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cluster:73 [2021/03/03 18:19]
hmeij07 [Mathematica] 		cluster:73 [2021/04/13 19:33]
hmeij07 [LAMMPS CPU/GPU]
Line 18: Line 18:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +====== OpenHPC ======
 +
 +So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
 +
 +  * whitetail tar ball for centos7/warewulf (no slurm)
 +  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
 +  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
 +  * https://github.com/warewulf/warewulf3 (master git zip file)
 +
 +====== OneAPI ======
 +
 +  * Requires CentOS 7 so queues mwgpu, amber128, exx96
 +
 +  * Production version is installed in /share/apps/CENTOS7/intel/openapi (via **n78**)
 +  * source /share/apps/CENTOS/intel/oneapi/setvars.sh
 +
 +<code>
 +# which icc icx icpc icpx dpcpp ifort ifx mpirun mpicc python clang clang++
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/icc
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/icx
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/icpc
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/icpx
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/dpcpp
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/intel64/ifort
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/ifx
 +/share/apps/CENTOS7/intel/oneapi/intelpython/latest/bin/mpirun
 +/share/apps/CENTOS7/intel/oneapi/mpi/2021.1.1/bin/mpicc
 +/share/apps/CENTOS7/intel/oneapi/intelpython/latest/bin/python
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/clang
 +/share/apps/CENTOS7/intel/oneapi/compiler/2021.1.1/linux/bin/clang++
 +# in addition these were installed
 +/share/apps/CENTOS7/intel/oneapi/mkl/2021.1.1
 +/share/apps/CENTOS7/intel/oneapi/pytorch/1.5.0
 +/share/apps/CENTOS7/intel/oneapi/tensorflow/2.2.0
 +</code>
 +
 +  * Test version is installed on local disk on host **greentail52**
 +  * source /opt/intel/oneapi/setvars.sh
 +  * Read [[cluster:203|ICC vs ICX]]
 +
 +
 +====== StringTie2 ======
 +
 +  * Requires CentOS 7 so queues mwgpu, amber128, exx96
 +  * /share/apps/CENTOS7/stringtie2/stringtie2 binarie
 +  * https://github.com/skovaka/stringtie2
  
 ====== Rstudio ====== ====== Rstudio ======
Line 1289: Line 1336:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** USER_QUIP **
 +
 +This is a version of lammps (29Oct20, last stable) that contains all packages with user-quip.
 +
 +It does compile with MPI (mpif90), not ifort, in CentOS7 ... was tricky, solution for MPI was the ''mpifort --showme:link'' answer
 +
 +  * Requires CentOS 7 so queues: mwgpu, amber128, exx96 for cpu-only binaries
 +  * Rwequires CentOS7 plus Cuda 10.2 so queue: exx96 for cpu+gpu binaries
 +
 +Read, if you wish  
 +
 +  * /share/apps/CENTOS7/lammps/QUIP-public.install 
 +  * /share/apps/CENTOS7/lammps/29Oct2020.install 
 +
 +**Environments**
 +
 +<code>
 +
 +# serial - cpu only (although quippy compiled, it refused to install)
 +# MPI STUBS is compiled in
 +
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_serial-with-quip.cpu -h
 +
 +# mpi - cpu only
 +# OpenMPI
 +
 +export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu -h
 +
 +
 +# serial - cpu+gpu
 +
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
 +export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +export CUDA_HOME=/usr/local/cuda
 +export PATH=/usr/local/cuda/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_double_double -h
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_single_double -h
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_single_single -h
 +
 +</code>
  
 ** CPU only ** -Centos6 ** CPU only ** -Centos6
Line 3004: Line 3109:
 ===== Intel  ===== ===== Intel  =====
  
-UPDATE, 2016 parallel studio cluster edition installed+UPDATE 2021 
 +latest version of icc/icx and ifort/ifx are inside OneAPI, search this page 
 + 
 +UPDATE 2016  
 +parallel studio cluster edition installed
  
   * 2 ifort and 2 icc float licenses   * 2 ifort and 2 icc float licenses
Line 3032: Line 3141:
  
 ====== Cluster Math Kernel Libraries ====== ====== Cluster Math Kernel Libraries ======
 +
 +  * latest version in OneAPI, search this page
  
   * see Intel parallel studio   * see Intel parallel studio
Line 3041: Line 3152:
  
 ====== Intel Threading Building Blocks ====== ====== Intel Threading Building Blocks ======
 +
 +  * latest version is in OneAPI, search this pages
  
   * see Intel parallel studio   * see Intel parallel studio
Line 3055: Line 3168:
  
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
-    * R2020a, campus wide license so no more restrictions on licenses +    * R2020b, campus wide license so no more restrictions on licenses 
     * No Distributed Computing Engine or Matlab Parallel (for now)     * No Distributed Computing Engine or Matlab Parallel (for now)
-  * install dir: /share/apps/CENTOS7/matlab/R2020a+  * install dir: /share/apps/CENTOS7/matlab/R2020bISO
   * docs & www: http://mathworks.com   * docs & www: http://mathworks.com
 +  * CentOS7 required use on queues mwgpu, amber128 and exx96 
 +  * For GUI launch on greentail52
  
 Note: Note:
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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