From 39900b8aa62a76f2a1f27bfb91fef00bc509d65f Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 10:53:10 -0600 Subject: [PATCH 01/13] add poetry to julia maybe wip --- julia.nix | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/julia.nix b/julia.nix index 3a712f6..8ddc0e3 100644 --- a/julia.nix +++ b/julia.nix @@ -1,4 +1,4 @@ -{ stdenv, lib, fetchurl, zlib, glib, xorg, dbus, fontconfig, freetype, libGL, juliaVersion }: +{ poetry, stdenv, lib, fetchurl, zlib, glib, xorg, dbus, fontconfig, freetype, libGL, juliaVersion }: let versionShas = { @@ -24,6 +24,9 @@ let stdenv.mkDerivation { name = "julia-${version}"; src = src; + buildInputs = [ + poetry + ]; installPhase = '' mkdir $out cp -R * $out/ From 58bebdba2dff7a348483e70eb8776ba2bce62983 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 10:58:21 -0600 Subject: [PATCH 02/13] wip --- conda.nix | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conda.nix b/conda.nix index 3e99336..5ff8ef7 100644 --- a/conda.nix +++ b/conda.nix @@ -7,6 +7,7 @@ , libselinux , libarchive , libGL +, poetry , xorg , zlib # Conda installs its packages and environments under this directory @@ -14,7 +15,7 @@ # Conda manages most pkgs itself, but expects a few to be on the system. , condaDeps ? [ stdenv.cc xorg.libSM xorg.libICE xorg.libX11 xorg.libXau xorg.libXi xorg.libXrender libselinux libGL zlib] # Any extra nixpkgs you'd like available in the FHS env for Conda to use -, extraPkgs ? [ ] +, extraPkgs ? [ poetry ] }: let From 6b92e28b7ec15a4eadc66f94de56a2c876f2be09 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:02:19 -0600 Subject: [PATCH 03/13] wip --- fhs.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhs.nix b/fhs.nix index 7fec4f3..3a3df86 100644 --- a/fhs.nix +++ b/fhs.nix @@ -133,7 +133,7 @@ let with pkgs; [ (python3.withPackages (ps: with ps; [ - jupyter jupyterlab numpy scipy pandas matplotlib scikit-learn tox pygments + poetry jupyter jupyterlab numpy scipy pandas matplotlib scikit-learn tox pygments ])) ]; From bca28d6cdfc5cc0629d28da3ce8becd48ff70f9e Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:10:47 -0600 Subject: [PATCH 04/13] wip --- fhs.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhs.nix b/fhs.nix index 3a3df86..86caa53 100644 --- a/fhs.nix +++ b/fhs.nix @@ -3,7 +3,7 @@ , enableJulia ? true , juliaVersion ? "1.10.0" , enableConda ? false -, enablePython ? false +, enablePython ? true , enableQuarto ? true , condaInstallationPath ? "~/.conda" , condaJlEnv ? "conda_jl" From d4ec8f338817e321cc070a5b775fbb634afc1540 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:17:37 -0600 Subject: [PATCH 05/13] wip --- fhs.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhs.nix b/fhs.nix index 86caa53..9dbe23a 100644 --- a/fhs.nix +++ b/fhs.nix @@ -133,7 +133,7 @@ let with pkgs; [ (python3.withPackages (ps: with ps; [ - poetry jupyter jupyterlab numpy scipy pandas matplotlib scikit-learn tox pygments + poetry mlflow jupyter jupyterlab numpy scipy pandas matplotlib scikit-learn tox pygments ])) ]; From 8a278cb7a3256184b2ecc470301ba111d27faab6 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:21:41 -0600 Subject: [PATCH 06/13] wip --- conda.nix | 3 +-- julia.nix | 5 +---- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/conda.nix b/conda.nix index 5ff8ef7..3e99336 100644 --- a/conda.nix +++ b/conda.nix @@ -7,7 +7,6 @@ , libselinux , libarchive , libGL -, poetry , xorg , zlib # Conda installs its packages and environments under this directory @@ -15,7 +14,7 @@ # Conda manages most pkgs itself, but expects a few to be on the system. , condaDeps ? [ stdenv.cc xorg.libSM xorg.libICE xorg.libX11 xorg.libXau xorg.libXi xorg.libXrender libselinux libGL zlib] # Any extra nixpkgs you'd like available in the FHS env for Conda to use -, extraPkgs ? [ poetry ] +, extraPkgs ? [ ] }: let diff --git a/julia.nix b/julia.nix index 8ddc0e3..3a712f6 100644 --- a/julia.nix +++ b/julia.nix @@ -1,4 +1,4 @@ -{ poetry, stdenv, lib, fetchurl, zlib, glib, xorg, dbus, fontconfig, freetype, libGL, juliaVersion }: +{ stdenv, lib, fetchurl, zlib, glib, xorg, dbus, fontconfig, freetype, libGL, juliaVersion }: let versionShas = { @@ -24,9 +24,6 @@ let stdenv.mkDerivation { name = "julia-${version}"; src = src; - buildInputs = [ - poetry - ]; installPhase = '' mkdir $out cp -R * $out/ From 4dec8dc98893c2758d60b21cd55969b718c35fa9 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:22:19 -0600 Subject: [PATCH 07/13] wip --- fhs.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fhs.nix b/fhs.nix index 9dbe23a..5be71fb 100644 --- a/fhs.nix +++ b/fhs.nix @@ -133,7 +133,7 @@ let with pkgs; [ (python3.withPackages (ps: with ps; [ - poetry mlflow jupyter jupyterlab numpy scipy pandas matplotlib scikit-learn tox pygments + poetry-core mlflow jupyter jupyterlab numpy scipy pandas matplotlib scikit-learn tox pygments ])) ]; From ec105394843c925ef36981d174add20e067f4872 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:33:06 -0600 Subject: [PATCH 08/13] WIPip --- fhs.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/fhs.nix b/fhs.nix index 5be71fb..757eb92 100644 --- a/fhs.nix +++ b/fhs.nix @@ -42,6 +42,7 @@ let which texliveScheme ncurses + bubblewrap ] ++ lib.optional enableNode pkgs.nodejs; graphicalPackages = pkgs: From 8e706ed5a19cc7c9286920936e30156a879be3a6 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 11:35:36 -0600 Subject: [PATCH 09/13] wip --- fhs.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/fhs.nix b/fhs.nix index 757eb92..e5892a6 100644 --- a/fhs.nix +++ b/fhs.nix @@ -43,6 +43,7 @@ let texliveScheme ncurses bubblewrap + poetry ] ++ lib.optional enableNode pkgs.nodejs; graphicalPackages = pkgs: From f887c5049f8193586340e1c51e33466299d0e173 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 15:48:47 -0600 Subject: [PATCH 10/13] wip --- fhs.nix | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/fhs.nix b/fhs.nix index e5892a6..a2d2b32 100644 --- a/fhs.nix +++ b/fhs.nix @@ -173,6 +173,20 @@ let export CUDA_PATH=${pkgs.cudatoolkit_11} export LD_LIBRARY_PATH=${pkgs.cudatoolkit_11}/lib:${pkgs.cudnn_cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:${pkgs.zlib}/lib:$LD_LIBRARY_PATH export EXTRA_LDFLAGS="-L/lib -L${pkgs.linuxPackages.nvidia_x11}/lib" + + export CUDA_PATH=${pkgs.cudatoolkit} + export LD_LIBRARY_PATH=${pkgs.lib.makeLibraryPath [ + pkgs.glib + pkgs.linuxPackages.nvidia_x11 + pkgs.libz + pkgs.libGL + pkgs.stdenv.cc.cc + ]} + #export LD_LIBRARY_PATH=${pkgs.linuxPackages.nvidia_x11}/lib:${pkgs.stdenv.cc.cc.lib}/lib:${pkgs.cudatoolkit.lib}/lib:${pkgs.cudatoolkit}/lib + #export RUNPATH=${pkgs.linuxPackages.nvidia_x11}/lib:${pkgs.stdenv.cc.cc.lib}/lib:${pkgs.cudatoolkit}/lib/stubs:${pkgs.cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:$LD_LIBRARY_PATH + #export LD_LIBRARY_PATH=${pkgs.linuxPackages.nvidia_x11}/lib:${pkgs.ncurses5}/lib:${pkgs.stdenv.cc.cc.lib}/lib + export EXTRA_LDFLAGS="-L/lib -L${pkgs.linuxPackages.nvidia_x11}/lib" + export EXTRA_CCFLAGS="-I/usr/include" ''; envvars = std_envvars + optionalString enableGraphical graphical_envvars From a4e3e49efecb7db3625021e20bdcbc7f3d31abb2 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 15:56:21 -0600 Subject: [PATCH 11/13] wip --- fhs.nix | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/fhs.nix b/fhs.nix index a2d2b32..a765aec 100644 --- a/fhs.nix +++ b/fhs.nix @@ -173,20 +173,22 @@ let export CUDA_PATH=${pkgs.cudatoolkit_11} export LD_LIBRARY_PATH=${pkgs.cudatoolkit_11}/lib:${pkgs.cudnn_cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:${pkgs.zlib}/lib:$LD_LIBRARY_PATH export EXTRA_LDFLAGS="-L/lib -L${pkgs.linuxPackages.nvidia_x11}/lib" - - export CUDA_PATH=${pkgs.cudatoolkit} - export LD_LIBRARY_PATH=${pkgs.lib.makeLibraryPath [ - pkgs.glib - pkgs.linuxPackages.nvidia_x11 - pkgs.libz - pkgs.libGL - pkgs.stdenv.cc.cc - ]} - #export LD_LIBRARY_PATH=${pkgs.linuxPackages.nvidia_x11}/lib:${pkgs.stdenv.cc.cc.lib}/lib:${pkgs.cudatoolkit.lib}/lib:${pkgs.cudatoolkit}/lib - #export RUNPATH=${pkgs.linuxPackages.nvidia_x11}/lib:${pkgs.stdenv.cc.cc.lib}/lib:${pkgs.cudatoolkit}/lib/stubs:${pkgs.cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:$LD_LIBRARY_PATH - #export LD_LIBRARY_PATH=${pkgs.linuxPackages.nvidia_x11}/lib:${pkgs.ncurses5}/lib:${pkgs.stdenv.cc.cc.lib}/lib - export EXTRA_LDFLAGS="-L/lib -L${pkgs.linuxPackages.nvidia_x11}/lib" - export EXTRA_CCFLAGS="-I/usr/include" + export LD_LIBRARY_PATH=${pkgs.stdenv.lib.makeLibraryPath [ + stdenv.cc.cc + zlib + glib + xorg.libXi + xorg.libxcb + xorg.libXrender + xorg.libX11 + xorg.libSM + xorg.libICE + xorg.libXext + dbus + fontconfig + freetype + libGL + ]}:$LD_LIBRARY_PATH ''; envvars = std_envvars + optionalString enableGraphical graphical_envvars From a86b19499ff58b77d1a282df7f43b7187fdc9bed Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 16:01:51 -0600 Subject: [PATCH 12/13] WIPip --- fhs.nix | 26 +++++++++----------------- 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/fhs.nix b/fhs.nix index a765aec..d745131 100644 --- a/fhs.nix +++ b/fhs.nix @@ -171,24 +171,16 @@ let nvidia_envvars = '' export CUDA_PATH=${pkgs.cudatoolkit_11} - export LD_LIBRARY_PATH=${pkgs.cudatoolkit_11}/lib:${pkgs.cudnn_cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:${pkgs.zlib}/lib:$LD_LIBRARY_PATH + # export LD_LIBRARY_PATH=${pkgs.cudatoolkit_11}/lib:${pkgs.cudnn_cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:${pkgs.zlib}/lib:$LD_LIBRARY_PATH export EXTRA_LDFLAGS="-L/lib -L${pkgs.linuxPackages.nvidia_x11}/lib" - export LD_LIBRARY_PATH=${pkgs.stdenv.lib.makeLibraryPath [ - stdenv.cc.cc - zlib - glib - xorg.libXi - xorg.libxcb - xorg.libXrender - xorg.libX11 - xorg.libSM - xorg.libICE - xorg.libXext - dbus - fontconfig - freetype - libGL - ]}:$LD_LIBRARY_PATH + export CUDA_PATH=${pkgs.cudatoolkit} + export LD_LIBRARY_PATH=${pkgs.lib.makeLibraryPath [ + pkgs.glib + pkgs.linuxPackages.nvidia_x11 + pkgs.libz + pkgs.libGL + pkgs.stdenv.cc.cc + ]} ''; envvars = std_envvars + optionalString enableGraphical graphical_envvars From 3c0614cc4538537e6dd9046ee3758a0bc3540a86 Mon Sep 17 00:00:00 2001 From: Matt Camp Date: Thu, 8 Feb 2024 16:04:22 -0600 Subject: [PATCH 13/13] wip --- fhs.nix | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/fhs.nix b/fhs.nix index d745131..50ddb39 100644 --- a/fhs.nix +++ b/fhs.nix @@ -12,7 +12,7 @@ , enableNVIDIA ? false , enableNode ? false , commandName ? "scientific-fhs" -, commandScript ? "bash" +, commandScript ? "zsh" , texliveScheme ? pkgs.texlive.combined.scheme-minimal , extraOutputsToInstall ? ["man" "dev"] }: @@ -171,16 +171,8 @@ let nvidia_envvars = '' export CUDA_PATH=${pkgs.cudatoolkit_11} - # export LD_LIBRARY_PATH=${pkgs.cudatoolkit_11}/lib:${pkgs.cudnn_cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:${pkgs.zlib}/lib:$LD_LIBRARY_PATH + export LD_LIBRARY_PATH=${pkgs.cudatoolkit_11}/lib:${pkgs.cudnn_cudatoolkit_11}/lib:${pkgs.cudatoolkit_11.lib}/lib:${pkgs.zlib}/lib:$LD_LIBRARY_PATH export EXTRA_LDFLAGS="-L/lib -L${pkgs.linuxPackages.nvidia_x11}/lib" - export CUDA_PATH=${pkgs.cudatoolkit} - export LD_LIBRARY_PATH=${pkgs.lib.makeLibraryPath [ - pkgs.glib - pkgs.linuxPackages.nvidia_x11 - pkgs.libz - pkgs.libGL - pkgs.stdenv.cc.cc - ]} ''; envvars = std_envvars + optionalString enableGraphical graphical_envvars