DokuWiki

User Tools

Site Tools

Trace:
cluster:73

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
cluster:73 [2022/12/01 18:57]
hmeij07 [HPC SDK] 		cluster:73 [2023/07/04 12:24]
hmeij07 [Sequencing Tools #3]
Line 30: Line 30:
   * http://www.usadellab.org/cms/?page=trimmomatic   * http://www.usadellab.org/cms/?page=trimmomatic
   * binary download and stage   * binary download and stage
 +  * java -jar trimmomatic-0.39.jar ...
  
 <code> <code>
Line 345: Line 346:
 ** Flye ** ** 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. 
 + 
 +  * v2.9.2 (June 2023) 
 +  * python bin/flye 
 +    * chnage the PATHS accordingly 
 + 
 +<code> 
 + 
 +/share/apps/CENTOS7/flye/2.9.2/bin/flye --version 
 +2.9.2-b1794 
 + 
 +</code>
  
   * v2.9.1 (October 2022)   * v2.9.1 (October 2022)
Line 372: Line 384:
 </code> </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 ** ** Filtlong **
Line 718: Line 718:
 fasteners-0.18 mmtf-python-1.1.3  fasteners-0.18 mmtf-python-1.1.3 
 mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4 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> </code>
Line 787: Line 821:
 -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      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 -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> </code>
Line 2057: Line 2111:
  
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]] [[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)   * program: mcc, math, mathematica (v 12.2)
Line 2254: Line 2312:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** 25Apr2023**
 +
 +  * /share/apps/CENTOS7/lammps/25Arp2023
 +  * lmp_serial and lmp_mpi
 +  * 3 cuda versions with 3 different precision settings
 +  * 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>
 +
 +# 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 gcc
 +
 +
 +# 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:$LD_LIBRARY_PATH
 + which nvcc
 +
 +# related for starrlab
 +# https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
 +
 +[hmeij@cottontail2 ~]$ 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
 +>>> 
 +
 +
 +</code>
  
 ** USER_QUIP ** ** USER_QUIP **
Line 4098: Line 4207:
 ====== Matlab ====== ====== Matlab ======
  
 +  * installed R2023a
  
 +  * installed R2022a
 +
 +  * installed R2021a
  
   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''   * program: Matlab, link to binary is 'matlab' in ''/share/apps/bin''
Line 4118: Line 4231:
  
 ====== Stata ====== ====== 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    * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se 
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
CC Attribution-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki