Segmentation Fault when installing via conda

[kylekam]

🐛 Bugs / Unexpected behaviors

May be similar to this issue #317. The main difference being that the segmentation fault occurs during the "conda install pytorch" command. There's several github issues that reference a segfault but they've occured on a Windows system rather than a Linux system.

Instructions To Reproduce the Issue:

Please include the following (depending on what the issue is):

1. Any changes you made (git diff) or code you wrote

None. Just follow the install instructions on Linux and it crashes on "conda install pytorch3d -c pytorch3d".

2. The exact command(s) you ran:
3. What you observed (including the full logs):

(pytorch3d) kam@brachio:~/libs$ conda install pytorch3d -c pytorch3d
Channels:
 - pytorch3d
 - defaults
 - nvidia
 - pytorch
 - iopath
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: - Segmentation fault (core dumped)
(pytorch3d) kam@brachio:~/libs$ 

[bottler]

This is weird. Can you paste the output of conda info and conda list?

[kylekam]

conda list

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
blas                      1.0                         mkl  
brotli-python             1.0.9            py39h6a678d5_8  
bzip2                     1.0.8                h5eee18b_6  
ca-certificates           2024.9.24            h06a4308_0  
certifi                   2024.8.30        py39h06a4308_0  
charset-normalizer        3.3.2              pyhd3eb1b0_0  
cuda                      11.6.1                        0    nvidia
cuda-cccl                 11.6.55              hf6102b2_0    nvidia
cuda-command-line-tools   11.6.2                        0    nvidia
cuda-compiler             11.6.2                        0    nvidia
cuda-cudart               11.6.55              he381448_0    nvidia
cuda-cudart-dev           11.6.55              h42ad0f4_0    nvidia
cuda-cuobjdump            11.6.124             h2eeebcb_0    nvidia
cuda-cupti                11.6.124             h86345e5_0    nvidia
cuda-cuxxfilt             11.6.124             hecbf4f6_0    nvidia
cuda-driver-dev           11.6.55                       0    nvidia
cuda-gdb                  12.6.77                       0    nvidia
cuda-libraries            11.6.1                        0    nvidia
cuda-libraries-dev        11.6.1                        0    nvidia
cuda-memcheck             11.8.86                       0    nvidia
cuda-nsight               12.6.77                       0    nvidia
cuda-nsight-compute       12.4.1                        0    nvidia
cuda-nvcc                 11.6.124             hbba6d2d_0    nvidia
cuda-nvdisasm             12.6.77                       0    nvidia
cuda-nvml-dev             11.6.55              haa9ef22_0    nvidia
cuda-nvprof               12.6.80                       0    nvidia
cuda-nvprune              11.6.124             he22ec0a_0    nvidia
cuda-nvrtc                11.6.124             h020bade_0    nvidia
cuda-nvrtc-dev            11.6.124             h249d397_0    nvidia
cuda-nvtx                 11.6.124             h0630a44_0    nvidia
cuda-nvvp                 12.6.80                       0    nvidia
cuda-runtime              11.6.1                        0    nvidia
cuda-samples              11.6.101             h8efea70_0    nvidia
cuda-sanitizer-api        12.6.77                       0    nvidia
cuda-toolkit              11.6.1                        0    nvidia
cuda-tools                11.6.1                        0    nvidia
cuda-version              12.6                          3    nvidia
cuda-visual-tools         11.6.1                        0    nvidia
dbus                      1.13.18              hb2f20db_0  
expat                     2.6.3                h6a678d5_0  
ffmpeg                    4.3                  hf484d3e_0    pytorch
fontconfig                2.14.1               h55d465d_3  
freetype                  2.12.1               h4a9f257_0  
gds-tools                 1.11.1.6                      0    nvidia
glib                      2.78.4               h6a678d5_0  
glib-tools                2.78.4               h6a678d5_0  
gmp                       6.2.1                h295c915_3  
gnutls                    3.6.15               he1e5248_0  
icu                       73.1                 h6a678d5_0  
idna                      3.7              py39h06a4308_0  
intel-openmp              2023.1.0         hdb19cb5_46306  
iopath                    0.1.9                      py39    iopath
jpeg                      9e                   h5eee18b_3  
lame                      3.100                h7b6447c_0  
lcms2                     2.12                 h3be6417_0  
ld_impl_linux-64          2.40                 h12ee557_0  
lerc                      3.0                  h295c915_0  
libcublas                 11.9.2.110           h5e84587_0    nvidia
libcublas-dev             11.9.2.110           h5c901ab_0    nvidia
libcufft                  10.7.1.112           hf425ae0_0    nvidia
libcufft-dev              10.7.1.112           ha5ce4c0_0    nvidia
libcufile                 1.11.1.6                      0    nvidia
libcufile-dev             1.11.1.6                      0    nvidia
libcurand                 10.3.7.77                     0    nvidia
libcurand-dev             10.3.7.77                     0    nvidia
libcusolver               11.3.4.124           h33c3c4e_0    nvidia
libcusparse               11.7.2.124           h7538f96_0    nvidia
libcusparse-dev           11.7.2.124           hbbe9722_0    nvidia
libdeflate                1.17                 h5eee18b_1  
libffi                    3.4.4                h6a678d5_1  
libgcc-ng                 11.2.0               h1234567_1  
libglib                   2.78.4               hdc74915_0  
libgomp                   11.2.0               h1234567_1  
libiconv                  1.16                 h5eee18b_3  
libidn2                   2.3.4                h5eee18b_0  
libnpp                    11.6.3.124           hd2722f0_0    nvidia
libnpp-dev                11.6.3.124           h3c42840_0    nvidia
libnvjpeg                 11.6.2.124           hd473ad6_0    nvidia
libnvjpeg-dev             11.6.2.124           hb5906b9_0    nvidia
libpng                    1.6.39               h5eee18b_0  
libstdcxx-ng              11.2.0               h1234567_1  
libtasn1                  4.19.0               h5eee18b_0  
libtiff                   4.5.1                h6a678d5_0  
libunistring              0.9.10               h27cfd23_0  
libuuid                   1.41.5               h5eee18b_0  
libwebp-base              1.3.2                h5eee18b_0  
libxcb                    1.15                 h7f8727e_0  
libxkbcommon              1.0.1                h097e994_2  
libxml2                   2.13.1               hfdd30dd_2  
lz4-c                     1.9.4                h6a678d5_1  
mkl                       2023.1.0         h213fc3f_46344  
mkl-service               2.4.0            py39h5eee18b_1  
mkl_fft                   1.3.10           py39h5eee18b_0  
mkl_random                1.2.7            py39h1128e8f_0  
ncurses                   6.4                  h6a678d5_0  
nettle                    3.7.3                hbbd107a_1  
nsight-compute            2024.3.2.3                    0    nvidia
nspr                      4.35                 h6a678d5_0  
nss                       3.89.1               h6a678d5_0  
numpy                     2.0.1            py39h5f9d8c6_1  
numpy-base                2.0.1            py39hb5e798b_1  
openh264                  2.1.1                h4ff587b_0  
openjpeg                  2.5.2                he7f1fd0_0  
openssl                   3.0.15               h5eee18b_0  
pcre2                     10.42                hebb0a14_1  
pillow                    10.4.0           py39h5eee18b_0  
pip                       24.2             py39h06a4308_0  
portalocker               2.3.0            py39h06a4308_1  
pysocks                   1.7.1            py39h06a4308_0  
python                    3.9.20               he870216_1  
pytorch                   1.13.0          py3.9_cuda11.6_cudnn8.3.2_0    pytorch
pytorch-cuda              11.6                 h867d48c_1    pytorch
pytorch-mutex             1.0                        cuda    pytorch
readline                  8.2                  h5eee18b_0  
requests                  2.32.3           py39h06a4308_0  
setuptools                75.1.0           py39h06a4308_0  
sqlite                    3.45.3               h5eee18b_0  
tbb                       2021.8.0             hdb19cb5_0  
tk                        8.6.14               h39e8969_0  
torchvision               0.14.0               py39_cu116    pytorch
tqdm                      4.66.5           py39h2f386ee_0  
typing_extensions         4.11.0           py39h06a4308_0  
tzdata                    2024b                h04d1e81_0  
urllib3                   2.2.3            py39h06a4308_0  
wheel                     0.44.0           py39h06a4308_0  
xz                        5.4.6                h5eee18b_1  
zlib                      1.2.13               h5eee18b_1  
zstd                      1.5.6                hc292b87_0

conda info

     active environment : pytorch3d
    active env location : /home/kylekam/anaconda3/envs/pytorch3d
            shell level : 4
       user config file : /home/kylekam/.condarc
 populated config files : 
          conda version : 24.1.2
    conda-build version : 24.1.2
         python version : 3.11.7.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen
                          __conda=24.1.2=0
                          __cuda=12.1=0
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /home/kylekam/anaconda3  (writable)
      conda av data dir : /home/kylekam/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/kylekam/anaconda3/pkgs
                          /home/kylekam/.conda/pkgs
       envs directories : /home/kylekam/anaconda3/envs
                          /home/kylekam/.conda/envs
               platform : linux-64
             user-agent : conda/24.1.2 requests/2.31.0 CPython/3.11.7 Linux/5.15.0-73-generic ubuntu/22.04.4 glibc/2.35 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.6 aau/0.4.3 c/jKJTMlAZrgs2yej7w-GggQ s/y90H47jWma4PtltFoJpbEA e/ZFd8gySp99t1-i16jHXAiw
                UID:GID : 1008:1008
             netrc file : None
           offline mode : False

[leilai125]

it happens to me too

[bottler]

The latest relevant conda package to your dependencies is https://anaconda.org/pytorch3d/pytorch3d/0.7.5/download/linux-64/pytorch3d-0.7.5-py39_cu116_pyt1130.tar.bz2 I think. I think conda is crashing while trying to discover that fact. Can you try downloading that file and then installing in with conda install <filename>?

[Chen-Suyi]

I followed INSTALL.md. The same issue happened to me as well when I use conda install pytorch3d -c pytorch3d, and here is my conda info and conda list

conda info

active environment : cryoai
active env location : /home/suyi/apps/miniconda3/envs/cryoai
        shell level : 1
   user config file : /home/suyi/.condarc

populated config files : /home/suyi/.condarc
conda version : 24.7.1
conda-build version : not installed
python version : 3.12.4.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake
__conda=24.7.1=0
__cuda=12.2=0
__glibc=2.35=0
__linux=6.5.0=0
__unix=0=0
base environment : /home/suyi/apps/miniconda3 (writable)
conda av data dir : /home/suyi/apps/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/suyi/apps/miniconda3/pkgs
/home/suyi/.conda/pkgs
envs directories : /home/suyi/apps/miniconda3/envs
/home/suyi/.conda/envs
platform : linux-64
user-agent : conda/24.7.1 requests/2.32.3 CPython/3.12.4 Linux/6.5.0-41-generic ubuntu/22.04.1 glibc/2.35 solver/libmamba conda-libmamba-solver/24.7.0 libmambapy/1.5.8 aau/0.4.4 c/. s/. e/.
UID:GID : 1024:1024
netrc file : None
offline mode : False

conda list

packages in environment at /home/suyi/apps/miniconda3/envs/cryoai:

Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
blas 1.0 mkl
brotli-python 1.0.9 py39h6a678d5_8
bzip2 1.0.8 h5eee18b_6
ca-certificates 2024.9.24 h06a4308_0
certifi 2024.8.30 py39h06a4308_0
charset-normalizer 3.3.2 pyhd3eb1b0_0
cuda-cudart 12.1.105 0 nvidia
cuda-cupti 12.1.105 0 nvidia
cuda-libraries 12.1.0 0 nvidia
cuda-nvrtc 12.1.105 0 nvidia
cuda-nvtx 12.1.105 0 nvidia
cuda-opencl 12.6.77 0 nvidia
cuda-runtime 12.1.0 0 nvidia
cuda-version 12.6 3 nvidia
ffmpeg 4.3 hf484d3e_0 pytorch
filelock 3.13.1 py39h06a4308_0
freetype 2.12.1 h4a9f257_0
gmp 6.2.1 h295c915_3
gmpy2 2.1.2 py39heeb90bb_0
gnutls 3.6.15 he1e5248_0
idna 3.7 py39h06a4308_0
intel-openmp 2023.1.0 hdb19cb5_46306
iopath 0.1.9 py39 iopath
jinja2 3.1.4 py39h06a4308_1
jpeg 9e h5eee18b_3
lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.40 h12ee557_0
lerc 3.0 h295c915_0
libcublas 12.1.0.26 0 nvidia
libcufft 11.0.2.4 0 nvidia
libcufile 1.11.1.6 0 nvidia
libcurand 10.3.7.77 0 nvidia
libcusolver 11.4.4.55 0 nvidia
libcusparse 12.0.2.55 0 nvidia
libdeflate 1.17 h5eee18b_1
libffi 3.4.4 h6a678d5_1
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libiconv 1.16 h5eee18b_3
libidn2 2.3.4 h5eee18b_0
libjpeg-turbo 2.0.0 h9bf148f_0 pytorch
libnpp 12.0.2.50 0 nvidia
libnvjitlink 12.1.105 0 nvidia
libnvjpeg 12.1.1.14 0 nvidia
libpng 1.6.39 h5eee18b_0
libstdcxx-ng 11.2.0 h1234567_1
libtasn1 4.19.0 h5eee18b_0
libtiff 4.5.1 h6a678d5_0
libunistring 0.9.10 h27cfd23_0
libwebp-base 1.3.2 h5eee18b_1
llvm-openmp 14.0.6 h9e868ea_0
lz4-c 1.9.4 h6a678d5_1
markupsafe 2.1.3 py39h5eee18b_0
mkl 2023.1.0 h213fc3f_46344
mkl-service 2.4.0 py39h5eee18b_1
mkl_fft 1.3.11 py39h5eee18b_0
mkl_random 1.2.8 py39h1128e8f_0
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpmath 1.3.0 py39h06a4308_0
ncurses 6.4 h6a678d5_0
nettle 3.7.3 hbbd107a_1
networkx 3.2.1 py39h06a4308_0
numpy 2.0.1 py39h5f9d8c6_1
numpy-base 2.0.1 py39hb5e798b_1
nvidiacub 1.10.0 0 bottler
openh264 2.1.1 h4ff587b_0
openjpeg 2.5.2 he7f1fd0_0
openssl 3.0.15 h5eee18b_0
pillow 11.0.0 py39hfdbf927_0
pip 24.2 py39h06a4308_0
portalocker 2.3.0 py39h06a4308_1
pysocks 1.7.1 py39h06a4308_0
python 3.9.20 he870216_1
pytorch 2.4.0 py3.9_cuda12.1_cudnn9.1.0_0 pytorch
pytorch-cuda 12.1 ha16c6d3_6 pytorch
pytorch-mutex 1.0 cuda pytorch
pyyaml 6.0.2 py39h5eee18b_0
readline 8.2 h5eee18b_0
requests 2.32.3 py39h06a4308_1
setuptools 75.1.0 py39h06a4308_0
sqlite 3.45.3 h5eee18b_0
sympy 1.13.2 py39h06a4308_0
tbb 2021.8.0 hdb19cb5_0
tk 8.6.14 h39e8969_0
torchaudio 2.4.0 py39_cu121 pytorch
torchtriton 3.0.0 py39 pytorch
torchvision 0.19.0 py39_cu121 pytorch
tqdm 4.66.5 py39h2f386ee_0
typing_extensions 4.11.0 py39h06a4308_0
tzdata 2024b h04d1e81_0
urllib3 2.2.3 py39h06a4308_0
wheel 0.44.0 py39h06a4308_0
xz 5.4.6 h5eee18b_1
yaml 0.2.5 h7b6447c_0
zlib 1.2.13 h5eee18b_1
zstd 1.5.6 hc292b87_0

[bottler]

Can you also download the required package directly from https://anaconda.org/pytorch3d/pytorch3d/files?

[yukiumi13]

I have faced the same issue. In my case, I found that pytorch installed by anaconda is broken. I switched to pip and installed pytorch and pytorch3d successfully.