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cluster:73 [2022/06/28 16:12] hmeij07 [Miniconda3] |
cluster:73 [2023/11/16 13:57] hmeij07 [Miniconda3-py311] |
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on either cottontail2 or node n33 located at / | on either cottontail2 or node n33 located at / | ||
Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
+ | |||
+ | |||
+ | |||
+ | ====== Miniconda3-py311 ====== | ||
+ | |||
+ | * Starting a new branch, the other Miniconda3 section listed on this is quite loaded | ||
+ | * Python 3.11 | ||
+ | |||
+ | < | ||
+ | |||
+ | source / | ||
+ | or | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | which mpirun python conda | ||
+ | conda list | ||
+ | |||
+ | export CUDA_HOME=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | * conda install (same as what is listed on openhpc [[https:// | ||
+ | * cudatoolkit=10.2 cudnn=7 for exx96 queue | ||
+ | * same error, module cudatoolkit not found, but I found Cupy and it does load | ||
+ | * https:// | ||
+ | * thayerlab | ||
+ | |||
+ | < | ||
+ | |||
+ | # pollacklab | ||
+ | |||
+ | [hmeij@greentail52 ~]$ source / | ||
+ | |||
+ | [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 " | ||
+ | └────────────────────────────────────────────────────────────────────┘ | ||
+ | |||
+ | sage: exit | ||
+ | (sage) [hmeij@greentail52 ~]$ conda deactivate | ||
+ | [hmeij@greentail52 ~]$ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **mdtraj, matplotlib, pandas** | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ which python | ||
+ | / | ||
+ | | ||
+ | [hmeij@greentail52 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | ====== Masurca ====== | ||
+ | |||
+ | |||
+ | * module: masurca/ | ||
+ | * https:// | ||
+ | * supports openmp (maybe) | ||
+ | * queues mwgpu, exx96 (centos 7) | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | |||
+ | [hmeij@cottontail2 ~]$ masurca --version | ||
+ | version 4.1.0 | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | ====== Trimmomatic ====== | ||
+ | |||
+ | * http:// | ||
+ | * binary download and stage | ||
+ | * java -jar trimmomatic-0.39.jar ... | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | [root@cottontail Trimmomatic-0.39]# | ||
+ | total 176 | ||
+ | drwxr-xr-x 2 root root 8 Apr 8 2019 adapters | ||
+ | -rw-r--r-- 1 root root 35147 May 16 2018 LICENSE | ||
+ | -rw-r--r-- 1 root root 128502 Apr 8 2019 trimmomatic-0.39.jar | ||
+ | |||
+ | </ | ||
Line 223: | Line 329: | ||
Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). | Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). | ||
- | * Requires centos7 so queues mwgpu, amber128, exx96 | + | * Requires centos7 so queues mwgpu, |
* debug server greentail52 | * debug server greentail52 | ||
* PREFIX=/ | * PREFIX=/ | ||
Line 233: | Line 339: | ||
< | < | ||
- | # environment | + | # environment |
source / | source / | ||
export PATH=/ | export PATH=/ | ||
Line 244: | Line 350: | ||
which conda python pip mpirun gcc cmake | which conda python pip mpirun gcc cmake | ||
python --version | python --version | ||
+ | |||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
</ | </ | ||
Line 319: | Line 433: | ||
** Flye ** | ** Flye ** | ||
- | Somewhat annoying, no miniconda3 package, | + | Somewhat annoying, no miniconda3 package, |
- | * v2.9 | + | |
+ | | ||
+ | * python bin/flye | ||
+ | * change the PATHS accordingly | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | 2.9.2-b1794 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * v2.9.1 (October 2022) | ||
+ | * python bin/flye | ||
+ | * change the PATHs accordingly | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | 2.9.1-b1780 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * v2.9 (August 2021) | ||
* python bin/flye | * python bin/flye | ||
Line 335: | Line 472: | ||
</ | </ | ||
- | * https:// | ||
- | * miniconda3 | ||
- | * De novo assembler for single molecule sequencing reads using repeat graphs | ||
- | * v2.8.3 | ||
- | < | ||
- | |||
- | # To activate this environment, | ||
- | # $ conda activate flye | ||
- | # To deactivate an active environment, | ||
- | # $ conda deactivate | ||
- | |||
- | </ | ||
** Filtlong ** | ** Filtlong ** | ||
Line 379: | Line 504: | ||
</ | </ | ||
+ | ** BBmap ** | ||
+ | |||
+ | * location: / | ||
+ | * java programs | ||
+ | * https:// | ||
+ | |||
+ | ** Pilon ** | ||
+ | |||
+ | * location: / | ||
+ | * just one big jar file | ||
+ | * latest java is in $PATH | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 pilon]$ java -jar pilon-1.24.jar --help | ||
+ | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500 | ||
+ | |||
+ | Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam] | ||
+ | | ||
+ | pilon --help for option details | ||
+ | < | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** haslr ** | ||
+ | |||
+ | * miniconda3 env | ||
+ | * https:// | ||
+ | * conda install -c bioconda haslr | ||
+ | |||
+ | < | ||
+ | |||
+ | The following NEW packages will be INSTALLED: | ||
+ | |||
+ | _openmp_mutex | ||
+ | fastutils | ||
+ | haslr bioconda/ | ||
+ | k8 | ||
+ | libgomp | ||
+ | libzlib | ||
+ | minia bioconda/ | ||
+ | minimap2 | ||
+ | pluggy | ||
+ | ruamel.yaml | ||
+ | ruamel.yaml.clib | ||
+ | toolz conda-forge/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | Compiled from source, do **not** source miniconda3, we are using standalone pyhton3 | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | [hmeij@greentail52 20231006]$ which python | ||
+ | / | ||
+ | |||
+ | [hmeij@greentail52 20231006]$ pwd | ||
+ | / | ||
+ | |||
+ | [hmeij@greentail52 20231006]$ ll bin | ||
+ | total 11448 | ||
+ | -rwxr-xr-x 1 hmeij its | ||
+ | -rwxr-xr-x 1 hmeij its 3823032 Oct 6 15:04 haslr_assemble | ||
+ | -rwxr-xr-x 1 hmeij its 19949 Oct 6 14:48 haslr.py | ||
+ | -rwxr-xr-x 1 hmeij its 20969840 Oct 6 14:59 minia | ||
+ | -rwxr-xr-x 1 hmeij its 23856 Oct 6 15:01 minia_nooverlap | ||
+ | -rwxr-xr-x 1 hmeij its | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ** stLFR ** | ||
+ | |||
+ | * same centos 7 environment | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | cd / | ||
+ | |||
+ | [hmeij@greentail52 20230929]$ ./ | ||
+ | Version: | ||
+ | 1.00 | ||
+ | |||
+ | Contact: | ||
+ | dengli1@genomics.cn && guolidong@genomics.cn | ||
+ | |||
+ | Usage: | ||
+ | stLFR_GapCloser [options] | ||
+ | ... | ||
+ | |||
+ | |||
+ | # and another request by Luis | ||
+ | # https:// | ||
+ | |||
+ | [hmeij@greentail52 stLFR]$ pwd | ||
+ | / | ||
+ | [hmeij@greentail52 stLFR]$ ll GapCloser-bin-v1.12-r6/ | ||
+ | total 175 | ||
+ | -rwxr-xr-x 1 hmeij its 184713 Jan 11 2013 GapCloser | ||
+ | -rw-r--r-- 1 hmeij its 44533 Jan 11 2013 GapCloser_Manual.pdf | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** BUSCO ** | ||
+ | |||
+ | * https:// | ||
+ | * conda package fails on glib 2.17, weird | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@n79 ~]$ docker images | ||
+ | REPOSITORY | ||
+ | ezlabgva/ | ||
+ | |||
+ | |||
+ | [hmeij@n79 busco_wd]$ docker run --rm -v $(pwd):/ | ||
+ | 2023-10-28 20:30:00 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 10/28/2023 20:30:00 ***** | ||
+ | 2023-10-28 20:30:00 INFO: | ||
+ | 2023-10-28 20:30:00 INFO: Mode is genome | ||
+ | 2023-10-28 20:30:00 INFO: ' | ||
+ | 2023-10-28 20:30:00 INFO: | ||
+ | |||
+ | that's a problem, trying to reach the internet ... | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** picard ** | ||
+ | |||
+ | * https:// | ||
+ | * Warning: using Java 20 but only Java 17 has been tested. | ||
+ | |||
+ | < | ||
+ | |||
+ | picard centos7, weird | ||
+ | > Failed to load native library ' | ||
+ | |||
+ | picard centos8 | ||
+ | |||
+ | [hmeij@cottontail2 20231108]$ pwd | ||
+ | / | ||
+ | |||
+ | [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]$ | ||
+ | |||
+ | |||
+ | </ | ||
====== Galario CPU+GPU ====== | ====== Galario CPU+GPU ====== | ||
Line 669: | Line 950: | ||
IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * https:// | ||
+ | * calterlab, annika (used pip to install) | ||
+ | |||
+ | < | ||
+ | |||
+ | Successfully installed | ||
+ | GridDataFormats-1.0.1 MDAnalysis-2.3.0 | ||
+ | fasteners-0.18 mmtf-python-1.1.3 | ||
+ | mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4 | ||
+ | |||
+ | </ | ||
+ | |||
+ | For **Lammps** (starrlab) 23April2023, | ||
+ | |||
+ | * / | ||
+ | * make yes-ml-pace | ||
+ | * make yes-gpu | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | # Note: you must add this line to you env | ||
+ | export 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 | ||
+ | / | ||
+ | [hmeij@greentail52 ~]$ pip list | grep tensorflow | ||
+ | mesh-tensorflow | ||
+ | tensorflow | ||
+ | tensorflow-addons | ||
+ | tensorflow-datasets | ||
+ | tensorflow-estimator | ||
+ | tensorflow-gan | ||
+ | tensorflow-hub | ||
+ | tensorflow-io-gcs-filesystem 0.32.0 | ||
+ | tensorflow-metadata | ||
+ | tensorflow-probability | ||
+ | [hmeij@greentail52 ~]$ which pacemaker | ||
+ | / | ||
</ | </ | ||
Line 683: | Line 1010: | ||
* git clone https:// | * git clone https:// | ||
* python ./setup.py install | * python ./setup.py install | ||
- | * requires CentOS7 so queues mwgpu, amber128 and exx96 | + | * requires CentOS7 so queues mwgpu, |
* or for debugging use greentail52 | * or for debugging use greentail52 | ||
* / | * / | ||
Line 738: | Line 1065: | ||
-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 / | ||
+ | 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 | ||
+ | -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 | ||
+ | -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 | ||
+ | -rw-r--r-- 1 root root | ||
</ | </ | ||
Line 988: | Line 1335: | ||
pcangsd --version | pcangsd --version | ||
pcangsd 1.10 | pcangsd 1.10 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **angsd**, requires miniconda3, same environment as pcangsd | ||
+ | * http:// | ||
+ | * add location of angsd to PATH env | ||
+ | |||
+ | < | ||
+ | |||
+ | $ pwd | ||
+ | / | ||
+ | |||
+ | $ ls -l angsd | ||
+ | -rwxr-xr-x 1 hmeij its 5517248 Jul 6 14:11 angsd | ||
+ | |||
+ | $ ./ | ||
+ | -> angsd version: 0.940-dirty (htslib: 1.16) build(Jul | ||
</ | </ | ||
Line 1006: | Line 1370: | ||
</ | </ | ||
+ | |||
+ | |||
+ | * **qualimap ** | ||
+ | * http:// | ||
+ | * java & R app, probably will work in centos7 and rocky8 | ||
+ | * / | ||
+ | |||
+ | * **gatk** | ||
+ | * https:// | ||
+ | * java & R app. probably will work in centos7 and rocky8 | ||
+ | * / | ||
+ | |||
+ | 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 2008: | Line 2392: | ||
[[https:// | [[https:// | ||
+ | |||
+ | * program v13,2.1 installed | ||
+ | |||
+ | * program v13.2 installed | ||
* program: mcc, math, mathematica (v 12.2) | * program: mcc, math, mathematica (v 12.2) | ||
Line 2205: | Line 2593: | ||
====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** 25Apr2023** | ||
+ | |||
+ | * / | ||
+ | * lmp_serial and lmp_mpi | ||
+ | * 3 cuda versions with 3 different precision settings | ||
+ | * notes: / | ||
+ | * 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/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # CPU | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | which mpirun mpicc python gcc | ||
+ | |||
+ | |||
+ | # CPU + GPU (exx96 queue, may run on test and amber128 queues) | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | which nvcc | ||
+ | |||
+ | # related for starrlab | ||
+ | # https:// | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ module load miniconda3/ | ||
+ | [hmeij@cottontail2 ~]$ which pacemaker | ||
+ | / | ||
+ | [hmeij@cottontail2 ~]$ pacemaker --version | ||
+ | pacemaker/ | ||
+ | ace_evaluator | ||
+ | |||
+ | [hmeij@cottontail2 ~]$ python | ||
+ | Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21: | ||
+ | [GCC 9.4.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | |||
+ | </ | ||
** USER_QUIP ** | ** USER_QUIP ** | ||
Line 3262: | Line 3701: | ||
====== Amber ====== | ====== Amber ====== | ||
+ | |||
+ | ** Amber 22 ** | ||
+ | |||
+ | Details on how to run on CentOS7 can be found at | ||
+ | |||
+ | * https:// | ||
** Amber 20 ** | ** Amber 20 ** | ||
Line 3689: | Line 4134: | ||
< | < | ||
+ | |||
+ | # update | ||
+ | [hmeij@greentail52 ~]$ java --version | ||
+ | java 20.0.2 2023-07-18 | ||
+ | |||
+ | |||
export JAVAHOME=/ | export JAVAHOME=/ | ||
export CLASSPATH=$JAVAHOME/ | export CLASSPATH=$JAVAHOME/ | ||
Line 4043: | Line 4494: | ||
====== Matlab ====== | ====== Matlab ====== | ||
+ | * installed R2023a | ||
+ | * installed R2022a | ||
+ | |||
+ | * installed R2021a | ||
* program: Matlab, link to binary is ' | * program: Matlab, link to binary is ' | ||
Line 4063: | Line 4518: | ||
====== Stata ====== | ====== Stata ====== | ||
+ | |||
+ | * program stata[-mp|-se] in your $PATH, version 18 | ||
+ | * v17 will still run so add ' | ||
+ | * 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 |