# Pelle and issues for AEs

Rocky9 document: https://hackmd.io/@UPPMAX/rocky9sw

## Hardware

- pelle\* up 10-00:00:0 123 idle p\[1-115,201-206,251-252\]
- fat up 10-00:00:0 2 idle p\[251-252\] 96 (hyperthreads) 2 & 3TB
- gpu up 10-00:00:0 6 idle p\[201-206\]
- 201-4 64 (hyperthr) 377GB 10 L40
- 205-6 64 (hyperthr) 377GB 2 H100

## Software

### To install (oldest first)

#### User requests

- [ ] Amber with plumed [#315376](https://support.naiss.se/Ticket/Display.html?id=315376)
- [x] Diana almost done
- [ ] Vasp [#317063](https://support.naiss.se/Ticket/Display.html?id=317063)
- [x] Diana almost done

**[320167](https://support.naiss.se/Ticket/Display.html?id=320167) 30 Sep** ***Still NEW!!***
- [ ] pixy
- [ ] MAFFT (is 7.526 OK?)
- [ ] pblat
- [ ] ucsc-utilities
- [ ] vcflib
- [ ] vcftools (0.1.16/17 OK?)
- [ ] (R_packages)

**[321994](https://support.naiss.se/Ticket/Display.html?id=321994) 4 Nov**
- [ ] [Earl Grey](https://github.com/TobyBaril/EarlGrey)

**[322088](https://support.naiss.se/Ticket/Display.html?id=322088) 5 Nov**
To prioritize
- [ ] Megahit
- [x] MetaBat
- [x] MaxBin at a minimum.

Then
- [ ] VAMB,

then
- [ ] CONCOCT.

**[323947](https://support.naiss.se/Ticket/Display.html?id=323947) 10 Dec**
- [x] IQ-tree (2.4 and 3.0.1 OK?)
- [x] PCAngsd
- [ ] NGSAdmix
- [x] fastStructure (1.0-foss-2023a-Python-2.7.18 OK?)
- [x] STRUCTURE (2.3.4-GCC-13.3.0 OK?)
- [x] Fastp
- [ ] Genomescope 2.0
- [ ] KMC 3.2.2
- [ ] MSMC2
- [ ] Beta-PSMC
- [ ] SMC++
- [ ] rMATS-turbo 4.1.2

**[324101](https://support.naiss.se/Ticket/Display.html?id=324101)**
- [ ] [Pixy](https://pixy.readthedocs.io/en/latest/installation.html) 12 Dec

Some Structural Variants callers and associated tools that were on Rackham :

- [ ] [Parliament2](https://github.com/dnanexus-archive/parliament2) : (there was a singularity on Rackham)
- [ ] [SURVIVOR](https://github.com/fritzsedlazeck/SURVIVOR)
- [ ] [CNVnator](https://github.com/abyzovlab/CNVnator)
- [ ] [Manta](https://github.com/Illumina/manta)
- [ ] [Delly](https://github.com/dellytools/delly)
- [ ] [Lumpy](https://github.com/arq5x/lumpy-sv)

**[324113](https://support.naiss.se/Ticket/Display.html?id=324113)**
- [ ] mosdepth

___
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___

## Meeting Monday 14 Apr at 11-12

- add ``noarch`` in tree for, like, matlab
- more?
- EB tutorial by Doug (today)
- but also a file
- Priority of what softwares to be installed first
- Division of work

### Douglas overview of EB installation approach
- problem: you cannot have several toolchains at the same time
- runtime dependencies vs built-in in compilied executable rpaths (?)
- bioinformatics tools are often used together, too much work to make new toolchains for all
- solution:
- bioinformatic toolchains (yearly, 202Xa) when building
- also with specific versions of dependencies not shown in traditional tool-chain name
- set ``rpath`` instead manually??

## First meeting 8 Apr 11-12

### Topics to be covered
**Please add your concerns here!**

- Decision on module tree structure
- include legacy modules (currently Centos7-installed modules) via `module load legacy`
- (postinstall, makeroom)
- default `CLUSTER` for `legacy` modules
- `CLUSTER` will be ``pelle``
- How do we provision bianca when pelle is up?
- based on legacy (rackham5 perhaps)
- What is not supposed to be EB?
- See table [below](https://hackmd.io/PMixbGE_TE2mgjkJ1KbMbw#Where-to-put-data)
- Best way for
- R and packages (see table)
- we provide `-full` or `-maximal` subject-area bundles that expand on existing EB R bundles
- Python (see table)
- conda/**forge** (personal or module)
- Miniforge3 available as EB recipe
- think of Maja solutions later
- Priority of what softwares to be installed first
- Division of work
- Needs at the "system level"
- same as for Rockham
- pip, R/Rscript
- gcc, make, cmake, autoconf etc
- more?
- more?
- EB tutorial by Doug

## Present Architectures:
* `el9_broadwell`
* `el9_haswell`
* r1071 (IRHAM 1001-1075 have el9, the rest el7)
* `el9_westmere` (for `s229`, 4TB)
* needed
* a small possibility to upgrade new nmode to like 4 TB with vendor's penalty
* `el9_nehalem` (for `s230`, 2TB)
* not needed
* `el9_zen4` (?) (for the new AMD CPUs)
* `el9_icelake` (?) (Bianca 64-core nodes)

Preferred:

`/sw/arch -> /sw/architectures/el9_broadwell`
`/sw/arch -> /sw/architectures/el9_haswell`

### Directory structure

Suggested directory structure for `sw`:

[user@rackham5 SW-Directory-Structure]$ tree
/sw/
└── architectures/
    └── el9_broadwell/
        ├── eb4
        ├── eb5
        │   ├── eb5venv
        │   ├── modules
        │   └── software
        │       └── some-software
        │           └── some-version
        │               ├── bin
        │               ├── easybuild   # contains .log files generated by EasyBuild
        │               └── lib64
        ├── local/
        │   ├── modules
        │   └── software
        │       └── some-software
        │           └── some-version
        │               ├── bin
        │               ├── lib64
        │               └── localbuild   # contains README files of manual installations
        └── spack/    # if needed
    └── el9_nehalem/
        ├── eb4
            ├── ...
        ├── eb5
            ├── ...
        ├── local
            ├── ...
        └── spack    # if needed
            ├── ...
    └── el9_haswell/
        ├── ...
    └── .../
        ├── ...
└── eb_sources  # source files for EasyBuild
└── eb_recipes  # official development branch of easybuild-easyconfigs
└── apps     # legacy software from rackham/snowy/etc
└── bioinfo  # legacy software from rackham/snowy/etc
└── comp     # legacy software from rackham/snowy/etc
└── parallel # legacy software from rackham/snowy/etc
└── mf       # legacy software module files

### How to install

Program/tool|EasyBuild|As before
------------|---------|---------
matlab | check 2024b | x
Python | incl bundles (+stripped) | ?
julia | x
R | yes, combine EB bundles with own |
.. | .. | ..