---------- Forwarded message ---------
De : Osadchey Brown, Reilly <rosadche.bu.edu>
Date: lun. 20 févr. 2023 à 20:56
Subject: Re: [AMBER] Error - Amber 22 Installation with Cuda
To: AMBER Mailing List <amber.ambermd.org>, ABDELATIF MESSAOUDI <
amessaoudi.univ-batna.dz>
Hi Abdelatif,
For me, this was fixed by adding one line to the CMakeLists.txt file.
Please see the below text which shows the start of my CMakelists.txt file
and has the added line.
Best,
Reilly Osadchey Brown
cmake_minimum_required(VERSION 3.8.1)
project(Amber NONE)
#version number
#---------------------------------------------------------------------------------------------------------------------------------------------------------------------
set(Amber_MAJOR_VERSION 22)
set(Amber_MINOR_VERSION 0)
set(Amber_PATCH_VERSION 0)
set(Amber_VERSION
"${Amber_MAJOR_VERSION}.${Amber_MINOR_VERSION}.${Amber_PATCH_VERSION}")
# flag to submodules to tell them to not run their own version of
AmberCmakeConfig
set(INSIDE_AMBER TRUE)
#ADDED LINE TO FIX CUB ISSUE
add_compile_definitions(THRUST_IGNORE_CUB_VERSION_CHECK)
------------------------------
*From:* ABDELATIF MESSAOUDI via AMBER <
amber.ambermd.org>
*Sent:* 20 February 2023 14:37
*To:* AMBER Mailing List <amber.ambermd.org>
*Subject:* [AMBER] Error - Amber 22 Installation with Cuda
Dear AMBER users,
I am trying to install AMBER22 with Cuda. I am getting the error :
After running "./run_cmake" ; When I run "make install" I get the following
error :
Scanning dependencies of target pmemd_xray_contracts
[ 90%] Built target pmemd_xray_contracts
Scanning dependencies of target pmemd_xray_gpu
[ 90%] Built target pmemd_xray_gpu
Scanning dependencies of target pmemd_obj_cuda
Consolidate compiler generated dependencies of target pmemd_obj_cuda
[ 91%] Built target pmemd_obj_cuda
Scanning dependencies of target pmemd_obj_cuda_mpi
Consolidate compiler generated dependencies of target pmemd_obj_cuda_mpi
[ 93%] Built target pmemd_obj_cuda_mpi
[ 93%] Building NVCC (Device) object
src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir/pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o
In file included from
/usr/include/thrust/system/cuda/detail/execution_policy.h:35,
from /usr/include/thrust/iterator/detail/device_system_tag.h:23,
from /usr/include/thrust/iterator/detail/iterator_facade_category.h:22,
from /usr/include/thrust/iterator/iterator_facade.h:37,
from
/home/abdel/SOFT/amber22_src/src/pmemd/src/./cub/device/../iterator/arg_index_input_iterator.cuh:48,
from
/home/abdel/SOFT/amber22_src/src/pmemd/src/./cub/device/device_reduce.cuh:41,
from /home/abdel/SOFT/amber22_src/src/pmemd/src/./cub/cub.cuh:53,
from /home/abdel/SOFT/amber22_src/src/pmemd/src/cuda/kNLRadixSort.cu:14:
/usr/include/thrust/system/cuda/config.h:79:2: error: #error The version of
CUB in your include path is not compatible with this release of Thrust. CUB
is now included in the CUDA Toolkit, so you no longer need to use your own
checkout of CUB. Define THRUST_IGNORE_CUB_VERSION_CHECK to ignore this.
79 | #error The version of CUB in your include path is not compatible with
this release of Thrust. CUB is now included in the CUDA Toolkit, so you no
longer need to use your own checkout of CUB. Define
THRUST_IGNORE_CUB_VERSION_CHECK to ignore this.
| ^~~~~
CMake Error at
pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o.RELEASE.cmake:218 (message):
Error generating
/home/abdel/SOFT/amber22_src/build/src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir//./pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o
make[2]: ***
[src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir/build.make:1676 :
src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir/pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o]
Erreur 1
make[1]: *** [CMakeFiles/Makefile2:9879 :
src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir/all] Erreur 2
make: *** [Makefile:156 : all] Erreur 2
Best regards
Abdelatif Messaoudi
LCMVAR, University of Batna1, Algeria
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AMBER.ambermd.org
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Le sam. 4 mars 2023 à 09:02, Madhavan Jayaraman via AMBER <amber.ambermd.org>
a écrit :
> Hi
>
> I am trying to install Amber22 onto my ubuntu 22.04 machine running an
> RTX3060 and an AMD R5 3600. All necessary packages/compilers are installed,
> along with OpenMPI, MPI and CUDA 12.0. At 79% of the "make install" process
> there was a cmake error regarding CUSPARSE_MV_ALG_DEFAULT being undefined.
> I have asked some people and they suggested editing the run_cmake script
> however I am unsure of what changes should be made as this is my first time
> using a comp chem software.
>
> Below is the Error message,
> Many thanks,
> Madhavan.
>
> UNSW Sydney
>
> [ 78%] Built target libcpptraj_cuda
> Consolidate compiler generated dependencies of target ambpdb
> [ 78%] Built target ambpdb
> Scanning dependencies of target pbsa
> [ 79%] Built target pbsa
> Consolidate compiler generated dependencies of target simplepbsa
> [ 79%] Built target simplepbsa
> Consolidate compiler generated dependencies of target simplepbsa.MPI
> [ 79%] Built target simplepbsa.MPI
> [ 79%] Building NVCC (Device) object
> AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/pbsa.cuda_generated_cusparse_LinearSolvers.cu.o
> /home/madhavan/Desktop/amber/amber22_src/AmberTools/src/pbsa/cusparse_LinearSolvers.cu(78):
> error: identifier "CUSPARSE_MV_ALG_DEFAULT" is undefined
>
> /home/madhavan/Desktop/amber/amber22_src/AmberTools/src/pbsa/cusparse_LinearSolvers.cu(221):
> error: identifier "CUSPARSE_MV_ALG_DEFAULT" is undefined
>
> 2 errors detected in the compilation of
> "/home/madhavan/Desktop/amber/amber22_src/AmberTools/src/pbsa/cusparse_LinearSolvers.cu".
> CMake Error at
> pbsa.cuda_generated_cusparse_LinearSolvers.cu.o.RELEASE.cmake:278 (message):
> Error generating file
>
> /home/madhavan/Desktop/amber/amber22_src/build/AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir//./pbsa.cuda_generated_cusparse_LinearSolvers.cu.o
>
>
> make[2]: ***
> [AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/build.make:1429:
> AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/pbsa.cuda_generated_cusparse_LinearSolvers.cu.o]
> Error 1
> make[1]: *** [CMakeFiles/Makefile2:7432:
> AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/all] Error 2
> make: *** [Makefile:156: all] Error 2
>
> The run_cmake file is as follows:
>
> # Assume this is Linux:
>
> cmake $AMBER_PREFIX/amber22_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
> -DCOMPILER=GNU \
> -DMPI=TRUE -DOPENMP=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE \
> -D DLIB_USE_CUDA=1 -D USE_AVX_INSTRUCTIONS=1
> -DCUDA_NVCC_FLAGS="--expt-relaxed-constexpr"
> 2>&1 | tee cmake.log
>
> fi
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 06 2023 - 13:30:03 PST
