From ccddf5c3f4b6641ecce3a18291935569aeb3792d Mon Sep 17 00:00:00 2001 From: Xueshen Liu Date: Tue, 26 Sep 2023 16:55:27 -0500 Subject: [PATCH] add sample slurm --- gpu/.depend | 40 ++++++++++++++++++------------------ scripts/acc_integrated.slurm | 4 ++-- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/gpu/.depend b/gpu/.depend index 653311c0..cfefe771 100644 --- a/gpu/.depend +++ b/gpu/.depend @@ -1,49 +1,49 @@ -# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx1030 +# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx90a plchain.o: gpu/plchain.cu mmpriv.h minimap.h bseq.h kseq.h gpu/plmem.cuh \ gpu/hipify.cuh gpu/plchain.h gpu/plutils.h kalloc.h gpu/plrange.cuh \ - gpu/plscore.cuh gpu/debug.h + gpu/plscore.cuh -# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx1030 +# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx90a # __CLANG_OFFLOAD_BUNDLE____START__ host-x86_64-unknown-linux-gnu plchain.o: gpu/plchain.cu mmpriv.h minimap.h bseq.h kseq.h gpu/plmem.cuh \ gpu/hipify.cuh gpu/plchain.h gpu/plutils.h kalloc.h gpu/plrange.cuh \ - gpu/plscore.cuh gpu/debug.h + gpu/plscore.cuh # __CLANG_OFFLOAD_BUNDLE____END__ host-x86_64-unknown-linux-gnu -# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx1030 -plmem.o: gpu/plmem.cu gpu/plmem.cuh gpu/hipify.cuh gpu/plchain.h \ - gpu/plutils.h kalloc.h minimap.h gpu/plrange.cuh gpu/plscore.cuh \ - mmpriv.h bseq.h kseq.h cJSON/cJSON.h +# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx90a +plrange.o: gpu/plrange.cu gpu/plrange.cuh gpu/plmem.cuh gpu/hipify.cuh \ + gpu/plchain.h gpu/plutils.h kalloc.h minimap.h -# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx1030 +# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx90a # __CLANG_OFFLOAD_BUNDLE____START__ host-x86_64-unknown-linux-gnu -plmem.o: gpu/plmem.cu gpu/plmem.cuh gpu/hipify.cuh gpu/plchain.h \ - gpu/plutils.h kalloc.h minimap.h gpu/plrange.cuh gpu/plscore.cuh \ - mmpriv.h bseq.h kseq.h cJSON/cJSON.h +plrange.o: gpu/plrange.cu gpu/plrange.cuh gpu/plmem.cuh gpu/hipify.cuh \ + gpu/plchain.h gpu/plutils.h kalloc.h minimap.h # __CLANG_OFFLOAD_BUNDLE____END__ host-x86_64-unknown-linux-gnu -# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx1030 -plrange.o: gpu/plrange.cu gpu/plrange.cuh gpu/plmem.cuh gpu/hipify.cuh \ - gpu/plchain.h gpu/plutils.h kalloc.h minimap.h +# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx90a +plmem.o: gpu/plmem.cu gpu/plmem.cuh gpu/hipify.cuh gpu/plchain.h \ + gpu/plutils.h kalloc.h minimap.h gpu/plrange.cuh gpu/plscore.cuh \ + mmpriv.h bseq.h kseq.h cJSON/cJSON.h -# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx1030 +# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx90a # __CLANG_OFFLOAD_BUNDLE____START__ host-x86_64-unknown-linux-gnu -plrange.o: gpu/plrange.cu gpu/plrange.cuh gpu/plmem.cuh gpu/hipify.cuh \ - gpu/plchain.h gpu/plutils.h kalloc.h minimap.h +plmem.o: gpu/plmem.cu gpu/plmem.cuh gpu/hipify.cuh gpu/plchain.h \ + gpu/plutils.h kalloc.h minimap.h gpu/plrange.cuh gpu/plscore.cuh \ + mmpriv.h bseq.h kseq.h cJSON/cJSON.h # __CLANG_OFFLOAD_BUNDLE____END__ host-x86_64-unknown-linux-gnu -# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx1030 +# __CLANG_OFFLOAD_BUNDLE____START__ hip-amdgcn-amd-amdhsa-gfx90a plscore.o: gpu/plscore.cu gpu/plscore.cuh gpu/plmem.cuh gpu/hipify.cuh \ gpu/plchain.h gpu/plutils.h kalloc.h minimap.h mmpriv.h bseq.h kseq.h -# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx1030 +# __CLANG_OFFLOAD_BUNDLE____END__ hip-amdgcn-amd-amdhsa-gfx90a # __CLANG_OFFLOAD_BUNDLE____START__ host-x86_64-unknown-linux-gnu plscore.o: gpu/plscore.cu gpu/plscore.cuh gpu/plmem.cuh gpu/hipify.cuh \ diff --git a/scripts/acc_integrated.slurm b/scripts/acc_integrated.slurm index 4cd66069..3986be3e 100644 --- a/scripts/acc_integrated.slurm +++ b/scripts/acc_integrated.slurm @@ -27,8 +27,8 @@ cd /shared/prod/home/liuxs/bioinfo/minimap2/ make clean make GPU_CONFIG=gpu_config.json SHORT_BLOCK_SIZE=64 LONG_BLOCK_SIZE=1024 MID_BLOCK_SIZE=512 MID_CUT=1 LONG_CUT=100 # ./minimap2 -t 1 --max-chain-skip=2147483647 --gpu-chain /shareddata/umich_folder/data/ONT/hg38.mmi /shareddata/umich_folder/data/ONT/reads_4f452f4a-d82a-4580-981b-32d14b997217.fa -# ./minimap2 -t 1 --max-chain-skip=2147483647 --gpu-chain /shareddata/umich_folder/data/ONT/hg38.mmi /shareddata/umich_folder/data/ONT/random_500MBases_200kto300k.fa -./minimap2 -t 1 --max-chain-skip=2147483647 --gpu-chain /shareddata/umich_folder/data/ONT/hg38.mmi /shareddata/umich_folder/data/ONT/short_seg_reads_from_1kto10k_distri.fa +./minimap2 -t 1 --max-chain-skip=2147483647 --gpu-chain /shareddata/umich_folder/data/ONT/hg38.mmi /shareddata/umich_folder/data/ONT/random_500MBases_200kto300k.fa +# ./minimap2 -t 1 --max-chain-skip=2147483647 --gpu-chain /shareddata/umich_folder/data/ONT/hg38.mmi /shareddata/umich_folder/data/ONT/short_seg_reads_from_1kto10k_distri.fa # Optional: You can add post-processing commands here