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Questions tagged [mpi]

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0
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1answer
47 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 ...
0
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0answers
58 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 ...
1
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0answers
216 views

CentOS 7, VirtualBox, openmpi installation breaking GUI. Why? [closed]

I have a case where my installation of CentOS 7, hosted by a Windows 7 machine through an Oracle VM VirtualBox, is having its GUI installation crippled* by: yum install openmpi openmpi-devel In what ...
1
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0answers
155 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. ...
0
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0answers
104 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 ...
0
votes
1answer
415 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/...
1
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0answers
79 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 ...
1
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0answers
92 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 ...
1
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1answer
480 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 ...
1
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0answers
802 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 ...
1
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0answers
405 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 ...
1
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0answers
63 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 ...
1
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1answer
2k 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]: ...
3
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2answers
2k 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 ...
2
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1answer
14k 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 ...
2
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1answer
4k 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 ...
4
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1answer
3k 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 ...
2
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1answer
4k 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 ...
2
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4answers
126 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 ...
0
votes
1answer
485 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? ...
1
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0answers
495 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 ...
1
vote
1answer
8k 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 ...
0
votes
1answer
108 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 ...
1
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0answers
108 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 ...
3
votes
1answer
7k 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 ...
0
votes
1answer
297 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 ...
1
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3answers
4k 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 &...
2
votes
1answer
449 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 ...
0
votes
1answer
1k 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 ...
3
votes
1answer
715 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:...
1
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0answers
674 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 ...
5
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2answers
826 views

`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 ...
2
votes
1answer
2k views

How to run Abinit via MPI?

I'm trying to run Abinit in parallel, since in sequential mode it takes too much time. I have followed all steps in the abinit tutorials to run it in parallel, and they say to use OpenMPI, but I ...
4
votes
1answer
2k views

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 ...
2
votes
1answer
6k views

Why does 'make' complain about a missing rule when I try to build a program from source?

I am a Linux novice, and I am attempting to compile scientific software called DL_POLY_Classic. I downloaded the zip file dl_class_1.6.tar.gz and unzipped it using the command tar xvzf dl_class_1.6....
5
votes
2answers
846 views

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 ...