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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 ...
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1answer
108 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 ...
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2answers
115 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 ...
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0answers
73 views

mpd daemon prematurely ending jobs

I am a little out of my depth here so bear with me. 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 ...
0
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1answer
211 views

Execute John the Ripper on multiple processors using mpirun

I am a linux noob 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, ...
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1answer
157 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 ...
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0answers
239 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 ...
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2answers
307 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 ...
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1answer
888 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
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1answer
451 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
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1answer
2k 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 ...
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2answers
362 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 ...