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ERROR: Unknown compiler(s): [['gfortran'], ['flang-new'], ['flang'], ['nvfortran'], ['pgfortran'], ['ifort'], ['ifx'], ['g95']] #3

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opened 2026-06-10 10:41:33 +02:00 by Benjamin_Loison · 11 comments
Benjamin_Loison commented 2026-06-10 10:41:33 +02:00
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Following Benjamin_Loison/apptainer/issues/33#issuecomment-17184611.

DuckDuckGo search "Unknown compiler(s): [['gfortran'], ['flang-new'], ['flang'], ['nvfortran'], ['pgfortran'], ['ifort'], ['ifx'], ['g95']]".

Following [Benjamin_Loison/apptainer/issues/33#issuecomment-17184611](https://codeberg.org/Benjamin_Loison/apptainer/issues/33#issuecomment-17184611). DuckDuckGo search `"Unknown compiler(s): [['gfortran'], ['flang-new'], ['flang'], ['nvfortran'], ['pgfortran'], ['ifort'], ['ifx'], ['g95']]"`.
Benjamin_Loison commented 2026-06-10 10:43:20 +02:00
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The answer and comments to the Stack Overflow question 77607056 mention installing binaries.

The answer and comments to [the Stack Overflow question 77607056](https://stackoverflow.com/q/77607056) mention installing binaries.
Benjamin_Loison commented 2026-06-10 10:45:10 +02:00
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python3 --version

Python 3.13.5
```bash python3 --version ``` ``` Python 3.13.5 ```
Benjamin_Loison commented 2026-06-10 10:45:16 +02:00
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uname -p

unknown
```bash uname -p ``` ``` unknown ```
Benjamin_Loison commented 2026-06-10 10:45:27 +02:00
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uname -p

x86_64
```bash uname -p ``` ``` x86_64 ```
Benjamin_Loison commented 2026-06-10 10:46:04 +02:00
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uname --help | grep -e -p,

  -p, --processor          print the processor type (non-portable)

Outside container:

uname --processor

x86_64
```bash uname --help | grep -e -p, ``` ``` -p, --processor print the processor type (non-portable) ``` Outside container: ```bash uname --processor ``` ``` x86_64 ```
Benjamin_Loison commented 2026-06-10 10:46:38 +02:00
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Issue tracked at Benjamin_Loison/apptainer/issues/35.

Issue tracked at [Benjamin_Loison/apptainer/issues/35](https://codeberg.org/Benjamin_Loison/apptainer/issues/35).
Benjamin_Loison commented 2026-06-10 11:35:48 +02:00
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I quickly had a look to the Stack Overflow question 79146073 and its comments.

I quickly had a look to [the Stack Overflow question 79146073](https://stackoverflow.com/q/79146073) and its comments.
Benjamin_Loison commented 2026-06-10 13:05:06 +02:00
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uv pip install -r requirements.txt
Output: 
Using Python 3.14.4 environment at: /lustre/work/pdl16831/udlc74081/.venv_x86-64
Resolved 4 packages in 66ms
  × Failed to build `scipy==1.14.0`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `mesonpy.build_wheel` failed (exit status: 1)

      [stdout]
      + meson setup /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src
      /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md
      --native-file=/lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt/meson-python-native-file.ini
      The Meson build system
      Version: 1.11.1
      Source dir: /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src
      Build dir: /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt
      Build type: native build
      Project name: scipy
      Project version: 1.14.0
      C compiler for the host machine: cc (gcc 11.5.0 "cc (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      C linker for the host machine: cc ld.bfd 2.35.2-54
      C++ compiler for the host machine: c++ (gcc 11.5.0 "c++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      C++ linker for the host machine: c++ ld.bfd 2.35.2-54
      Cython compiler for the host machine: cython (cython 3.0.12)
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Program python found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python)
      Found pkg-config: YES (/usr/bin/pkg-config) 1.7.3
      Run-time dependency python found: YES 3.14
      Program cython found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/cython)
      Compiler for C supports arguments -Wno-unused-but-set-variable: YES
      Compiler for C supports arguments -Wno-unused-function: YES
      Compiler for C supports arguments -Wno-conversion: YES
      Compiler for C supports arguments -Wno-misleading-indentation: YES
      Library m found: YES
      Fortran compiler for the host machine: gfortran (gcc 11.5.0 "GNU Fortran (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      Fortran linker for the host machine: gfortran ld.bfd 2.35.2-54
      Compiler for Fortran supports arguments -Wno-conversion: YES
      Checking if "-Wl,--version-script" links: YES
      Program tools/generate_f2pymod.py found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python
      /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/tools/generate_f2pymod.py)
      Program scipy/_build_utils/tempita.py found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python
      /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/scipy/_build_utils/tempita.py)
      Program pythran found: YES 0.16.1 0.16.1 (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/pythran)
      Found CMake: /usr/bin/cmake (3.26.5)
      Run-time dependency xsimd found: NO  (tried pkg-config and cmake)
      Run-time dependency threads found: YES

      ../scipy/meson.build:48:17: ERROR: Command `/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python -c 'import os
      os.chdir(os.path.join("..", "tools"))
      import numpy as np
      try:
        incdir = os.path.relpath(np.get_include())
      except Exception:
        incdir = np.get_include()
      print(incdir)
        '` failed with status 1.

      A full log can be found at /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt/meson-logs/meson-log.txt


hint: Build failures usually indicate python -c 'import osackage or the build environment
Bash script: 
python -c 'import os
os.chdir(os.path.join("..", "tools"))
import numpy as np
try:
  incdir = os.path.relpath(np.get_include())
except Exception:
  incdir = np.get_include()
print(incdir)
  '
Output: 
Traceback (most recent call last):
  File "<string>", line 2, in <module>
    os.chdir(os.path.join("..", "tools"))
    ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '../tools'
```bash uv pip install -r requirements.txt ``` <details> <summary>Output:</summary> ``` Using Python 3.14.4 environment at: /lustre/work/pdl16831/udlc74081/.venv_x86-64 Resolved 4 packages in 66ms × Failed to build `scipy==1.14.0` ├─▶ The build backend returned an error ╰─▶ Call to `mesonpy.build_wheel` failed (exit status: 1) [stdout] + meson setup /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt/meson-python-native-file.ini The Meson build system Version: 1.11.1 Source dir: /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src Build dir: /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt Build type: native build Project name: scipy Project version: 1.14.0 C compiler for the host machine: cc (gcc 11.5.0 "cc (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)") C linker for the host machine: cc ld.bfd 2.35.2-54 C++ compiler for the host machine: c++ (gcc 11.5.0 "c++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)") C++ linker for the host machine: c++ ld.bfd 2.35.2-54 Cython compiler for the host machine: cython (cython 3.0.12) Host machine cpu family: x86_64 Host machine cpu: x86_64 Program python found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python) Found pkg-config: YES (/usr/bin/pkg-config) 1.7.3 Run-time dependency python found: YES 3.14 Program cython found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/cython) Compiler for C supports arguments -Wno-unused-but-set-variable: YES Compiler for C supports arguments -Wno-unused-function: YES Compiler for C supports arguments -Wno-conversion: YES Compiler for C supports arguments -Wno-misleading-indentation: YES Library m found: YES Fortran compiler for the host machine: gfortran (gcc 11.5.0 "GNU Fortran (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)") Fortran linker for the host machine: gfortran ld.bfd 2.35.2-54 Compiler for Fortran supports arguments -Wno-conversion: YES Checking if "-Wl,--version-script" links: YES Program tools/generate_f2pymod.py found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/tools/generate_f2pymod.py) Program scipy/_build_utils/tempita.py found: YES (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/scipy/_build_utils/tempita.py) Program pythran found: YES 0.16.1 0.16.1 (/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/pythran) Found CMake: /usr/bin/cmake (3.26.5) Run-time dependency xsimd found: NO (tried pkg-config and cmake) Run-time dependency threads found: YES ../scipy/meson.build:48:17: ERROR: Command `/lustre/work/pdl16831/udlc74081/.cache/uv/builds-v0/.tmpu4vwSN/bin/python -c 'import os os.chdir(os.path.join("..", "tools")) import numpy as np try: incdir = os.path.relpath(np.get_include()) except Exception: incdir = np.get_include() print(incdir) '` failed with status 1. A full log can be found at /lustre/work/pdl16831/udlc74081/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/.mesonpy-xxezvebt/meson-logs/meson-log.txt hint: Build failures usually indicate python -c 'import osackage or the build environment ``` </details> <details> <summary>Bash script:</summary> ```bash python -c 'import os os.chdir(os.path.join("..", "tools")) import numpy as np try: incdir = os.path.relpath(np.get_include()) except Exception: incdir = np.get_include() print(incdir) ' ``` </details> <details> <summary>Output:</summary> ``` Traceback (most recent call last): File "<string>", line 2, in <module> os.chdir(os.path.join("..", "tools")) ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '../tools' ``` </details>
Benjamin_Loison commented 2026-06-10 13:06:34 +02:00
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ls -lha ~/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/
Output: 
total 176K
drwxr-sr-x  8 udlc74081 pdl16831 4.0K Jun 10 13:03 .
drwxr-sr-x  3 udlc74081 pdl16831 4.0K Jun 10 00:50 ..
drwxr-sr-x  3 udlc74081 pdl16831 4.0K Jun 10 00:50 benchmarks
-rw-r--r--  1 udlc74081 pdl16831 1.9K Jun 10 00:50 .cirrus.star
-rw-r--r--  1 udlc74081 pdl16831 1.3K Jun 10 00:50 CITATION.bib
-rw-r--r--  1 udlc74081 pdl16831 1.1K Jun 10 00:50 CONTRIBUTING.rst
drwxr-sr-x  2 udlc74081 pdl16831 4.0K Jun 10 00:50 .devcontainer
-rw-r--r--  1 udlc74081 pdl16831  55K Jun 10 00:50 dev.py
drwxr-sr-x  3 udlc74081 pdl16831 4.0K Jun 10 00:50 doc
-rw-r--r--  1 udlc74081 pdl16831  13K Jun 10 00:50 LICENSES_bundled.txt
-rw-r--r--  1 udlc74081 pdl16831 1.5K Jun 10 00:50 LICENSE.txt
-rw-r--r--  1 udlc74081 pdl16831 6.1K Jun 10 00:50 meson.build
-rw-r--r--  1 udlc74081 pdl16831  759 Jun 10 00:50 meson_options.txt
-rw-r--r--  1 udlc74081 pdl16831  14K Jun 10 00:50 mypy.ini
-rw-r--r--  1 udlc74081 pdl16831 8.1K Jun 10 00:50 PKG-INFO
-rw-r--r--  1 udlc74081 pdl16831 5.6K Jun 10 00:50 pyproject.toml
-rw-r--r--  1 udlc74081 pdl16831  966 Jun 10 00:50 pytest.ini
-rw-r--r--  1 udlc74081 pdl16831 3.5K Jun 10 00:50 README.rst
drwxr-sr-x  2 udlc74081 pdl16831 4.0K Jun 10 00:50 requirements
drwxr-sr-x 22 udlc74081 pdl16831 4.0K Jun 10 00:50 scipy
drwxr-sr-x  3 udlc74081 pdl16831 4.0K Jun 10 00:50 tools
```bash ls -lha ~/.cache/uv/sdists-v9/pypi/scipy/1.14.0/FAKGoh_LOhakpiUT/src/ ``` <details> <summary>Output:</summary> ``` total 176K drwxr-sr-x 8 udlc74081 pdl16831 4.0K Jun 10 13:03 . drwxr-sr-x 3 udlc74081 pdl16831 4.0K Jun 10 00:50 .. drwxr-sr-x 3 udlc74081 pdl16831 4.0K Jun 10 00:50 benchmarks -rw-r--r-- 1 udlc74081 pdl16831 1.9K Jun 10 00:50 .cirrus.star -rw-r--r-- 1 udlc74081 pdl16831 1.3K Jun 10 00:50 CITATION.bib -rw-r--r-- 1 udlc74081 pdl16831 1.1K Jun 10 00:50 CONTRIBUTING.rst drwxr-sr-x 2 udlc74081 pdl16831 4.0K Jun 10 00:50 .devcontainer -rw-r--r-- 1 udlc74081 pdl16831 55K Jun 10 00:50 dev.py drwxr-sr-x 3 udlc74081 pdl16831 4.0K Jun 10 00:50 doc -rw-r--r-- 1 udlc74081 pdl16831 13K Jun 10 00:50 LICENSES_bundled.txt -rw-r--r-- 1 udlc74081 pdl16831 1.5K Jun 10 00:50 LICENSE.txt -rw-r--r-- 1 udlc74081 pdl16831 6.1K Jun 10 00:50 meson.build -rw-r--r-- 1 udlc74081 pdl16831 759 Jun 10 00:50 meson_options.txt -rw-r--r-- 1 udlc74081 pdl16831 14K Jun 10 00:50 mypy.ini -rw-r--r-- 1 udlc74081 pdl16831 8.1K Jun 10 00:50 PKG-INFO -rw-r--r-- 1 udlc74081 pdl16831 5.6K Jun 10 00:50 pyproject.toml -rw-r--r-- 1 udlc74081 pdl16831 966 Jun 10 00:50 pytest.ini -rw-r--r-- 1 udlc74081 pdl16831 3.5K Jun 10 00:50 README.rst drwxr-sr-x 2 udlc74081 pdl16831 4.0K Jun 10 00:50 requirements drwxr-sr-x 22 udlc74081 pdl16831 4.0K Jun 10 00:50 scipy drwxr-sr-x 3 udlc74081 pdl16831 4.0K Jun 10 00:50 tools ``` </details>
Benjamin_Loison commented 2026-06-10 13:07:46 +02:00
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ls -lah ~/.cache/uv/builds-v0/
Output: 
total 16K
drwxr-sr-x  4 udlc74081 pdl16831 4.0K Jun 10 13:03 .
drwxr-sr-x 11 udlc74081 pdl16831 4.0K Jun 10 13:02 ..
drwxr-sr-x  2 udlc74081 pdl16831 4.0K Jun 10 00:56 .tmpBgq1Vg
drwxr-sr-x  5 udlc74081 pdl16831 4.0K Jun 10 00:56 .tmpZE38OK
```bash ls -lah ~/.cache/uv/builds-v0/ ``` <details> <summary>Output:</summary> ``` total 16K drwxr-sr-x 4 udlc74081 pdl16831 4.0K Jun 10 13:03 . drwxr-sr-x 11 udlc74081 pdl16831 4.0K Jun 10 13:02 .. drwxr-sr-x 2 udlc74081 pdl16831 4.0K Jun 10 00:56 .tmpBgq1Vg drwxr-sr-x 5 udlc74081 pdl16831 4.0K Jun 10 00:56 .tmpZE38OK ``` </details>
Benjamin_Loison commented 2026-06-10 14:14:24 +02:00
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diff: 
diff --git a/requirements.txt b/requirements.txt
index 9dc82bc..1057c6a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 numpy #==2.3.2
 iio #==29
 PyWavelets #==1.9.0
-scipy==1.14.0
+scipy==1.17.1

uv pip install -r requirements.txt
Output: 
Using Python 3.14.4 environment at: /lustre/work/pdl16831/udlc74081/.venv_x86-64
Resolved 4 packages in 77ms
Installed 1 package in 179ms
 + pywavelets==1.9.0
<details> <summary><code>diff</code>:</summary> ```diff diff --git a/requirements.txt b/requirements.txt index 9dc82bc..1057c6a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ numpy #==2.3.2 iio #==29 PyWavelets #==1.9.0 -scipy==1.14.0 +scipy==1.17.1 ``` </details> ```bash uv pip install -r requirements.txt ``` <details> <summary>Output:</summary> ``` Using Python 3.14.4 environment at: /lustre/work/pdl16831/udlc74081/.venv_x86-64 Resolved 4 packages in 77ms Installed 1 package in 179ms + pywavelets==1.9.0 ``` </details>
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Reference: Benjamin_Loison/scipy#3