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Questions tagged [mpi]

MPI is the Message Passing Interface, a library for distributed memory parallel programming and the de facto standard method for using distributed memory clusters for high-performance technical computing. Questions about using MPI for parallel programming go under this tag; questions on, eg, installation problems with MPI implementations are best tagged with the appropriate implementation-specific tag, eg MPICH or OpenMPI.

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Package manager - is it possible to install packages with “variants”?

I am a data scientist coming from the macOS world planning to setup an Ubuntu server machine for data analysis. In the macOS world there are also package managers. My favorite one, MacPorts, allows ...
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17 views

No installation candidate for libopenmpi2

I've been trying to install openFOAM on 18.04 and get the following error after sudo apt-get install openfoam6: The following packages have unmet dependencies. openfoam6 : Depends: libopenmpi2 but ...
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28 views

Remove all previous version MPI and reinstall correctly it

I got some errors from mpi, mpich in UBUNTU 18.04, how can I remove all previous version MPI correctly. ||/ Name Version Architecture Description +++-==============-============-=======...
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1answer
31 views

Error while installing MPICH: C compiler cannot create executables

I am trying to install mpich 3.2.1 on ubuntu 16. When i execute ./configure --prefix=/opt/mpich 2>&1 | tee c.tx i get: checking for icc... no checking for pgcc... no checking for xlc... no ...
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1answer
82 views

Uninstall and install MPI

As far as I know, I cannot reinstall MPI from the terminal. For this reason, I want to know how I can repair MPI (uninstall and install MPI) using a security method in terminal? Thanks in Advance.
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30 views

How to set default mpicc

Recently, I have installed intel compiler, I loss the information for the set default mpicc, How can I set the following default in an easy way? CC variable not set, CC  = /usr/bin/mpicc CXX ...
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74 views

lam4-dev fails to install

Installing lam4-dev in a clean docker image with Ubuntu Bionic or Cosmic fails as below. Which dependency am I missing? Preparing to unpack .../lam4-dev_7.1.4-3.1build1_amd64.deb ... Unpacking lam4-...
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49 views

MPI: BLCR kernel module not present

how can I remove the bug of MPI in Ubuntu Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(474)...: MPID_Init(190)..........: channel initialization failed ...
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52 views

How to install ompi simultaneously with mpich?

I have mpich installed as the default MPI library. It is a part of my main project. Now I'd like to test some program that demands open-mpi be installed for compilation. I may not change something in ...
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114 views

Which MPI library are packages linked against? Open MPI?

Some packages in the Ubuntu repositories provide pre-compiled binaries of shared libraries (*.so). For example, the package fftw2 provides the FFTW library (version 2), including the MPI-related ...
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23 views

mpi exit code 65

I am running mpirun on a new (to me) refurbished workstation with 20 processors. I'm using Ubuntu 16.04 LTS. Occasionally it terminates with an exit code of 65 for no apparent reason. There is ...
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40 views

How could I switch OpenMPI library based on the gcc/g++ version?

Using the methods describe here I could easily switch gcc version with update-alternatives. Now, I have two versions of openmpi-3.1.1 that is compiled for each of them, namely: /home/user/me/.local/...
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1answer
340 views

Why does mpich not install correctly

I'm on 16.04. When I sudo apt-get install mpich and check the lib directory /usr/lib/mpich it contains the include dir as expected, but the lib directory within it: /usr/lib/mpich/lib is ...
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1answer
83 views

Open MPI Eclipse PTP -> failed to execute command: ompi_info , [closed]

I try to compile parallel programs using Open MPI 3.1 with Eclipse PTP 9.1.4 on Ubuntu 18.04. After building the project I follow the instructions of the Help-Eclipse Platform. The Step Run ...
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318 views

Using mpicc with update-alternatives

Since I am using CUDA 9.1 on Ubuntu 18.04, I need to use gcc-6 as suggested here. To deal with 2 versions of gcc (Ubuntu 18.04 comes with gcc-7), I have adopted the update-alternatives method as ...
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1answer
365 views

How to install debug symbol for OpenMPI on 16.04 [duplicate]

I couldn't find debug symbol in the official repo: $ apt-cache search openmpi gromacs-openmpi - Molecular dynamics sim, binaries for OpenMPI parallelization libblacs-openmpi1 - Basic Linear Algebra ...
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1answer
90 views

Computers hangs after running big script ubuntu mate 16.04

I am using ubuntu mate 16.04 and i recently ran a mpi script that was intended to overload my cpu. After running, and killing, the script I started running into issues: - A lot of simple commands (...
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2answers
2k views

mpirun: error while loading shared libraries: libopen-rte.so.12:

I have installed openmpi-bin and openmpi-common, and I get the following error when I run either mpirun or mpiexec: mpirun: error while loading shared libraries: libopen-rte.so.12 As I checked, this ...
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816 views

Error compilling program with makefile : undefined reference to symbol 'trunc@@GLIBC_2.2.5'

I am trying to compile a program on Linux+openmpi using a makefile but got this error: I have looked at answers to similar issues but can still fix it. /usr/bin/ld: outseis.o: undefined reference to ...
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39 views

GalIC-compilation and usage

Can anyone help me with GalIC code - compilation and usage, please. Downloaded from https://www.h-its.org/tap-software-en/galic-code/ In the README file, there are a list of non-standard libraries ...
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0answers
426 views

gfortran error :unrecognized option '-shared-intel'

I'm using a parallel fortran code that use MPI libraries (mpich or openmpi) and a "mpif90" compiler to run. When I try to compile the code, I encounter this comment: mpif90 -O3 -mcmodel=medium -...
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1answer
552 views

ubuntu 16.04 slurm srun failed with intel mpi?

I am trying to install slurm in a cluster running ubuntu 16.04. I am using intel mpi and the installation directory is located at the head node /opt/intel/impi_5.01. According to the slurm ...
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208 views

Problems compiling with openmpi after upgrade to v 1.10

I have been using openmpi to develop fortran90 parallel applications for a while. I usually install the default version of openmpi for developers from the repositories and it works out of the box. I ...
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1answer
10k views

Install OpenMPI from repository with GCC instead of Intel

I would like to install openmpi from repository and need to use it with GCC. The problem is I have installed intel libraries too and it causes problems like this: mpicc.openmpi --version mpicc....
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1answer
264 views

Ways to install programs in large clusters

For my internship I am currently setting up a cluster of laptops to run CFD applications using OpenFOAM. So far I've set it up installing SSH-client and NFS on both master and nodes. I've tested both ...
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1answer
465 views

Problems with mpirun (openmpi)

I have locally installed two openmpi versions on my cluster: openmpi-1.8.1 : when I run mpirun under this version, it gives me an error: librdmacm: Fatal: unable to open RDMA device librdmacm: Fatal:...
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186 views

How do I make h5py MPI-aware with the apt package system?

As I am trying to run parallel hdf5 with h5py and mpi4py, I am met with the following error: NameError: global name 'mpi4py' is not defined Googling suggests that this is because h5py is not "mpi-...
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0answers
1k views

Which Cluster Filesystem / Distributed Filesystem for Ubuntu 16.04

I have 5 servers, 16 threads running on each of them, producing a total of 80 files at the same time, which should finally be available for every other server in the same folder (it is a MPI ...
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1answer
7k views

How to check if the MPI already installed on my machine

I need to know how to check if MPI is already installed on my machine, and if not how much time it takes to be installed ?
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1answer
60 views

How to run a job in several machines that have Ubuntu as operating system

I need to run a job in several virtual machines exists in a specific cloud and I have the IP address for all of them and I configured the hostname for all of them. How to run a command in a network of ...
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1answer
769 views

Installing gfortran and mpich for a new Ubuntu user

I am a long-term Mac user who is considering switching to Ubuntu. I am not a system guru. I program in fortran and mpi for cfd applications on high-performance computers. I am considering ...
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2answers
1k views

How to set up a network of Ubuntu virtual machines via Virtualbox?

I am trying to create a network using 3 virtual Ubuntu machines (master, slave1, slave2). I hope posting this question here is acceptable. I'm not sure if the problem lies within Virtualbox ...
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1answer
7k views

Problem with mpiCC

I just downloaded openmpi 1.10.2 from https://www.open-mpi.org/software/ompi/v1.10/ and installed it on my ubuntu 14.04LTS(./configure then make all install). But when I try to use mpiCC to compile a ....
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1answer
550 views

Trouble linking libraries in FFTW

This error happens when I try to execute a Makefile: /usr/bin/ld: cannot find -lrfftw_mpi /usr/bin/ld: cannot find -lfftw_mpi /usr/bin/ld: cannot find -lrfftw collect2: error: ld returned 1 exit ...
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mpich2 installation error [duplicate]

i'm actually having a problem while installing mpich2. i'm using latest Ubuntu 14.04 LTS on 64 bit computer.i followed the steps in https://help.ubuntu.com/community/MpichCluster and https://...
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1answer
1k views

MPI Terminal Help manual..!

Is there is any possible way to get a developer manual help for the MPI commands in terminal. i tried mpi --help and mpich --help (because the mpi version command looks like mpich --version)but no use....
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1answer
686 views

ssh keeps asking for a password

I am trying to set up an MPI cluster, following Setting Up an MPICH2 Cluster in Ubuntu tutorial. At the end of step 7, it says that I should not receive a password request, which unfortunately is not ...
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0answers
53 views

Beowulf cluster hard disk problem

I built a Beowulf cluster using the message passing interface (MPI). When I send a message that contains the path for a specific file in the slave node, the slave can't access its local hard disk to ...
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1answer
56k views

installing openmpi on Ubuntu 14.04 [duplicate]

I am trying to instlal OpenMPI on my Ubuntu 14.04 LTS following this guide When I run the command sudo apt-get install -y autotools-dev g++ build-essential openmpi1.5-bin openmpi1.5-doc libopenmpi1.5-...
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2answers
149 views

missing library when running make?

I am trying to install a program on my machine (running Ubuntu 12.04), but I get the following error when I run make: Starting build... Working Directory : /home/laptop/mplabs_test Build Type :...
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1answer
444 views

Problem running octave with openmpi in juju

I am attempting to use openmpi from octave to start other octave instances on remote machines. When I run the scrip that should start the various processes, it complains about libraries being out of ...
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2answers
5k views

“cannot find -lmpi*” when compiling openmpi code

I had try to install openmpi 1.8.1 from the source code at Unbuntu 14.04 server. I would like to use mpi for large scale calculation on single machine with multi cores. The simple "Hello world" test ...
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2answers
2k views

Multiple hosts password problem using mpirun

So I am running a parallel c++ program by sending jobs from an Ubuntu machine to remote hosts (also Ubuntu), the command line I use on the terminal is something like: mpirun -np 4 --host host1,host2 ...
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2answers
318 views

mpdboot and mpdtrace gives Alarm Clock as a result

I try to execute mpdboot -n 2 -f /home/user/mpd.hosts and then mpdtrace However, both of them return: Alarm clock I have a virtual machine with mpd installed on it. I copied the .vdi (the hard ...
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1answer
165 views

Where to find openmpi-doc on my ubuntu 12.04?

I installed openmpi by apt-get install openmpi-doc. I think it is some folder that contain the document on openmpi? where can I find it? I just switched from Windows to Bbuntu, so a lot of things are ...
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1answer
1k views

Mpi file not recognized?

I am trying to compile some mpi files on Ubuntu I installed the library using this code sudo apt-get install libcr-dev mpich2 mpich2-doc and tried to compile this simple hello world program /* C ...
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1answer
9k views

Unable to locate package libopenmpi-dev on 12.04

While trying to install open mpi on my Ubuntu 12.04, I am getting error unable to locate package libopenmpi-dev. What to do? $ sudo apt-get install libopenmpi-dev openmpi-bin openmpi-doc unable to ...
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2answers
11k views

What is the difference MPI vs OpenMP? [closed]

I just want to know the differences between MPI vs OpenMP for a school project I have. I'm new on Ubuntu and i can't find a trustworthy website. I tried so many now. Please help me!