
using ClusterManagers
addprocs_slurm(36,job_name="jobname", account="some_acc_name", time="01:00:00", exename="/lustre/tetyda/home/pszufe/julia/usr/bin/julia")
Once you add the worker processes all what remains is to use the Distributed package to orchestrate your workload.

Related

how can I parallelize scaling a matrix (using the Seurat package) across multiple computing nodes?

I am working on scaling and clustering a matrix of single-nucleus RNA sequencing data (genes x cells) using the R package Seurat. My data is large, containing 11,500 genes and ~1.5mil cells. Due to the size of the data, the fastest way to scale the matrix would be to parallelize over multiple nodes (each containing 40 cores). I am computing on the Niagara cluster and can request as many cores as needed. My problem is that I can't figure out a way to effectively parallelize my code. I tried using the future package (which is recommended by Seurat) but that confines my data to one node, which is not enough. I also tried Rmpi, however that seemed to assign the same task to all the spawned workers, which was to scale the whole matrix and took too long. I have read about future.batchtools, but haven't been able to figure out the syntax.
I'll include the code I used for Rmpi and future.batchtools. I would appreciate any troubleshooting/alternative strategies to try.
Rmpi:
Seuratdata<-readRDS("/path/seuratobject.RDS")
mpi.universe.size()
mpi.spawn.Rslaves(nslaves=60)
mpi.bcast.cmd( id <- mpi.comm.rank() )
mpi.bcast.cmd( np <- mpi.comm.size() )
mpi.bcast.cmd( host <- mpi.get.processor.name() )
myfunc(data){
all.genes<-rownames(x=data)
Seuratdata<-ScaleData(data, features=all.genes)
}
Seuratdata<-mpi.remote.exec(cmd=myfunc, data=Seuratdata)
saveRDS(Seuratdata, file = "scaled_Seuratdata.rds")
mpi.close.Rslaves()
mpi.exit()
future.batchtools:
plan(tweak(batchtools_slurm, workers=80,resources=list(ncpus = 1, memory=10*1024^3,
walltime=10*60*60, partition='batch'), template = "./slurm.tmpl"))
Seuratdata<-readRDS("/path/seuratobject.RDS")
all.genes<-rownames(x=data)
Seuratdata<-ScaleData(Seuratdata, features=all.genes)
saveRDS(Seuratdata, file = "scaled_Seuratdata.rds")
If you've got SSH permission between compute nodes, then you can submit a main job to scheduler:
$ sbatch --partiton=batch --ntasks=100 --time=10:00:00 --mem=10G script.sh
which then calls your script.R, e.g. Rscript script.R, that looks like:
library(future)
plan(cluster)
...
This will spin up 100 PSOCK cluster workers on whatever compute nodes Slurm has allocated the job. This works, because plan(cluster) defaults to plan(cluster, workers = availableWorkers()) and availableWorkers() picks up the information in SLURM_JOB_NODELIST set by Slurm. You can add:
print(parallelly::availableWorkers())`
at the top to log which compute nodes.
However, there are two limitations:
plan(cluster) requires SSH access to the hosts in order to spin up the parallel workers on those hosts
R has a maximum number of 125 workers this way, cf. https://github.com/HenrikBengtsson/Wishlist-for-R/issues/28.

Details of foreach + doMPI: Multiple foreach loops in sequence in the same script?

In R, I am using the package foreach with doMPI in a wrapper script run an external model many times in parallel on a cluster. Each MPI process gets one parameter point for which to execute the model.
However, to run this, there's also a bit of pre- and post-processing -- making some folders first, and aggregating the results at the end. This is also parallelisable, but not with the same number of jobs as the main model runs.
The way I've handled it is by using multiple subsequent foreach loops in the script. First one that makes the folders, then when that's ended, another to run the model. And this is where, despite consulting the documentation, I am a little green on how the doMPI package works in detail, and how MPI works more generally, I guess: Am I guaranteed that all MPI processes in loop 1 finish before any work is done in loop 2? This would be a necessity for the script logic. If not, are there any magic MPI commands I could use to enforce my desired behaviour? Does it make any sense to close and reopen the cluster, even? Or is that stupid? Like,
foreach (i1=1:N1) %dopar% {
loopy loop number 1
}
# Stop the MPI cluster and start it again:
closeCluster(cl)
cl = startMPIcluster()
registerDoMPI(cl)
foreach (i2=1:N2) %dopar% {
loopy loop number 2
}
Thanks!

multinode processing in R

I am trying to run R code on an HPC, but not sure how to take advantage of multiple nodes. The specific HPC I am using has 100 nodes and 36 cores per node.
Here is an example of the code.
n = 3600 ### This would be my ideal. Set to 3 on my laptop
cl = makeCluster(n, "SOCK")
foreach(i in 1:length(files), packages=c("raster","dismo")) %dopar%
Myfunction(files=files[i],template=comm.path, out = outdir)
This code works on my laptop and on the login of the HPC, but it is only using 1 node. I just want to make sure I am taking advantage of all the cores that I can.
How specifically do I take advantage of multiple nodes, or is it done "behind the scenes"?
If you are serious with HPC clusters, use MPI cluster, not SOCK. MPI is the standard for non-shared memory computing, and most clusters are optimized for MPI.
In case of HPC you also need a job-script to start R. There are several ways to start it, you may use mpirun, or invoke the workers directly from R. Scheduler will set up the MPI environment and R will figure out which nodes to use. Start small, with say 4 workers, and increase the number until you have reached the optimal level. Most tasks cannot efficiently use 3600 cpus.
Finally, if you are using tens of CPU-s over MPI, I strongly recommend to use Rhpc instead of Rmpi package. it uses more efficient MPI communication and gives you quite a noticeable speed boost.
On a TORQUE-controlled system I am using something along the lines:
Rhpc_initialize()
nodefile <- Sys.getenv("PBS_NODEFILE")
nodes <- readLines(nodefile)
commSize <- length(nodes)
cl <- Rhpc_getHandle(commSize)
Rhpc_Export(cl, c("data"))
...
result <- Rhpc_lapply(cl, 1:1000, runMySimulation)
...
Rhpc_finalize()
The TORQUE-specific part is the nodefile part, in this way I know how many workers to create. In the jobscript I start R just as Rscript >>output.txt myScript.R.
As a side note: are you sure myfun(files, ...) is correct? Perhaps you mean myfun(files[i], ...)?
Let us know how it goes, I am happy to help :-)

Best way to pass local variables to ipyparallel cluster

I'm running a simulation in an ipython notebook that is composed of seven functions that are dependent of each other, and requires 13 different parameters. Some of the functions are called within other functions to allow one function to run the entire simulation. The simulation involves manipulating two parameters for a total of >20k iterations. Two simulations can be run asynchronously. Since each iteration is taking ~1.5 seconds, I'm investigating parallel processing.
When I first tried ipyparallel, I got a global name not defined error. Makes sense that local objects can't been found a worker. In an effort to avoid spending quite a bit of time going down a rabbit hole, what would be the easiest way to pass a whole bunch of objects to all of the workers? Are there other gotchas to consider when using ipyparallel in this way?
There is a bit more detail in this related question, but the gist is: interactively defined modules resolve in the interactive namespace (__main__), which is different on the engine and client. You can send functions to the engine with view.push(dict(func=func, func2=func2)), in which case they will be found. The alternative is to define your functions in a module or package that you ensure is installed on all the engines.
For instance, in a script:
def bar(x):
return x * x
def foo(y):
return bar(y)
view.apply(foo, 5) # NameError on bar
view.push(dict(bar=bar)) # send bar
view.apply(foo, 5) # 25
Often when using IPython parallel from a notebook or larger script, one of the early steps is seeding the namespace of the engines:
rc[:].push(dict(
f1=f1,
f2=f2,
const=const,
))
If you have more than a few names to push this way, it might be time to consider defining these functions in a module, and distributing that instead.

Is it possible, in R parallel::mcparallel, to limit the number of cores used at any one time?

In R, the mcparallel() function in the parallel package forks off a new task to a worker each time it is called. If my machine has N (physical) cores, and I fork off 2N tasks, for example, then each core starts off running two tasks, which is not desirable. I would rather like to be able to start running N tasks on N workers, and then, as each tasks finishes, submit the next task to the now-available core. Is there an easy way to do this?
My tasks take different amounts of time, so it is not an option to fork off the tasks serial in batches of N. There might be some workarounds, such as checking the number of active cores and then submitting new tasks when they become free, but does anyone know of a simple solution?
I have tried setting cl <- makeForkCluster(nnodes=N), which does indeed set N cores going, but these are not then used by mcparallel(). Indeed, there appears to be no way to feed cl into mcparallel(). The latter has an option mc.affinity, but it's unclear how to use this and it doesn't seem to do what I want anyway (and according to the documentation its functionality is machine dependent).
you have at least 2 possibilities:
As mentioned above you can use mcparallel's parameters "mc.cores" or "mc.affinity".
On AMD platforms "mc.affinity" is preferred since two cores share same clock.
For example an FX-8350 has 8 cores, but core 0 has same clock as core 1. If you start a task for 2 cores only it is better to assign it to cores 0 and 1 rather than 0 and 2. "mc.affinity" makes that. The price is loosing load balancing.
"mc.affinity" is present in recent versions of the package. See changelog to find when introduced.
Also you can use OS's tool for setting affinity, e.g. "taskset":
/usr/bin/taskset -c 0-1 /usr/bin/R ...
Here you make your script to run on cores 0 and 1 only.
Keep in mind Linux numbers its cores starting from "0". Package parallel conforms to R's indexing and first core is core number 1.
I'd suggest taking advantage of the higher level functions in parallel that include this functionality instead of trying to force low level functions to do what you want.
In this case, try writing your tasks as different arguments of a single function. Then you can use mclapply() with the mc.preschedule parameter set to TRUE and the mc.cores parameter set to the number of threads you want to use at a time. Each time a task finishes and a thread closes, a new thread will be created, operating on the next available task.
Even if each task uses a completely different bit of code, you can create a list of functions and pass that to a wrapper function. For example, the following code executes two functions at a time.
f1 <- function(x) {x^2}
f2 <- function(x) {2*x}
f3 <- function(x) {3*x}
f4 <- function(x) {x*3}
params <- list(f1,f2,f3,f4)
wrapper <- function(f,inx){f(inx)}
output <- mclapply(params,FUN=calling,mc.preschedule=TRUE,mc.cores=2,inx=5)
If need be you could make params a list of lists including various parameters to be passed to each function as well as the function definition. I've used this approach frequently with various tasks of different lengths and it works well.
Of course, it may be that your various tasks are just different calls to the same function, in which case you can use mclapply directly without having to write a wrapper function.

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