Brief description of tools/files: I am trying to install gromac 2026.0 with conda forge in anaconda environment.
The first part is sucessfull installation through conda
The next is the error with pip install gmxapi
(gmx_cuda) mayur@prorthozyme:~$ gmx --version
:-) GROMACS - gmx, 2026.0-conda_forge (-:
Executable: /home/mayur/anaconda3/envs/gmx_cuda/bin.AVX2_256/gmx
Data prefix: /home/mayur/anaconda3/envs/gmx_cuda
Working dir: /home/mayur
Command line:
gmx --version
GROMACS version: 2026.0-conda_forge
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
MPI version: built in
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NBNxM GPU setup: super-cluster 2x2x2 / cluster 8 (cluster-pair splitting on)
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.11-sse2-avx
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP: disabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Colvars support: enabled (version 2025-10-13)
CP2K support: disabled
Torch support: disabled
Plumed support: enabled
C compiler: /home/conda/feedstock_root/build_artifacts/gromacs_1770909930561/_build_env/bin/x86_64-conda-linux-gnu-cc GNU 14.3.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /home/conda/feedstock_root/build_artifacts/gromacs_1770909930561/_build_env/bin/x86_64-conda-linux-gnu-c++ GNU 14.3.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG
BLAS library: Internal
LAPACK library: Internal
CUDA compiler: /home/mayur/anaconda3/envs/gmx_cuda/bin/nvcc (NVIDIA 12.9.86)
CUDA compiler flags: -O3 -DNDEBUG -use_fast_math -static-global-template-stub=false -Xptxas=-warn-double-usage -Xptxas=-Werror -diag-suppress=177 -use_fast_math -static-global-template-stub=false -Xptxas=-warn-double-usage -Xptxas=-Werror -diag-suppress=177 -O3 -DNDEBUG
CUDA targets: 50;52-real;60-real;61-real;70-real;75-real;80-real;86-real;89-real;90-real;120
CUDA driver: 13.10
CUDA runtime: 12.90
NVSHMEM: disabled
(gmx_cuda) mayur@prorthozyme:~$ pip install --no-cache-dir gmxapi
Collecting gmxapi
Downloading gmxapi-0.4.2.tar.gz (207 kB)
Installing build dependencies … done
Getting requirements to build wheel … done
Preparing metadata (pyproject.toml) … done
Requirement already satisfied: mpi4py in ./.local/lib/python3.10/site-packages (from gmxapi) (4.1.1)
Requirement already satisfied: packaging in ./.local/lib/python3.10/site-packages (from gmxapi) (26.1)
Requirement already satisfied: pybind11 in ./.local/lib/python3.10/site-packages (from gmxapi) (2.12.1)
Requirement already satisfied: networkx>=2.0 in ./anaconda3/envs/gmx_cuda/lib/python3.10/site-packages (from gmxapi) (3.4.2)
Requirement already satisfied: numpy>1.7 in ./anaconda3/envs/gmx_cuda/lib/python3.10/site-packages (from gmxapi) (2.2.6)
Building wheels for collected packages: gmxapi
Building wheel for gmxapi (pyproject.toml) … error
error: subprocess-exited-with-error
× Building wheel for gmxapi (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [130 lines of output]
:74: SetuptoolsDeprecationWarning: Deprecated API usage.
!!
********************************************************************************
As setuptools moves its configuration towards `pyproject.toml`,
`setuptools.config.read_configuration` became deprecated.
For the time being, you can use the `setuptools.config.setupcfg` module
to access a backward compatible API, but this module is provisional
and might be removed in the future.
To read project metadata, consider using
``build.util.project_wheel_metadata`` (https://pypi.org/project/build/).
For simple scenarios, you can also try parsing the file directly
with the help of ``configparser``.
********************************************************************************
!!
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/exceptions.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/datamodel.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/version.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/abc.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/runtime.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/_transform.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/utility.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/testsupport.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/typing.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/__init__.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/_logging.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/operation.py -> build/lib.linux-x86_64-cpython-310/gmxapi
copying src/gmxapi/commandline.py -> build/lib.linux-x86_64-cpython-310/gmxapi
creating build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/abc.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/mdrun.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/workflow.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/context.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/modify_input.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/fileio.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/__init__.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
copying src/gmxapi/simulation/read_tpr.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation
running build_ext
loading initial cache file /home/mayur/anaconda3/envs/gmx_cuda/share/cmake/gromacs/gromacs-hints.cmake
-- The C compiler identification is unknown
-- The CXX compiler identification is unknown
CMake Error at CMakeLists.txt:42 (project):
The CMAKE_C_COMPILER:
/home/conda/feedstock_root/build_artifacts/gromacs_1770909930561/_build_env/bin/x86_64-conda-linux-gnu-cc
is not a full path to an existing compiler tool.
Tell CMake where to find the compiler by setting either the environment
variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
the compiler, or to the compiler name if it is in the PATH.
CMake Error at CMakeLists.txt:42 (project):
The CMAKE_CXX_COMPILER:
/home/conda/feedstock_root/build_artifacts/gromacs_1770909930561/_build_env/bin/x86_64-conda-linux-gnu-c++
is not a full path to an existing compiler tool.
Tell CMake where to find the compiler by setting either the environment
variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
to the compiler, or to the compiler name if it is in the PATH.
-- Configuring incomplete, errors occurred!
Traceback (most recent call last):
File "/home/mayur/anaconda3/envs/gmx_cuda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
main()
File "/home/mayur/anaconda3/envs/gmx_cuda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
json_out["return_val"] = hook(**hook_input["kwargs"])
File "/home/mayur/anaconda3/envs/gmx_cuda/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
return _build_backend().build_wheel(
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 441, in build_wheel
return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 429, in _build
return self._build_with_temp_dir(
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 410, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 317, in run_setup
exec(code, locals())
File "<string>", line 415, in <module>
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 117, in setup
return distutils.core.setup(**attrs) # type: ignore[return-value]
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 186, in setup
return run_commands(dist)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1000, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1107, in run_command
super().run_command(command)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
self.run_command("build")
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1107, in run_command
super().run_command(command)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1107, in run_command
super().run_command(command)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
cmd_obj.run()
File "<string>", line 232, in run
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 97, in run
_build_ext.run(self)
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 367, in run
self.build_extensions()
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 483, in build_extensions
self._build_extensions_serial()
File "/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 509, in _build_extensions_serial
self.build_extension(ext)
File "<string>", line 210, in build_extension
File "/home/mayur/anaconda3/envs/gmx_cuda/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-xvb8x3xl/gmxapi_e92db02a555c45e2b42bd5575a492fbc', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-xvb8x3xl/gmxapi_e92db02a555c45e2b42bd5575a492fbc/build/lib.linux-x86_64-cpython-310/gmxapi/', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_AR=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-ar', '-DCMAKE_CXX_COMPILER_AR=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-gcc-ar', '-DCMAKE_C_COMPILER_AR=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-gcc-ar', '-DCMAKE_RANLIB=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-ranlib', '-DCMAKE_CXX_COMPILER_RANLIB=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-gcc-ranlib', '-DCMAKE_C_COMPILER_RANLIB=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-gcc-ranlib', '-DCMAKE_LINKER=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-ld', '-DCMAKE_STRIP=/home/mayur/anaconda3/envs/gmx_cuda/bin/x86_64-conda-linux-gnu-strip', '-DCMAKE_BUILD_TYPE=Release', '-Dgmxapi_ROOT=/home/mayur/anaconda3/envs/gmx_cuda', '-D_setuppy_cmake_hints=/home/mayur/anaconda3/envs/gmx_cuda/share/cmake/gromacs/gromacs-hints.cmake', '-C', '/home/mayur/anaconda3/envs/gmx_cuda/share/cmake/gromacs/gromacs-hints.cmake', '-Dpybind11_ROOT=/tmp/pip-build-env-4gymhjhx/overlay/lib/python3.10/site-packages/pybind11/share/cmake/pybind11']' returned non-zero exit status 1.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for gmxapi
Failed to build gmxapi
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> gmxapi
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