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--- cluster:156 [2017/04/03 18:21] – [OpenHPC Tools] hmeij07
+++ cluster:156 [2017/04/05 14:42] (current) – [OpenHPC page 3] hmeij07
@@ Line 2: / Line 2: @@
 **[[cluster:0|Back]]**
-==== OpenHPC Tools ====
+==== OpenHPC page 3 ====
+** Tools **
 <code>
@@ Line 10: / Line 12: @@
 yum -y install EasyBuild-ohpc
 yum -y install spack-ohpc
+yum -y install R_base-ohpc
 </code>
+  * "Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs" (memcheck)
+    * http://valgrind.org/
   * "Welcome to the documentation of EasyBuild, a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way."
     * https://easybuild.readthedocs.io/en/latest/
   * "Spack is a package management tool designed to support multiple versions and configurations of software on a wide variety of platforms and environments."
     * http://spack.readthedocs.io/en/latest/tutorial_sc16.html
+    * ''/opt/ohpc/admin/spack/0.8.17/bin/spack''
+  * R_base contains ''R'' and ''Rscript''
+** Compilers **
+<code>
+yum install gnu-compilers-ohpc
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/c++
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/cpp
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/g++
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc-ar
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc-nm
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc-ranlib
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcov
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcov-tool
+/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gfortran
+</code>
+**MPIs**
+  * Both for ethernet and infiniband networks
+<code>
+yum -y install openmpi-gnu-ohpc mvapich2-gnu-ohpc mpich-gnu-ohpc
+/opt/ohpc/pub/mpi/openmpi-gnu/1.10.4/bin/mpicc
+/opt/ohpc/pub/mpi/openmpi-gnu/1.10.4/bin/mpirun
+/opt/ohpc/pub/mpi/mvapich2-gnu/2.2/bin/mpicc
+/opt/ohpc/pub/mpi/mvapich2-gnu/2.2/bin/mpirun
+/opt/ohpc/pub/mpi/mpich-gnu-ohpc/3.2/bin/mpicc
+/opt/ohpc/pub/mpi/mpich-gnu-ohpc/3.2/bin/mpirun
+</code>
+** Perf Tools **
+  * ''yum -y groupinstall ohpc-perf-tools-gnu''
+  * 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.
+<code>
+# 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
+</code>
+Finish with installing Intel's Parallel Data Studio (icc/ifort).
+{{:cluster:install_guide-centos7.2-slurm-1.2-x86_64.pdf|install_guide-centos7.2-slurm-1.2-x86_64.pdf}}
+As user ''test''
+<code>
+module avail
+module spider
+which mpicc
+module load gnu/5.4.0
+module load openmpi/1.10.4
+which gcc
+which mpicc
+mpicc -O3 /opt/ohpc/pub/examples/mpi/hello.c
+cp /opt/ohpc/pub/examples/slurm/job.mpi .
+which prun
+find /opt/ohpc/pub -name prun
+module spider prun
+module load prun/1.1
+which prun
+sbatch job.mpi
+squeue
+</code>
+You do need to install the Infiniband section so you can run over ethernet with OpenMPI
+<code>
+  yum  -y groupinstall "Infiniband Support"
+  yum -y install infinipath-psm
+  systemctl enable rdma
+  systemctl start rdma
+# recipe is missing this: flavor openmpi
+  yum -y --installroot=/data/ohpc/images/centos7.2 install libibverbs opensm-libs infinipath-psm
+# remake vnfs
+</code>
+The following shows up when running MPI over ethernet
+<code>
+[prun] Master compute host = n29
+[prun] Resource manager = slurm
+[prun] Launch cmd = mpirun ./a.out
+--------------------------------------------------------------------------
+[[49978,1],4]: A high-performance Open MPI point-to-point messaging module
+was unable to find any relevant network interfaces:
+Module: OpenFabrics (openib)
+  Host: n31
+Another transport will be used instead, although this may result in
+lower performance.
+--------------------------------------------------------------------------
+ Hello, world (8 procs total)
+    --> Process #   2 of   8 is alive. -> n29.localdomain
+    --> Process #   3 of   8 is alive. -> n29.localdomain
+    --> Process #   0 of   8 is alive. -> n29.localdomain
+    --> Process #   1 of   8 is alive. -> n29.localdomain
+    --> Process #   6 of   8 is alive. -> n31.localdomain
+    --> Process #   7 of   8 is alive. -> n31.localdomain
+    --> Process #   4 of   8 is alive. -> n31.localdomain
+    --> Process #   5 of   8 is alive. -> n31.localdomain
+</code>
+See page 4 for ib0 configuration which is incomplete on the recipe.
+[[cluster:154|OpenHPC page 1]] - [[cluster:155|OpenHPC page 2]] - page 3 - [[cluster:160|OpenHPC page 4]]
 \\
 **[[cluster:0|Back]]**