From 9577cbf23b11f4be8120e3fecb31d3f44602cd65 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Thu, 16 Oct 2025 17:42:42 +0800
Subject: [PATCH 1/2] megahit

---
 .../1.2.9/megahit.arm.cpu.hpckit.config       | 91 +++++++++++++++++++
 1 file changed, 91 insertions(+)
 create mode 100644 templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config

diff --git a/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config b/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config
new file mode 100644
index 00000000..22f21d81
--- /dev/null
+++ b/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config
@@ -0,0 +1,91 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+megahit/1.2.9 https://codeload.github.com/voutcn/megahit/tar.gz/v1.2.9 megahit-1.2.9.tar.gz
+sse2neon/1.5.0 https://codeload.github.com/DLTcollab/sse2neon/tar.gz/refs/tags/v1.5.0 sse2neon-1.5.0.tar.gz
+SRR1976948 https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1976948.abundtrim.subset.pe.fq.gz
+SRR1977249 https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1977249.abundtrim.subset.pe.fq.gz
+
+[DEPENDENCY]
+set -e
+set -x
+yum install -y cmake gzip zlib bzip2
+./jarvis -install hpckit/25.0.0 com
+module use ./software/compiler/hpckit/25.0.0/HPCKit/25.0.0/modulefiles
+module add bisheng/compiler4.2.0/bishengmodule bisheng/hmpi25.0.0/hmpi
+export CC=`which mpicc`
+export CXX=`which mpicxx`
+export FC=`which mpifort`
+export F77=`which mpifort`
+rm -rf MEGAHIT
+mkdir -p MEGAHIT
+cd MEGAHIT
+tar -xzvf ${JARVIS_DOWNLOAD}/megahit-1.2.9.tar.gz
+tar -xzvf ${JARVIS_DOWNLOAD}/sse2neon-1.5.0.tar.gz
+
+
+[ENV]
+module use ./software/compiler/hpckit/25.0.0/HPCKit/25.0.0/modulefiles
+module add bisheng/compiler4.2.0/bishengmodule bisheng/hmpi25.0.0/hmpi
+export CC=`which mpicc`
+export CXX=`which mpicxx`
+export FC=`which mpifort`
+export F77=`which mpifort`
+export PATH=${JARVIS_ROOT}/MEGAHIT/bin:$PATH
+
+
+[APP]
+app_name = megahit
+build_dir = ${JARVIS_ROOT}/MEGAHIT/megahit-1.2.9
+binary_dir = 
+case_dir = ${JARVIS_ROOT}/MEGAHIT/testcase
+
+[BUILD]
+
+cd ${JARVIS_ROOT}/MEGAHIT/megahit-1.2.9
+sed -i '6s/-std=c++11/& -march=armv8.2-a/' CMakeLists.txt
+sed -i '76s/-mbmi2 -DUSE_BMI2 -mpopcnt//g' CMakeLists.txt
+sed -i '77s/-mpopcnt//g' CMakeLists.txt
+cd ./src/utils/
+git clone https://github.com/xiaotao-star/KunpengTrans.h.git
+mv KunpengTrans.h KunpengTrans
+cp ./KunpengTrans/KunpengTrans.h ./
+sed -i '4i\#if defined(__aarch64__)\n  #include "KunpengTrans.h"\n#endif' cpu_dispatch.h
+sed -i '18i\#if defined(__x86_64__)' cpu_dispatch.h
+sed -i '22i\#elif defined(__aarch64__)\n  {\n    eax = 1;\n    GetSupportedCPUID(&eax,&ebx,&ecx,&edx);\n  }\n#endif' cpu_dispatch.h
+sed -i '39i\#if defined(__x86_64__)' cpu_dispatch.h
+sed -i '43i\#elif defined(__aarch64__)\n  {\n    eax = 7;\n    ecx = 0;\n    GetSupportedCPUID(&eax,&ebx,&ecx,&edx);\n  }\n#endif' cpu_dispatch.h
+cd ../kmlib/
+sed -i 's/<x86intrin.h>/<sse2neon.h>/g' kmrns.h
+cd ../
+cp ${JARVIS_ROOT}/MEGAHIT/sse2neon-1.5.0/sse2neon.h ./
+cd ../
+rm -rf build
+mkdir -p build
+cd build
+CC=`which gcc` CXX=`which g++` cmake -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/MEGAHIT -DCMAKE_BUILD_TYPE=Release ../
+make -j 16
+make install
+export PATH=${JARVIS_ROOT}/MEGAHIT/bin:$PATH
+
+cd ${JARVIS_ROOT}/MEGAHIT/
+rm -rf testcase
+mkdir testcase && cd testcase
+cp ${JARVIS_DOWNLOAD}/SRR1976948.abundtrim.subset.pe.fq.gz ./
+cp ${JARVIS_DOWNLOAD}/SRR1977249.abundtrim.subset.pe.fq.gz ./
+
+
+[CLEAN]
+make clean
+
+[RUN]
+run = megahit -t 128 --12 SRR1976948.abundtrim.subset.pe.fq.gz SRR1977249.abundtrim.subset.pe.fq.gz > megahit.log
+binary =
+nodes = 1
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
+
-- 
Gitee


From 95a9e9e3902e123f791e9b1dd5c90ab0fe51002c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Mon, 20 Oct 2025 19:18:50 +0800
Subject: [PATCH 2/2] megahit

---
 templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config b/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config
index 22f21d81..cfabdea9 100644
--- a/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config
+++ b/templates/megahit/1.2.9/megahit.arm.cpu.hpckit.config
@@ -6,6 +6,7 @@ megahit/1.2.9 https://codeload.github.com/voutcn/megahit/tar.gz/v1.2.9 megahit-1
 sse2neon/1.5.0 https://codeload.github.com/DLTcollab/sse2neon/tar.gz/refs/tags/v1.5.0 sse2neon-1.5.0.tar.gz
 SRR1976948 https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1976948.abundtrim.subset.pe.fq.gz
 SRR1977249 https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1977249.abundtrim.subset.pe.fq.gz
+KunpengTrans.h https://raw.githubusercontent.com/xiaotao-star/KunpengTrans.h/refs/heads/main/KunpengTrans.h
 
 [DEPENDENCY]
 set -e
@@ -48,9 +49,7 @@ sed -i '6s/-std=c++11/& -march=armv8.2-a/' CMakeLists.txt
 sed -i '76s/-mbmi2 -DUSE_BMI2 -mpopcnt//g' CMakeLists.txt
 sed -i '77s/-mpopcnt//g' CMakeLists.txt
 cd ./src/utils/
-git clone https://github.com/xiaotao-star/KunpengTrans.h.git
-mv KunpengTrans.h KunpengTrans
-cp ./KunpengTrans/KunpengTrans.h ./
+cp ${JARVIS_DOWNLOAD}/KunpengTrans.h ./
 sed -i '4i\#if defined(__aarch64__)\n  #include "KunpengTrans.h"\n#endif' cpu_dispatch.h
 sed -i '18i\#if defined(__x86_64__)' cpu_dispatch.h
 sed -i '22i\#elif defined(__aarch64__)\n  {\n    eax = 1;\n    GetSupportedCPUID(&eax,&ebx,&ecx,&edx);\n  }\n#endif' cpu_dispatch.h
-- 
Gitee