DokuWiki

User Tools

Site Tools

Trace:
cluster:73

Warning: Undefined array key -1 in /usr/share/dokuwiki/inc/html.php on line 1458

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
cluster:73 [2023/10/12 15:29]
hmeij07 [Sequencing Tools #3] 		cluster:73 [2024/02/16 11:17] (current)
hmeij07 [LAMMPS CPU/GPU]
Line 54: Line 54:
   * thayerlab   * thayerlab
  
 +<code>
 +
 +# pollacklab
 +
 +[hmeij@greentail52 ~]$ source /share/apps/CENTOS7/miniconda3-py311/etc/profile.d/conda.sh
 +
 +[hmeij@greentail52 ~]$ conda activate sage
 +
 +(sage) [hmeij@greentail52 ~]$ sage --version
 +SageMath version 10.0, Release Date: 2023-05-20
 +
 +(sage) [hmeij@greentail52 ~]$ sage
 +┌────────────────────────────────────────────────────────────────────┐
 +│ SageMath version 10.0, Release Date: 2023-05-20                    │
 +│ 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>
  
  
Line 587: Line 637:
 REPOSITORY                         TAG                            IMAGE ID            CREATED             SIZE REPOSITORY                         TAG                            IMAGE ID            CREATED             SIZE
 ezlabgva/busco                     v5.5.0_cv1                     30d3e831aba7        2 months ago        2.88GB ezlabgva/busco                     v5.5.0_cv1                     30d3e831aba7        2 months ago        2.88GB
 +
 +
 +[hmeij@n79 busco_wd]$ docker run --rm -v $(pwd):/busco_wd -u $(id -u):$(id -g) ezlabgva/busco:v5.5.0_cv1 busco -i /busco_wd/assembly.fasta -l actinopterygii_odb10 -o Busco_Output -m geno -f
 +2023-10-28 20:30:00 INFO:       ***** Start a BUSCO v5.5.0 analysis, current time: 10/28/2023 20:30:00 *****
 +2023-10-28 20:30:00 INFO:       Configuring BUSCO with local environment
 +2023-10-28 20:30:00 INFO:       Mode is genome
 +2023-10-28 20:30:00 INFO:       'Force' option selected; overwriting previous results directory
 +2023-10-28 20:30:00 INFO:       Downloading information on latest versions of BUSCO data...
 +
 +that's a problem, trying to reach the internet ...
  
 </code> </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 ====== ====== Galario CPU+GPU ======
  
Line 1300: Line 1384:
  
 </code> </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 2503: Line 2607:
  
 ====== LAMMPS CPU/GPU ====== ====== 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** ** 25Apr2023**
cluster/73.1697138985.txt.gz · Last modified: 2023/10/12 15:29 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