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cluster:156 [2017/04/03 18:21] hmeij07 [OpenHPC Tools] |
cluster:156 [2017/04/04 18:59] hmeij07 [OpenHPC page 3] |
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**[[cluster: | **[[cluster: | ||
- | ==== OpenHPC | + | ==== OpenHPC |
+ | |||
+ | ** Tools ** | ||
< | < | ||
Line 10: | Line 12: | ||
yum -y install EasyBuild-ohpc | yum -y install EasyBuild-ohpc | ||
yum -y install spack-ohpc | yum -y install spack-ohpc | ||
+ | yum -y install R_base-ohpc | ||
</ | </ | ||
+ | * " | ||
+ | * http:// | ||
* " | * " | ||
* https:// | * https:// | ||
* "Spack is a package management tool designed to support multiple versions and configurations of software on a wide variety of platforms and environments." | * "Spack is a package management tool designed to support multiple versions and configurations of software on a wide variety of platforms and environments." | ||
* http:// | * http:// | ||
+ | * ''/ | ||
+ | * R_base contains '' | ||
+ | ** Compilers ** | ||
+ | |||
+ | < | ||
+ | |||
+ | yum install gnu-compilers-ohpc | ||
+ | |||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | **MPIs** | ||
+ | |||
+ | * Both for ethernet and infiniband networks | ||
+ | |||
+ | < | ||
+ | |||
+ | yum -y install openmpi-gnu-ohpc mvapich2-gnu-ohpc mpich-gnu-ohpc | ||
+ | |||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | ** Perf Tools ** | ||
+ | |||
+ | * '' | ||
+ | * Appendix C | ||
+ | |||
+ | **3rd Party & Libs Tools** | ||
+ | |||
+ | * OpenHPC provides package aliases for these 3rd party libraries and utilities that can | ||
+ | be used to install available libraries for use with the GNU compiler family toolchain. | ||
+ | |||
+ | < | ||
+ | |||
+ | # Install libs for all available GNU compiler family toolchain | ||
+ | yum -y groupinstall ohpc-serial-libs-gnu | ||
+ | yum -y groupinstall ohpc-io-libs-gnu | ||
+ | yum -y groupinstall ohpc-python-libs-gnu | ||
+ | yum -y groupinstall ohpc-runtimes-gnu | ||
+ | # Install parallel libs for all available MPI toolchains | ||
+ | yum -y groupinstall ohpc-parallel-libs-gnu-mpich | ||
+ | yum -y groupinstall ohpc-parallel-libs-gnu-mvapich2 | ||
+ | yum -y groupinstall ohpc-parallel-libs-gnu-openmpi | ||
+ | |||
+ | # things like | ||
+ | # netcdf, hdf5, numpy and scipy for python, fftw, scalapack | ||
+ | |||
+ | </ | ||
+ | |||
+ | Finish with installing Intel' | ||
+ | |||
+ | {{: | ||
+ | |||
+ | As user '' | ||
+ | |||
+ | < | ||
+ | |||
+ | module avail | ||
+ | module spider | ||
+ | which mpicc | ||
+ | module load gnu/5.4.0 | ||
+ | module load openmpi/ | ||
+ | which gcc | ||
+ | which mpicc | ||
+ | mpicc -O3 / | ||
+ | cp / | ||
+ | which prun | ||
+ | find / | ||
+ | module spider prun | ||
+ | module load prun/1.1 | ||
+ | which prun | ||
+ | sbatch job.mpi | ||
+ | squeue | ||
+ | |||
+ | </ | ||
+ | |||
+ | You do need to install the Infiniband section so you can run over ethernet with OpenMPI | ||
+ | |||
+ | < | ||
+ | |||
+ | yum -y groupinstall " | ||
+ | yum -y install infinipath-psm | ||
+ | systemctl enable rdma | ||
+ | systemctl start rdma | ||
+ | |||
+ | # recipe is missing this | ||
+ | |||
+ | yum -y --installroot=/ | ||
+ | |||
+ | # remake vnfs | ||
+ | </ | ||
\\ | \\ | ||
**[[cluster: | **[[cluster: |