MPI require I deploy mpi program to each machine. Currently, I put the mpi program in nfs, but this method has 2 issues, one is nfs has latency issue and the other is nfs not suitable for large cluster. I know that I could use some linux shell commands to sync up my program to each node, but looks like not so convenient. especially, when I change the program frequently. Is there any easy method to to that ?
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3 Answers
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There's nothing wrong with NFS or any other network filing system in large clusters. It just means your file server isn't sized for the job. If you replace NFS with anything like ssh, ftp, scripts, or whatever and change nothing else, I don't think that'll make any significant difference. Also, if the loading time is a significant and bothersome component of the overall runtime then why use MPI in the first place?
OK, enough of playing devils advocate. One thing you can do is to have nodes load your program onto other nodes in a binary tree type arrangement. You'll need a script that will copy the executable to two other nodes along with a copy of the script, start that script running asynchronously on those nodes and then runs the executable locally. The result would be a chain reaction of copying and running spreading across the network. The only difficult bit is in choosing which nodes to copy to so that each one is visited just once. It will be a lot faster.
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Depending on the nature of the application and the nature of the NFS network, using a shared file system for both the MPI implementation and the application "should" be able to scale with reasonable performance, to a point. Keep in mind that there is some NFS caching at the node level, so multiple ranks on the same node will not each have to traverse the network to reach the files.
In general terms, I tend to advise that NFS be discontinued at about 128 nodes or 1024 ranks in favor of local installations. That advice changes if the NFS is delivered with 10GigE, IPoIB, or if a high performance file system like SFS or GPFS is used.
If you are committed to local installations, then tools like rsync, or scp are good candidates to distribute the bits. Script the final result. You can even do a tar to shared, and remote command (e.g. ssh, clush) un-tar to local disc. The "solution" only needs to be robust, not polished or elegant.
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I'll also chime in to say the NFS should be just fine in this use-case, unless you have a cluster of over 100-200 nodes.
If you just want a lightweight tool for doing many-node parallel operations, I'd suggest pdsh. pdsh is a very common tool on HPC clusters. It includes a command called pdcp for doing parallel node copies, i.e.
pdcp -w node[00-99] myfile /path/to/destination/myfile
Where the nodenames are node00, node01, ... node99.
Similarly, you use the pdsh command to run a command in parallel across all the nodes. I.e.,
pdsh -w node[00-99] /path/to/my/executable
Alternatively, if you're looking for something a little less ad-hoc for doing these operations, I can recommend Ansible as an easy and lightweight configuration management and deployment tool. It's not as simple to get started as pdsh, but might be more manageable in the long run...
For example, a simple Ansible playbook to copy a tarball to all nodes, extract it, and then execute a binary might look like:
---
- hosts: computenodes
user: myname
vars:
num_procs: 32
tasks:
- name: copy and extract tarball to deployment location
action: unarchive src=myapp.tar.gz dest=/path/to/deploy/
- name: execute app
action: command mpirun -np {{num_procs}} /path/to/deploy/myapp.exe
MPI_Barrierat the start so all nodes synch up before they start doing their work. – rath