Hi,
I am trying to install open3d on my system and I am running in to different challenges. I am new to Nix/NixOS and am learning as I go. Online I found a gist that I took as inspiration, but that one is installing a prior version of open3D, so I have been adapting it.
As far as I can tell from my log, my issues are with the build of nccl-2.12.10-1-cuda-11.7 failing if I include tensorflow as a build buildInput.
And If I leave tensorflow out, then then the autoPatchlfHook failes to find the following binaries.
libglapi.so.0 -> kms_swrast_dri.so
libdrm.so.2 -> kms_swrast_dri.so
libLLVM-10.so.1 -> kms_swrast_dri.so
libzstd.so.1 -> kms_swrast_dri.so
libglapi.so.0 -> libEGL.so.1
libdrm.so.2 -> libEGL.so.1
libglapi.so.0 -> libgallium_dri.so
libdrm.so.2 -> libgallium_dri.so
libLLVM-10.so.1 -> libgallium_dri.so
libzstd.so.1 -> libgallium_dri.so
libglapi.so.0 -> libGL.so.1
libdrm.so.2 -> libGL.so.1
libXxf86vm.so.1 -> libGL.so.1
libglapi.so.0 -> swrast_dri.so
libdrm.so.2 -> swrast_dri.so
libLLVM-10.so.1 -> swrast_dri.so
libzstd.so.1 -> swrast_dri.so
I am on system.stateVersion = "22.11";
and here is what I believe is relevant form my config file.
The unstable channel I am referencing is unstable https://nixos.org/channels/nixpkgs-unstable
If you have any pointers as to what I could try or see what I am doing wrong, I’d be happy for any hint.
{ config, pkgs, lib, fetchPypi, fetchurl, ... }:
let
unstable = import <nixos-unstable> {
config.allowUnfree = true;
config.cudaSupport = true;
};
my_python = unstable.pkgs.python3.override {
packageOverrides = self: super: {
nbformat = super.buildPythonPackage rec {
pname = "nbformat";
version = "5.7.0";
format = "wheel";
src = pkgs.fetchurl {
url = "https://files.pythonhosted.org/packages/5c/9f/957655d02f43b8bff77e6da08c94472b1229c13e7455bbd662163c9b78c0/nbformat-5.7.0-py3-none-any.whl";
sha256 = "sha256-GwXsLFUsLxrcdF9O3c4erIyp/9Wbuf2FnoJ+qgMTGfk=";
};
buildInputs = with super; [
fastjsonschema
jupyter_core
jsonschema
];
propagatedBuildInputs = with super; [
fastjsonschema
jupyter_core
jsonschema
];
};
};
};
in
{
nixpkgs.config = {
allowUnfree = true;
cudaSupport = true;
};
# List packages installed in system profile. To search, run:
environment.systemPackages = with pkgs; [
linuxPackages.nvidia_x11
cudaPackages.cudatoolkit
cudaPackages.cudnn
conda
(my_python.withPackages( ps: with ps; [
pip
numpy
torch-bin
matplotlib
pandas
ipywidgets
# tensorflow
# tensorflowWithCuda
(
buildPythonPackage rec {
pname = "open3d";
version = "0.17.0";
format = "pyproject";
src = unstable.fetchurl {
url ="https://github.com/isl-org/Open3D/releases/download/v0.16.0/open3d-devel-linux-x86_64-cxx11-abi-cuda-0.16.0.tar.xz";
sha256 = "sha256-0HnwgZPfeDNy+0bKL/pT1u9q4413Jeht48MUyHQMAxA=";
};
nativeBuildInputs = [
autoPatchelfHook
];
}
)
(
buildPythonPackage rec {
pname = "open3d";
version = "0.17.0";
format = "wheel";
src = unstable.python3Packages.fetchPypi {
inherit pname version format;
sha256 = "sha256-PcMAaXMgu2iCRsXQn2gQRYFcMyIlaFc/GWSy11ZDFlc=";
dist = "cp310";
python = "cp310";
abi = "cp310";
platform = "manylinux_2_27_x86_64";
};
# patchPhase = ''
# ${unzip}/bin/unzip ./dist/open3d-0.17.0-cp310-cp310-manylinux_2_27_x86_64.whl -d tmp
# rm ./dist/open3d-0.17.0-cp310-cp310-manylinux_2_27_x86_64.whl
# sed -i 's/sklearn/scikit-learn/g' tmp/open3d-0.17.0.dist-info/METADATA
# cd tmp
# ${zip}/bin/zip -0 -r ../dist/open3d-0.17.0-cp310-cp310-manylinux_2_27_x86_64.whl ./*
# cd ../
# ';
nativeBuildInputs = [
autoPatchelfHook
];
buildInputs = with pkgs; [
# so deps
stdenv.cc.cc.lib
libusb.out
cudaPackages.cudatoolkit
libtorch-bin
libGL
(my_python.withPackages( ps: with ps; [
torch-bin
tensorboard
tensorflow-bin
]))
];
propagatedBuildInputs = [
# py deps
(my_python.withPackages(
ps: with ps; [
dash
configargparse
pyquaternion
ipywidgets
tqdm
pyyaml
pandas
plyfile
scipy
scikitlearn
numpy
addict
matplotlib
tensorboard
nbformat
]))
];
})
]))
];
}
I thought it might be helpful if I add the build log with the errors.
The first one is with tensorflow included, and to me it seems that there is an issue with CUDA support.
Although CUDA seems to work just fine for me in pyTorch.
include/debug.h:34:77: note: in definition of macro 'WARN'
34 | #define WARN(...) ncclDebugLog(NCCL_LOG_WARN, NCCL_ALL, __FILE__, __LINE__, __VA_ARGS__)
| ^~~~~~~~~~~
include/alloc.h:158:3: note: in expansion of macro 'CUDACHECK'
158 | CUDACHECK(cudaThreadExchangeStreamCaptureMode(&mode));
| ^~~~~~~~~
include/checks.h:24:53: error: 'cudaGetErrorString' was not declared in this scope; did you mean 'cuGetErrorString'?
24 | WARN("Cuda failure '%s'", cudaGetErrorString(err)); \
| ~~~~~~~~~~~~~~~~~~^~~~~
include/debug.h:34:77: note: in definition of macro 'WARN'
34 | #define WARN(...) ncclDebugLog(NCCL_LOG_WARN, NCCL_ALL, __FILE__, __LINE__, __VA_ARGS__)
| ^~~~~~~~~~~
include/alloc.h:159:3: note: in expansion of macro 'CUDACHECKGOTO'
159 | CUDACHECKGOTO(cudaFree(ptr), result, finish);
| ^~~~~~~~~~~~~
include/checks.h:16:53: error: 'cudaGetErrorString' was not declared in this scope; did you mean 'cuGetErrorString'?
16 | WARN("Cuda failure '%s'", cudaGetErrorString(err)); \
| ~~~~~~~~~~~~~~~~~~^~~~~
include/debug.h:34:77: note: in definition of macro 'WARN'
34 | #define WARN(...) ncclDebugLog(NCCL_LOG_WARN, NCCL_ALL, __FILE__, __LINE__, __VA_ARGS__)
| ^~~~~~~~~~~
include/alloc.h:161:3: note: in expansion of macro 'CUDACHECK'
161 | CUDACHECK(cudaThreadExchangeStreamCaptureMode(&mode));
| ^~~~~~~~~
make[1]: *** [Makefile:120: /build/source/build/obj/enqueue.o] Error 1
make[1]: Leaving directory '/build/source/src'
make: *** [Makefile:25: src.build] Error 2
error: builder for '/nix/store/9yqjl3wqd5n92y1zjsahcsj0bl4aspyg-nccl-2.16.5-1-cuda-11.drv' failed with exit code 2
error: 1 dependencies of derivation '/nix/store/mrg93381myi59y29br39hcs464kl2p6l-bazel-build-jaxlib-0.3.22-deps.tar.gz.drv' failed to build
error: 2 dependencies of derivation '/nix/store/6zsszdn1cciv334l6h00jffv628sqhx5-bazel-build-jaxlib-0.3.22.drv' failed to build
error: 2 dependencies of derivation '/nix/store/247xv7haia8v59s2fgs1q1mgp968b75w-python3.10-jaxlib-0.3.22.drv' failed to build
error: 1 dependencies of derivation '/nix/store/6kjnzjavz88z5zypks6d0lgxm8k0dahx-python3.10-jax-0.4.1.drv' failed to build
error: 1 dependencies of derivation '/nix/store/g1jvj6l6rhqlqfxaz8lcasbcfxca94n3-python3.10-tensorflow-gpu-2.12.0.drv' failed to build
error: 2 dependencies of derivation '/nix/store/4mr03lgbic446yc72zj1ma57x1n1l115-python3-3.10.10-env.drv' failed to build
error: 1 dependencies of derivation '/nix/store/mpmqvjcd8ljxf2n9kdhgn6yqp4wcrkb4-python3.10-open3d-0.17.0.drv' failed to build
error: 2 dependencies of derivation '/nix/store/g6lcb7jql4ypaig67fy087bpgympgy5j-python3-3.10.10-env.drv' failed to build
error: 1 dependencies of derivation '/nix/store/78amws50vanwf7kvvjdin1gr65cla2g9-system-path.drv' failed to build
error: 1 dependencies of derivation '/nix/store/sdqb88ps8w8f4rfrm157aj2vj05n5i22-dbus-1.drv' failed to build
error: 1 dependencies of derivation '/nix/store/z5wacjp4n4177ikbanaw69g7fqcygpp9-unit-accounts-daemon.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/1kmmpzcry1rmsldd0kyr67raw3176lqj-unit-polkit.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/sycza7vzgx31iy8v2hx83ycg78ywxb3z-unit-systemd-fsck-.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/473xnva59n14yb179qj7cv84npifwglq-unit-dbus.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/ia31zpka3yc6s9ga6cmk189ibmd3p8y7-unit-dbus.service.drv' failed to build
error: 4 dependencies of derivation '/nix/store/vjb13w6050pd5zbaxp833b55b5643nkk-system-units.drv' failed to build
error: 1 dependencies of derivation '/nix/store/cymlqx76wp3qwfp5yanzrs41sg7f58p7-user-units.drv' failed to build
error: 4 dependencies of derivation '/nix/store/4pb4icy0vznmpv4qbjcaincas97xvknx-etc.drv' failed to build
error: 2 dependencies of derivation '/nix/store/pkckqm1lfhlk859mbviaa6j1mk32y9jr-nixos-system-nixos-22.11.3781.cd749f58ba8.drv' failed to build
The second one. Here I omitted tensorflow and now I seem to be missing some binaries that look as though they relate to openGL
setting RPATH to: /nix/store/zqix2nszqij97ldlryzw7qypx43fp5kv-libtorch-1.12.1/lib:/nix/store/6plx60y4x4q2lfp6n7190kaihyxr7m1w-gcc-11.3.0-lib/lib
searching for dependencies of /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/cpu/pybind.cpython-310-x86_64-linux-gnu.so
libudev.so.1 -> found: /nix/store/x53598nbd84lz90f10zdw8w6g2a98qw6-systemd-minimal-251.15/lib
libgomp.so.1 -> found: /nix/store/6plx60y4x4q2lfp6n7190kaihyxr7m1w-gcc-11.3.0-lib/lib
libX11.so.6 -> found: /nix/store/33qdhi8l6f4ixqzdc387w9gwdxrdsara-libX11-1.8.4/lib
libstdc++.so.6 -> found: /nix/store/6plx60y4x4q2lfp6n7190kaihyxr7m1w-gcc-11.3.0-lib/lib
libc++.so.1 -> found: /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d
libGL.so.1 -> found: /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d
libgcc_s.so.1 -> found: /nix/store/6plx60y4x4q2lfp6n7190kaihyxr7m1w-gcc-11.3.0-lib/lib
setting RPATH to: /nix/store/x53598nbd84lz90f10zdw8w6g2a98qw6-systemd-minimal-251.15/lib:/nix/store/6plx60y4x4q2lfp6n7190kaihyxr7m1w-gcc-11.3.0-lib/lib:/nix/store/33qdhi8l6f4ixqzdc387w9gwdxrdsara-libX11-1.8.4/lib:/nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d
auto-patchelf: 19 dependencies could not be satisfied
error: auto-patchelf could not satisfy dependency libglapi.so.0 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/kms_swrast_dri.so
error: auto-patchelf could not satisfy dependency libdrm.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/kms_swrast_dri.so
error: auto-patchelf could not satisfy dependency libLLVM-10.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/kms_swrast_dri.so
error: auto-patchelf could not satisfy dependency libzstd.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/kms_swrast_dri.so
error: auto-patchelf could not satisfy dependency libglapi.so.0 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libEGL.so.1
error: auto-patchelf could not satisfy dependency libdrm.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libEGL.so.1
error: auto-patchelf could not satisfy dependency libglapi.so.0 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libgallium_dri.so
error: auto-patchelf could not satisfy dependency libdrm.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libgallium_dri.so
error: auto-patchelf could not satisfy dependency libLLVM-10.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libgallium_dri.so
error: auto-patchelf could not satisfy dependency libzstd.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libgallium_dri.so
error: auto-patchelf could not satisfy dependency libglapi.so.0 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libGL.so.1
error: auto-patchelf could not satisfy dependency libdrm.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libGL.so.1
error: auto-patchelf could not satisfy dependency libXxf86vm.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/libGL.so.1
error: auto-patchelf could not satisfy dependency libglapi.so.0 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/swrast_dri.so
error: auto-patchelf could not satisfy dependency libdrm.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/swrast_dri.so
error: auto-patchelf could not satisfy dependency libLLVM-10.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/swrast_dri.so
error: auto-patchelf could not satisfy dependency libzstd.so.1 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/swrast_dri.so
error: auto-patchelf could not satisfy dependency libtensorflow_framework.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/cuda/open3d_tf_ops.so
error: auto-patchelf could not satisfy dependency libtensorflow_framework.so.2 wanted by /nix/store/zhrg5nn412h76y5l80z9c37hqcc98w90-python3.10-open3d-0.17.0/lib/python3.10/site-packages/open3d/cpu/open3d_tf_ops.so
auto-patchelf failed to find all the required dependencies.
Add the missing dependencies to --libs or use `--ignore-missing="foo.so.1 bar.so etc.so"`.
/nix/store/5s1yg5l36wzgy1dj0vv1ibarc4g7vrdr-stdenv-linux/setup: line 79: pop_var_context: head of shell_variables not a function context
/nix/store/5s1yg5l36wzgy1dj0vv1ibarc4g7vrdr-stdenv-linux/setup: line 1457: pop_var_context: head of shell_variables not a function context
/nix/store/5s1yg5l36wzgy1dj0vv1ibarc4g7vrdr-stdenv-linux/setup: line 1594: pop_var_context: head of shell_variables not a function context
error: builder for '/nix/store/9sh9yjq6ahb63pc8aqdz45xiz1hg212i-python3.10-open3d-0.17.0.drv' failed with exit code 1
error: 2 dependencies of derivation '/nix/store/q447a12jdyk6ycpi92wvb72qh3cgnn8r-python3-3.10.10-env.drv' failed to build
error: 1 dependencies of derivation '/nix/store/mlgjwl5qg9jf9hmj5c0lcsf29xdgxgy5-system-path.drv' failed to build
error: 1 dependencies of derivation '/nix/store/64gcl7vvxpyrhr3iy0nfr9hpcpl8wap4-dbus-1.drv' failed to build
error: 1 dependencies of derivation '/nix/store/flqz1s269qcj3q11hfbdq0yhkfb5yda1-unit-accounts-daemon.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/hlxp7pw6p5y6vi77mgn19331iaqwhv6x-unit-polkit.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/720qnib9lnwm7f3sj15vhgv7ni85390m-unit-systemd-fsck-.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/rzanv5sc49zzl2am29ddydmgi3p6hglp-unit-dbus.service.drv' failed to build
error: 1 dependencies of derivation '/nix/store/xicyxmw94y22jkdbdg47birnl9vc9ifc-unit-dbus.service.drv' failed to build
error: 4 dependencies of derivation '/nix/store/98nnnl4c4d2yjwzwrcffkqx5rqpww7gx-system-units.drv' failed to build
error: 1 dependencies of derivation '/nix/store/34bxyiymyzvas2ph9jasz3wp5j2pxbdb-user-units.drv' failed to build
error: 4 dependencies of derivation '/nix/store/y61pg4n3gjhydmmkhxp0n0jpck03qvwy-etc.drv' failed to build
error: 2 dependencies of derivation '/nix/store/zkyi3mqhk9dhidaiynh7pwdf5mym4mzf-nixos-system-nixos-22.11.3781.cd749f58ba8.drv' failed to build
I think I ended up solving it.
Turns out I was missing the mesa, zstd and libtensorflow packages.
I still have an issue with nix not finding libLLVM-10.so.1 which I think might have something to do with the build dependency of mesa but ignoring it has so far not produced any issues.
For reference this is my config file:
{ config, pkgs, lib, fetchPypi, fetchurl, ... }:
let
unstable = import <nixos-unstable> {
config.allowUnfree = true;
config.cudaSupport = true;
};
my_python = unstable.pkgs.python3.override {
packageOverrides = self: super: {
nbformat = super.buildPythonPackage rec {
pname = "nbformat";
version = "5.7.0";
format = "wheel";
src = pkgs.fetchurl {
url = "https://files.pythonhosted.org/packages/5c/9f/957655d02f43b8bff77e6da08c94472b1229c13e7455bbd662163c9b78c0/nbformat-5.7.0-py3-none-any.whl";
sha256 = "sha256-GwXsLFUsLxrcdF9O3c4erIyp/9Wbuf2FnoJ+qgMTGfk=";
};
buildInputs = with super; [
fastjsonschema
jupyter_core
jsonschema
];
propagatedBuildInputs = with super; [
fastjsonschema
jsonschema
];
};
};
};
ml_python_packages = ps: with ps; [
pip
ipykernel
numpy
torch-bin
matplotlib
pandas
ipywidgets
tensorflowWithoutCuda
gpustat
plotly
dash
scikitlearn
addict
tqdm
(
buildPythonPackage rec {
pname = "open3d";
version = "0.17.0";
format = "wheel";
src = unstable.python3Packages.fetchPypi {
inherit pname version format;
sha256 = "sha256-PcMAaXMgu2iCRsXQn2gQRYFcMyIlaFc/GWSy11ZDFlc=";
dist = "cp310";
python = "cp310";
abi = "cp310";
platform = "manylinux_2_27_x86_64";
};
nativeBuildInputs = [
pkgs.autoPatchelfHook
];
autoPatchelfIgnoreMissingDeps = [
"libLLVM-10.so.1"
];
buildInputs = with pkgs; [
mesa
zstd
#libllvm
stdenv.cc.cc.lib
libusb.out
cudaPackages.cudatoolkit
cudaPackages.nccl
libtorch-bin
libtensorflow
];
propagatedBuildInputs = [
(my_python.withPackages(
ps: with ps; [
nbformat
werkzeug
dash
ipywidgets
matplotlib
pyyaml
tqdm
configargparse
addict
scikitlearn
pyquaternion
pandas
#tensorflowWithoutCuda
]))
];
})
];
in
{
nixpkgs.config = {
allowUnfree = true;
cudaSupport = true;
};
# List packages installed in system profile. To search, run:
environment.systemPackages = with pkgs; [
linuxPackages.nvidia_x11
cudaPackages.cudatoolkit
cudaPackages.cudnn
conda
nvtop
ctop
(my_python.withPackages ml_python_packages)
];
}