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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E: Unable to locate package libcr-dev

I am trying to run a script (astrophysics stuff) using mpirun. I executed the command: mpirun -n 3 ./harm and got this error: /usr/local/bin/hydra_pmi_proxy: error while loading shared libraries: ...
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26 views

Invalid MIT-MAGIC-COOKIE-1 key when running MPI programs on Ubuntu 20.04

So i am trying to run a program using sst (SST-Simulator) which also uses MPI internally. The program runs fine but everytime i use "sst" i get this unwanted terminal output: Invalid MIT-...
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199 views

Can not install openmpi with intel oneapi

I have oneapi installed and environments set. mpiifort works as well as ifor -V, which returns the correct compiler version. I am trying to setup openmpi with itel compiler as it is required by ...
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0answers
89 views

OpenMPI - Update alternatives

I have troubles with openmpi crashing. The installed/repository version is "mpirun (Open MPI) 3.1.3". Consequently I have locally built a "mpirun (Open MPI) 4.1.0" which does not ...
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2answers
102 views

Multiprocess per single core

I have 6 cores and want to run 12 processes in the same time in parallel .. I'm using mpirun but sucked and confused in the option that I will use for multiprocess per core .. the command of 6 ...
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1answer
418 views

mpirun dosent work with openFoam (suddenly) [closed]

my mpirun on Ubuntu 20.04 dosent work anymore. I used it a few weeks back and it works good and well. I just wanted to use it a few minutes ago and it doesent work. I decompose the case first and then ...
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34 views

MPIRUN thread detection failed after upgrade

I have used MPI Fortran with UBUNTU for a long time. My DELL PC has 8 nodes and 16 threads. mpirun worked with -n 16 well and gave good results. However after an upgrade (?) it stopped doing this. Now ...
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121 views

libopen-rte.so.7 not found

I am trying to use openmpi. While i run, i face that output: mpirun: error while loading shared libraries: libopen-rte.so.7: cannot open shared object file: No such file or directory In this site, ...
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1k views

Problem with version of Open MPI

Scenario I am working with third party library TCLB to do my Master Thesis in the field of computational physic. As I know it depends on few other libraries and packages such as R, python2.7, ...
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43 views

mpirun in kubuntu 20.4 stucks

I installed kubuntu20.4.1 with openmpi 4.0.3-0 in two different computers. Compiling with mpif90 works, but mpirun stucks with no output in both systems. Even mpirun command without parameters stucks ...
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28 views

Issue with Install of Openfoam breaking mpi

I use several CFD programs on ubuntu. These are openfoam and SU2. Currently I am using more SU2. However, after the install of openfoam I noticed that mpirun command which i use to run SU2 cases did ...
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1answer
3k views

“Invalid MIT-MAGIC-COOKIE-1 key” message - MPI on Ubuntu 20.04

Running a program that uses MPI gives me an "Invalid MIT-MAGIC-COOKIE-1 key" warning on Ubuntu 20.04. I only recently upgraded; I was having no such issues when I was using 19.10. I want to ...
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227 views

Have problems about mpi after upgrade to 20.04

I upgraded to 20.04 from 19.10. On 20.04, I encounter the problem that CMAKE cannot find MPI, which was not a problem on 19.10. By using my own makefile, ld cannot find lmpi neither. It seems that at /...
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1answer
502 views

Installing libopnempi-dev on WSL with Ubuntu 20.04 failing

I'm currently testing the waters on developing software with C++ and MPI and need some help. I'm trying to install the openmpi headers on my machine on WSL with a Ubuntu 20.04. I can't seem to get ...
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381 views

Why doesn't Ubuntu 18.04 have latest OpenMPI packages? [duplicate]

I'm running WSL 18.04 I am trying to use EPOCH particle in cell code but get: Error: OpenMPI 2.1.1 detected. This contains a serious bug and should not be used. So i'm trying to update my OpenMPI. ...
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107 views

Unable to run mpi4py program on multiple machines

I have a very simple mpi python program from mpi4py import MPI comm = MPI.COMM_WORLD rank = comm.rank name = MPI.Get_processor_name() print('name: ', name, ' rank: ', rank) MPI.Finalize I have ...
2
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1answer
369 views

Xeon Phi and Ubuntu Server

I am looking at a surprising number of low-cost $100 Xeon Phi "cluster in a board" PCI cards on eBay. Can these be used from an Ubuntu Server host to dispatch numerical computing tasks, or ...
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448 views

MIT MAGIC KEY 1 error when running MPI programs compiled with openmpi 4.0.3 under Ubuntu 20.04

I am facing a weird issue. Whenever I run programs compiled with openmpi (version 4.0.3, the default on ubuntu 20.04 LTS), the following line is printed on the terminal Invalid MIT-MAGIC-COOKIE key. ...
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1answer
10k views

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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1answer
1k 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 libopenmpi-...
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3answers
582 views

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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1answer
322 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
59 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
108 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
1k 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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1answer
2k 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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1answer
147 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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0answers
1k 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
839 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
6k 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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550 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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298 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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150 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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0answers
404 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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76 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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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 ...
2
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1answer
278 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
618 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
145 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
6k 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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0answers
2k 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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0answers
59 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
923 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
810 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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0answers
422 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 ...
8
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1answer
31k 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
480 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
656 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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0answers
248 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 ...