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Questions tagged [mpi]

53 questions
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Parallel vs Distributed vs Traditional File system

I am trying to understand the differences between these three file system at a very basic level. Distributed FS: HDFS Parallel FS : Lustre Traditional FS : ext4/ext3/ NTFS/FAT etc. I want to know what are the basic conceptual differences…
puneet336
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6
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MPI program causes "invalid MIT-magic-cookie-1 key" warning to show

I'm setting up a new development environment that requires high performance computing. I installed mpi and openmpi on this new machine (Ubuntu 20.04), and I wrote the following code in python as a sort of "hello world" style test. from mpi4py import…
SoyBison
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`mpirun -np N`: what if `N` is larger than my physical cores?

Say I have a 4-core workstation, what would Linux (Ubuntu) do if I execute mpirun -np 9 XXX Will 9 run immediately together, or they will run 4 after 4? I suppose that using 9 is not good, because the remainder 1 will make the computer confused,…
Daniel
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2 answers

Run mpirun and ssh-add remotely on the same session

I am developing a program that is running on multiple machines using MPI. I have machines on Amazon EC2 where I can start mpirun from one of them (the master). Everything works as I expect if I ssh to the master machine, then trigger ssh-agent and…
0xFF
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4
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1 answer

SSH/OpenMPI: Permission Denied with mpirun but fine with ssh

I am trying to setup a cluster of four nodes (all running Fedora 22) with OpenMPI. On the master node, I've created a password-less key (~/.ssh/id_dsa) and copied ~/.ssh/id_dsa.pub to each of the three slave nodes' ~/.ssh/authorized_keys. So, from…
davewy
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4
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1 answer

mpirun fails to recognize program in $PATH

Somehow mpirun fails to acknowledge my $PATH. The program PyroDist, that I have in $PATH, works: $ PyroDist Can't find asked option -in PyroDist - pairwise distance matrix from flowgrams -in string flow file name -out stub …
Martin
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1 answer

mpirun with ssh and X11

At present we're trying to write a program which uses mpirun to launch multiple X11 clients. If the programs are text-only, then using the following command, we can run proceses on a list of computers: mpirun -np 4 --hostfile hostlist date Here…
speciousfool
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3
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1 answer

Openmpi installation

I have just started to use Linux Mint for academic reasons and ran into an error as I was trying to install openmpi-2.0.1. I am getting following error as I am trying to make check make[4]: Leaving directory…
Kuljeet Keshav
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3
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2 answers

How to give all computers connected to a network switch internet?

I want to make a cluster computer out of Raspberry Pis (with a network switch/hub, and mpiexec), and have run into the issue about how they will get internet access. Since it would be a hassle for all of them to have their own adapters and cables, I…
Flare Cat
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3
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1 answer

mpi.h not found

I tried to compile the Hello World program in C, inside Eclipse PTP, but it gives me an error related to mpi.h. I have included /usr/local/include and /usr/local/lib in my paths, and also tried running a search with find / -name mpi.h. I still get a…
Dalia Shouman
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3
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1 answer

Using MPI with a .sh script?

I have a runPR.sh script as below DIR=/directory/buildagain/bin/Project FILELIST=$1 while read FILE do echo "Processing ${FILE}..." ./makeInp.sh ${FILE} ${FILE} >INP/${FILE}.inp ${DIR} -PR INP/${FILE}.inp done < ${FILELIST} For…
user4352158
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Why I got error: `error while loading shared libraries: libmpich.so.3`?

I installed mpich-3.0.4 not in a default location. I installed it based on the mpich installer's guidance. However when I try to run: mpiexec -n 4 -f machinefile ./mpich-3.0.4/examples/cpi It gives me an error, which…
Santosa Sandy
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2
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3 answers

Kill a nohup mpi process

I have started a program in parallel using the command: nohup mpirun -7 mylongprogram.py & I now want to terminate the program. When I want to kill the process by the command: kill -9 I see that another process with a different PID…
gora
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1 answer

mpd daemon prematurely ending jobs

I am trying to configure mpirun and mpiexec to run software called Materials Studio on a 1 node, 2 processor, 12 core cluster. The submission scheme is PBS. I had everything set up properly (with some help) and where I could submit jobs and they…
sjensen
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2
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1 answer

Very new to slurm. How to get slurm to run multiple core jobs on my linux cluster?

I've been trying to move some existing processes to a revamped linux cluster that now runs on slurm. I thought I have it done, but my problem now is trying to get multiple cores to run. Here is my submission script. #!/bin/bash # #SBATCH…
ted y
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