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cluster:73 [2022/12/01 18:58] hmeij07 [Trimmomatic] |
cluster:73 [2023/06/01 14:24] hmeij07 [Sequencing Tools #3] |
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** 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, so local install, use minconda3 environment as listed top of this section (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 | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | 2.9.2-b1794 | ||
+ | |||
+ | </ | ||
* v2.9.1 (October 2022) | * v2.9.1 (October 2022) | ||
Line 788: | Line 799: | ||
-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 | ||
</ | </ | ||
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====== 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 | ||
+ | |||
+ | < | ||
+ | |||
+ | # 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 ** |