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sagemath / sage

Main repository of SageMath
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Codespace (conda) setup fails with `No space left on device` #36952

Closed mkoeppe closed 7 months ago

mkoeppe commented 8 months ago 
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  + kiwisolver                                1.4.5  py311h9547e67_1        conda-forge     Cached
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  + debugpy                                   1.8.0  py311hb755f60_1        conda-forge     Cached
  + cython                                    3.0.7  py311hb755f60_0        conda-forge     Cached
  + cysignals                                1.11.2  py311h82528dc_3        conda-forge     Cached
  + cvxopt                                    1.3.2  py311h2b3fd1d_1        conda-forge     Cached
  + python-lrcalc                               2.1  py311ha362b79_5        conda-forge     Cached
  + gmpy2                                     2.1.2  py311h6a5fa03_1        conda-forge     Cached
  + pytz-deprecation-shim               0.1.0.post0  py311h38be061_4        conda-forge     Cached
  + fonttools                                4.47.0  py311h459d7ec_0        conda-forge     Cached
  + cffi                                     1.16.0  py311hb3a22ac_0        conda-forge     Cached
  + jupyter_core                              5.5.1  py311h38be061_0        conda-forge     Cached
  + sip                                      6.7.12  py311hb755f60_0        conda-forge     Cached
  + gstreamer                                1.22.8  h98fc4e7_0             conda-forge     Cached
  + pybind11                                 2.11.1  py311h9547e67_2        conda-forge     Cached
  + contourpy                                 1.2.0  py311h9547e67_0        conda-forge     Cached
  + scipy                                    1.11.4  py311h64a7726_0        conda-forge     Cached
  + pythran                                  0.14.0  py311h92ebd52_1        conda-forge     Cached
  + memory-allocator                          0.1.3  py311h459d7ec_0        conda-forge     Cached
  + primecountpy                              0.1.0  py311h9547e67_4        conda-forge     Cached
  + fpylll                                    0.6.0  py311hcfae7cf_1        conda-forge     Cached
  + cypari2                                   2.1.3  py311hd2352ae_2        conda-forge     Cached
  + pplpy                                     0.8.9  py311h85abca9_0        conda-forge     Cached
  + argon2-cffi-bindings                     21.2.0  py311h459d7ec_4        conda-forge     Cached
  + pyqt5-sip                               12.12.2  py311hb755f60_5        conda-forge     Cached
  + gst-plugins-base                         1.22.8  h8e1006c_0             conda-forge     Cached
  + matplotlib-base                           3.8.2  py311h54ef318_0        conda-forge     Cached
  + qt-main                                  5.15.8  h82b777d_17            conda-forge     Cached
  + pyqt                                     5.15.9  py311hf0fb5b6_5        conda-forge     Cached
  + matplotlib                                3.8.2  py311h38be061_0        conda-forge     Cached
  + referencing                              0.32.0  pyhd8ed1ab_0           conda-forge     Cached
  + tox                                      4.11.4  pyhd8ed1ab_0           conda-forge     Cached
  + urllib3                                   2.1.0  pyhd8ed1ab_0           conda-forge     Cached
  + terminado                                0.18.0  pyh0d859eb_0           conda-forge     Cached
  + jinja2                                    3.1.2  pyhd8ed1ab_1           conda-forge     Cached
  + sympy                                      1.12  pypyh9d50eac_103       conda-forge     Cached
  + jupyter_client                            8.6.0  pyhd8ed1ab_0           conda-forge     Cached
  + argon2-cffi                              23.1.0  pyhd8ed1ab_0           conda-forge     Cached
  + ipympl                                    0.9.3  pyhd8ed1ab_0           conda-forge     Cached
  + jsonschema-specifications             2023.11.2  pyhd8ed1ab_0           conda-forge     Cached
  + requests                                 2.31.0  pyhd8ed1ab_0           conda-forge     Cached
  + jupyter_server_terminals                  0.5.0  pyhd8ed1ab_0           conda-forge     Cached
  + ipykernel                                6.26.0  pyhf8b6a83_0           conda-forge     Cached
  + jsonschema                               4.20.0  pyhd8ed1ab_0           conda-forge     Cached
  + sphinx                                    7.2.6  pyhd8ed1ab_0           conda-forge     Cached
  + sphinxcontrib-applehelp                   1.0.7  pyhd8ed1ab_0           conda-forge     Cached
  + jsonschema-with-format-nongpl            4.20.0  pyhd8ed1ab_0           conda-forge     Cached
  + nbformat                                  5.9.2  pyhd8ed1ab_0           conda-forge     Cached
  + sphinxcontrib-devhelp                     1.0.5  pyhd8ed1ab_0           conda-forge     Cached
  + jupyter_events                            0.9.0  pyhd8ed1ab_0           conda-forge     Cached
  + nbclient                                  0.8.0  pyhd8ed1ab_0           conda-forge     Cached
  + sphinxcontrib-qthelp                      1.0.6  pyhd8ed1ab_0           conda-forge     Cached
  + nbconvert-core                           7.13.1  pyhd8ed1ab_0           conda-forge     Cached
  + sphinxcontrib-htmlhelp                    2.0.4  pyhd8ed1ab_0           conda-forge     Cached
  + jupyter_server                           2.12.1  pyhd8ed1ab_0           conda-forge     Cached
  + nbconvert-pandoc                         7.13.1  pyhd8ed1ab_0           conda-forge     Cached
  + sphinxcontrib-serializinghtml             1.1.9  pyhd8ed1ab_0           conda-forge     Cached
  + jupyter-lsp                               2.2.1  pyhd8ed1ab_0           conda-forge     Cached
  + jupyterlab_server                        2.25.2  pyhd8ed1ab_0           conda-forge     Cached
  + notebook-shim                             0.2.3  pyhd8ed1ab_0           conda-forge     Cached
  + nbconvert                                7.13.1  pyhd8ed1ab_0           conda-forge     Cached
  + esbonio                                  0.16.3  pyhd8ed1ab_0           conda-forge     Cached
  + sphinxcontrib-websupport                  1.2.6  pyhd8ed1ab_0           conda-forge     Cached
  + sphinx-copybutton                         0.5.2  pyhd8ed1ab_0           conda-forge     Cached
  + sphinx-basic-ng                         1.0.0b2  pyhd8ed1ab_1           conda-forge     Cached
  + jupyterlab                                4.0.9  pyhd8ed1ab_0           conda-forge     Cached
  + furo                                  2023.9.10  pyhd8ed1ab_0           conda-forge     Cached
  + notebook                                  7.0.6  pyhd8ed1ab_0           conda-forge     Cached
  + rpy2                                     3.5.11  py311r43h1f0f07a_3     conda-forge     Cached
  + jupyter_sphinx                            0.4.0  py311h38be061_1        conda-forge     Cached

  Summary:

  Install: 475 packages

  Total download: 5MB

────────────────────────────────────────────────────────────────────────────────────────────────────

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error    libmamba Error opening for reading "/opt/conda/pkgs/conway-polynomials-0.8-pyhd8ed1ab_0/info/index.json": No such file or directory
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critical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/brial-1.2.12-pyh694c41f_1]
error    libmamba Error opening for reading "/opt/conda/pkgs/autoconf-2.71-pl5321h2b4cb7a_1/info/index.json": No such file or directory
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error    libmamba Error opening for reading "/opt/conda/pkgs/brial-1.2.12-pyh694c41f_1/info/index.json": No such file or directory
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critical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/jupyterlab_widgets-3.0.9-pyhd8ed1ab_0]
error    libmamba Error opening for reading "/opt/conda/pkgs/charset-normalizer-3.3.2-pyhd8ed1ab_0/info/index.json": No such file or directory
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error    libmamba Error opening for reading "/opt/conda/pkgs/jupyterlab_widgets-3.0.9-pyhd8ed1ab_0/info/index.json": No such file or directory
error    libmamba Error when extracting package: [json.exception.parse_err
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error    libmamba Error opening for reading "/opt/conda/pkgs/entrypoints-0.4-pyhd8ed1ab_0/info/index.json": No such file or directory
error    libmamba Error when extracting package: [json.exception.parse_err
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Extracting  (30) ━━━━╸━━━━━━━━━━━━━━━━━━       9 appnope                    3.6scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/sympy-1.12-pypyh9d50eac_103]
error    libmamba Error opening for reading "/opt/conda/pkgs/sympy-1.12-pypyh9d50eac_103/info/index.json": No such file or directory
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Extracting  (29) ━━━━╸━━━━━━━━━━━━━━━━━━      10 argon2-cffi                4.1scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/pyqt5-sip-12.12.2-py311hb755f60_5]
error    libmamba Error opening for reading "/opt/conda/pkgs/pyqt5-sip-12.12.2-py311hb755f60_5/info/index.json": No such file or directory
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Extracting  (28) ━━━━━╸━━━━━━━━━━━━━━━━━      11 argon2-cffi                4.3scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/pyproject-api-1.6.1-pyhd8ed1ab_0]
error    libmamba Error opening for reading "/opt/conda/pkgs/pyproject-api-1.6.1-pyhd8ed1ab_0/info/index.json": No such file or directory
error    libmamba Error when extracting package: [json.exception.parse_err
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error    libmamba Error opening for reading "/opt/conda/pkgs/soupsieve-2.5-pyhd8ed1ab_1/info/index.json": No such file or directory
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error    libmamba Error opening for reading "/opt/conda/pkgs/pycparser-2.21-pyhd8ed1ab_0/info/index.json": No such file or directory
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Extracting  (25) ━━━━━━━╸━━━━━━━━━━━━━━━      14 binutils_impl_linux-64     5.4scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/jupyterlab_server-2.25.2-pyhd8ed1ab_0]
error    libmamba Error opening for reading "/opt/conda/pkgs/jupyterlab_server-2.25.2-pyhd8ed1ab_0/info/index.json": No such file or directory
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Extracting  (24) ━━━━━━━╸━━━━━━━━━━━━━━━      15 decorator                  5.7scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0]
error    libmamba Error opening for reading "/opt/conda/pkgs/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0/info/index.json": No such file or directory
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Extracting  (23) ━━━━━━━━╸━━━━━━━━━━━━━━      16 gxx_impl_linux-64          6.1scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/gxx_linux-64-12.3.0-h8a814eb_2]
error    libmamba Error opening for reading "/opt/conda/pkgs/gxx_linux-64-12.3.0-h8a814eb_2/info/index.json": No such file or directory
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Extracting  (22) ━━━━━━━━━╸━━━━━━━━━━━━━      17 harfbuzz                   6.5scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/decorator-5.1.1-pyhd8ed1ab_0]
error    libmamba Error opening for reading "/opt/conda/pkgs/decorator-5.1.1-pyhd8ed1ab_0/info/index.json": No such file or directory
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Extracting  (21) ━━━━━━━━━╸━━━━━━━━━━━━━      18 jupyter_server             6.9scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/ntl-11.4.3-hef3c4d3_1]
error    libmamba Error opening for reading "/opt/conda/pkgs/ntl-11.4.3-hef3c4d3_1/info/index.json": No such file or directory
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Extracting  (20) ━━━━━━━━━━╸━━━━━━━━━━━━      19 jupyter_sphinx           
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Extracting  (19) ━━━━━━━━━━╸━━━━━━━━━━━━      20 libgcrypt                  7.6scritical libmamba filesystem error: cannot create directories: No space left on device [/opt/conda/pkgs/asttokens-2.4.1-pyhd8ed1ab_0]
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mkoeppe commented 8 months ago

With #36953, running df gives:

Filesystem      Size  Used Avail Use% Mounted on
overlay          32G   23G  7.5G  76% /
tmpfs            64M     0   64M   0% /dev
shm              64M     0   64M   0% /dev/shm
/dev/sda1        44G   52K   42G   1% /tmp
/dev/root        29G   22G  7.2G  76% /vscode
/dev/loop3       32G   23G  7.5G  76% /workspaces
tmpfs           3.9G     0  3.9G   0% /proc/acpi
tmpfs           3.9G     0  3.9G   0% /proc/scsi                         
tmpfs           3.9G     0  3.9G   0% /sys/firmware
tobiasdiez commented 8 months ago

The conda packages should only take about 2 * 7gb of space. That should still give plenty of space to build sage. Also it looks like that it already fails for you at the download, which would mean that it has less then 7gb to start with. Strange.

Did you analyze what takes so much space, except for the conda packages?

mkoeppe commented 8 months ago

I've fixed it in https://github.com/sagemath/sage/pull/36953, needs review.

tobiasdiez commented 8 months ago

I've seen that PR. But removing the conda package cache is not a nice solution. It would also not fix the space problem if you build or update the conda env later in the codespace.

mkoeppe commented 8 months ago

not a nice solution

Why would you think that. Try to explain your thinking.