From ac2bea271d0aef12b805352f0eb27e5b8ecef858 Mon Sep 17 00:00:00 2001
From: wanghanwen <1564586847@qq.com>
Date: Sat, 11 Jun 2022 10:44:28 +0800
Subject: [PATCH 1/2] =?UTF-8?q?=E6=96=B0=E5=A2=9Ewrf=E3=80=81abinit?=
 =?UTF-8?q?=E6=AF=95=E6=98=87=E7=BC=96=E8=AF=91=E8=84=9A=E6=9C=AC=EF=BC=8C?=
 =?UTF-8?q?=E6=96=B0=E5=A2=9Ereadme=E9=80=82=E9=85=8D=E5=88=97=E8=A1=A8?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 README.md                                     |  47 ++++++-
 software/compiler/bisheng/2.1.0/installed     |   1 -
 software/compiler/gcc/9.3.1/installed         |   1 -
 software/compiler/kgcc/10.3.1/installed       |   1 -
 software/compiler/kgcc/9.3.1/installed        |   1 -
 software/compiler/python3/installed           |   1 -
 .../bisheng/.data.abinit.arm.gpu.config.swp   | Bin 0 -> 16384 bytes
 .../8.10.3/bisheng/data.abinit.arm.gpu.config | 120 ++++++++++++++++++
 .../wrf/4.2/bisheng/data.wrf.arm.cpu.config   | 114 +++++++++++++++++
 templates/wrf/4.2/data.wrf.arm.cpu.config     | 117 +++++++++++++++++
 10 files changed, 393 insertions(+), 10 deletions(-)
 delete mode 100644 software/compiler/bisheng/2.1.0/installed
 delete mode 100644 software/compiler/gcc/9.3.1/installed
 delete mode 100644 software/compiler/kgcc/10.3.1/installed
 delete mode 100644 software/compiler/kgcc/9.3.1/installed
 delete mode 100644 software/compiler/python3/installed
 create mode 100644 templates/abinit/8.10.3/bisheng/.data.abinit.arm.gpu.config.swp
 create mode 100644 templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config
 create mode 100644 templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config
 create mode 100644 templates/wrf/4.2/data.wrf.arm.cpu.config

diff --git a/README.md b/README.md
index bda24f3..6cea069 100644
--- a/README.md
+++ b/README.md
@@ -38,8 +38,6 @@
 
 ### 已验证HPC应用
 
-分子动力学领域：
-
 - [x] CP2K
 
 - [x] Amber
@@ -48,14 +46,53 @@
 
 - [x] VASP
 
-气象领域：
+- [x] ABINIT
+
+- [x] SIESTA
+
+气象海洋领域：
+
+- [x] CMAQ
+
+- [x] fvcom
+
+- [x] SPECFEM3D_GLOBE
 
-- [x] WRF
+- [x] udunits
 
 流体力学领域：
 
 - [x] OpenFOAM
 
+- [x] SU2
+
+- [x] miniFE
+
+计算化学领域：
+
+- [x] CP2K
+
+- [x] nwchem
+
+量子力学领域：
+
+- [x] octopus
+
+生命科学领域：
+
+- [x] bedtools
+
+- [x] blast
+
+- [x] bwa
+
+- [x] gatk
+
+- [x] octave
+
+- [x] picard
+
+- [x] relion
 
 ### 使用说明
 
@@ -234,4 +271,4 @@ eg: ./jarvis -container openeuler:openeuler
 
 揭开HPC应用的神秘面纱：https://zhuanlan.zhihu.com/p/489828346
 
-我和容器有个约会：https://zhuanlan.zhihu.com/p/499544308
\ No newline at end of file
+我和容器有个约会：https://zhuanlan.zhihu.com/p/499544308
diff --git a/software/compiler/bisheng/2.1.0/installed b/software/compiler/bisheng/2.1.0/installed
deleted file mode 100644
index 56a6051..0000000
--- a/software/compiler/bisheng/2.1.0/installed
+++ /dev/null
@@ -1 +0,0 @@
-1
\ No newline at end of file
diff --git a/software/compiler/gcc/9.3.1/installed b/software/compiler/gcc/9.3.1/installed
deleted file mode 100644
index c227083..0000000
--- a/software/compiler/gcc/9.3.1/installed
+++ /dev/null
@@ -1 +0,0 @@
-0
\ No newline at end of file
diff --git a/software/compiler/kgcc/10.3.1/installed b/software/compiler/kgcc/10.3.1/installed
deleted file mode 100644
index c227083..0000000
--- a/software/compiler/kgcc/10.3.1/installed
+++ /dev/null
@@ -1 +0,0 @@
-0
\ No newline at end of file
diff --git a/software/compiler/kgcc/9.3.1/installed b/software/compiler/kgcc/9.3.1/installed
deleted file mode 100644
index c227083..0000000
--- a/software/compiler/kgcc/9.3.1/installed
+++ /dev/null
@@ -1 +0,0 @@
-0
\ No newline at end of file
diff --git a/software/compiler/python3/installed b/software/compiler/python3/installed
deleted file mode 100644
index c227083..0000000
--- a/software/compiler/python3/installed
+++ /dev/null
@@ -1 +0,0 @@
-0
\ No newline at end of file
diff --git a/templates/abinit/8.10.3/bisheng/.data.abinit.arm.gpu.config.swp b/templates/abinit/8.10.3/bisheng/.data.abinit.arm.gpu.config.swp
new file mode 100644
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diff --git a/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config b/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config
new file mode 100644
index 0000000..c12aa77
--- /dev/null
+++ b/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config
@@ -0,0 +1,120 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+abinit/8.10.3 https://www.abinit.org/sites/default/files/packages/abinit-8.10.3.tar.gz
+atompaw/4.0.1.0 http://forge.abinit.org/fallbacks/atompaw-4.0.1.0.tar.gz
+bigdft/1.7.1.25 http://forge.abinit.org/fallbacks/bigdft-1.7.1.25.tar.gz
+libxc/3.0.0 http://forge.abinit.org/fallbacks/libxc-3.0.0.tar.gz
+wannier90/2.0.1.1 http://forge.abinit.org/fallbacks/wannier90-2.0.1.1.tar.gz
+abinit_package https://github.com/abinit/abinit/files/3586400/0001-Patching-m_polynomial_coeff.F90-for-ability-to-compi.patch.txt abinit_patch-8.10.3.patch
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/2.1.0 com
+module load bisheng2/2.1.0
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install hmpi/1.1.1 clang
+module load hmpi1/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+./jarvis -install package/hdf5/1.10.1 clang+mpi
+./jarvis -install package/pnetcdf/1.11.2 clang+mpi
+./jarvis -install package/netcdf/4.7.0 clang+mpi
+./jarvis -install package/openblas/0.3.18 clang
+
+
+[ENV]
+module use ./software/modulefiles
+module purge
+#module load kgcc9/9.3.1
+module load bisheng2/2.1.0
+module load hmpi1/1.1.1
+module load hdf5/1.10.1  
+module load pnetcdf/1.11.2   
+module load netcdf/4.7.0
+module load openblas/0.3.18
+export CC=mpicc CXX=mpicxx FC=mpifort
+
+[APP]
+app_name = abinit
+build_dir = $JARVIS_ROOT
+binary_dir = $JARVIS_ROOT/software/apps/bisheng2/hmpi1/abinit
+case_dir = $JARVIS_ROOT/software/apps/bisheng2/hmpi1/abinit
+
+[BUILD]
+set -x
+set -e
+
+#mkdir -p $JARVIS_ROOT/software/apps/bisheng2/hmpi1/abinit
+#rm -rf $JARVIS_ROOT/software/apps/bisheng2/hmpi1/abinit/*
+#cd $JARVIS_ROOT/software/apps/bisheng2/hmpi1/abinit
+
+cd ${JARVIS_TMP}
+#ABINIT_INSTALL_DIR="$JARVIS_ROOT/software/apps/kgcc9/hmpi1/abinit/"
+
+MPI_HOME=`which mpicc`
+MPI_HOME=${MPI_HOME%/*/*}
+
+
+hdf5_path=`which h5diff`
+hdf5_path=${hdf5_path%/*/*}
+netcdf_path=`nc-config --prefix`
+pnetcdf_path=`pnetcdf-config --prefix`
+
+array=(${LD_LIBRARY_PATH//:/ })
+for var in ${array[@]}
+do
+   if [[ $var =~ "openblas" ]];then
+           openblas_path=${var%/*}
+   fi
+done
+
+
+export CPPFLAGS=" -I${hdf5_path}/include -I${pnetcdf_path}/include -I${netcdf_path}/include -I$MPI_HOME/include"
+
+export CFLAGS=" -I${hdf5_path}/include -I${pnetcdf_path}/include -I${netcdf_path}/include -I$MPI_HOME/include "
+
+export CXXFLAGS=" -I${hdf5_path}/include -I${pnetcdf_path}/include -I${netcdf_path}/include -I$MPI_HOME/include "
+
+export FCFLAGS=" -I${hdf5_path}/include -I${pnetcdf_path}/include"
+
+export FFLAGS=" -I${hdf5_path}/include -I${pnetcdf_path}/include"
+
+export LDFLAGS=" -L${hdf5_path}/lib -L${pnetcdf_path}/lib -L${netcdf_path}/lib"
+
+rm -rf abinit-8.10.3
+tar -zxvf $JARVIS_DOWNLOAD/abinit-8.10.3.tar.gz
+cd abinit-8.10.3
+temp_path=`pwd`
+
+sed -i "16443a generic)\\n       abi_fc_vendor_hnt=\"generic\"\\n       abi_fc_version_hnt=\"default\"\\n       abi_sys_spec_hnt=\"default\"\\n       FCFLAGS_32BITS='-m32'\\n       FCFLAGS_64BITS='-m64'\\n       FCFLAGS_BIGENDIAN='-fconvert=big-endian -frecord-marker=4'\\n       FCFLAGS_FIXEDFORM='-ffixed-form'\\n       FCFLAGS_FREEFORM='-ffree-form'\\n       FCFLAGS_PIC='-fPIC'\\n       FCFLAGS_MODDIR='-J\$(abinit_moddir)'\\n       FCFLAGS_HINTS='-ffree-line-length-none'\\n       FCFLAGS_OPENMP='-fopenmp'\\n       ;;" configure
+
+sed -i '21618s/#define HAVE_FC_INT_QUAD 1//g' configure
+
+#cp $JARVIS_DOWNLOAD/abinit_patch-8.10.3.patch  ./
+#cd ./src
+#patch -p2 < ../abinit_patch-8.10.3.patch
+#cd ..
+
+mkdir extral
+cd extral
+cp $JARVIS_DOWNLOAD/atompaw-4.0.1.0.tar.gz ./
+cp $JARVIS_DOWNLOAD/bigdft-1.7.1.25.tar.gz ./
+cp $JARVIS_DOWNLOAD/libxc-3.0.0.tar.gz ./
+cp $JARVIS_DOWNLOAD/wannier90-2.0.1.1.tar.gz ./
+cd ..
+mkdir build
+cd build
+../configure FC=mpif90 --enable-mpi --with-mpi-prefix=$MPI_HOME --with-dft-flavor="libxc+atompaw" --with-trio-flavor="netcdf" --with-tardir=$temp_path/extral --with-netcdf-incs="-I${netcdf_path}/include" --with-netcdf-libs="-L${netcdf_path}/lib -lnetcdf -L${netcdf_path}/lib -lnetcdff" FCFLAGS="-g -O2 -ffree-line-length-none" --with-linalg-libs="-L${openblas_path}/ -lblas -llapack" 
+
+FC=mpif90 CC=mpicc CXX=mpicxx make multi multi_nprocs=96
+
+
+[CLEAN]
+./clean_build
+
+[RUN]
+run =
+binary =
+nodes = 1
diff --git a/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config b/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config
new file mode 100644
index 0000000..e357ad4
--- /dev/null
+++ b/templates/wrf/4.2/bisheng/data.wrf.arm.cpu.config
@@ -0,0 +1,114 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+wrf/4.2 https://github.com/wrf-model/WRF/archive/refs/tags/v4.2.tar.gz wrf-4.2.tar.gz
+
+[DEPENDENCY]
+module purge
+module use ./software/modulefiles
+./jarvis -install bisheng/2.1.0 com
+module load bisheng2/2.1.0
+export CC=clang CXX=clang++ FC=flang
+
+./jarvis -install hmpi/1.1.1 clang
+module load hmpi1/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+./jarvis -install hdf5/1.10.1 clang+mpi
+./jarvis -install package/pnetcdf/1.11.2 clang+mpi
+./jarvis -install package/netcdf/4.7.0 clang+mpi
+./jarvis -install optimized-routines/20.02/clang clang+mpi
+
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+module load hmpi1/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+module load hdf5/1.10.1
+module load pnetcdf/1.11.2
+module load netcdf/4.7.0
+module load optimized-routines-clang/20.02
+
+[APP]
+app_name = WRF	
+build_dir = ${JARVIS_ROOT}
+binary_dir = ${JARVIS_ROOT}/software/apps/bisheng2/hmpi1/wrf
+case_dir = ${JARVIS_ROOT}/software/apps/bisheng2/hmpi1/wrf
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf WRF-4.2
+tar -zxvf $JARVIS_DOWNLOAD/wrf-4.2.tar.gz
+cd WRF-4.2
+
+export HDF5=`which h5diff`
+export HDF5=${HDF5%/*/*}
+export NETCDF=`nc-config --prefix`
+export PNETCDF=`pnetcdf-config --prefix`
+
+
+export CPPFLAGS="-I$HDF5/include -I$PNETCDF/include -I$NETCDF/include"
+export LDFLAGS="-L$HDF5/lib -L$PNETCDF/lib -L$NETCDF/lib -lnetcdf -lnetcdff -lpnetcdf -lhdf5_hl -lhdf5 -lz"
+export WRFIO_NCD_LARGE_FILE_SUPPORT=1
+
+sed -i $((`sed -n '$=' arch/configure.defaults`-2)),$((`sed -n '$=' arch/configure.defaults`))d arch/configure.defaults
+
+cat >> arch/configure.defaults <<EOF
+################################################## #########
+#ARCH   Linux   aarch64,LLVM OpenMPI #serial smpar dmpar dm+sm
+DESCRIPTION     =       LLVM (\$SFC/\$SCC):AArch64
+DMPARALLEL      =        1
+OMPCPP          =        -D_OPENMP
+OMP             =        -fopenmp
+OMPCC           =        -fopenmp
+SFC             =       flang
+SCC             =       clang
+CCOMP           =       clang
+DM_FC           =       mpif90
+DM_CC           =       mpicc -DMPI2_SUPPORT
+FC              =       CONFIGURE_FC
+CC              =       CONFIGURE_CC
+LD              =       \$(FC)
+RWORDSIZE       =       CONFIGURE_RWORDSIZE
+PROMOTION       =       
+ARCH_LOCAL      =       
+CFLAGS_LOCAL    =       -w -O3 -c 
+LDFLAGS_LOCAL   =	-fopenmp -Wl,--build-id
+FCOPTIM         =       -O3 -mcpu=tsv110 -fvectorize -funroll-loops -mllvm -unroll-indirect-loads=true -L/usr/local/kml/lib -lkm -lmathlib -lm
+FCREDUCEDOPT    =       \$(FCOPTIM)
+FCNOOPT         =       -O0 -fopenmp -frecursive
+FCDEBUG         = 	#-g \$(FCNOOPT)
+FORMAT_FIXED    =       -ffixed-form
+FORMAT_FREE     =       -ffree-form 
+FCSUFFIX        =
+BYTESWAPIO      =       -fconvert=big-endian    
+FCBASEOPTS      =       -w \$(FORMAT_FREE) \$(BYTESWAPIO)
+MODULE_SRCH_FLAG =	-module \$(WRF_SRC_ROOT_DIR)/main
+TRADFLAG        =      -traditional-cpp
+CPP             =      /lib/cpp 
+AR              =      ar
+ARFLAGS         =      ru
+M4              =      m4 -B 14000
+RANLIB          =      ranlib
+CC_TOOLS        =      \$(SCC)
+###########################################################
+#ARCH  NULL
+EOF
+
+echo 4 | ./configure
+
+sed -ri "1537s/derf/erf/g" ./phys/module_mp_SBM_polar_radar.F
+
+./compile em_real 2>&1 | tee -a compile.log 
+
+
+
+[CLEAN]
+
+[RUN]
+run = 
+binary = 
+nodes = 1
+
diff --git a/templates/wrf/4.2/data.wrf.arm.cpu.config b/templates/wrf/4.2/data.wrf.arm.cpu.config
new file mode 100644
index 0000000..03b096e
--- /dev/null
+++ b/templates/wrf/4.2/data.wrf.arm.cpu.config
@@ -0,0 +1,117 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+wrf/4.2 https://github.com/wrf-model/WRF/archive/refs/tags/v4.2.tar.gz wrf-4.2.tar.gz
+
+[DEPENDENCY]
+module purge
+module use ./software/modulefiles
+./jarvis -install kgcc/9.3.1 com
+module load kgcc9/9.3.1
+export CC=gcc CXX=g++ FC=gfortran
+
+./jarvis -install hmpi/1.1.1 gcc
+module load hmpi1/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+./jarvis -install hdf5/1.10.1 gcc+mpi
+./jarvis -install package/pnetcdf/1.11.2 gcc+mpi
+./jarvis -install package/netcdf/4.7.0 gcc+mpi
+./jarvis -install optimized-routines/20.02 gcc+mpi
+
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load kgcc9/9.3.1
+module load hmpi1/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+module load pnetcdf/1.11.2
+module load netcdf/4.7.0
+module load optimized-routines/20.02
+
+[APP]
+app_name = WRF	
+build_dir = ${JARVIS_ROOT}
+binary_dir = ${JARVIS_ROOT}/software/apps/bisheng2/hmpi1/wrf
+case_dir = ${JARVIS_ROOT}/software/apps/bisheng2/hmpi1/wrf
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf WRF-4.2
+tar -zxvf $JARVIS_DOWNLOAD/wrf-4.2.tar.gz
+cd WRF-4.2
+
+export HDF5=`which h5diff`
+export HDF5=${HDF5%/*/*}
+export NETCDF=`nc-config --prefix`
+export PNETCDF=`pnetcdf-config --prefix`
+
+
+export CPPFLAGS="-I$HDF5/include -I$PNETCDF/include -I$NETCDF/include"
+export LDFLAGS="-L$HDF5/lib -L$PNETCDF/lib -L$NETCDF/lib -lnetcdf -lnetcdff -lpnetcdf -lhdf5_hl -lhdf5 -lz"
+export WRFIO_NCD_LARGE_FILE_SUPPORT=1
+
+sed -i $((`sed -n '$=' arch/configure.defaults`-2)),$((`sed -n '$=' arch/configure.defaults`))d arch/configure.defaults
+
+mathlib_path=$JARVIS_ROOT/software/compiler/kgcc/9.3.1/lib64/libhpc
+cat >> arch/configure.defaults <<EOF
+################################################## #########
+#ARCH   Linux   aarch64,gnu OpenMPI #serial smpar dmpar dm+sm
+DESCRIPTION     =       GNU (\$SFC/\$SCC)
+DMPARALLEL      =        1
+OMPCPP          =        -D_OPENMP
+OMP             =        -fopenmp
+OMPCC           =        -fopenmp
+SFC             =       gfortran
+SCC             =       gcc
+CCOMP           =       gcc
+DM_FC           =       mpif90 -f90=\$(SFC)
+DM_CC           =       mpicc -cc=\$(SCC) -DMPI2_SUPPORT
+FC              =       CONFIGURE_FC
+CC              =       CONFIGURE_CC
+LD              =       \$(FC)
+RWORDSIZE       =       CONFIGURE_RWORDSIZE
+PROMOTION       =       #-fdefault-real-8
+ARCH_LOCAL      =       -DNONSTANDARD_SYSTEM_SUBR  -DWRF_USE_CLM
+CFLAGS_LOCAL    =       -w -O3 -c -march=armv8.2-a -L$mathlib_path -lmathlib
+LDFLAGS_LOCAL   =
+CPLUSPLUSLIB    =
+ESMF_LDFLAG     =      \$(CPLUSPLUSLIB)
+FCOPTIM         =       -O3 -ftree-vectorize -funroll-loops -mcpu=tsv110 -march=armv8.2-a -L$mathlib_path -lmathlib
+FCREDUCEDOPT    =       \$(FCOPTIM)
+FCNOOPT         =       -O0
+FCDEBUG         =       # -g \$(FCNOOPT)  # -fbacktrace -ggdb-fcheck=bounds,do,mem,pointer -ffpe-trap=invalid,zero,overflow
+FORMAT_FIXED    =       -ffixed-form
+FORMAT_FREE     =       -ffree-form -ffree-line-length-none
+FCSUFFIX        =
+BYTESWAPIO      =       -fconvert=big-endian -frecord-marker=4
+FCBASEOPTS_NO_G =       -w \$(FORMAT_FREE) \$(BYTESWAPIO)
+FCBASEOPTS      =       \$(FCBASEOPTS_NO_G) \$(FCDEBUG)
+MODULE_SRCH_FLAG =
+TRADFLAG        =      -traditional
+CPP             =      /lib/cpp -P
+AR              =      ar
+ARFLAGS         =      ru
+M4              =      m4 -G
+RANLIB          =      ranlib
+RLFLAGS         =
+CC_TOOLS        =      \$(SCC)
+
+###########################################################
+#ARCH  NULL
+EOF
+
+echo 4 | ./configure
+
+./compile em_real 2>&1 | tee -a compile.log 
+
+
+
+[CLEAN]
+
+[RUN]
+run = 
+binary = 
+nodes = 1
+
-- 
Gitee


From a255b6aed7347dc08d108fb75be1536fec31c4e4 Mon Sep 17 00:00:00 2001
From: wanghanwen <wanghanwen3@huawei.com>
Date: Sat, 11 Jun 2022 02:50:16 +0000
Subject: [PATCH 2/2] update README.md.

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 6cea069..d11bde8 100644
--- a/README.md
+++ b/README.md
@@ -52,6 +52,8 @@
 
 气象海洋领域：
 
+- [x] WRF
+
 - [x] CMAQ
 
 - [x] fvcom
-- 
Gitee