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
Related
I have installed openmpi and slurm in two nodes. i want to use slurm to run mpi jobs. When i use srun to run non-mpi jobs, everything is ok. However, i got some errors when i use salloc to run mpi jobs. Environment and codes are as follows.
Env:
slurm 17.02.1-2
mpirun (Open MPI) 2.1.0
test.sh
#!/bin/bash
MACHINEFILE="nodes.$SLURM_JOB_ID"
# Generate Machinefile for mpich such that hosts are in the same
# order as if run via srun
#
srun -l /bin/hostname | sort -n | awk '{print $2}' > $MACHINEFILE
source /home/slurm/allreduce/tf/tf-allreduce/bin/activate
mpirun -np $SLURM_NTASKS -machinefile $MACHINEFILE test
rm $MACHINEFILE
command
salloc -N2 -n2 bash test.sh
ERROR
salloc: Granted job allocation 97
--------------------------------------------------------------------------
An ORTE daemon has unexpectedly failed after launch and before
communicating back to mpirun. This could be caused by a number
of factors, including an inability to create a connection back
to mpirun due to a lack of common network interfaces and/or no
route found between them. Please check network connectivity
(including firewalls and network routing requirements).
--------------------------------------------------------------------------
salloc: Relinquishing job allocation 97
Anyone can help? Thanks.
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.
I am trying to run a compiled program that is supposed to be running on multiple processors. But with the same data, sometimes this program runs in parallel and sometimes it won't (with the identical PBS script file!). I am suspecting that something is wrong with some of the compute nodes that won't let it run on parallel (I don't get to choose the compute node I want). How can I troubleshoot if this is a bug in the program or it is problem with the compute node?
As per the sys admin's adivce, I am using ulimit -s 100000, but this don't change anything. Also, this program is not an mpi program (runs only on a single node, with multiple processors).
The code that I run is as follows:
quorum_error_correct_reads -q 68 \
--contaminant=/data004/software/GIF/packages/masurca/2.3.0rc1/bin/../share/adapter.jf \
-m 1 -s 1 -g 1 -a 3 --thread=32 -w 10 -e 3 \
quorum_mer_db.jf aa.renamed.fastq ab.renamed.fastq ac.renamed.fastq ad.renamed.fastq ae.renamed.fastq af.renamed.fastq ag.renamed.fastq \
--no-discard -o pe.cor --verbose
Thanks for any advice you can offer. I will greatly appreciate your help!
PS: I don't have sudo access.
EDIT: I know it is supposed to be using multiple processors because, when I SSH into the node and do top -c I can see (above command) sometimes running like 3200 % CPU (all the time) and sometimes only 100 % CPU all the time. This is the only step involved and there are no other sub-process within this program. Also, I am using HPC, where I submit the job to a compute node, each with 32 procs, 512GB RAM.
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.