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---
Jones de Andrade
(jdandrade.iq.ufrgs.br)
DFQ/IQ/UFRGS
Lattes: http://lattes.cnpq.br/6675936210583999
Orcid: https://orcid.org/0000-0003-3429-8119
ResearcherID: https://publons.com/researcher/AAC-5337-2019/
Em 2023-11-10 16:54, Scott Brozell via AMBER escreveu:
> Hi,
>
> Thanks for the reports.
> Of course, we are also interested in testing, benchmarking, and other
> results of using Amber with the latest cuda 12 versions.
>
> Note that the additional cuda version check is
> ===
> CMake Error at
> AmberTools/src/quick/quick-cmake/QUICKCudaConfig.cmake:94 (message):
> Error: Unsupported CUDA version. quick requires CUDA version >= 8.0
> and <=
> 12.0. Please upgrade your CUDA installation or disable building with
> CUDA.
> ===
>
> In addition to modifying that cmake source file one can also disable
> building QUICK; add this to your cmake command either on the command
> line
> or in your run_cmake file:
> ===
> -DBUILD_QUICK=FALSE
> ===
>
> scott
>
> On Fri, Nov 10, 2023 at 07:14:10PM +0000, Mingxuan Jiang via AMBER
> wrote:
>> Dear Todd,
>>
>> This worked wonderfully.
>>
>> I just changed the 12.X to 12.4 for the following additional files:
>>
>> In the amber22_src/AmberTools/src/quick/quick-cmake/ folder
>>
>> in addition to what you have suggested, and everything seemed to
>> install well, to 100%.
>>
>> When I ran some minimization scripts, and they ran to completion.
>>
>> pmemd.cuda -O -i min.in -o min_f_CTS.out -p pypy.prmtop -c pypy.inpcrd
>> -r pypy_out.rst -ref pypy.inpcrd -x pypy_out.nc
>>
>> The only warning I got was:
>>
>> Note: The following floating-point exceptions are signalling:
>> IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
>>
>> Is this something of concern?
>>
>> If necessary, I can attach the input files.
>>
>>
>> Thank you!
>>
>> Best wishes,
>> Mingxuan Jiang
>>
>>
>> From: Todd Minehardt <todd.minehardt.gmail.com>
>> Date: Friday, 10 November 2023 at 14:00
>> To: Mingxuan Jiang <Mingxuan.Jiang.cruk.cam.ac.uk>, AMBER Mailing List
>> <amber.ambermd.org>
>> Subject: Re: [AMBER] CUDA version for AMBER22
>> Mingxuan,
>>
>> There is no need to roll back your CUDA 12.3 library, I have recently
>> recompiled AmberTools 23 with CUDA 12.3. It works just fine.
>>
>> You just need to edit a few files.
>>
>> First, edit the file cmake/CudaConfig.cmake and change line 76 to
>> read:
>>
>> elseif((${CUDA_VERSION} VERSION_GREATER_EQUAL 12.0) AND
>> (${CUDA_VERSION} VERSION_LESS_EQUAL 12.3))
>>
>> and rebuild.
>>
>> There will be a few other instances during your build process that
>> exit as before (I cannot recall off the top of my head which files
>> they emanate from), and repeat the process of editing the code in the
>> same way (i.e., change VERSION_LESS to VERSION_LESS_EQUAL and 12.1 to
>> 12.3).
>>
>> Cheers,
>>
>> Todd
>>
>> On Fri, Nov 10, 2023 at 3:53???AM Mingxuan Jiang via AMBER
>> <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
>> Dear Sir/Mdm,
>>
>> I am Ming, a PhD student from CRUKCI, and a user of AMBER for a few
>> years now.
>>
>> Recently, our HPC cluster has upgraded to CUDA-12.3, and I was hoping
>> to compile AMBER22. However, when running ./run_cmake,
>>
>> The following message was received:
>>
>> Basically, the cuda version is too high on the HPC. What would be the
>> best way to resolve this?
>>
>>
>> --
>> **************************************************************************
>>
>> -- Starting configuration of Amber version 22.0.0...
>>
>> -- CMake Version: 3.20.2
>>
>> -- For how to use this build system, please read this wiki:
>>
>> --
>> http://ambermd.org/pmwiki/pmwiki.php/Main/CMake<https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fambermd.org%2fpmwiki%2fpmwiki.php%2fMain%2fCMake&c=E,1,i7cWOz-8ow8JlxxHZOC99dt2WZUEjAtTR9fcEel2fiEZ3fuaC7BcvrqDbTTYOAMd1SDQvMlBW4jRKQiYFB_vlAtxYVVnQ10hHpqIaaPNCwMDEw,,&typo=1>
>>
>> -- For a list of important CMake variables, check here:
>>
>> --
>> http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options<https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fambermd.org%2fpmwiki%2fpmwiki.php%2fMain%2fCMake-Common-Options&c=E,1,JabDTcvBeNM1AcPUPee8HsK6asOdoSgzuMKMzBJWl8al7VTiBofM40DtIdI3IoWdLWe1J-xtakALAtH1OxVa319m_kvZj9zgmFqpJuUCcDPi594,&typo=1>
>>
>> --
>> **************************************************************************
>>
>> -- Amber source found, building AmberTools and Amber
>>
>> -- Looking for pthread.h
>>
>> -- Looking for pthread.h - found
>>
>> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
>>
>> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
>>
>> -- Looking for pthread_create in pthreads
>>
>> -- Looking for pthread_create in pthreads - not found
>>
>> -- Looking for pthread_create in pthread
>>
>> -- Looking for pthread_create in pthread - found
>>
>> -- Found Threads: TRUE
>>
>> -- Found CUDA: /usr/local/cuda (found version "12.3")
>>
>> -- CUDA version 12.3 detected
>>
>> CMake Error at cmake/CudaConfig.cmake:84 (message):
>>
>> Error: Untested CUDA version. AMBER currently requires CUDA version
>> >= 7.5
>>
>> and <= 12.1.
>>
>> Call Stack (most recent call first):
>>
>> CMakeLists.txt:119 (include)
>>
>>
>>
>>
>>
>> -- Configuring incomplete, errors occurred!
>>
>> See also
>> "/Users/jiang02/new_amber/amber22_src/build/CMakeFiles/CMakeOutput.log".
>>
>> See also
>> "/Users/jiang02/new_amber/amber22_src/build/CMakeFiles/CMakeError.log".
>>
>>
>>
>> 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
>> /Users/jiang02/new_amber/amber22/amber.sh<https://linkprotect.cudasvc.com/url?a=https%3a%2f%2famber.sh&c=E,1,PRJQV7h47oLdpihxmMIc9GJ9CClJyiSvAFpnqkwAZzy6sYmDiqX_oiidSkGWoH-DCpWCxWfuetbYif0HDYrDN0-B1DfwMSalYZLqBOrcqjT4rd3C4E4jhJ1Kmw,,&typo=1&ancr_add=1>
>>
>>
>>
>> Consider adding the last line to your login startup script, e.g.
>> ~/.bashrc
>
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Received on Sun Nov 12 2023 - 01:30:02 PST