Differences

This shows you the differences between two versions of the page.

--- cluster:73 [2020/12/14 14:45]
hmeij07 [DMTCP]
+++ cluster:73 [2021/04/12 19:17]
hmeij07 [LAMMPS CPU/GPU]
@@ Line 18: / Line 18: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 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 ======
+  * http://our-sanscratch-server:8787/
+  * https://support.rstudio.com/hc/en-us/articles/200552316-Configuring-the-Server
+  * centos7 R v 3.6.0
+  * use your HPC username and credentials
 ====== DMTCP =====
@@ Line 24: / Line 78: @@
   * this came from the CRAC source, trying to install gpu checkpoint tool
   * [[cluster:198|GPU checkpoint/restart]]
+  * but plugin will not compile, checking with developers 12 Dec 2020
   * Installed as package ins OS on all nodes
@@ Line 226: / Line 281: @@
   * most packages found on this page
   * picked up mpirun from miniconda2 apps (that may be a problem)
+  * Added to 3.8.3 "acpipe"
+  * https://github.com/alanwilter/acpype
+ --- //[[hmeij@wesleyan.edu|Henk]] 2021/02/18 14:41//
 <code>
@@ Line 1080: / Line 1140: @@
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
-  * program: mcc, math, mathematica (v 12.1)
+  * program: mcc, math, mathematica (v 12.2)
-  * install dir: /share/apps/CENTOS6/mathematica/12.1
+  * install dir: /share/apps/CENTOS7/mathematica/12.2
   * docs: on the web
   * www:  http://www.wolfram.com/mathematica/
-  * Campus wide license, use any queue.
+  * Centos7, use queues mwgpu, amber128 or exx96
+  * For GUI launch on greentail52
   * Parallel kernels
@@ Line 1275: / Line 1336: @@
 ====== LAMMPS CPU/GPU ======
+** USER_QUIP **
+This is a version of lammps (29Oct20, last stable) that contains all packages with user-quip.
+It does not compile with MPI, nor ifort in CentOS7, so there is only a "serial" version.
+  * Requires CentOS 7 so queues: mwgpu, amber128, exx96
+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)
+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
+# serial - cpu+gpu
+(to come, hopefully)
+</code>
 ** CPU only ** -Centos6
@@ Line 2265: / Line 2354: @@
 ====== Amber ======
+** Amber 20 **
+  * Two versions compiled,
+    * one for cuda 8.0/mpich3 for queue amber128
+    * one for queues mwgpu and exx96 (cuda 9.2/openmpi).
+  * Consult the run.amber20 script to set up environment
+    * /share/apps/CENTOS7/amber/amber20/run.amber20
+  * Both are installed in /usr/local/amber20
 ** AMBER 18 **
@@ Line 2977: / Line 3079: @@
 ===== 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
@@ Line 3005: / Line 3111: @@
 ====== Cluster Math Kernel Libraries ======
+  * latest version in OneAPI, search this page
   * see Intel parallel studio
@@ Line 3014: / Line 3122: @@
 ====== Intel Threading Building Blocks ======
+  * latest version is in OneAPI, search this pages
   * see Intel parallel studio
@@ Line 3028: / Line 3138: @@
   * 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)
-  * install dir: /share/apps/CENTOS7/matlab/R2020a
+  * install dir: /share/apps/CENTOS7/matlab/R2020bISO
   * docs & www: http://mathworks.com
+  * CentOS7 required use on queues mwgpu, amber128 and exx96
+  * For GUI launch on greentail52
 Note:

DokuWiki

User Tools

Site Tools

Differences

Page Tools