From f289136b484909dd172ad3399ba1f7e60d35848a Mon Sep 17 00:00:00 2001 From: jsfhd <2162443403@qq.com> Date: Tue, 15 Apr 2025 17:38:09 +0800 Subject: [PATCH 1/2] add relion-3.1.2 templates --- .../3.1.2/data.relion.arm.sve.cpu.config | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 templates/relion/3.1.2/data.relion.arm.sve.cpu.config 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 0000000..60a21f4 --- /dev/null +++ b/templates/relion/3.1.2/data.relion.arm.sve.cpu.config @@ -0,0 +1,92 @@ +[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 wxWidgets/3.0.5 clang+mpi +#./jarvis -install ctffind/4.1.14/clang clang+mpi +./jarvis -install fftw/3.3.8 clang+mpi + + +[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] +#mkdir -p ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 +#tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz --strip-components 1 -C ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 + +#cd ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 + +cd ${JARVIS_TMP} +rm -rf relion-3.1.2 +tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz +cd relion-3.1.2 +mkdir build && cd build + +cmake -DCMAKE_C_FLAGS="-g -O3 -fopenmp -mllvm -force-customized-pipeline -mllvm -replace-sqrt-compare-by-square=true -fopenmp -mllvm -aarch64-enable-loop-data-prefetch=false -Wno-deprecated-declarations -msve-vector-bits=512 " -DCMAKE_CXX_FLAGS=" -g -O3 -fopenmp -mllvm -force-customized-pipeline -mllvm -replace-sqrt-compare-by-square=true -fopenmp -mllvm -aarch64-enable-loop-data-prefetch=false -Wno-deprecated-declarations -msve-vector-bits=512" -DFFTW_PATH=${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/include -DFFTW_INCLUDES=$JARVIS_ROOT/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/include -DFFTW_LIBRARIES="${JARVIS_ROOT}/software/libs/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib/libfftw3.so ${JARVIS_ROOT}/software/libs/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib/libfftw3f.so" -DCMAKE_INSTALL_PREFIX=${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 " $LOG_FILE + +mpirun --allow-run-as-root --map-by ppr:${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 $trdnum --gpu 0 -pool 100 --dont_combine_weights_via_disc --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --maxsig 500 --fast_subsets --o class3d/test_1N_25it_32-4_1_1gp + + + +[JOB] +#!/bin/bash +#DSUB -n relion_test +#DSUB --mpi hmpi +#DSUB -N 1 +#DSUB -R cpu=128 +#DSUB -o relion.%J.out +#DSUB -e relion.%J.err + + +#定义日志文件 +LOG_FILE="relion-proformance.log" + +#清空日志文件 +>"$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 -- Gitee From c76297d866ea451c1535a276a249e17524d4a56a Mon Sep 17 00:00:00 2001 From: jsfhd <2162443403@qq.com> Date: Wed, 14 May 2025 10:01:01 +0800 Subject: [PATCH 2/2] add relion-3.1.2 templates --- .../3.1.2/data.relion.arm.sve.cpu.config | 20 ++++++++----------- 1 file changed, 8 insertions(+), 12 deletions(-) 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 index 60a21f4..bee79bd 100644 --- a/templates/relion/3.1.2/data.relion.arm.sve.cpu.config +++ b/templates/relion/3.1.2/data.relion.arm.sve.cpu.config @@ -12,10 +12,12 @@ module load bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi export CC=mpicc CXX=mpicxx FC=mpifort -#./jarvis -install wxWidgets/3.0.5 clang+mpi -#./jarvis -install ctffind/4.1.14/clang clang+mpi ./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 @@ -34,18 +36,13 @@ binary_dir = ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2/b case_dir = ${JARVIS_ROOT}/case/relion_benchmark [BUILD] -#mkdir -p ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 -#tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz --strip-components 1 -C ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 - -#cd ${JARVIS_ROOT}/software/apps/bisheng4.1.0-hmpi2.4.3/relion-3.1.2 cd ${JARVIS_TMP} -rm -rf relion-3.1.2 -tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz cd relion-3.1.2 mkdir build && cd build -cmake -DCMAKE_C_FLAGS="-g -O3 -fopenmp -mllvm -force-customized-pipeline -mllvm -replace-sqrt-compare-by-square=true -fopenmp -mllvm -aarch64-enable-loop-data-prefetch=false -Wno-deprecated-declarations -msve-vector-bits=512 " -DCMAKE_CXX_FLAGS=" -g -O3 -fopenmp -mllvm -force-customized-pipeline -mllvm -replace-sqrt-compare-by-square=true -fopenmp -mllvm -aarch64-enable-loop-data-prefetch=false -Wno-deprecated-declarations -msve-vector-bits=512" -DFFTW_PATH=${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/include -DFFTW_INCLUDES=$JARVIS_ROOT/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/include -DFFTW_LIBRARIES="${JARVIS_ROOT}/software/libs/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib/libfftw3.so ${JARVIS_ROOT}/software/libs/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib/libfftw3f.so" -DCMAKE_INSTALL_PREFIX=${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 ../ +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 @@ -66,9 +63,8 @@ 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 " $LOG_FILE +$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 " $LOG_FILE -mpirun --allow-run-as-root --map-by ppr:${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 $trdnum --gpu 0 -pool 100 --dont_combine_weights_via_disc --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --maxsig 500 --fast_subsets --o class3d/test_1N_25it_32-4_1_1gp @@ -89,4 +85,4 @@ LOG_FILE="relion-proformance.log" >"$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 " $LOG_FILE +$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 -- Gitee