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--- cluster:73 [2023/10/31 14:16] – [Miniconda3-py311] hmeij07
+++ cluster:73 [2025/08/29 18:41] (current) – [Mathematica] hmeij07
@@ Line 24: / Line 24: @@
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== Julia ======
+  * https://julialang.org/
+  * /share/apps/julia/julia-1/10.4
+  * link in /share/apps/bin
+  * runs on centos7 and rocky8
@@ Line 70: / Line 78: @@
 │ Using Python 3.11.4. Type "help()" for help.                       │
 └────────────────────────────────────────────────────────────────────┘
+sage: exit
+(sage) [hmeij@greentail52 ~]$ conda deactivate
+[hmeij@greentail52 ~]$
 </code>
+  * **mdtraj, matplotlib, pandas**
+<code>
+[hmeij@greentail52 ~]$ which python
+/share/apps/CENTOS7/miniconda3-py311/bin/python
+[hmeij@greentail52 ~]$ python
+Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import mdtraj as mt
+>>>
+</code>
+  * ** seaborn**
+  * https://seaborn.pydata.org/index.html
+  * also in miniconda3/py311 on rock8 module (used pip3)
+<code>
+  patsy              conda-forge/noarch::patsy-0.5.4-pyhd8ed1ab_0
+  seaborn            conda-forge/noarch::seaborn-0.13.0-hd8ed1ab_0
+  seaborn-base       conda-forge/noarch::seaborn-base-0.13.0-pyhd8ed1ab_0
+  statsmodels        conda-forge/linux-64::statsmodels-0.14.0-py311h1f0f07a_3
+</code>
+  * joblib (thayerlab)
+<code>
+  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
+</code>
@@ Line 618: / Line 667: @@
 </code>
+** picard **
+  * https://github.com/broadinstitute/picard
+  * Warning: using Java 20 but only Java 17 has been tested.
+<code>
+picard centos7, weird
+> Failed to load native library 'libnative-platform.so' for Linux amd64.
+picard centos8
+[hmeij@cottontail2 20231108]$ pwd
+/share/apps/CENTOS8/picard/20231108
+[hmeij@cottontail2 20231108]$ ls -l build/libs/
+total 119872
+-rw-r--r-- 1 hmeij its 62520451 Nov  8 11:46 picard-3.1.0-3-ga9194bd97-SNAPSHOT-all.jar
+-rw-r--r-- 1 hmeij its  1856980 Nov  8 11:01 picard-3.1.0-3-ga9194bd97-SNAPSHOT.jar
+-rw-r--r-- 1 hmeij its 62520451 Nov  8 11:46 picard.jar
+[hmeij@cottontail2 20231108]$
+</code>
 ====== Galario CPU+GPU ======
@@ Line 1328: / Line 1401: @@
 </code>
+  * **qualimap **
+  * http://qualimap.conesalab.org/
+  * java & R app, probably will work in centos7 and rocky8
+  * /share/apps/CENTOS7/qualimap/2.3
+  * **gatk**
+  * https://github.com/broadinstitute/gatk
+  * java & R app. probably will work in centos7 and rocky8
+  *  /share/apps/CENTOS7/gatk/4.4.0.0
+For both apps above java is v20, developers want and tested v17
+For both apps you may find R local in operating system or a recent versions at
+  * (rocky 8) module load R/4.1.2
@@ Line 1444: / Line 1537: @@
 # drop all the packages in from previous versions
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#python3
+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
+which pip3 python3
+/share/apps/CENTOS7/python/3.8.3/bin/pip3
+/share/apps/CENTOS7/python/3.8.3/bin/python3
 </code>
@@ Line 2331: / Line 2432: @@
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
-  * program v13,2.1 installed
+Requires CentOS8 now ...
-  * program v13.2 installed
+  * program: mcc, math, mathematica in /share/apps/bin
-  * program: mcc, math, mathematica (v 12.2)
-  * install dir: /share/apps/CENTOS7/mathematica/12.2
-  * docs: on the web
-  * www:  http://www.wolfram.com/mathematica/
-  * Centos7, use queues mwgpu, amber128 or exx96
-  * For GUI launch on greentail52
   * Parallel kernels
@@ Line 2531: / Line 2626: @@
 ====== LAMMPS CPU/GPU ======
+** 7Feb2024 **
+  * /share/apps/CENTOS7/lammps/7Feb2024 (feature version vs latest stable)
+  * lmp_serial and lmp_mpi
+  * 3 cuda versions with 3 different precision settings
+  * compiled against cuda 10.2 on exx96, may work in mwgpu cuda-11.2
+  * notes: /share/apps/CENTOS7/lammps/7Feb2024.install (setup env, look for export statements)
+  * does **not** support openmp, look for the OpenHPC version for that
 ** 25Apr2023**
@@ Line 4432: / Line 4537: @@
 ====== Matlab ======
-  * installed R2023a
+Requires CentOS 8 now ...
-  * installed R2022a
+  * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
-  * installed R2021a
-  * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
-    * 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/R2020bISO
-  * docs & www: http://mathworks.com
-  * CentOS7 required use on queues mwgpu, amber128 and exx96
-  * For GUI launch on greentail52
 Note: