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--- cluster:73 [2020/01/14 14:57]
hmeij07 [Paleogenomics Tools]
+++ cluster:73 [2020/04/02 18:45]
hmeij07 [LAMMPS CPU/GPU]
@@ Line 2: / Line 2: @@
 **[[cluster:0|Back]]**
+====== Software ======
 The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing).
@@ Line 10: / Line 10: @@
 Most of the compilations have been performed by Intel's icc/ifort compilers.
-The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33.
+Old compilations, mostly located in /share/apps, are RHEL 5.5 \\
+Newer compilations are done with CentOS 6.10 (since summer 2013) \\
+on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
+Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== Deep Learning Software Stack ======
+  * queue ''exx96'' provides access to docker containers and
+    * **digits, tensorflow, pytorch, caffe, rapidsai**
+    * cuda (several versions)
+    * jupyterlab
+    * portainer
+  * consult [[cluster:193|Docker Containers Usage]]
 ====== Paleogenomics Tools ======
@@ Line 40: / Line 52: @@
 </code>
+  * https://www.beast2.org/
+  * BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
+<code>
+# with local java jre1.8.0_212
+export PATH=/share/apps/CENTOS6/beast/2.6.0/bin:$PATH
+</code>
 ====== CD-HIT ======
@@ Line 118: / Line 141: @@
 ====== Python3 ======
+Added to both versions\\
+pycuda\\
+ --- //[[hmeij@wesleyan.edu|Henk]] 2020/02/18 08:45//
+Added to both 3.5.2 versions\\
+Successfully installed\\
+boto-2.49.0 boto3-1.12.0 botocore-1.15.0 gensim-3.8.1 jmespath-0.9.4 s3transfer-0.3.3 smart-open-1.9.0\\
+joblib, scikit-learn, sklearn\\
+\\
+Requirement already satisfied:\\
+keras keras-preprocessing keras-applications\\
+tensorflow (requires centos7)\\
+ --- //[[hmeij@wesleyan.edu|Henk]] 2020/02/17 13:02//
 Added to both 3.5.2 versions\\
@@ Line 1117: / Line 1155: @@
 ====== LAMMPS CPU/GPU ======
+  * /share/apps/CENTOS7/lammps/3Mar2020
+    * lmp_mpi-[double-double|single-double|single-single]
+  * consult this file for packages installed and compilations
+    * /share/apps/CENTOS7/lammps/03Mar2020.install
+    * CUDA_ARCH = sm_75 (probably only works on queue exx96)
+  * sample script in ~hmeij/k20redo/run.rtx.lammps
+<code>
+# simple colloid example
+CPU run -n1
+Performance: 493311 tau/day, 1141 timesteps/s
+GPU run gpu4=1 double-double: 1.1x
+Performance: 571354 tau/day, 1322 timesteps/s
+GPU run gpu4=1 single-double: 1.2x
+Performance: 608498 tau/day, 1408 timesteps/s
+GPU run gpu4=1 single-single: 1.3x
+Performance: 623405 tau/day, 1443 timesteps/s
+</code>
     * /share/apps/CENTOS6/lammps/22Aug18
       * consult [[cluster:161|lammps-11Aug17]] page
@@ Line 1861: / Line 1918: @@
 ====== R & R/parallel ======
+  * https://edwards.sdsu.edu/research/c11-on-centos-6/
+    * C11++ on CentOS6, two version of gcc
+    * read the R-3.6.1_configure file in ''/share/apps/src/cottontail2''
+<code>
+install.packages('lme4', dependencies = TRUE)
+install.packages('tidyverse', dependencies = TRUE)
+install.packages('mice', dependencies = TRUE)
+install.packages('rpart', dependencies = TRUE)
+install.packages('party', dependencies = TRUE)
+install.packages('caret', dependencies = TRUE)
+install.packages('nnet', dependencies = TRUE)
+install.packages('e1071', dependencies = TRUE)
+install.packages('xgboost', dependencies = TRUE)
+install.packages('kernlab', dependencies = TRUE)
+install.packages('randomForest', dependencies = TRUE)
+</code>
   * R 3.6.1 (running against "packages", had to comment out libcurl version check)
@@ Line 2001: / Line 2077: @@
 ====== Amber ======
+** AMBER 18 **
+  * **/share/apps/CENTOS7/amber/amber18**
+  * compiled on ''n33'' with a ''/usr/local/n37-cuda-9.2'' soft link
+  * view compile steps at /share/apps/CENTOS7/amber/amber18.install
+  * when submitting on ''exx96'' we're mixing
+    * 10.2 cuda drivers
+    * 9.2 toolkits
+  * some speed results below K20 vs RTX2080s, Amber 16 vs 18
+  * sample jobs at ~hmeij/k20redo/run.amber[16|18]
+<code>
+# compiled on n33
+[hmeij@n33 amber18]$ ls -l bin/pmemd*
+-rwxr-xr-x 1 hmeij its  3549803 Mar 30 10:19 bin/pmemd
+lrwxrwxrwx 1 hmeij its       15 Mar 30 11:57 bin/pmemd.cuda -> pmemd.cuda_SPFP
+-rwxr-xr-x 1 hmeij its 93895208 Mar 30 12:11 bin/pmemd.cuda_DPFP
+-rwxr-xr-x 1 hmeij its 94734272 Mar 30 13:07 bin/pmemd.cuda_DPFP.MPI
+lrwxrwxrwx 1 hmeij its       19 Mar 30 12:51 bin/pmemd.cuda.MPI -> pmemd.cuda_SPFP.MPI
+-rwxr-xr-x 1 hmeij its 75579744 Mar 30 11:57 bin/pmemd.cuda_SPFP
+-rwxr-xr-x 1 hmeij its 76418760 Mar 30 12:51 bin/pmemd.cuda_SPFP.MPI
+-rwxr-xr-x 1 hmeij its  4304392 Mar 30 11:23 bin/pmemd.MPI
+# some quick results
+|     Average timings for all steps:
+~hmeij/k20redo/run.amber18 - mwgpu - K20
+|         ns/day =       2.84   seconds/ns =   30385.24
+~hmeij/k20redo/run.amber18 - exx96 - RTX2080S
+|         ns/day =      11.66   seconds/ns =    7408.08
+~hmeij/k20redo/run.amber16 - exx96 - RTX2080S
+|         ns/day =       7.09   seconds/ns =   12185.91
+</code>
 **AMBER 16**
@@ Line 2595: / Line 2709: @@
 For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page ...
+  * program: GCC v 9.2.0
+  * /share/apps/CENTOS6/9.2.0
+  * note: libgomp disabled for nanopolish compile attempt
+<code>
+  wget ftp://ftp.nluug.nl/mirror/languages/gcc/releases/gcc-9.2.0/gcc-9.2.0.tar.gz
+  tar zxvf gcc-9.2.0.tar.gz
+  cd gcc-9.2.0
+  ./contrib/download_prerequisites
+  ./configure --prefix=/share/apps/CENTOS6/gcc/9.2.0 --disable-libgomp --disable-multilib
+  make
+  make install
+</code>
   * program: GCC v 4.8.4

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