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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MPICH installation

I searching on internet how to download the MPICH in my laptop, and something is going wrong... I don't know what is happening. I am using ubuntu 18.04. Someone know any good installation video, or ...
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Building configured OpenMPI 2.1.1-8 with debuild

I´m trying to build a configured version of OpenMPI-bin ver. 2.1.1-8 that has support of Slurm-manager. The steps I´ve taken are: $apt-get source openmpi-bin $dpkg-source -x openmpi-*.dsc $cd ...
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1answer
122 views

mpif.h not found error [install openmpi]

I was trying to install openpi on ubuntu. I have an Ubuntu 18.04.4 LTS (64 bit) desktop. I installed openmpi using sudo apt-get install openmpi-bin openmpi-common openmpi-doc libopenmpi2 ...
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3answers
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Is there any conflict between nohup and mpirun?

I want to start a big simulation on an ubuntu desktop computer. I have physical (not remote) access to this PC. This simulation may take some weeks. The command to start the process is: mpirun -np ...
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Using other mpirun environment variable [duplicate]

I'm running some code in Ubuntu and I have alredy installed every required package, my question is: How can I ask to my program to use the new MPI I have alredy installed echo $PATH /usr/local/sbin:/...
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1answer
100 views

Setting up custom modulefiles in environment-modules on ubuntu 18.04 LTS

Using environment-modules, I am trying to set up custom environment modules for installation of a software by using intel compiler and openmpi. I am not familiar with the method of creating a custom ...
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1answer
46 views

Machines with identical number of vCPUs, one gives MPI Error, the other does not

TLDR Two machines with the same number of vCPUs allow different number of MPI threads. Why? I am running two Ubuntu instances: Deep Learning Base AMI (Ubuntu 18.04) Version 20.2 (ami-...
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1answer
86 views

Deleted mpicc.openmpi file by mistake [duplicate]

In my infinite wisdom, I deleted the file 'mpicc.openmpi' file in my /usr/bin/ folder by mistake. I tried installing OpenMPI as well as GCC. But don't know how to get back to normalcy. Can anyone ...
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1answer
462 views

Fortran error: Cannot allocate memory

I am having some trouble with a code I have parallelized. The code is written in Fortran90, and I parallelized it using mpi. I won't post the code because its more than 10 thousand lines long. ...
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35 views

wanted to install g++ and mpirun but facing error to connect

i am installing Lammps.and after installation my lmp_mpi is not executable. mpirun is also not installed properlly. please help me i am beginner and need to install it for my academic purpose. ...
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195 views

Ubuntu 18.04.3 system hangs upon killing mpirun

Background: Earlier this year I started a new job for which I have a centrally managed workstation that dual-boots Ubuntu 18.0.4 LTS and Windows. I am a sudoer for the Ubuntu system. Although I've ...
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xeon processors hangs when using even half treads

We have an HPC system with 32 cores zeon processor and about 100 Gb RAM. The problem is that the system hangs or works very slowly even with using 16 cores and half RAM. Its OS is ubuntu 16.04 LTS. ...
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Building modified Openmpi-bin 3.1.2 with Ubuntu 18.10

I am trying to configure openmpi-bin to cope with slurm. This can be made using the --with-slurm when calling the configure-script in the source-dir. I have taken the following steps: apt-get source ...
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49 views

mpirun exit with no error

I am using specfem3d package. It is a parallel package. Everything is ok when I run my code alone in our PC. But when my friend also run his program, my runs will kill with no error. I run my program ...
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1answer
726 views

Downgrade openmpi v2.1.1 to v2.0.2

I have installed openmpi on ubuntu 18.04.2 LTS using $sudo apt-get install libopenmpi-dev $ mpirun -version mpirun (Open MPI) 2.1.1 How can I downgrade it to v2.0.2 Thank you!
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707 views

Problems in executing mpi with machinefile Ubuntu 18.04

following these guidelines MpichClusterUbuntu, I'm trying to execute my very first mpi program with a PC with Ubuntu 18.04.01 Server Edition and a laptop with Ubuntu 18.04.02 Desktop. Till step 11 of ...
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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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718 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
612 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
4k 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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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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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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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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305 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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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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1answer
2k 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
220 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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1answer
565 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
126 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
4k 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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1k 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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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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709 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
733 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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313 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
17k 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
416 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
607 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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227 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
2k 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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2answers
10k 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
72 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
1k 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
10k 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
860 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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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
972 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
63 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
65k 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-...