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--- cluster:73 [2022/11/07 18:57]
hmeij07 [Miniconda3]
+++ cluster:73 [2023/04/27 12:52]
hmeij07 [LAMMPS CPU/GPU]
@@ Line 23: / Line 23: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== Trimmomatic ======
+  * http://www.usadellab.org/cms/?page=trimmomatic
+  * binary download and stage
+  * java -jar trimmomatic-0.39.jar ...
+<code>
+/share/apps/CENTOS6/Trimmomatic-0.39/
+[root@cottontail Trimmomatic-0.39]# ll
+total 176
+drwxr-xr-x 2 root root      8 Apr  8  2019 adapters
+-rw-r--r-- 1 root root  35147 May 16  2018 LICENSE
+-rw-r--r-- 1 root root 128502 Apr  8  2019 trimmomatic-0.39.jar
+</code>
@@ Line 688: / Line 707: @@
 IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020
-# https://userguide.mdanalysis.org/stable/installation.html
-# calterlab, annika
+</code>
+  * https://userguide.mdanalysis.org/stable/installation.html
+  * calterlab, annika (used pip to install)
+<code>
 Successfully installed
@@ Line 695: / Line 719: @@
 fasteners-0.18 mmtf-python-1.1.3
 mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4
 </code>
@@ Line 763: / Line 788: @@
 -rw-r--r-- 1 root root      10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm
 -rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar
+# this is all that is needed for ohpc base compute client
+# see the recipe for cct2 and follow compute node only ingredients
+[root@cottontail2 ~]# ll /share/apps/src/cottontail2/ohpc-compute/
+total 95196
+-rw-r--r-- 1 root root  2696360 Feb 10 09:21 hwloc-ohpc-2.7.0-3.9.ohpc.2.6.x86_64.rpm
+-rw-r--r-- 1 root root   266252 Feb 10 09:22 lmod-ohpc-8.7.6-12.3.ohpc.2.6.x86_64.rpm
+-rw-r--r-- 1 root root     7268 Feb 10 09:22 ohpc-base-compute-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm
+-rw-r--r-- 1 root root     8204 Feb 10 09:23 ohpc-filesystem-2.6-2.3.ohpc.2.6.noarch.rpm
+-rw-r--r-- 1 root root    10720 Feb 10 09:23 ohpc-release-2-1.el8.x86_64.rpm
+-rw-r--r-- 1 root root     7124 Feb 10 09:27 ohpc-slurm-client-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm
+-rw-r--r-- 1 root root 74326532 Feb 10 09:23 singularity-ohpc-3.7.1-5.1.ohpc.2.1.x86_64.rpm
+-rw-r--r-- 1 root root    22168 Feb 10 09:24 slurm-contribs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
+-rw-r--r-- 1 root root   247392 Feb 10 09:24 slurm-example-configs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
+-rw-r--r-- 1 root root 18764472 Feb 10 09:24 slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
+-rw-r--r-- 1 root root   176480 Feb 10 09:28 slurm-pam_slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
+-rw-r--r-- 1 root root   785112 Feb 10 09:25 slurm-slurmd-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 </code>
@@ Line 2230: / Line 2275: @@
 ====== LAMMPS CPU/GPU ======
+** 25Apr2023**
+  * /share/apps/CENTOS7/lammps/25Arp2023
+  * lmp_serial and lmp_mpi
+  * 3 cuda versions with 3 different precision settings
+  * recipe: /share/apps/CENTOS7//lammps/25Apr2023.install
+<code>
+# CPU
+ 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
+ which mpirun mpicc python
+# CPU + GPU (exx96 queue, may run on test and amber128 queues)
+ 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
+ which nvcc
+</code>
 ** USER_QUIP **

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