Dear Amber experts,
I have problems compiling ambertools 25 and pmemd 24 on my machine with openSUSE Leap 15.6 and an RTX A5000 GPU. I am aware that Amber 26 might come soon, but I wanted to make a final version of Amber 25.
There were no issues the last time I did this on the same machine, in August 2025, with patchlevel 02 of both programs.
More specifically:
In ambertools25_src/build: after ./run_cmake with -DMPI=TRUE, make install fails somewhere in the context of mpi4py - see below (make -i runs through, probably with something missing…):
----------
…
copying src/mpi4py/util/dtlib.pyi -> /ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/AmberTools/src/mpi4py-3.1.4/CMakeFiles/mpi4py-build/lib.linux-x86_64-cpython-312/mpi4py/util
running build_clib
Traceback (most recent call last):
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/AmberTools/src/mpi4py-3.1.4/setup.py", line 642, in <module>
main()
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/AmberTools/src/mpi4py-3.1.4/setup.py", line 639, in main
run_setup()
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/AmberTools/src/mpi4py-3.1.4/setup.py", line 490, in run_setup
setup(
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/AmberTools/src/mpi4py-3.1.4/conf/mpidistutils.py", line 508, in setup
return fcn_setup(**attrs)
^^^^^^^^^^^^^^^^^^
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/__init__.py", line 117, in setup
return distutils.core.setup(**attrs) # type: ignore[return-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 186, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
dist.run_commands()
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1000, in run_commands
self.run_command(cmd)
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/dist.py", line 1107, in run_command
super().run_command(command)
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
cmd_obj.run()
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
self.distribution.run_command(command)
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/dist.py", line 1107, in run_command
super().run_command(command)
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/build/CMakeFiles/miniconda/install/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
cmd_obj.run()
File "/ccc/SOFT/Amber/amber25_2026-04/ambertools25_src/AmberTools/src/mpi4py-3.1.4/conf/mpidistutils.py", line 946, in run
self.compiler = new_compiler(compiler=self.compiler,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: new_compiler() got an unexpected keyword argument 'dry_run'
make[2]: *** [AmberTools/src/mpi4py-3.1.4/CMakeFiles/mpi4py.dir/build.make:203: AmberTools/src/mpi4py-3.1.4/CMakeFiles/mpi4py-build/mpi4py-build.stamp] Error 1
make[1]: *** [CMakeFiles/Makefile2:3426: AmberTools/src/mpi4py-3.1.4/CMakeFiles/mpi4py.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
--------------
The other problem that I have is in pmemd24_src/build, when running ./run_cmake with -DMPI=FALSE -DCUDA=TRUE .
$CUDA_HOME points to cuda-12.8:
3:16pm[ccc068]/build>echo $CUDA_HOME/
/usr/local/cuda/
3:17pm[ccc068]/build>ll /usr/local/cuda
lrwxrwxrwx 1 root root 22 Nov 15 2021 /usr/local/cuda -> /etc/alternatives/cuda
3:17pm[ccc068]/build>ll /etc/alternatives/cuda
lrwxrwxrwx 1 root root 20 Apr 21 17:32 /etc/alternatives/cuda -> /usr/local/cuda-12.8
When running ./cmake_run , the highest CUDA version available on the system is found, not the one defined in $CUDA_HOME:
--------------
-- **************************************************************************
-- Starting configuration of Amber version 24.0.0...
-- CMake Version: 3.28.3
-- For how to use this build system, please read this wiki:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
-- For a list of important CMake variables, check here:
--
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
-- **************************************************************************
-- Amber source found, building AmberTools and Amber
CMake Warning (dev) at cmake/CudaConfig.cmake:12 (find_package):
Policy CMP0146 is not set: The FindCUDA module is removed. Run "cmake
--help-policy CMP0146" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:129 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- CUDA version 13.0 detected
CMake Error at cmake/CudaConfig.cmake:83 (message):
Error: Untested CUDA version. AMBER currently requires CUDA version >= 7.5
and < 12.9.
Call Stack (most recent call first):
CMakeLists.txt:129 (include)
-- Configuring incomplete, errors occurred!
If errors are reported, search for 'CMake Error' in the cmake.log file.
If the cmake build report looks OK, you should now do the following:
make install
source /ccc/SOFT/Amber/amber25_2026-04/amber24/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
-------------
Any help would be greatly appreciated!
Many thanks and best wishes,
Frank
--
Dr. Frank Beierlein
Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU)
Zentrum für Nationales Hochleistungsrechnen (NHR.FAU)
Computer-Chemie-Centrum (CCC)
Naegelsbachstr. 25, Room 2.109
91052 Erlangen, Deutschland/Germany
Tel. +49(0)-9131-85 20415 / +49(0)-9131-85 89914
frank.beierlein.fau.de
https://chemistry.nat.fau.eu/beierlein
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Received on Thu Apr 23 2026 - 07:30:02 PDT
