[CP2K-user] [CP2K:20293] Re: Running cp2k on GPU

Johann Pototschnig pototschnig.johann at gmail.com
Tue Jun 11 11:07:07 UTC 2024
Previous message (by thread): [CP2K-user] [CP2K:20289] Re: Running cp2k on GPU
Next message (by thread): [CP2K-user] [CP2K:20303] Re: Running cp2k on GPU
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Which GPU bindings did you end up using?

Did you compare to submission scripts for your cluster for which the GPU is 
used?


On Monday, June 10, 2024 at 6:31:45 PM UTC+2 Hemanth Haridas wrote:

> I tried running cp2k as described in the previous email, but the code 
> still does not run on the gpu, and the GPU usage is still zero.
>
> Sincererly,
> Hemanth
>
> On Friday, June 7, 2024 at 11:02:42 AM UTC-6 Johann Pototschnig wrote:
>
>> For cuda it is rather:
>> https://github.com/tom-papatheodore/hello_jobstep
>>
>> On Friday, June 7, 2024 at 6:52:33 PM UTC+2 Johann Pototschnig wrote:
>>
>>> It links to cuda, there should be no problem, but you are missing the 
>>> mpirun / srun:
>>>
>>> mpirun -n 1 -x OMP_NUM_THREADS=$...  /cp2k_plumed_gpu/cp2k-2024.1/exe/local_cuda/cp2k.psmp 
>>> -i colvars.inp -o colvars.out
>>>
>>>
>>> depending on your system there might be additional options for 
>>> mpirun/srun necessary. 
>>>
>>> The following program can help to figure out bindings:
>>> https://code.ornl.gov/olcf/hello_jobstep
>>>
>>> On Friday, June 7, 2024 at 5:18:47 PM UTC+2 Hemanth Haridas wrote:
>>>
>>>> CC          = 
>>>> /gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/bin/mpicc
>>>>
>>>> CXX         = 
>>>> /gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/bin/mpic++
>>>>
>>>> AR          = ar -r
>>>>
>>>> FC          = 
>>>> /gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/bin/mpifort
>>>>
>>>> LD          = 
>>>> /gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/bin/mpifort
>>>>
>>>> #
>>>>
>>>> DFLAGS      = -D__OFFLOAD_CUDA -D__DBCSR_ACC  -D__LIBXSMM  -D__parallel 
>>>> -D__MKL -D__FFTW3  -D__SCALAPACK -D__LIBINT -D__LIBXC -D__LIBGRPP -D__GSL 
>>>> -D__PLUMED2 -D__SPGLIB  -D__OFFLOAD_GEMM  -D__SPLA
>>>>
>>>> #
>>>>
>>>> WFLAGS      = -Werror=aliasing -Werror=ampersand -Werror=c-binding-type 
>>>> -Werror=intrinsic-shadow -Werror=intrinsics-std -Werror=line-truncation 
>>>> -Werror=tabs -Werror=target-lifetime -Werror=underflow 
>>>> -Werror=unused-but-set-variable -Werror=unused-variable 
>>>> -Werror=unused-dummy-argument -Werror=unused-parameter -Werror=unused-label 
>>>> -Werror=conversion -Werror=zerotrip -Wno-maybe-uninitialized 
>>>> -Wuninitialized -Wuse-without-only
>>>>
>>>> #
>>>>
>>>> FCDEBFLAGS  = -fbacktrace -ffree-form -fimplicit-none -std=f2008
>>>>
>>>> CFLAGS      = -fno-omit-frame-pointer -fopenmp -g -mtune=native  -O3 
>>>> -funroll-loops $(PROFOPT)  
>>>> -I/gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/include 
>>>> -pthread  -m64 
>>>> -I/gcc-8.5.0/intel-oneapi-mkl-2023.2.0-etwucm5d3s2qu7eiuaaxastbiukj2ori/mkl/2023.2.0/include 
>>>> -I/gcc-8.5.0/intel-oneapi-mkl-2023.2.0-etwucm5d3s2qu7eiuaaxastbiukj2ori/mkl/2023.2.0/include/fftw 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxc-6.2.2/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libgrpp-main-20231215/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxsmm-1.17/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/gsl-2.7/include' 
>>>> -I/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/spglib-1.16.2/include 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/SpLA-1.5.5/include/spla' 
>>>> -std=c11 -Wall -Wextra -Werror -Wno-vla-parameter 
>>>> -Wno-deprecated-declarations $(DFLAGS) 
>>>> -I/gcc-8.5.0/cuda-11.8.0-3wlxktsbgw2ui4wvdnsy7w7xyxlkkwju/include
>>>>
>>>> FCFLAGS     = -fno-omit-frame-pointer -fopenmp -g -mtune=native  -O3 
>>>> -funroll-loops $(PROFOPT)  
>>>> -I/gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/include 
>>>> -pthread  -m64 
>>>> -I/gcc-8.5.0/intel-oneapi-mkl-2023.2.0-etwucm5d3s2qu7eiuaaxastbiukj2ori/mkl/2023.2.0/include 
>>>> -I/gcc-8.5.0/intel-oneapi-mkl-2023.2.0-etwucm5d3s2qu7eiuaaxastbiukj2ori/mkl/2023.2.0/include/fftw 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxc-6.2.2/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libgrpp-main-20231215/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxsmm-1.17/include' 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/gsl-2.7/include' 
>>>> -I/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/spglib-1.16.2/include 
>>>> -I'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/SpLA-1.5.5/include/spla' 
>>>> $(FCDEBFLAGS) $(WFLAGS) $(DFLAGS)
>>>>
>>>> CXXFLAGS    = -O2 -fPIC -fno-omit-frame-pointer -fopenmp -g 
>>>> -march=native -mtune=native --std=c++14 $(DFLAGS) 
>>>> -Wno-deprecated-declarations 
>>>> -I/gcc-8.5.0/cuda-11.8.0-3wlxktsbgw2ui4wvdnsy7w7xyxlkkwju/include
>>>>
>>>> #
>>>>
>>>> LDFLAGS     =  $(FCFLAGS) -Wl,--enable-new-dtags -pthread 
>>>> -L/gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/lib 
>>>> -L/gcc-8.5.0/ucx-1.14.0-cupo7hrn2exqqwfyatdigeuiiqijaulw/lib -L/uufs/
>>>> chpc.utah.edu/sys/spack/v019/linux-rocky8-x86_64/gcc-8.5.0/zlib-1.2.13-dcpzngybj4fisn6ojapnels3yfwcxqgk/lib 
>>>> -Wl,-rpath 
>>>> -Wl,/gcc-8.5.0/openmpi-4.1.6-chhfokbbf3fbb2t4uo7ns4ukaripskzj/lib 
>>>> -Wl,-rpath -Wl,/gcc-8.5.0/ucx-1.14.0-cupo7hrn2exqqwfyatdigeuiiqijaulw/lib 
>>>> -Wl,-rpath -Wl,/gcc-8.5.0/zlib-1.2.13-dcpzngybj4fisn6ojapnels3yfwcxqgk/lib  
>>>>   
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxc-6.2.2/lib' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxc-6.2.2/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libgrpp-main-20231215/lib' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libgrpp-main-20231215/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxsmm-1.17/lib' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/libxsmm-1.17/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/gsl-2.7/lib' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/gsl-2.7/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/plumed-2.9.0/lib' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/plumed-2.9.0/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/spglib-1.16.2/lib' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/spglib-1.16.2/lib' 
>>>> -L'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/SpLA-1.5.5/lib/cuda' 
>>>> -Wl,-rpath,'/cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/SpLA-1.5.5/lib/cuda' 
>>>> -L'/gcc-8.5.0/cuda-11.8.0-3wlxktsbgw2ui4wvdnsy7w7xyxlkkwju/targets/x86_64-linux/lib' 
>>>> -Wl,-rpath,'/gcc-8.5.0/cuda-11.8.0-3wlxktsbgw2ui4wvdnsy7w7xyxlkkwju/targets/x86_64-linux/lib' 
>>>> -L'/usr/lib64' -Wl,-rpath,'/usr/lib64'
>>>>
>>>> LDFLAGS_C   =
>>>>
>>>> LIBS        = -lspla -lsymspg -l:libplumed.a -ldl -lstdc++ -lz -ldl 
>>>> -lgsl -lxsmmf -lxsmm -ldl -lpthread -llibgrpp -lxcf03 -lxc -lint2   
>>>> -lmpi_cxx -lmpi  
>>>> -L/gcc-8.5.0/intel-oneapi-mkl-2023.2.0-etwucm5d3s2qu7eiuaaxastbiukj2ori/mkl/2023.2.0/lib/intel64 
>>>> -Wl,-rpath,/gcc-8.5.0/intel-oneapi-mkl-2023.2.0-etwucm5d3s2qu7eiuaaxastbiukj2ori/mkl/2023.2.0/lib/intel64 
>>>> -lmkl_scalapack_lp64 -Wl,--start-group -lmkl_gf_lp64 -lmkl_sequential 
>>>> -lmkl_core -lmkl_blacs_openmpi_lp64 -Wl,--end-group -lpthread -lm -ldl 
>>>> -lstdc++ -lcudart -lnvrtc -lcuda -lcufft -lcublas -lrt
>>>>
>>>> #
>>>>
>>>> GPUVER        = A100
>>>>
>>>> OFFLOAD_CC    = nvcc
>>>>
>>>> OFFLOAD_FLAGS = -g -arch sm_80 -O3 -allow-unsupported-compiler 
>>>> -Xcompiler='-fopenmp -Wall -Wextra -Werror' --std=c++11 $(DFLAGS)
>>>>
>>>> OFFLOAD_TARGET = cuda
>>>>
>>>> #
>>>>
>>>> FYPPFLAGS   = -n --line-marker-format=gfortran5
>>>> On Friday, June 7, 2024 at 1:51:34 AM UTC-6 Johann Pototschnig wrote:
>>>>
>>>>> Can you provide the local_cuda.psmp  file which you find in the arch 
>>>>> folder?
>>>>>
>>>>> On Thursday, June 6, 2024 at 9:10:38 PM UTC+2 Hemanth Haridas wrote:
>>>>>
>>>>>> I am trying to run CP2K on a linux cluster with GPU support. I have 
>>>>>> successfully complied the code with CUDA support. But the utilization of 
>>>>>> GPU is zero, even though the program is running , meaning that the code is 
>>>>>> running on cpu cores.
>>>>>>
>>>>>> This is the script that I am using to run cp2k 
>>>>>>
>>>>>> #!/bin/bash
>>>>>>
>>>>>> #SBATCH --job-name=LiCl                 ### Job Name
>>>>>>
>>>>>> #SBATCH --output=cp2k.out               ### File in which to store 
>>>>>> job output
>>>>>>
>>>>>> #SBATCH --error=cp2k.err                ### File in which to store 
>>>>>> job error messages
>>>>>>
>>>>>> #SBATCH --time=3-00:00:00               ### Wall clock time limit in 
>>>>>> Days-HH:MM:SS              
>>>>>>
>>>>>> #SBATCH --ntasks=64
>>>>>>
>>>>>> #SBATCH --gres=gpu:1
>>>>>>
>>>>>> #SBATCH --cpus-per-task=1
>>>>>>
>>>>>>
>>>>>> module load gcc cuda/11.8.0 openmpi/4.1.6-gpu intel-oneapi-mkl/2022.0
>>>>>> .2
>>>>>>
>>>>>>
>>>>>> source /cp2k_plumed_gpu/cp2k-2024.1/tools/toolchain/install/setup
>>>>>>
>>>>>>
>>>>>> export* OMP_NUM_THREADS=*$SLURM_NTASKS
>>>>>>
>>>>>>
>>>>>> /cp2k_plumed_gpu/cp2k-2024.1/exe/local_cuda/cp2k.psmp -i colvars.inp 
>>>>>> -o colvars.out
>>>>>>
>>>>>>
>>>>>> Are there any additional flags that I need to use to run the code on 
>>>>>> GPUs?
>>>>>>
>>>>>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/d3f8f2e2-f956-4477-b398-d11a78e5ed27n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20240611/a119eeb5/attachment-0001.htm>
Previous message (by thread): [CP2K-user] [CP2K:20289] Re: Running cp2k on GPU
Next message (by thread): [CP2K-user] [CP2K:20303] Re: Running cp2k on GPU
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the CP2K-user mailing list