From aadc57ca94b2327a3acbdd32a5cd811c59a88de8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Fri, 16 May 2025 17:11:23 +0800
Subject: [PATCH 1/6] openbabel

---
 ...data.openbabel.arm.cpu.bisheng.hmpi.config | 68 +++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config

diff --git a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
new file mode 100644
index 0000000..d4aa4ba
--- /dev/null
+++ b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
@@ -0,0 +1,68 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+OpenBabel/3.1.1 https://github.com/openbabel/openbabel/archive/refs/tags/openbabel-3-1-1.tar.gz
+boost/1.72.0 https://nchc.dl.sourceforge.net/project/boost/boost/1.72.0/boost_1_72_0.tar.bz2
+
+[DEPENDENCY]
+set -e
+set -x
+
+yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ -y 
+./jarvis -install hpckit/2024.12.30 any
+module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
+module purge
+module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+tar -xf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.bz2
+tar -vzxf ${JARVIS_DOWNLOAD}/openbabel-3-1-1.tar.gz
+mkdir -p boost/1_72_0
+cd boost_1_72_0/
+sed -i "60c #ifdef PTHREAD_STACK_MIN" boost/thread/pthread/thread_data.hpp
+sed -i "61c \\\tif (size<static_cast<std::size_t>(PTHREAD_STACK_MIN)) size=PTHREAD_STACK_MIN;" boost/thread/pthread/thread_data.hpp
+sed -i "59c #if 1" boost/mpl/aux_/integral_wrapper.hpp
+./bootstrap.sh --with-toolset=clang --prefix=${JARVIS_ROOT}/boost/1_72_0
+sed -i '$ a\using mpi : mpicxx ;' project-config.jam
+./b2 install --prefix=${JARVIS_ROOT}/boost/1_72_0 toolset=clang
+export Boost_INCLUDE_PATH=${JARVIS_ROOT}/boost/1_72_0/include
+
+
+[ENV]
+yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ -y
+module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
+module purge
+module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = OpenBabel
+build_dir = ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/
+binary_dir = ${JARVIS_ROOT}/openbabel-3.1.1-install/bin/
+case_dir = ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/test/files
+
+[BUILD]
+wget https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
+tar xvf eigen-3.4.0.tar.gz
+mkdir build
+cd build
+cmake .. -DEIGEN3_INCLUDE_DIR=${JARVIS_ROOT}/openbabel-openbabel-3-1-1/eigen-3.4.0 -DBoost_INCLUDE_DIR=${Boost_INCLUDE_PATH} -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/openbabel-3.1.1-install
+make -j
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run = time -p
+binary = obabel -i cif *.cif -o cif
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From e727b8981c77e5bc743b7295d3d4ef9805fccaca 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, 19 May 2025 10:07:23 +0800
Subject: [PATCH 2/6] openbabel

---
 .../openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
index d4aa4ba..83793f9 100644
--- a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
+++ b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
@@ -31,7 +31,6 @@ export Boost_INCLUDE_PATH=${JARVIS_ROOT}/boost/1_72_0/include
 
 
 [ENV]
-yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ -y
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
 module purge
 module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi
-- 
Gitee


From b70e51234046a189341ea3b879121763129234d5 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, 19 May 2025 10:19:01 +0800
Subject: [PATCH 3/6] openbabel

---
 .../3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config      | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
index 83793f9..dbbce4a 100644
--- a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
+++ b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
@@ -4,6 +4,7 @@
 [DOWNLOAD]
 OpenBabel/3.1.1 https://github.com/openbabel/openbabel/archive/refs/tags/openbabel-3-1-1.tar.gz
 boost/1.72.0 https://nchc.dl.sourceforge.net/project/boost/boost/1.72.0/boost_1_72_0.tar.bz2
+eigen/3.4.0 https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
 
 [DEPENDENCY]
 set -e
@@ -28,7 +29,8 @@ sed -i "59c #if 1" boost/mpl/aux_/integral_wrapper.hpp
 sed -i '$ a\using mpi : mpicxx ;' project-config.jam
 ./b2 install --prefix=${JARVIS_ROOT}/boost/1_72_0 toolset=clang
 export Boost_INCLUDE_PATH=${JARVIS_ROOT}/boost/1_72_0/include
-
+tar xvf ${JARVIS_DOWNLOAD}/eigen-3.4.0.tar.gz
+mv eigen-3.4.0 ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/ 
 
 [ENV]
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
@@ -45,8 +47,8 @@ binary_dir = ${JARVIS_ROOT}/openbabel-3.1.1-install/bin/
 case_dir = ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/test/files
 
 [BUILD]
-wget https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
-tar xvf eigen-3.4.0.tar.gz
+#wget https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
+#tar xvf eigen-3.4.0.tar.gz
 mkdir build
 cd build
 cmake .. -DEIGEN3_INCLUDE_DIR=${JARVIS_ROOT}/openbabel-openbabel-3-1-1/eigen-3.4.0 -DBoost_INCLUDE_DIR=${Boost_INCLUDE_PATH} -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/openbabel-3.1.1-install
-- 
Gitee


From 6308c1cb4493308f2eae954c8188e10484919358 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, 19 May 2025 11:09:12 +0800
Subject: [PATCH 4/6] openbabel

---
 .../openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
index dbbce4a..2109653 100644
--- a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
+++ b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
@@ -10,7 +10,7 @@ eigen/3.4.0 https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
 set -e
 set -x
 
-yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ -y 
+yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ python3-devel -y 
 ./jarvis -install hpckit/2024.12.30 any
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
 module purge
@@ -54,6 +54,7 @@ cd build
 cmake .. -DEIGEN3_INCLUDE_DIR=${JARVIS_ROOT}/openbabel-openbabel-3-1-1/eigen-3.4.0 -DBoost_INCLUDE_DIR=${Boost_INCLUDE_PATH} -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/openbabel-3.1.1-install
 make -j
 make install
+export LD_LIBRARY_PATH=${JARVIS_ROOT}/openbabel-3.1.1-install/lib64:$LD_LIBRARY_PATH
 
 [CLEAN]
 make clean
-- 
Gitee


From 9618cb59a1faa563e9f707ff1746f740f9e9e6b8 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, 19 May 2025 11:47:48 +0800
Subject: [PATCH 5/6] openbabel

---
 .../openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config  | 2 --
 1 file changed, 2 deletions(-)

diff --git a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
index 2109653..567fb90 100644
--- a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
+++ b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
@@ -47,8 +47,6 @@ binary_dir = ${JARVIS_ROOT}/openbabel-3.1.1-install/bin/
 case_dir = ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/test/files
 
 [BUILD]
-#wget https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
-#tar xvf eigen-3.4.0.tar.gz
 mkdir build
 cd build
 cmake .. -DEIGEN3_INCLUDE_DIR=${JARVIS_ROOT}/openbabel-openbabel-3-1-1/eigen-3.4.0 -DBoost_INCLUDE_DIR=${Boost_INCLUDE_PATH} -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/openbabel-3.1.1-install
-- 
Gitee


From fdf0c085520b5d0c8ba0aa15b327880f338e484e 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, 12 Jun 2025 11:58:13 +0800
Subject: [PATCH 6/6] openbabel

---
 ...data.openbabel.arm.cpu.bisheng.hmpi.config | 24 ++++++++-----------
 1 file changed, 10 insertions(+), 14 deletions(-)

diff --git a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
index 567fb90..6ab7007 100644
--- a/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
+++ b/templates/openbabel/3.1.1/data.openbabel.arm.cpu.bisheng.hmpi.config
@@ -3,14 +3,13 @@
 
 [DOWNLOAD]
 OpenBabel/3.1.1 https://github.com/openbabel/openbabel/archive/refs/tags/openbabel-3-1-1.tar.gz
-boost/1.72.0 https://nchc.dl.sourceforge.net/project/boost/boost/1.72.0/boost_1_72_0.tar.bz2
 eigen/3.4.0 https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
 
 [DEPENDENCY]
 set -e
 set -x
 
-yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ python3-devel -y 
+yum install zlib-devel git cmake make git vim tar time glibc-headers gcc-c++ python3-devel -y
 ./jarvis -install hpckit/2024.12.30 any
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
 module purge
@@ -18,19 +17,13 @@ module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi
 export CC=`which clang`
 export CXX=`which clang++`
 export FC=`which flang`
-tar -xf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.bz2
+./jarvis -install boost/1.72.0/clang clang
+module use software/moduledeps/bisheng4.1.0
+module load boost-clang/1.72.0
+export Boost_INCLUDE_PATH=${BOOST_CLANG_PATH}/include
 tar -vzxf ${JARVIS_DOWNLOAD}/openbabel-3-1-1.tar.gz
-mkdir -p boost/1_72_0
-cd boost_1_72_0/
-sed -i "60c #ifdef PTHREAD_STACK_MIN" boost/thread/pthread/thread_data.hpp
-sed -i "61c \\\tif (size<static_cast<std::size_t>(PTHREAD_STACK_MIN)) size=PTHREAD_STACK_MIN;" boost/thread/pthread/thread_data.hpp
-sed -i "59c #if 1" boost/mpl/aux_/integral_wrapper.hpp
-./bootstrap.sh --with-toolset=clang --prefix=${JARVIS_ROOT}/boost/1_72_0
-sed -i '$ a\using mpi : mpicxx ;' project-config.jam
-./b2 install --prefix=${JARVIS_ROOT}/boost/1_72_0 toolset=clang
-export Boost_INCLUDE_PATH=${JARVIS_ROOT}/boost/1_72_0/include
 tar xvf ${JARVIS_DOWNLOAD}/eigen-3.4.0.tar.gz
-mv eigen-3.4.0 ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/ 
+mv eigen-3.4.0 ${JARVIS_ROOT}/openbabel-openbabel-3-1-1/
 
 [ENV]
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
@@ -39,6 +32,9 @@ module add bisheng/compiler4.1.0/bishengmodule bisheng/hmpi2.4.3/hmpi
 export CC=`which clang`
 export CXX=`which clang++`
 export FC=`which flang`
+module use software/moduledeps/bisheng4.1.0
+module load boost-clang/1.72.0
+export Boost_INCLUDE_PATH=${BOOST_CLANG_PATH}/include
 
 [APP]
 app_name = OpenBabel
@@ -63,6 +59,6 @@ binary = obabel -i cif *.cif -o cif
 nodes = 1
 
 [PERF]
-perf= 
+perf=
 nsys=
 ncu=--target-processes all
-- 
Gitee