Since the beginning of November, I'm stuck in to run a parallel job in a Linux cluster. I already search A LOT on the internet searching for information but I simply can't progress. When I start to search for parallelism in R using cluster I discovered the Rmpi. It looked quite simple, but now I don't now more what to do. I have a script to send my job:
#PBS -S /bin/bash
#PBS -N ANN_residencial
#PBS -q linux.q
#PBS -l nodes=8:ppn=8
cd $PBS_O_WORKDIR
source /hpc/modulos/bash/R-3.3.0.sh
export LD_LIBRARY_PATH=/hpc/nlopt-2.4.2/lib:$LD_LIBRARY_PATH
export CPPFLAGS='-I/hpc/nlopt-2.4.2/include '$CPPFLAGS
export PKG_CONFIG_PATH=/hpc/nlopt-2.4.2/lib/pkgconfig:$PKG_CONFIG_PATH
# OPENMPI 1.10 + GCC 5.3
source /hpc/modulos/bash/openmpi-1.10-gcc53.sh
mpiexec --mca orte_base_help_aggregate 0 -np 1 -hostfile ${PBS_NODEFILE} /hpc/R-3.3.0/bin/R --slave -f sunhpc_mpi.r
And this is the beginning of my R program:
library(caret)
library(Rmpi)
library(doMPI)
cl <- startMPIcluster()
registerDoMPI(cl)
So here is my questions:
1- Is this way I should initialize the processes (i.e. using starMPIcluster whitout a parameter and using at the command line -np 1)?
2- Why when I use this commands the MPI complains with it's frase?
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process....
OBS: He said that for all the 64 processes (because there are 8 nodes with 8 cpus and I'm creating 63 processes)
3- Why when I use this commands on a machine of 60 CPU's he just spawn two workers?
Finally, I got it!
To run a parallel program in R using the Rmpi in a cluster you need to configure the job script according to the system. Next on the command line:
mpiexec --mca orte_base_help_aggregate 0 -np 1 -hostfile ${PBS_NODEFILE} /hpc/R-3.3.0/bin/R --slave -f sunhpc_mpi.r
You have to modify to:
mpiexec -np NUM_PROC -hostfile ${PBS_NODEFILE} /hpc/R-3.3.0/bin/R --slave -f sunhpc_mpi.r
On the R code, you must not detail anything 'startMPIcluster()' So, the code will exactly as I wrote above.
Related
I am trying to test a script I have developed locally on an interactive HPC node, and I keep running in this strange issue that mclapply works only on a single core. I see several R processes spawned in htop (as many as the number of the cores), but they all occupy only one core.
Here is how I obtain the interactive node:
srun -n 16 -N 1 -t 5 --pty bash -il
Is there a setting I am missing? How can I make this work? What can I check?
P.S. I just tested and the other programs that rely on forking to do parallel processing (say pigz) are afflicted by the same issue as well. Those that rely on MPI and messaging work properly, it seems.
Yes, you are missing a setting. Try:
srun -N 1 -n 1 -c 16 -t 5 --pty bash -il
The problem is that you are running the parallel commands within a bash shell that is allocated on a single core, so the bash process is spawned on only one of the cores requested by srun.
Otherwise, you can first allocate your resources using salloc and once you obtain them run your actual command. For instance:
salloc -N 1 -n 1 -c 16 -t 5
srun pigz file.ext
I'm trying to get a code to run in parallel using mpirun, in the PBS queue. The script I'm using is below:
#!/bin/bash
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=4
#PBS -l walltime=4:10:00
#PBS -N job
#PBS -j oe
/usr/bin/mpirun -np 4 a.out
where a.out is the executable. The problem is that the mpirun I'm using is the one on the main node of the cluster. I want to use an mpirun installed on my own compute nodes, which is also in /usr/bin/mpirun.
I tried just copying mpirun in the folder and running with the line
./mpirun -np 4 hello.out
and that worked for some simple "hello world" program, but it doesn't work for the more complex code. It also works from my compute node if I just type
/usr/bin/mpirun -np 4 a.out
How do I use the mpirun of the compute node in the PBS script? I simply cannot use the stuff on the main node because it's an old linux version I'm not ready to change.
I have PBS command something like this
#PBS -N marcell_single_cell
#PBS -l nodes=1:ppn=1
#PBS -l walltime=20000:00:00
#PBS -e stderr.log
#PBS -o stdout.log
# Specific the shell types
#PBS -S /bin/bash
# Specific the queue type
#PBS -q dque
#uncomment this if you want to debug the process
#set -vx
cd $PBS_O_WORKDIR
ulimit -s unlimited
NPROCS=`wc -l < $PBS_NODEFILE`
#export PATH=$PBS_O_PATH
echo This job has allocated $NPROCS nodes
echo Cleaning old files...
rm -rf *.png *.plt *.log
echo Cleaning success
/opt/Lib/openmpi-2.1.3/bin/mpirun -np $NPROCS /scratch4/marcell/CellMLSimulator/bin/CellMLSimulator -ionmodel grandi2010 -solverType CVode -irepeat 4 -dt 0.01
gnuplot -p plotting.gnu
It got error something like this, thrown by the PBS error log.
/var/spool/torque/mom_priv/jobs/6265.node01.SC: line 28: gnuplot: command not found
I've already make sure that the path of GNUPlot is already been added to the PATH environment variable.
However, the strange part is, if I interchange the sequence of command, like gnuplot first and then mpirun, there isn't any error. I suspect that some commands after mpirun need some special configs, but I dunno how to do that
Already following this solution, but no avail.
sleep command not found in torque pbs but works in shell
EDITED:
it seems that the before and after mpirun still got error. and this is the which result:
which: no gnuplot in (/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/pgi/linux86-64/9.0-4/bin:/opt/openmpi/bin:/usr/kerberos/bin:/prog/tools/grace/grace/bin:/home/prog/ansys_inc/v121/fluent/bin:/bin:/usr/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64:/scratch7/feber/jdk1.8.0_101:/scratch7/feber/code/apache-maven/bin:/usr/local/bin:/scratch7/cml/bin)
It's strange, since when I try to find the gnuplot, there is one in the /usr/local/bin
ls -l /usr/local/bin/gnuplot
-rwxr-xr-x 1 root root 3262113 Sep 18 2017 /usr/local/bin/gnuplot
moreover, if I run those commands without PBS, it seems executed as I expected:
/scratch4/marcell/CellMLSimulator/bin/CellMLSimulator -ionmodel grandi2010 -solverType CVode -irepeat 4 -dt 0.01
gnuplot -p plotting.gnu
It's very likely that your system has different "login/head nodes" and "compute nodes". This is a commonly used practice in many supercomputing clusters. While you build and launch your application from the head node, it gets executed on one or more compute nodes.
The compute nodes can have different hardware and software compared to the head nodes. In your case, gnuplot is installed only on the head node, as you can see from the different outputs of which gnuplot. To solve this, you have three approaches:
Request the system administrators to install gnuplot on the compute nodes.
Build and install your own version of gnuplot in a file-system accessible from the compute nodes. It could be your home directory or somewhere else depending on your cluster. In general, the filesystem where your application is will be available. In your case, anywhere under /scratch4/marcell/ would probably work.
Run gnuplot on the head node after the MPI jobs finish as a post-processing step. PBS/Torque does not provide a direct way to do this. You'll need to write a separate bash (not PBS) script to do this.
I am doing MPI programming on a cluster with 8 nodes and each having a Intel Xeon hexcore processor. I need three processors for my mpi code.
I submit the job using qsub. When I check on which processors the job is running using "qstat -n" it says something like cn004/0*3 .
So does this mean it is running it on only one processor ??
Because it is not speeding up than when I use a single processor(This is when the domain size is the same for both cases)
The script i use for submitting is as follows
#! /bin/bash
#PBS -o logfile.log
#PBS -e errorfile.err
#PBS -l cput=40:00:00
#PBS -lselect=1:ncpus=3:ngpus=3
#PBS -lplace=excl
cat $PBS_NODEFILE
cd $PBS_O_WORKDIR
mpicc -g -W -c -I /usr/local/cuda/include mpi1.c
mpicc -g -W mpi1.o -L /usr/local/cuda/lib64 -lOpenCL
mpirun -np 3 ./a.out
"qstat -n" it says something like cn004/0*3.
Q: So does this mean it is running it on only one processor ??
The short answer is "no". This does not mean that it runs on one processor.
"cn004/0*3" should be interpreted as "The job is allocated three cpu cores. And if we were to number the cores from 0 to 5 then the cores allocated would have numbers 0,1,and 2".
If another job were to run on the node it would receive the next three consecutive numbers "3,4, and 5". In the qstat -n output this would look like "cn004/3*3".
You use the directive place=excl to ensure that other jobs would not get the node, so essentially all the six cores are available.
Now for your second question:
Q: it is not speeding up than when I use a single processor
In order to answer this question we need to know if the algorithm is parallelized correctly.
I'm trying to run a MPI job on a cluster with torque and openmpi 1.3.2 installed and I'm always getting the following error:
"mpirun was unable to launch the specified application as it could not find an executable:
Executable: -p
Node: compute-101-10.local
while attempting to start process rank 0."
I'm using the following script to do the qsub:
#PBS -N mphello
#PBS -l walltime=0:00:30
#PBS -l nodes=compute-101-10+compute-101-15
cd $PBS_O_WORKDIR
mpirun -npersocket 1 -H compute-101-10,compute-101-15 /home/username/mpi_teste/mphello
Any idea why this happens?
What I want is to run 1 process in each node (compute-101-10 and compute-101-15). What am I getting wrong here?
I've already tried several combinations of the mpirun command, but either the program runs on only one node or it gives me the above error...
Thanks in advance!
The -npersocket option did not exist in OpenMPI 1.2.
The diagnostics that OpenMPI reported
mpirun was unable to launch the specified application as it could not
find an executable: Executable: -p
is exactly what mpirun in OpenMPI 1.2 would say if called with this option.
Running mpirun --version will determine which version of OpenMPI is default on the compute nodes.
The problem is that the -npersocket flag is only supported by Open MPI 1.3.2 and the cluster where I'm running my code only has Open MPI 1.2 which doesn't support that flag.
A possible way around is to use the flag -loadbalance and specify the nodes where i want the code to run with the flag -H node1,node2,node3,... like this:
mpirun -loadbalance -H node1,node2,...,nodep -np number_of_processes program_name
that way each node will run number_of_processes/p processes, where p the number of nodes where the processes will be run.