add sample slurm

Minimap2onGPU · Sep 26, 2023 · ccddf5c · ccddf5c
1 parent 7b65403
commit ccddf5c
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diff --git 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
@@ -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