All Questions
Tagged with openmpi cluster-computing
47 questions
0
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94
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Segmentation Fault When Sending Arrays Over a Certain Size with Open MPI
I am writing a program to run with an ifiniband and intel-based cluster using openmpi, pmix, and SLURM scheduling.
When I run my program on the cluster with an input matrix over 38x38 on each node, I ...
0
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0
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149
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mpiexec was unable to launch the specified application as it could not find an executable (np)
can anyone help me out with this?
Everytime I do qsub file.pbs i get this error:
mpiexec was unable to launch the specified application as it could not find an executable:
Executable: –np
This is my ...
- 233
1
vote
0
answers
290
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"Snakemake" call mpirun using multiple nodes and a slurm-clusterprofile
I am writing a snakemake-workflow which calls a process using mpirun in a slurm-job using a docker-image. It is necessary to use multiple computing nodes and lots of processes. I am using a slurm-...
- 11
16
votes
3
answers
49k
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GPU allocation in Slurm: --gres vs --gpus-per-task, and mpirun vs srun
There are two ways to allocate GPUs in Slurm: either the general --gres=gpu:N parameter, or the specific parameters like --gpus-per-task=N. There are also two ways to launch MPI tasks in a batch ...
- 1,372
1
vote
1
answer
1k
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Issues when running MPI program on two cluster nodes
I have a very simple MPI program:
int my_rank;
int my_new_rank;
int size;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
MPI_Comm_size(MPI_COMM_WORLD, &...
- 926
2
votes
1
answer
767
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OpenMP code is using only 4 threads instead of the specified 72
I have a program written by someone else that uses OpenMP. I am running it on a cluster that uses Slurm as its job manager. Despite setting OMP_NUM_THREADS=72 and properly requesting 72 cores for the ...
1
vote
2
answers
1k
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Difference between -n and -np when running MPI script?
I'm learning how to use MPI, and am confused on the difference between -n and -np when calling a script. For reference, I am trying to run the script on a Slurm cluster with OpenMPI 3.
For instance, ...
- 188
1
vote
1
answer
34
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Manually launch OpenMPI jobs
I have a cluster that does not allow direct ssh access, but does permit me to submit commands through a proprietary interface.
Is there any way to either manually launch OpenMPI jobs, or ...
- 11.8k
0
votes
1
answer
4k
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Openmpi setting btl flags --mca btl tcp vs --mca btl_tcp_if_include eth1
I am looking the documentation of how to set btl flags to use network specific protocol and specific connection.
I am seeing the btl selection general documentation documentation, but a bit confused. ...
- 2,407
1
vote
1
answer
2k
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openmpi runtime error: Hello World run on hosts
I'm trying to setup a cluster. Up to now I'm testing it only with 1 master and 1 slave. Running the script from the master it starts printing the HelloWorld, but then I get the following error:
...
0
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0
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65
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Limit to number of Broadcasts on a cluster?
I have a problem with a loop containing mpi broadcast line. After 1000th iterations, the broadcast line stops or hangs the execution (waiting for the transmission presumably).
See the following code:
...
- 1
0
votes
1
answer
317
views
Best practice for job resource scaling (environment) on cluster computing?
I am quite new to programming on a cluster and am having great difficulty finding my way around. I am on SGE with bash cluster and using OpenMPI.
I have a task where I want to run several variations ...
- 1,649
1
vote
1
answer
772
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MPI: Pin each instance to certain cores on each node
I want to execute several instances of my program with OpenMPI 2.11. Each instance runs on its own node (-N 1) on my cluster. This works fine. I now want to pin each program-instance to the first 2 ...
- 346
1
vote
1
answer
137
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How to run an external library into different nodes?[MPI]
I need to write a C MPI code that use many functions of a library (specifically, it's Parasail), but my cluster has three different processors, a front-end with Intel Xeon, 16 nodes with Intel i3 and ...
- 13
0
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0
answers
5k
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How to invoke InfiniBand with OpenMPI
I would like to know how to invoke InfiniBand hardware on CentOS 6x cluster with OpenMPI (static libs.) for running my C++ code. This is how I compile and run:
/usr/local/open-mpi/1.10.7/bin/mpic++ -...
- 193