HiI am trying to install pmemd26 on Ubuntu 25I am getting the following Warning during configuration
CMake Warning at src/pmemd/src/xray/CMakeLists.txt:25 (message):
PMEMD_XRAY_CPU_FFT_BACKEND=NONE disables xray functionality of `pmemd`
executable
and subsequent error during make install
6 errors detected in the compilation of "/opt/pmemd26_src/src/pmemd/src/xray/cuda/src/xray/xray_non_bulk.cu".
CMake Error at pmemd_xray_cuda_generated_xray_non_bulk.cu.o.RELEASE.cmake:278 (message):
Error generating file
/opt/pmemd26_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_xray_non_bulk.cu.o
Can someone help me
NOTE: Cuda-12.8.2 used along with gcc gcc (Ubuntu 14.3.0-8ubuntu1) 14.3.0
Regards
Raghuvir
> On 9 May 2026, at 00:30, amber-request.ambermd.org wrote:
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> Today's Topics:
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> 1. ambermd.org is Down (Zihao Bai)
> 2. Re: Compilation Issues - also with pmemd26 (Beierlein, Frank)
> 3. Re: Compilation Issues - also with pmemd26 (David Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 8 May 2026 02:10:09 +0000
> From: Zihao Bai <zbai29.wisc.edu>
> To: Carlos Simmerling via AMBER <amber.ambermd.org>
> Subject: [AMBER] ambermd.org is Down
> Message-ID:
> <PH0PR06MB74646D803AF41A91F15319A9B53D2.PH0PR06MB7464.namprd06.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Amber Team,
>
> The website https://ambermd.org/ is down. So, update_amber does not work.
>
> Best regards,
> Zihao
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 8 May 2026 09:43:45 +0000
> From: "Beierlein, Frank" <frank.beierlein.fau.de>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Compilation Issues - also with pmemd26
> Message-ID: <8543911A-A763-409E-BC4C-43240452C6B9.fau.de>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Amber Experts,
>
> I still have problems when trying to run_cmake for prmemd.cuda, as I previously mailed to this list. Upgrading to Amber 26 did not change anything.
>
> The highest version of Cuda that is available on the system ist found, and not the one defined in $CUDA_HOME:
>
> 11:24am[ccc068]/build>pwd
> /ccc/SOFT/Amber/amber26_2026-05/pmemd26_src/build
> 11:24am[ccc068]/build>echo $CUDA_HOME/
> /usr/local/cuda/
> 11:24am[ccc068]/build>ll /usr/local/cuda
> lrwxrwxrwx 1 root root 22 Nov 15 2021 /usr/local/cuda -> /etc/alternatives/cuda
> 11:25am[ccc068]/build>ll /etc/alternatives/cuda
> lrwxrwxrwx 1 root root 20 May 6 16:29 /etc/alternatives/cuda -> /usr/local/cuda-12.8
> 11:25am[ccc068]/build>echo $path
> /usr/local/cuda/bin /usr/lib64/mpi/gcc/openmpi4/bin /home/local/beierl/.local/bin /home/local/beierl/bin /usr/bin /bin /usr/sbin /sbin /usr/local/bin /usr/lib/mit/bin /usr/lib/mit/sbin /ccc/SOFT/bin
> 11:25am[ccc068]/build>echo $LD_LIBRARY_PATH
> /usr/local/cuda/lib64:/usr/lib64/mpi/gcc/openmpi4/lib64
> 11:25am[ccc068]/build>./run_cmake |& tee run_cmake_CUDA_fb.log
> -- **************************************************************************
> -- 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
> -- CUDA version 13.0 detected
> CMake Error at cmake/CudaConfig.cmake:85 (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/amber26/pmemd26/amber.sh
>
> Consider adding the last line to your login startup script, e.g. ~/.bashrc
>
>
>
>
> Any help would be appreciated very much.
>
> Many thanks and best wishes,
> Frank
>
>
> On 28 Apr 2026, at 15:35, Frank Beierlein <frank.beierlein.fau.de> wrote:
>
> Dear Matt, All,
>
> Many thanks for pointing this out.
>
> In the second part of my mail I had described a problem that occurs when I run ./run_cmake in pmemd24_src/build with -DMPI=FALSE -DCUDA=TRUE .
>
> Any suggestions to solve this would also be very much appreciated.
>
> Many thanks and best wishes,
> Frank
>
>
> On 4/23/26 17:46, Matt Thompson wrote:
> You're probably using SetupTools 81+ which removed that keyword. It was released in February and Miniconda probably pulls it down. Try downgrading to 80.x
>
> https://setuptools.pypa.io/en/stable/history.html#v81-0-0
>
> Matt
>
> On Thu, Apr 23, 2026 at 9:01?AM Beierlein, Frank via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
> ...
>
>
> 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 f?r 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<mailto:frank.beierlein.fau.de>
>
> https://chemistry.nat.fau.eu/beierlein
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> --
> Dr. Frank Beierlein
>
> Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU)
> Zentrum fuer 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<mailto:frank.beierlein.fau.de>
>
> https://chemistry.nat.fau.eu/beierlein
>
>
> --
> Dr. Frank Beierlein
>
> Friedrich-Alexander-Universitaet Erlangen-Nuernberg (FAU)
> Zentrum f?r 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
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 8 May 2026 08:53:28 -0600
> From: David Case <dacase1.gmail.com>
> To: "Beierlein, Frank" <frank.beierlein.fau.de>, AMBER Mailing List
> <amber.ambermd.org>
> Subject: Re: [AMBER] Compilation Issues - also with pmemd26
> Message-ID:
> <CADHyprRUNg21T0YzhFSWkLcgihsOMH39VBsNUJiKY+mo_7ceXw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Fri, May 8, 2026 at 3:47?AM Beierlein, Frank via AMBER <amber.ambermd.org>
> wrote:
>
>>
>>
>> The highest version of Cuda that is available on the system is found, and
>> not the one defined in $CUDA_HOME:
>>
>
> Do you have permissions to temporarily rename whatever link is pointing to
> Cuda13? And, where is Cuda13 on your system?
>
> Amber is using on (old-ish) FindCuda,cmake package, which we did not
> write. I hope that someone else on the list can provide better
> recommendations.
>
> ...regards...dac
>
>>
>>
>
>
> ------------------------------
>
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> ------------------------------
>
> End of AMBER Digest, Vol 4956, Issue 1
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Received on Fri May 08 2026 - 22:30:02 PDT
