From 673187dd7e2375725d793fa73081b16fa688d89b Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Thu, 10 Apr 2025 20:40:27 +0800
Subject: [PATCH 1/2] Add templates app BerkeleyGW-3.0.1

---
 .../berkeleygw.arm.bisheng.hpckit.config      | 84 +++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config

diff --git a/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config b/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config
new file mode 100644
index 0000000..3c72e1c
--- /dev/null
+++ b/templates/berkeleygw/3.0.1/berkeleygw.arm.bisheng.hpckit.config
@@ -0,0 +1,84 @@
+[SERVER]
+11.11.11.11
+
+# Go: https://berkeleygw.org/download/
+# Download: BerkeleyGW-3.0.1.tar.gz
+# Manually-upload: ../hpcrunner/downloads/
+[DOWNLOAD]
+BerkeleyGW/3.0.1
+
+[DEPENDENCY]
+module purge
+./jarvis -install hpckit/2024.12.30 any
+module use ./software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles
+module use ./software/moduledeps
+module load bisheng/compiler4.1.0/bishengmodule
+module load bisheng/hmpi2.4.3/hmpi
+export CC=mpicc
+export CXX=mpicxx
+export FC=mpifort
+export F77=mpifort
+export F90=mpifort
+./jarvis -install fftw/3.3.8 bisheng+mpi
+module load bisheng4.1.0-hmpi2.4.3/fftw/3.3.8
+module load bisheng/kml2.5.0/kml
+
+tar -zxvf ${JARVIS_DOWNLOAD}/BerkeleyGW-3.0.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD}
+mkdir -p ${JARVIS_ROOT}/software/apps/berkeleygw
+
+[ENV]
+module purge
+module use ./software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles
+module use ./software/moduledeps
+module load bisheng/compiler4.1.0/bishengmodule
+module load bisheng/hmpi2.4.3/hmpi
+module load bisheng/kml2.5.0/kml
+module load bisheng4.1.0-hmpi2.4.3/fftw/3.3.8
+
+[APP]
+app_name = BerkeleyGW
+build_dir = ${JARVIS_TMP_DOWNLOAD}/BerkeleyGW-3.0.1
+binary_dir = ${JARVIS_ROOT}/software/apps/berkeleygw/bin
+case_dir = ${JARVIS_TMP_DOWNLOAD}/BerkeleyGW-3.0.1/testsuite/CUBE
+
+[BUILD]
+touch arch.mk
+
+cat << EOF > arch.mk
+COMPFLAG     = -DGNU
+PARAFLAG     = -DMPI
+MATHFLAG     = -DUSESCALAPACK -DUSEFFTW3
+FCPP         = cpp -C -nostdinc
+F90free      = mpif90 -ffree-form -ffree-line-length-none -Wall -pedantic-errors -fopenmp
+LINK         = mpif90
+FOPTS        = -O3
+FNOOPTS      = \$(FOPTS)
+MOD_OPT      = -J
+INCFLAG      = -I
+C_PARAFLAG   = -DPARA
+CC_COMP      = mpicxx -Wall
+C_COMP       = mpicc -Wall
+C_LINK       = mpicxx
+C_OPTS       = -O3
+C_DEBUGFLAG  =
+REMOVE       = /bin/rm -f
+FFTWLIB      = \${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/lib/libfftw3.a
+FFTWINCLUDE  = \${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.3/fftw/3.3.8/include
+LAPACKLIB    = -L\${JARVIS_UTILS}/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib/neon -lklapack_full -L\${JARVIS_UTILS}/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib/neon/kblas/pthread -lkblas
+SCALAPACKLIB = -L\${JARVIS_UTILS}/hpckit/2024.12.30/HPCKit/24.12.30/kml/bisheng/lib/neon -lkscalapack_full \$(LAPACKLIB)
+TESTSCRIPT   = make check-parallel
+EOF
+
+make all-flavors
+make install INSTDIR=${JARVIS_ROOT}/software/apps/berkeleygw
+
+cd ${JARVIS_TMP_DOWNLOAD}/BerkeleyGW-3.0.1/testsuite/CUBE/
+tar -zxvf homo.cube.tgz
+
+[CLEAN]
+make clean
+
+[RUN]
+run = time mpirun --allow-run-as-root -np $(nproc)
+binary = surface.x surface.inp
+nodes = 1
-- 
Gitee


From 7fdf98b92cdd3ac1658d9020c00148feaf37d7bf Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Thu, 10 Apr 2025 21:30:42 +0800
Subject: [PATCH 2/2] Add templates app blastz-2004-12-27

---
 .../blastz/2004-12-27/blastz.arm.kgcc.config  | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 templates/blastz/2004-12-27/blastz.arm.kgcc.config

diff --git a/templates/blastz/2004-12-27/blastz.arm.kgcc.config b/templates/blastz/2004-12-27/blastz.arm.kgcc.config
new file mode 100644
index 0000000..457c73e
--- /dev/null
+++ b/templates/blastz/2004-12-27/blastz.arm.kgcc.config
@@ -0,0 +1,46 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+blastz/2004-12-27 https://www.bx.psu.edu/miller_lab/dist/blastz-2004-12-27.deprecated.tar.gz
+hg38/ http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr4.fa.gz hg38.chr4.fa.gz
+galGal3/ http://hgdownload.soe.ucsc.edu/goldenPath/galGal3/chromosomes/chr4.fa.gz galGal3.chr4.fa.gz
+
+[DEPENDENCY]
+module purge
+module use ./software/modulefiles
+./jarvis -install kgcc/10.3.1 com
+module load kgcc/10.3.1
+
+mkdir -p ${JARVIS_ROOT}/software/apps
+tar -zxvf ${JARVIS_DOWNLOAD}/blastz-2004-12-27.deprecated.tar.gz -C ${JARVIS_ROOT}/software/apps/
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load kgcc/10.3.1
+
+[APP]
+app_name = blastz
+build_dir = ${JARVIS_ROOT}/software/apps/blastz-source
+binary_dir = ${JARVIS_ROOT}/software/apps/blastz-source
+case_dir = ${JARVIS_ROOT}/software/apps/blastz-source/testfile
+
+[BUILD]
+sed -i 's/CFLAGS= -O/CFLAGS= -O3 -march=armv8.2-a -mtune=tsv110 -flto/g' Makefile
+sed -i '11c //char *argv0;' args.c
+CC=`which gcc` make
+${JARVIS_ROOT}/software/apps/blastz-source/blastz --help
+
+mkdir -p testfile
+cd testfile/
+cp -ar ${JARVIS_DOWNLOAD}/*.fa.gz .
+gzip -d hg38.chr4.fa.gz
+gzip -d galGal3.chr4.fa.gz
+
+[CLEAN]
+
+[RUN]
+run = time
+binary = blastz hg38.chr4.fa galGal3.chr4.fa C=3 T=2 Z=10 > hg38_c4-vs-galGal3_c4-kp7265.out
+nodes = 1
-- 
Gitee