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MPI program doesn't start right away (Fedora)

sorry I'm not sure if this is better asked here or Stack Overflow, but this is with a fresh Fedora 39 install, and I've tested it with the packages (installed via dnf) mpich-devel, openmpi-devel and (...
tmph's user avatar
  • 111
4 votes
0 answers
377 views

TCP/IP Network in Ubuntu 22.04 Becomes Unresponsive After Heavy Network Load from MPI Program

I have two identical servers running Ubuntu 22.04.3 LTS. Both systems have 2x AMD 9654 CPUs with 192 total cores and 512 GB of RAM. Each server has two 10G ethernet ports built into the motherboard. ...
Michael S. Emanuel's user avatar
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0 answers
35 views

OpenMPI built from source not working on a raspberry pi + mac cluster

I am trying to use macbook m1 as the master in a cluster of 4 raspberry pies (workers, connected to each other with a switch which is connected to my home router to which the mac is connected via wifi)...
Coddy's user avatar
  • 113
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0 answers
107 views

How to find out MPI vendor

How do I find out what MPI (MPICH, OpenMPI, etc) is installed? MPI location (returned by which mpiexec) is cryptic and does not hint a vendor. mpiexec --version returns mpiexec version 1.1.8 mpiexec -...
user2052436's user avatar
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1 answer
108 views

mpirun kill parallel processes when lose internet connection ssh

When I'm connected via ssh and are parallel processes running and it loses the internet connection all parallel processes. When I reconnect I find the following message in log file: -------------------...
gvd's user avatar
  • 111
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0 answers
148 views

MPI job stopped with ssh disconnected

I have been using MPI in THCP diskless sever. However, when I run jobs with MPI, sometimes the process die because of SSH disconnected. client_loop: send disconnect: Broken pipe There is no error or ...
JeongYeong Kim's user avatar
0 votes
1 answer
316 views

calling vim with mpiexec says "Warning: Output is not to a terminal / Warning: Input is not from a terminal"

My question is a bit technical. For specific reason, I need to call vim after mpiexec. Example : mpiexec -n 1 vim mytext.txt But this gives the following warning message: Vim: Warning: Output is not ...
Kiven Jecquas's user avatar
0 votes
1 answer
452 views

Calling mpirun from bash file does not recognize $VAR format...?

While trying to run the following .sh file I get an error from mpirun: The file: (additional python config omitted for brevity) NB_MPI_WORKERS=2 SEED=0 mpirun --n ${NB_MPI_WORKERS} python start.py --...
Mandias's user avatar
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0 answers
2k views

Problem with intel MPI

I just installed intel oneApi and the intel MPI was included in it. I can now compile my fortran code with mpiifort, but when I try to run it with intel mpirun, with just `` it throws this error. ...
Eular's user avatar
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94 views

`mpirun -n 2 ./a.x`, the two processes was stuck by epoll_wait, why?

I run a mpi progrem with mpirun -n 2 ./a.x. However, these two processes was stuck. And it is always get stuck and seldom(actually only once) pass through. I find follow information by strace and ...
Runfeng Jin's user avatar
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0 answers
84 views

Slurm 18 allocates MPI jobs to the same CPUs on the node

For some reason when launching an mpi job with SLURM on CentOS8 cluster, slurm ties mpi processes to CPUs always starting from CPU0. Say there are 128 CPU cores on a compute node. I launch mpi job ...
Alex P's user avatar
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2 votes
1 answer
243 views

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 ...
ted y's user avatar
  • 21
0 votes
2 answers
88 views

how to manage %files section in spec without environment variables

I am creating a package for a software using MPICH. The binaries must be installed on the mpich directory. This directory depends on the mpich version (/usr/lib64/mpich-3.2/ or /usr/lib64/mpich/). For ...
Bruno Guerraz's user avatar
2 votes
1 answer
6k views

nohup ends when I close the SSH terminal and doesn't show up on ps/job when running

I have an AWS EC2 Ubuntu 20.04 instance, accessed via puTTY SSH. Running a Python process via OpenMPI through the following command on non root: nohup mpirun python3 job.py When the shell is open it ...
Sad CRUD Developer's user avatar
0 votes
1 answer
354 views

Debian : MPI code - Intel compiler - [Hardware Error]: Unified Memory Controller Error: DRAM ECC error

When running an executable compiled with intel mpiicc, I get, after 30 minutes of running, the following errors : kernel:[29585.573874] [Hardware Error]: Corrected error, no action required. Message ...
youpilat13's user avatar
0 votes
1 answer
2k views

Install multiple MPI libraries and switch between them on Ubuntu

For educational purposes I'd like to set up several MPI libraries, e.g. OpenMPI, MPICH, and Intel MPI along with different backend compilers (gcc, clang, icc) on the same machine running Ubuntu 18.04....
mentalmushroom's user avatar
6 votes
0 answers
3k views

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 ...
SoyBison's user avatar
1 vote
1 answer
313 views

Combining gnu parallel and mpirun: how to take care of the max number of cores?

I have a machine with 32 cores where a I want to run some mpi jobs with a variable number of cores (this is because the problem requires that). Is there a way to make gnu parallel aware of the number ...
iluvatar's user avatar
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2 votes
1 answer
1k views

How to distribute cores using mpirun

I am trying to execute two processes at the same time on a VPS which has 16 cores and I'd like each job to utilize 8 cores each and max out the number of available cores. So I thought that I could ...
gusgrave's user avatar
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0 votes
0 answers
95 views

How RAM is distributed among processes in MPI?

For example for a 4GB RAM and 2 processes, each process will take 2 GB of memory?
Arvanitis's user avatar
0 votes
1 answer
1k views

How to understand PBS output "mem" and "vmem" keep the same when the task is x-fold increased with mpirun -np x task

Here is a simple experiment I tried: Given a task called "sim.exe" which doing a model simulation, I then use MPI to launch x "sim.exe" simultaneously on one node (shared memory system). I have tried ...
LouisXW's user avatar
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0 answers
798 views

ORTE_ERROR_LOG, what does it mean?

1 [node18:02644] [[37701,0],0] ORTE_ERROR_LOG: File open failure in file ras_tm_module.c at line 142 2 [node18:02644] [[37701,0],0] ORTE_ERROR_LOG: File open failure in file ras_tm_module.c at line ...
Prasad Mani's user avatar
1 vote
1 answer
660 views

NFS server seems to kick diskless nodes off

I'm currently helping setting up a lab that will use diskless nodes for some MPI and CUDA computing. The distribution of choice is CentOS 7. To set up the diskless nodes I've followed the guide here. ...
user-2147482617's user avatar
0 votes
0 answers
244 views

Reset gfortran / MPI installation on Ubuntu 16.04

It seems that an anaconda update has messed up my gfortran / MPI installation. I have tried reinstalling both gfortran and openmpi. Compilation of my code is successful, but on run time I get ...
painfulenglish's user avatar
0 votes
1 answer
2k views

slurm: srun & sbatch different performance with the same settings

In a slurm system, when I use srun command to run the program. It runs very slow and seems like only one processor works. srun --pty -A free -J test -N 1 -n 1 -c 1 mpirun -np 16 $FEAPHOME8_3/...
Rilin Shen's user avatar
1 vote
0 answers
253 views

Configuration of Hostfiles on Master node and Slave nodes on Linux system for MPI job run

I am new to MPI. I an using MPICH 3.2 to parallelize my programs. Currently I am trying to run some basic available programs on different physical nodes. I am using the poisson_mpi.f90 to get this ...
Soumyaranjan's user avatar
0 votes
0 answers
131 views

high performance computing cluster setup

In my lab, we have several servers used for the simulation programs, but they worked independently. Now I want to combine them to become a cluster using MPICH to make them communicate. But there ...
zmwang's user avatar
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1 vote
3 answers
2k views

Install MPICH on CentOS error could not determine the size of a Fortran INTEGER

I followed the this installation guide to install MPICH on my machine. I got the following error while configure: configure: error: Unable to configure with Fortran support because configure could ...
Abolfazl's user avatar
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1 vote
0 answers
1k views

install Open MPI on CentOS 6.8 "requires a C99 compiler error"

I am trying to install Open MPI 2.1.0 version on our CentOS machine. I followed these steps: tar -xvf openmpi-* cd openmpi-* ./configure --prefix="/home/$USER/.openmpi" *** C compiler and ...
Abolfazl's user avatar
  • 123
1 vote
0 answers
1k views

MPICC with different versions of GCC

I need to use MPICH with different versions of GCC. Is it possible to change GCC without having to recompile MPI? Example I'd like to do something like this: mpicc --compiler=/usr/bin/gcc-5 Is it ...
Eenoku's user avatar
  • 1,195
1 vote
0 answers
95 views

Problem executing HPCC and IMB benchmarks on IBM platform HPC

I want to execute the IMB 2017 and HPCC 1.5.0 benchmarks on our HPC to be sure that all is configured correctly. we have 32 compute nodes, each one with 16 cores and 32GB of memory. each node have a ...
Wodel's user avatar
  • 31
3 votes
1 answer
3k views

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]: ...
Kuljeet Keshav's user avatar
3 votes
2 answers
4k views

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 ...
Flare Cat's user avatar
  • 165
4 votes
2 answers
24k views

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 ...
Dalia Shouman's user avatar
4 votes
1 answer
6k views

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 ...
davewy's user avatar
  • 153
7 votes
2 answers
6k views

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 ...
puneet336's user avatar
  • 188
3 votes
1 answer
9k views

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 ...
user4352158's user avatar
2 votes
4 answers
449 views

Does it make a difference (e.g. performance-wise) if I execute a command from a bash script (vs the command line)?

Is there any difference between the following (e.g. performance-wise): $ make && cp bin/myexecutable inputfile.txt $workdir && cd $workdir $ <series of sed commands to modify ...
nathanielng's user avatar
0 votes
1 answer
723 views

How to use programs with MPI?

Is it possible to use programs with MPI for example blender? Is it a mpi program by only adding the source file "mpi.h" or is there any way to simply convert an existing program for the use with mpi? ...
rudolf97's user avatar
  • 141
1 vote
0 answers
973 views

permission denied for mpicc

I am trying to install and make[1]: /usr/bin/mpicc: Permission denied make[1]: *** [molmatch.o] Error 1 make: *** [all] Error 2 I have mpicc installed in /usr/bin/mpicc and checked the paths in ...
user3011008's user avatar
2 votes
1 answer
13k views

Failed to bind to '127.0.0.1:6600': Address already in use

I'm using ubuntu 12.10 for my MPI(message passing interface) configuration I have installed mpd after installation I have start mpd, it is started normally no error message display but when I'm trying ...
dora sa's user avatar
  • 21
0 votes
1 answer
176 views

slow down of mpi by Torque

I'm running Torque with Open MPI on a cluster with 30 nodes and 360 cores. I have found that the wall time of mpirun -np N ~./myjob and qsub -l nodes=1:ppn=N mpirun -np N ~./myjob differs ...
Arsen's user avatar
  • 1
1 vote
0 answers
134 views

How to debug MPI timing problems

While running Gromacs benchmarks in different setups (intra-node vs 2, 3, and 4 nodes connected with Infiniband), we have noticed severe performance degradation. In order to investigate, we have ...
Ansgar Esztermann's user avatar
3 votes
1 answer
9k views

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 ...
Santosa Sandy's user avatar
0 votes
1 answer
393 views

ERROR: cube viewer is not available! [closed]

I have installed and configured the following: cube-4.2.1 opari2-1.1.1 papi-5.2.0 scalasca-2.0 scorep-1.2.1 I am trying to run scalasca -examine, but I get the following error: ERROR: cube viewer ...
Alexander Talavari's user avatar
2 votes
3 answers
8k views

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 &...
gora's user avatar
  • 21
2 votes
1 answer
574 views

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 ...
sjensen's user avatar
  • 121
0 votes
1 answer
2k views

Execute John the Ripper on multiple processors using mpirun

I am trying to optimize John the Ripper for a security class. I am trying to use both processors to run John by using the mpirun program as suggested in this tutorial. I installed mpirun, but when I ...
bernie2436's user avatar
  • 6,705
3 votes
1 answer
1k views

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:...
speciousfool's user avatar
1 vote
0 answers
754 views

MPI mpdboot error

I have a problem with MPI in a 3-box cluster with machines named head, node1 and node2 respectively. I install a newer version on node2 and the problems arises. When I include only head and node2 in ...
Summer_More_More_Tea's user avatar