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--- cluster:73 [2020/07/13 14:53]
hmeij07 [Gromacs]
+++ cluster:73 [2020/10/26 19:27]
hmeij07 [LAMMPS CPU/GPU]
@@ Line 3: / Line 3: @@
 ====== Software ======
+IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/home/apps'' **should be replaced with** ''/share/apps'' **which points to** ''/zfshomes/apps''
+ --- //[[hmeij@wesleyan.edu|Henk]] 2020/07/31 15:08//
 The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing).
@@ Line 14: / Line 18: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== EMBOSS ======
+  * /share/apps/CENTOS6/EMBOSS
+  * /share/apps/CENTOS6/EMBOSS/6.6.0.install (read to setup env)
+  * https://www.ebi.ac.uk/services
+  * jfabry/kthayer
 ====== Sequencing Tools #2 ======
@@ Line 944: / Line 955: @@
 ====== Gromacs =====
-Gromacs-2018 for GPU (RTX2080)
+Gromacs-2020.3 for GPU (RTX2080S)
+  * ''exx96'' queue
+  * see /share/apps/CENTOS7/gromacs/2020.3.install for env
+  * change env in script below
+Gromacs-2018 for GPU (RTX2080S)
   * ''exx96'' queue
   * **/zfshomes/hmeij/k20redo/run.rtx sample script**
@@ Line 1054: / Line 1070: @@
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
-  * program: mcc, math, mathematica (v 11.0.1)
+  * program: mcc, math, mathematica (v 12.1)
-  * install dir: /share/apps/CENTOS6/mathematica/11.0.1
+  * install dir: /share/apps/CENTOS6/mathematica/12.1
   * docs: on the web
   * www:  http://www.wolfram.com/mathematica/
+  * Campus wide license, use any queue.
   * Parallel kernels
@@ Line 1064: / Line 1081: @@
     * http://reference.wolfram.com/mathematica/guide/ParallelComputing.html
-Job submissions should go to queue //mathematica// which containes licensed nodes (all the hp12 nodes for now).
 ====== Eigen =====
@@ Line 1248: / Line 1265: @@
 ====== LAMMPS CPU/GPU ======
+** CPU only OR CPU+GPU for ''exx96'' queue - CentOS7
+  * git download of latest did not work (lots of fortran errors?)
+  * latest tarball is still 3Mar2020 (?)
+  * added user-eaxc (but had to remove package python)
+  * please read **/share/apps/CENTOS7/lammps/3Mar2020.install **
+<code>
+# CPU
+/share/apps/CENTOS7/lammps/3Mar2020/lmp_serial+user-omp+user-reaxc
+/share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi+user-omp+user-reaxc
+# CPU+GPU
+/share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi-single-single_kokkos_cuda_mpi+user-omp+user-reaxc
+# env
+ 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 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 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:$LD_LIBRARY_PATH
+<code>
+** CPU ONLY v2 CentOS7 **
+  * add user-opm on next compile ... done ... binaries with string +user-omp
+  * /share/apps/CENTOS7/lammps/3Mar2020
+    * lmp_serial, lmp_mpi
+  * //latest// openmpi version as of today v4.0.4
+  * consult this file for packages installed and compilations
+    * /share/apps/CENTOS7/lammps/03Mar2020.install
+    * should work only on exx96 and mwgpu queues
+<code>
+ export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
+ export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
+</code>
 ** CPU ONLY **
@@ Line 1260: / Line 1322: @@
 ** CPU or GPU **
+  * added lmp_mpi-single-single+user-omp
   * /share/apps/CENTOS7/lammps/3Mar2020

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