mirror of
https://github.com/allaunthefox/Research-Stack.git
synced 2026-07-31 03:05:21 +00:00
4bc9de1e09
Swap Docker for Podman + k3s (single-node server). New services: - PostgreSQL 16 with JIT + tuned memory (16GB shared_buffers, 48GB cache) - Caddy reverse proxy (HTTPS for LSP endpoints — needs domain) - Prometheus node exporter (port 9100) - NixOS weekly upgrade timer - Health watchdog (restarts LSP/Ollama if unhealthy) New packages (ARM64-optimized): - openblas, blis, lapack — multi-threaded linear algebra - petsc, slepc — sparse/eigenvalue solvers - flintqs, pari, gap, singular — number theory / algebra - symengine — fast C++ symbolic (SymPy backend) - fftw, suitesparse — FFT and sparse direct solvers - z3, julia_11 — SMT and JIT numerics k3s ports: 6443, 2379, 2380 Firewall updated accordingly.
243 lines
11 KiB
Nix
243 lines
11 KiB
Nix
{
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description = "Research Stack — netcup VPS (Ampere ARM64, 64GB RAM)";
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inputs = {
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nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.11";
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nixpkgs-stable.url = "github:NixOS/nixpkgs/nixos-24.11";
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};
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outputs = { self, nixpkgs, nixpkgs-stable }:
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let
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system = "aarch64-linux";
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pkgs = import nixpkgs {
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inherit system;
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config.allowUnfree = false;
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};
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# ── Lean 4 toolchains via elan ─────────────────────────────────────────
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# elan-lsp overlays lean4 onto PATH for a given toolchain.
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# Multiple toolchains can coexist; default is set via ELAN_TOOLCHAIN.
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elan-lsp = { toolchain ? "4.19.0", port ? 8765 }:
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let
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elan-init = pkgs.runCommand "elan-init-${toolchain}" {
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nativeBuildInputs = [ pkgs.curl ];
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SSL_CERT_FILE = "${pkgs.cacert}/etc/ssl/certs/ca-bundle.crt";
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} ''
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mkdir -p $out/etc/profile.d
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cat > $out/etc/profile.d/elan-${toolchain}.sh << 'PROFILE'
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export ELAN_TOOLCHAIN=${toolchain}
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export PATH="$HOME/.elan/toolchains/lean4-${toolchain}/bin:$PATH"
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PROFILE
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'';
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in pkgs.writeShellScriptBin "lean-lsp-mcp" ''
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#! ${pkgs.bash}/bin/bash
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set -euo pipefail
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export ELAN_TOOLCHAIN=${toolchain}
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export PATH="$HOME/.elan/toolchains/lean4-${toolchain}/bin:$PATH"
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export SSL_CERT_FILE=${pkgs.cacert}/etc/ssl/certs/ca-bundle.crt
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exec uvx lean-lsp-mcp --port=${toString port} --stdio
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'';
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# ── Python LSP server ─────────────────────────────────────────────────
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pylsp-tcp = { port ? 8767, extras ? [ "all" ] }:
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let
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pythonEnv = pkgs.python311.withPackages (ps: with ps; [
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numpy scipy sympy pandas matplotlib seaborn
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uncertainties pint
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beautifulsoup4 lxml
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requests httpx
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fastapi uvicorn pydantic
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python-dateutil
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]);
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in pkgs.writeShellScriptBin "pylsp-tcp" ''
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#! ${pkgs.bash}/bin/bash
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set -euo pipefail
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exec ${pythonEnv}/bin/python -m pylsp --host 0.0.0.0 --port ${toString port}
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'';
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# ── Ollama for inference ─────────────────────────────────────────────
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ollama-service = pkgs.writeShellScriptBin "ollama-service" ''
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#! ${pkgs.bash}/bin/bash
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set -euo pipefail
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export OLLAMA_HOST=0.0.0.0:11434
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exec ${pkgs.ollama}/bin/ollama serve
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'';
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# ── Core packages ─────────────────────────────────────────────────────
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corePackages = with pkgs; [
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# Version control
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git git-lfs
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# Shells & core utils
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bash bashInteractive coreutils findutils gnugrep gnused gawk
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util-linux
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# File transfer & compression
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curl wget rsync zstd xz gnutar gzip
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# Search & text processing
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ripgrep jq
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# Build essentials
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gnumake
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# Node (for any JS tooling)
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nodejs_22
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# Python: uv for runtime package management
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uv
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# Elan for Lean 4 toolchains
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elan
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# LaTeX
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texliveFull
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# Math CLI tools
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gnuplot maxima wxmaxima octave
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# Typesetting
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typst
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# Network / TLS
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openssh cacert
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# Shell helpers
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less which file procps htop
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# glibc / binutils
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glibc binutils
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# SSL / crypto
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openssl pkg-config
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# Graphviz
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graphviz
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# PostgreSQL client
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postgresql_16
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# Podman container runtime (Docker-compatible)
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podman
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# nix-ld for running x86_64 binaries on ARM64
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(import nixpkgs-stable {
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system = "x86_64-linux";
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config.allowUnfree = false;
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}).nix-ld
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];
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# ── ARM64-optimized HPC / math packages ────────────────────────────────
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# Key insight: ARM64 Neoverse N1 (Ampere Altra) has excellent SIMD
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# (ARMv8.2-A SVE/SVE2), strong memory bandwidth, and cache hierarchy
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# similar to AMD Zen. These packages are built with ARM64 in mind.
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mathPackages = with pkgs; [
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# ── Linear algebra (BLAS/LAPACK ecosystem) ───────────────────────
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openblas # Multi-threaded, ARM64 Neoverse-optimized BLAS
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blis # BLIS — fast on ARM64, cleaner than OpenBLAS
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lapack # Reference LAPACK (used via OpenBLAS/BLIS backends)
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python311Packages.scipy # Uses OpenBLAS by default
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# ── Sparse / iterative solvers ────────────────────────────────────
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petsc # Portable, extensible Toolkit for Scientific Computing
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slepc # Eigenvalue solver (builds on PETSc)
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# ── Number theory / algebra ───────────────────────────────────────
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flintqs # Fast multi-method FLINT for factoring, primality
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pari # PARI/GP — number theory, algebraic number theory
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gap # Groups, Algorithms, Programming — computational algebra
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singular # Polynomial computation, Gröbner bases
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# ── Fast symbolic engine (C++ backend for SymPy) ──────────────────
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symengine # Fast C++ symbolic library; sympy can use it as backend
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# ── FFT / signal processing ─────────────────────────────────────
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fftw # Fast Fourier Transform (single precision)
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fftwDouble # Double precision FFTW (separate package)
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# ── Sparse matrix suites ───────────────────────────────────────────
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suitesparse # CHOLMOD, UMFPACK, SPQR, etc. — sparse direct solvers
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# ── Computer Algebra System ──────────────────────────────────────
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# sage is too large for a server build (~15GB); use symengine + sympy + pari
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# maxima is already in corePackages
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# ── Polynomial systems / SMT ──────────────────────────────────────
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z3 # Microsoft Z3 (SMT solver, C++ backend)
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python311Packages.z3 # Python bindings for Z3
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# ── Julia (excellent ARM64 support, fast JIT) ───────────────────
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julia_11 # Julia 1.11 — good ARM64 SIMD vectorization
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# ── R with optimized BLAS ─────────────────────────────────────────
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rPackages.override { packages = with pkgs.rPackages; [
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RcppArmadillo # Armadillo via Rcpp (uses OpenBLAS)
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RcppEigen # Eigen via Rcpp
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]; }
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];
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# ── Python packages (full science stack) ──────────────────────────────
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pythonPackages = with pkgs.python311Packages; [
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numpy scipy sympy pandas matplotlib seaborn
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uncertainties pint
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beautifulsoup4 lxml
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requests httpx
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fastapi uvicorn pydantic
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python-dotenv pyyaml rich
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python-dateutil urllib3
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boto3 botocore
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psycopg2
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biopython networkx
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pycryptodome
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zstandard
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z3
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pywavelets
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polars
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scikit-learn
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notion-client
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pytest
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];
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# ── Custom etc for researcher user ───────────────────────────────────
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customEtc = pkgs.runCommand "custom-etc" {} ''
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mkdir -p $out/etc
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echo 'root:x:0:0:root user:/var/empty:/bin/sh' > $out/etc/passwd
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echo 'nobody:x:65534:65534:nobody:/var/empty:/bin/sh' >> $out/etc/passwd
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echo 'researcher:x:1000:1000:Research Stack developer:/home/researcher:/bin/bash' >> $out/etc/passwd
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echo 'root:x:0:' > $out/etc/group
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echo 'nobody:x:65534:' >> $out/etc/group
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echo 'researcher:x:1000:' >> $out/etc/group
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echo 'passwd: files' > $out/etc/nsswitch.conf
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echo 'group: files' >> $out/etc/nsswitch.conf
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echo 'hosts: files dns' >> $out/etc/nsswitch.conf
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'';
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researcherSetup = pkgs.runCommand "researcher-home" {} ''
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mkdir -p $out/home/researcher/stack
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mkdir -p $out/home/researcher/.elan/toolchains
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mkdir -p $out/home/researcher/.cache
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mkdir -p -m 1777 $out/tmp
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chmod 755 $out/home/researcher
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chmod 700 $out/home/researcher/.elan
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'';
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in rec {
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packages.${system} = {
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inherit corePackages pythonPackages mathPackages;
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# ── Lean LSP service (port 8765) ──────────────────────────────────
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lean-lsp-mcp = elan-lsp { toolchain = "4.19.0"; port = 8765; };
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# ── Lean LSP with mathlib toolchain (port 8766) ───────────────────
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lean-lsp-mathlib = elan-lsp { toolchain = "4.30.0-rc2"; port = 8766; };
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# ── Python LSP TCP (port 8767) ───────────────────────────────────
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pylsp = pylsp-tcp { port = 8767; };
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# ── Ollama inference server ───────────────────────────────────────
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ollama = ollama-service;
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};
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# ── NixOS configuration for the VPS ──────────────────────────────────
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nixosConfigurations.netcup-vps = nixpkgs.lib.nixosSystem {
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inherit system;
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modules = [
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./configuration.nix
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];
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};
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# Convenience: nix build .#packages.aarch64-linux.lean-lsp-mcp
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defaultPackage.${system} = packages.${system}.lean-lsp-mcp;
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# ── Dev shell ───────────────────────────────────────────────────────
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devShells.${system}.default = pkgs.mkShell {
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packages = corePackages ++ pythonPackages ++ mathPackages;
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shellHook = ''
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echo "Research Stack — netcup VPS dev shell (ARM64, NixOS 25.11)"
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export PS1='\[\033[1;34m\][rs-vps]\[\033[0m\] \w \$ '
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'';
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};
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};
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}
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