diff --git a/templates/relion/3.1.2/data.relion.arm.sve.cpu.config b/templates/relion/3.1.2/data.relion.arm.sve.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..bee79bd00f0fd1337f2e0c42eabdd95bcc629f10 --- /dev/null +++ b/templates/relion/3.1.2/data.relion.arm.sve.cpu.config @@ -0,0 +1,88 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz + +[DEPENDENCY] +./jarvis -install package/hpckit/2024.12.30/ any +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module purge +module load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi + +export CC=mpicc CXX=mpicxx FC=mpifort + +./jarvis -install fftw/3.3.8 clang+mpi + +cd ${JARVIS_TMP} +rm -rf relion-3.1.2 +tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz + + +[ENV] +module purge +module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles +module load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi +module use software/moduledeps/bisheng4.1.0-hmpi2.4.3/ +module load fftw/3.3.8 + +export PATH=${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2/bin:$PATH + + +[APP] +app_name = relion +build_dir = ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 +binary_dir = ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2/bin +case_dir = ${JARVIS_ROOT}/case/relion_benchmark + +[BUILD] + +cd ${JARVIS_TMP} +cd relion-3.1.2 +mkdir build && cd build + +cmake -DCMAKE_C_FLAGS="-g -O3 -fopenmp -mllvm -force-customized-pipeline -mllvm -replace-sqrt-compare-by-square=true -fopenmp -mllvm -aarch64-enable-loop-data-prefetch=false -Wno-deprecated-declarations -msve-vector-bits=512 " -DCMAKE_CXX_FLAGS=" -g -O3 -fopenmp -mllvm -force-customized-pipeline -mllvm -replace-sqrt-compare-by-square=true -fopenmp -mllvm -aarch64-enable-loop-data-prefetch=false -Wno-deprecated-declarations -msve-vector-bits=512" -DFFTW_PATH=${KML_PATH}/include -DFFTW_INCLUDES=${KML_PATH}/include -DFFTW_LIBRARIES="${FFTW_PATH}/lib/libfftw3.so ${FFTW_PATH}/lib/libfftw3f.so" -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 -DCUDA=OFF -DBUILD_SHARED_LIBS=OFF -DGUI=OFF -DFETCH_WEIGHTS=OFF -DFORCE_OWN_FFTW=OFF -DALTCPU=ON -DCMAKE_BUILD_TYPE=release ../ + +make -j +make install + +[RUN] +run = +binary = +nodes = 1 + +[BATCH] +#定义日志文件 +LOG_FILE="cesm-proformance.log" +#清空日志文件 +>"$LOG_FILE" +#创建输出目录 +mkdir -p class3d + +trdnum=8 +mynp=16 + +#执行每个命令并统计性能 +$RUN_TOOL "mpirun " "time -p mpirun --allow-run-as-root --map-by ppr:${mynp}:node:pe=${trdnum} -x OMP_NUM_THREADS=${trdnum} --bind-to core --rank-by core -x UCX_TLS=self,sm -mca pml ucx -mca btl ^vade,tcp,openib,uct relion_refine_mpi --j $trdnum --gpu 0 -pool 100 --dont_combine_weights_via_disc --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --maxsig 500 --fast_subsets --o class3d/test_1N_25it_32-4_1_1gp " $LOG_FILE + + + + +[JOB] +#!/bin/bash +#DSUB -n relion_test +#DSUB --mpi hmpi +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -o relion.%J.out +#DSUB -e relion.%J.err + + +#定义日志文件 +LOG_FILE="relion-proformance.log" + +#清空日志文件 +>"$LOG_FILE" + +#执行每个命令并统计性能 +$RUN_TOOL "mpirun " "time -p mpirun --allow-run-as-root -np ${allnp} --map-by ppr:${mynp}:node:pe=${trdnum} -x OMP_NUM_THREADS=${trdnum} --bind-to core --rank-by core -x UCX_TLS=self,sm -mca pml ucx -mca btl ^vade,tcp,openib,uct relion_refine_mpi --j $trdnum --gpu 0 -pool 100 --dont_combine_weights_via_disc --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --maxsig 500 --fast_subsets --o class3d/test_1N_25it_32-4_1_1gp " $LOG_FILE