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--- cluster:73 [2023/04/27 12:57]
hmeij07 old revision restored (2023/04/26 16:20)
+++ cluster:73 [2023/07/12 14:15]
hmeij07 [Trimmomatic]
@@ Line 26: / Line 26: @@
-====== Trimmomatic ======
+===== Masurca =====
+    module: masurca/4.1.0
+    https://github.com/alekseyzimin/masurca/releases
+    supports openmp (maybe)
+    queues mwgpu, exx96 (centos 7)
+<code>
+export PATH=/share/apps/CENTOS7/masurca/4.1.0/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/masurca/4.1.0/lib:$LD_LIBRARY_PATH
+</code>
+===== Trimmomatic =====
   * http://www.usadellab.org/cms/?page=trimmomatic
@@ Line 346: / Line 362: @@
 ** Flye **
-Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2)
+Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52.
+  * setup env as for all packages in #3, see top of section
+  * v2.9.2 (June 2023)
+  * python bin/flye
+    * change the PATHS accordingly
+<code>
+/share/apps/CENTOS7/flye/2.9.2/bin/flye --version
+.9.2-b1794
+</code>
   * v2.9.1 (October 2022)
@@ Line 373: / Line 401: @@
 </code>
-  * https://github.com/fenderglass/Flye
-  * miniconda3
-  * De novo assembler for single molecule sequencing reads using repeat graphs
-  * v2.8.3
-<code>
-# To activate this environment, use
-#     $ conda activate flye
-# To deactivate an active environment, use
-#     $ conda deactivate
-</code>
 ** Filtlong **
@@ Line 719: / Line 735: @@
 fasteners-0.18 mmtf-python-1.1.3
 mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4
+</code>
+For **Lammps** (starrlab) 23April2023, consult install file
+  *  /share/apps/CENTOS7/lammps/25Apr2023.install
+  * make yes-ml-pace
+  * make yes-gpu
+  * https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
+<code>
+# Note: you must add this line to you env
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/pkgs/cudatoolkit-11.0.221-h6bb024c_0/lib:$LD_LIBRARY_PATH
+# Note2: had to install 'conda install cudnn' and make two links
+to higher level libraries (a must not do)
+for libcudnn.so.8 and libcusolver.so.11
+[hmeij@greentail52 ~]$ which python
+/share/apps/CENTOS7/amber/miniconda3/bin/python
+[hmeij@greentail52 ~]$ pip list | grep tensorflow
+mesh-tensorflow              0.1.19
+tensorflow                   2.8.0
+tensorflow-addons            0.15.0
+tensorflow-datasets          4.4.0
+tensorflow-estimator         2.7.0
+tensorflow-gan               2.1.0
+tensorflow-hub               0.12.0
+tensorflow-io-gcs-filesystem 0.32.0
+tensorflow-metadata          1.4.0
+tensorflow-probability       0.15.0
+[hmeij@greentail52 ~]$ which pacemaker
+/usr/bin/which: no pacemaker in (...failed to install
 </code>
@@ Line 1058: / Line 1108: @@
 pcangsd --version
 pcangsd 1.10
+</code>
+  * **angsd**, requires miniconda3, same environment as pcangsd
+  * http://www.popgen.dk/angsd/index.php/RealSFS
+  * add location of angsd to PATH env
+<code>
+$ pwd
+/share/apps/CENTOS7/angsd/0.940/angsd
+$ ls -l angsd
+-rwxr-xr-x 1 hmeij its 5517248 Jul  6 14:11 angsd
+$ ./angsd
+	-> angsd version: 0.940-dirty (htslib: 1.16) build(Jul  6 2023 14:11:30)
 </code>
@@ Line 2078: / Line 2145: @@
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
+  * program v13,2.1 installed
+  * program v13.2 installed
   * program: mcc, math, mathematica (v 12.2)
@@ Line 2281: / Line 2352: @@
   * lmp_serial and lmp_mpi
   * 3 cuda versions with 3 different precision settings
-  * notes: /share/apps/CENTOS7//lammps/25Apr2023.install
+  * notes: /share/apps/CENTOS7/lammps/25Apr2023.install
+  * does **not** support openmp, look for the OpenHPC version for that
+  * 05/24/2023 remade with package CREATION added
+  * also read miniconda3 section for tensorflow/pacemaker info
 <code>
@@ Line 2287: / Line 2361: @@
 # CPU
+ export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin/:$PATH
+ export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$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 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
+ which mpirun mpicc python gcc
 # CPU + GPU (exx96 queue, may run on test and amber128 queues)
@@ Line 2300: / Line 2377: @@
  export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
  which nvcc
+# related for starrlab
+# https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
+[hmeij@cottontail2 ~]$ module load miniconda3/py39
+[hmeij@cottontail2 ~]$ which pacemaker
+/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker
+[hmeij@cottontail2 ~]$ pacemaker --version
+pacemaker/pyace version: 0.2.7+77.g8b40c11
+ace_evaluator   version: 2022.6.27
+[hmeij@cottontail2 ~]$ python
+Python 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:24:11)
+[GCC 9.4.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import pyace as py
+>>>
@@ Line 4147: / Line 4241: @@
 ====== Matlab ======
+  * installed R2023a
+  * installed R2022a
+  * installed R2021a
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
@@ Line 4167: / Line 4265: @@
 ====== Stata ======
+  * program stata[-mp|-se] in your $PATH, version 18
+  * v17 will still run so add '17' to the command like 'stata-mp17'
+  * so that makes for 12 licenses 8-)
   * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se

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