The mpi tag has no usage guidance.
5
votes
2answers
552 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 ...
5
votes
2answers
472 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 ...
4
votes
1answer
718 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 ...
3
votes
1answer
3k 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 ...
3
votes
1answer
310 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 ...
2
votes
1answer
3k 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 ...
2
votes
4answers
66 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 ...
2
votes
1answer
1k 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 ...
2
votes
1answer
190 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 ...
1
vote
1answer
114 views
Using MPI with a .sh script?
I am a beginner with Unix and MPI. I have a runPR.sh script as below
DIR=/directory/buildagain/bin/Project
FILELIST=$1
while read FILE
do
echo "Processing ${FILE}..."
./makeInp.sh ...
1
vote
1answer
2k 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 ...
1
vote
0answers
46 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 ...
1
vote
0answers
425 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 ...
0
votes
1answer
488 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, ...
0
votes
0answers
13 views
Installing Infiniband on Ubuntu 12.04 (still need to downgrade kernel )?
We plan to install HPC cluster on Ubuntu 12.04 ( and this version cannot be changed for various reasons ). I've read this manual: http://techs.enovance.com/6285/a-quick-tour-of-infiniband
And now I'm ...
0
votes
0answers
74 views
Parallel vs Distributed vs Traditional File system
I am trying to understand the difference between these three file system at a very basic level.
Distributed FS: HDFS
Parallel FS : Lustre
Tradational FS : ext4/ext3/ NTFS/FAT etc.
I want to ...
0
votes
0answers
58 views
Fatal error in MPI (rank 1 PID 13862)
I am running a program in a server with Ubuntu 3.16 that requires to specify the number of node and cpus per node to be used. It runs with mpirun. Some details about the server first:
Architecture: ...
0
votes
1answer
36 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?
...
0
votes
0answers
77 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 make ...
0
votes
1answer
49 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 ...
0
votes
2answers
631 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 ...
