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--- cluster:73 [2021/11/22 17:15]
hmeij07 [Hoomd]
+++ cluster:73 [2022/04/07 14:50]
hmeij07
@@ Line 3: / Line 3: @@
 ====== Software ======
+[[cluster:215|OpenHPC Software]] for **Rocky 8**
+Below is all centos 6 and/or 7, which may or may not run in 8.
 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''
@@ Line 18: / Line 23: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== HPC SDK ======
+    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:212
+    * Nvidia SDK v 22.2
+====== Magenta ======
+An open source research project exploring the role of machine learning as a tool in the creative process.  Magenta is distributed as an open source Python library, powered by TensorFlow. This library includes utilities for manipulating source data (primarily music and images), using this data to train machine learning models, and finally generating new content from these models.
+  * https://magenta.tensorflow.org/
+  * installed in miniconda3's python3
+  * queues: mwgpu, amber128, exx96
+  * (MUSC/hgonzalez)
 ====== EasyBuild ======
@@ Line 110: / Line 130: @@
 cudatoolkit               11.0.221             h6bb024c_0
 hoomd                     2.9.4           gpu_py38h02d30ca_1    conda-forge
+# ahh, hamed found an error
+conda install -c conda-forge cudatoolkit=10.2
+The following packages will be DOWNGRADED:
+  cudatoolkit                           11.0.221-h6bb024c_0 --> 10.2.89-hfd86e86_1
+  hoomd                            2.9.4-gpu_py38h02d30ca_1 --> 2.9.4-gpu_py38h5bdc439_1
 </code>
@@ Line 564: / Line 594: @@
 </code>
+Then
+ --- //[[hmeij@wesleyan.edu|Henk]] 2021/11/24 13:16//
+<code>
+# using pip3
+Successfully installed magenta-2.1.3 python-rtmidi-1.1.2
+Successfully installed keras-2.7.0 libclang-12.0.0 tensorboard-2.7.0 \
+tensorflow-2.7.0 tensorflow-estimator-2.7.0 tensorflow-io-gcs-filesystem-0.22.0
+</code>
+Added\\
+ --- //[[hmeij@wesleyan.edu|Henk]] 2022/01/03 14:35//\\
+# https://github.com/merenlab/anvio/issues/1479
+<code>
+conda install -c bioconda samtools=1.9 --force-reinstall
+The following NEW packages will be INSTALLED:
+  gettext            conda-forge/linux-64::gettext-0.19.8.1-hf34092f_1004
+  htslib             bioconda/linux-64::htslib-1.9-h4da6232_3
+  libdeflate         bioconda/linux-64::libdeflate-1.2-h516909a_1
+  libglib            conda-forge/linux-64::libglib-2.66.3-hbe7bbb4_0
+  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
+The following packages will be UPDATED:
+  cffi                pkgs/main::cffi-1.14.3-py38h261ae71_2 --> conda-forge::cffi-1.14.4-py38ha312104_0
+  libedit            pkgs/main::libedit-3.1.20191231-h14c3~ --> conda-forge::libedit-3.1.20191231-h46ee950_2
+  samtools                                            1.7-1 --> 1.9-h10a08f8_12
+The following packages will be SUPERSEDED by a higher-priority channel:
+  glib                    pkgs/main::glib-2.69.0-h5202010_0 --> conda-forge::glib-2.66.3-h58526e2_0
+  libffi                   pkgs/main::libffi-3.3-he6710b0_2 --> conda-forge::libffi-3.2.1-he1b5a44_1007
+  ncurses                 pkgs/main::ncurses-6.2-he6710b0_1 --> conda-forge::ncurses-6.1-hf484d3e_1002
+  python                 pkgs/main::python-3.8.5-h7579374_1 --> conda-forge::python-3.8.3-cpython_he5300dc_0
+  sqlite                pkgs/main::sqlite-3.33.0-h62c20be_0 --> conda-forge::sqlite-3.32.3-hcee41ef_1
+$ samtools --version
+samtools 1.9
+Using htslib 1.9
+Copyright (C) 2018 Genome Research Ltd.
+</code>
 ====== pytraj ======
@@ Line 615: / Line 697: @@
 ====== OpenHPC ======
-So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
+So I remember where I put the tar repo file
-  * whitetail tar ball for centos7/warewulf (no slurm)
+  * OpenHPC v2.4
-  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
+  * Rocky 8.5
-  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
+  * Slurm 20.11.8
-  * https://github.com/warewulf/warewulf3 (master git zip file)
+  * Warewulf 3.9
+  * x86_64
+<code>
+[root@cottontail2 ~]# ll /share/apps/src/cottontail2/openhpc/
+total 8290421
+-rw------- 1 root root     562276 Mar 17 09:34 Install_guide-Rocky8-Warewulf-SLURM-2.4-x86_64.pdf
+-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
+</code>
 ====== OneAPI ======
@@ Line 831: / Line 924: @@
 </code>
+  * **mapDamage2**
+  * https://github.com/ginolhac/mapDamage/issues/25
+  * docker container is broke
+  * requires centos6 so queues hp12, mw128  .. may run elsewhere?
+  * conda install -c 'bioconda' mapdamage2
+<code>
+# env
+export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
+export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
+The following NEW packages will be INSTALLED:
+  mapdamage2         bioconda/linux-64::mapdamage2-2.0.6-1
+  pysam              bioconda/linux-64::pysam-0.16.0.1-py27hc729bab_3
+  seqtk              bioconda/linux-64::seqtk-1.3-h5bf99c6_3
+[hmeij@petaltail ~]$ mapDamage --version
+.0.6
+</code>
@@ Line 2925: / Line 3041: @@
   * 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''
+    * read the R-3.6.1_configure file in ''/share/apps/CENTOS6/R/R-3.6.1_configure''
 <code>

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