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To submit a precompiled binary to run on HabaneroTerremoto, the script will look just as it does in the Hello World example. The difference is that you will call your executable file instead of the shell commands "echo", "sleep", and "date".
C/C++/Fortran MPI
Intel Parallel Studio
Habanero Terremoto supports Intel Parallel Studio which provides a version of MPI derived from MPICH2. We encourage users to avail themselves of Intel MPI because it is faster and more modern than other versions. Also, all nodes on the cluster have Infiniband transport and that is the fabric that MPI jobs avail themselves of - which is another reason for a substantial boost of efficiency on the cluster.
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In order to take advantage of Terremoto architecture, your program should be (re)compiled on the cluster even if you used Intel for compiling it on another cluster (like Habanero). It is important to compile with the compiler provided by the module mentioned above. Note that you may have to set additional environment variables in order to successfully compile your program.
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$ sbatch pi_mpi.sh |
OpenMPI
Habanero Terremoto supports also OpenMPI from the GNU family.
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Important note: On Yeti, where Matlab was single thread by default, it appeared that the more recent versions of Matlab took liberties to grab all the cores within a node even when fewer (or even only one) cores were specified as above. On HabaneroTerremoto, we believe this has been addressed by implementing a system mechanism which enforces the proper usage of the number of specified cores.
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7. From your local system, open a second connection to Habanero Terremoto that forwards a local port to the remote node and port. Replace UNI below with your uni.
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$ ssh -L 8080:10.43.4.206:8888 UNI@habaneroUNI@moto.rcs.columbia.edu |
8. Open a browser session on your desktop and enter the URL 'localhost:8080' (i.e. the string within the single quotes) into its search field. You should now see the notebook.