From 80aed1a91c1d1df8d0585288df8a0e82152e7175 Mon Sep 17 00:00:00 2001
From: wanghanwen <1564586847@qq.com>
Date: Fri, 12 Apr 2024 14:53:31 +0800
Subject: [PATCH 1/9] =?UTF-8?q?=E6=96=B0=E5=A2=9Erelion=20bisheng3.2.0=20m?=
 =?UTF-8?q?ini=E5=AE=89=E8=A3=85=E8=84=9A=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../3.1.2/data.relion.mini.arm.cpu.config     | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 templates/relion/3.1.2/data.relion.mini.arm.cpu.config

diff --git a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
new file mode 100644
index 0000000..a957165
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
@@ -0,0 +1,49 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/3.2.0-mini com
+module add bisheng/3.2.0-mini
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module add wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+./jarvis -install hmpi/2.3.0 clang
+
+[ENV]
+module purge
+module use ${JARVIS_ROOT}/software/modulefiles
+module add bisheng/3.2.0-mini
+module add wxWidgets/3.0.5
+module add ctffind-clang/4.1.14
+module add hmpi/2.3.0
+export CC=clang CXX=clang++ FC=flang
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+cd relion-3.1.2
+mkdir build && cd build
+#yum install -y libtiff-* fltk* fltk-devel*
+#yum -y install xorg-x11-xauth
+cmake -DCUDA=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
-- 
Gitee


From d95314ebdf5dbccf7129b21871cac9acbf4a98b7 Mon Sep 17 00:00:00 2001
From: wanghanwen <1564586847@qq.com>
Date: Fri, 12 Apr 2024 17:37:50 +0800
Subject: [PATCH 2/9] =?UTF-8?q?=E4=BF=AE=E6=94=B9relion=E8=84=9A=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 templates/relion/3.1.2/data.relion.mini.arm.cpu.config | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
index a957165..02fc0e5 100644
--- a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
+++ b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
@@ -11,6 +11,7 @@ module purge
 module add bisheng/3.2.0-mini
 export CC=clang CXX=clang++ FC=flang
 ./jarvis -install wxWidgets/3.0.5 clang
+module use ./software/moduledeps/bisheng3.2.0
 module add wxWidgets/3.0.5
 ./jarvis -install ctffind/4.1.14/clang clang
 ./jarvis -install hmpi/2.3.0 clang
@@ -18,6 +19,7 @@ module add wxWidgets/3.0.5
 [ENV]
 module purge
 module use ${JARVIS_ROOT}/software/modulefiles
+module use ${JARVIS_ROOT}/software/moduledeps/bisheng3.2.0
 module add bisheng/3.2.0-mini
 module add wxWidgets/3.0.5
 module add ctffind-clang/4.1.14
@@ -35,6 +37,10 @@ cd ${JARVIS_TMP}
 rm -rf relion-3.1.2
 tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
 cd relion-3.1.2
+sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
 mkdir build && cd build
 #yum install -y libtiff-* fltk* fltk-devel*
 #yum -y install xorg-x11-xauth
-- 
Gitee


From 29f061dc4e438814831aac9fd5fdbd2ef658c374 Mon Sep 17 00:00:00 2001
From: wanghanwen <1564586847@qq.com>
Date: Fri, 12 Apr 2024 17:48:58 +0800
Subject: [PATCH 3/9] =?UTF-8?q?=E4=BF=AE=E6=94=B9relion=E8=84=9A=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 templates/relion/3.1.2/data.relion.mini.arm.cpu.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
index 02fc0e5..eedb52d 100644
--- a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
+++ b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
@@ -42,8 +42,8 @@ sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -forc
 sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
 sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
 mkdir build && cd build
-#yum install -y libtiff-* fltk* fltk-devel*
-#yum -y install xorg-x11-xauth
+yum install -y libtiff-* fltk* fltk-devel*
+yum -y install xorg-x11-xauth
 cmake -DCUDA=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
 make -j
 make install
-- 
Gitee


From 83b28150bc50d916a4842fcf829bc166f9e0fb76 Mon Sep 17 00:00:00 2001
From: wanghanwen <1564586847@qq.com>
Date: Mon, 15 Apr 2024 20:08:08 +0800
Subject: [PATCH 4/9] =?UTF-8?q?relion=E6=B7=BB=E5=8A=A0sve=E8=84=9A?=
 =?UTF-8?q?=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../3.1.2/data.relion.mini.arm.cpu.config     | 12 ++--
 .../3.1.2/data.relion.mini.sve.arm.cpu.config | 55 +++++++++++++++++++
 2 files changed, 61 insertions(+), 6 deletions(-)
 create mode 100644 templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config

diff --git a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
index eedb52d..3db752e 100644
--- a/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
+++ b/templates/relion/3.1.2/data.relion.mini.arm.cpu.config
@@ -18,8 +18,8 @@ module add wxWidgets/3.0.5
 
 [ENV]
 module purge
-module use ${JARVIS_ROOT}/software/modulefiles
-module use ${JARVIS_ROOT}/software/moduledeps/bisheng3.2.0
+module use software/modulefiles
+module use software/moduledeps/bisheng3.2.0
 module add bisheng/3.2.0-mini
 module add wxWidgets/3.0.5
 module add ctffind-clang/4.1.14
@@ -37,10 +37,10 @@ cd ${JARVIS_TMP}
 rm -rf relion-3.1.2
 tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
 cd relion-3.1.2
-sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
-sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
-sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
-sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
 mkdir build && cd build
 yum install -y libtiff-* fltk* fltk-devel*
 yum -y install xorg-x11-xauth
diff --git a/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config
new file mode 100644
index 0000000..4072547
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.mini.sve.arm.cpu.config
@@ -0,0 +1,55 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/3.2.0-mini com
+module add bisheng/3.2.0-mini
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module use ./software/moduledeps/bisheng3.2.0
+module add wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+./jarvis -install hmpi/2.3.0 clang
+
+[ENV]
+module purge
+module use software/modulefiles
+module use software/moduledeps/bisheng3.2.0
+module add bisheng/3.2.0-mini
+module add wxWidgets/3.0.5
+module add ctffind-clang/4.1.14
+module add hmpi/2.3.0
+export CC=clang CXX=clang++ FC=flang
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+cd relion-3.1.2
+sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+mkdir build && cd build
+yum install -y libtiff-* fltk* fltk-devel*
+yum -y install xorg-x11-xauth
+cmake -DCUDA=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
-- 
Gitee


From 019948f887aa0d37097bba37ebd54c7728e6114c Mon Sep 17 00:00:00 2001
From: jsfhd <2162443403@qq.com>
Date: Wed, 17 Apr 2024 11:46:53 +0800
Subject: [PATCH 5/9] =?UTF-8?q?relion=E4=BC=98=E5=8C=96?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../3.1.2/data.relion.mini.all.arm.cpu.config | 60 +++++++++++++++++++
 .../data.relion.mini.altcpu.arm.cpu.config    | 60 +++++++++++++++++++
 2 files changed, 120 insertions(+)
 create mode 100644 templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config
 create mode 100644 templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config

diff --git a/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config
new file mode 100644
index 0000000..56a410b
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.mini.all.arm.cpu.config
@@ -0,0 +1,60 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/3.2.0-mini com
+module add bisheng/3.2.0-mini
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module use ./software/moduledeps/bisheng3.2.0
+module add wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+./jarvis -install hmpi/2.3.0 clang
+
+[ENV]
+module purge
+module use software/modulefiles
+module use software/moduledeps/bisheng3.2.0
+module add bisheng/3.2.0-mini
+module add wxWidgets/3.0.5
+module add ctffind-clang/4.1.14
+module add hmpi/2.3.0
+export CC=clang CXX=clang++ FC=flang
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+cd relion-3.1.2
+#sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+
+sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+sed -i "12i set(CMAKE_C_FLAGS \"-O3 -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+mkdir build && cd build
+yum install -y libtiff-* fltk* fltk-devel* tbb-devel
+yum -y install xorg-x11-xauth
+cmake -DCUDA=OFF -DGUI=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
diff --git a/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config
new file mode 100644
index 0000000..1edd31d
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.mini.altcpu.arm.cpu.config
@@ -0,0 +1,60 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/3.2.0-mini com
+module add bisheng/3.2.0-mini
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module use ./software/moduledeps/bisheng3.2.0
+module add wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+./jarvis -install hmpi/2.3.0 clang
+
+[ENV]
+module purge
+module use software/modulefiles
+module use software/moduledeps/bisheng3.2.0
+module add bisheng/3.2.0-mini
+module add wxWidgets/3.0.5
+module add ctffind-clang/4.1.14
+module add hmpi/2.3.0
+export CC=clang CXX=clang++ FC=flang
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+cd relion-3.1.2
+#sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+
+#sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+#sed -i "12i set(CMAKE_C_FLAGS \"-O3 -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+#sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+mkdir build && cd build
+yum install -y libtiff-* fltk* fltk-devel* tbb-devel
+yum -y install xorg-x11-xauth
+cmake -DCUDA=OFF -DGUI=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
-- 
Gitee


From 03fc22c39f1ffffd156c8f6b534a7982d4546253 Mon Sep 17 00:00:00 2001
From: berserker111 <2162443403@qq.com>
Date: Thu, 18 Apr 2024 14:41:06 +0800
Subject: [PATCH 6/9] =?UTF-8?q?=E4=BC=98=E5=8C=96relion=E6=BA=90=E7=A0=81?=
 =?UTF-8?q?=E4=B8=AD=E5=BE=AA=E7=8E=AF=E9=80=BB=E8=BE=91?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../data.relion.mini.loop.arm.cpu.config      | 61 +++++++++++++++++++
 templates/relion/3.1.2/patch_relion           | 37 +++++++++++
 2 files changed, 98 insertions(+)
 create mode 100644 templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config
 create mode 100644 templates/relion/3.1.2/patch_relion

diff --git a/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config
new file mode 100644
index 0000000..c1f3983
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.mini.loop.arm.cpu.config
@@ -0,0 +1,61 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/3.2.0-mini com
+module add bisheng/3.2.0-mini
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module use ./software/moduledeps/bisheng3.2.0
+module add wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+./jarvis -install hmpi/2.3.0 clang
+
+[ENV]
+module purge
+module use software/modulefiles
+module use software/moduledeps/bisheng3.2.0
+module add bisheng/3.2.0-mini
+module add wxWidgets/3.0.5
+module add ctffind-clang/4.1.14
+module add hmpi/2.3.0
+export CC=clang CXX=clang++ FC=flang
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+patch -p0 < ${JARVIS_ROOT}/templates/relion/3.1.2/patch_relion
+cd relion-3.1.2
+#sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+
+#sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+#sed -i "12i set(CMAKE_C_FLAGS \"-O3 -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+#sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+#sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+mkdir build && cd build
+yum install -y libtiff-* fltk* fltk-devel* tbb-devel
+yum -y install xorg-x11-xauth
+cmake -DCUDA=OFF -DGUI=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
diff --git a/templates/relion/3.1.2/patch_relion b/templates/relion/3.1.2/patch_relion
new file mode 100644
index 0000000..aebf898
--- /dev/null
+++ b/templates/relion/3.1.2/patch_relion
@@ -0,0 +1,37 @@
+--- relion-3.1.2/src/multidim_array.h	2021-02-24 18:22:57.000000000 +0800
++++ relion_new-3.1.2/src/multidim_array.h	2024-04-18 11:36:44.573735000 +0800
+@@ -1151,23 +1151,21 @@
+         }
+ 
+         // Copy needed elements, fill with 0 if necessary
++        long int j_lower_limit = XSIZE(*this) > Xdim ? Xdim : XSIZE(*this);
++        long int j_upper_limit = XSIZE(*this) < Xdim ? Xdim : XSIZE(*this);
+         for (long int l = 0; l < Ndim; l++)
+             for (long int k = 0; k < Zdim; k++)
+                 for (long int i = 0; i < Ydim; i++)
+-                    for (long int j = 0; j < Xdim; j++)
++                {
++                    for (long int j = 0; j < j_lower_limit; j++)
+                     {
+-                        T val;
+-                        if (k >= ZSIZE(*this))
+-                            val = 0;
+-                        else if (i >= YSIZE(*this))
+-                            val = 0;
+-                        else if (j >= XSIZE(*this))
+-                            val = 0;
+-                        else
+-                            val = DIRECT_A3D_ELEM(*this, k, i, j);
+-                        new_data[l*ZYXdim + k*YXdim+i*Xdim+j] = val;
++                        bool flag = (k >= ZSIZE(*this)) || (i >= YSIZE(*this));
++                        new_data[l*ZYXdim + k*YXdim+i*Xdim+j] = flag ? (T)0 : DIRECT_A3D_ELEM(*this,k,i,j);
+                     }
+-
++                    for(long int j = XSIZE(*this);j < j_upper_limit; j++)
+                     {
++                        new_data[l*ZYXdim + k*YXdim+i*Xdim+j]
++                    }
++                }
+         // deallocate old vector
+         coreDeallocate();
+ 
-- 
Gitee


From a2be90aee171cee337a0409cf8bf3a6ef02dcc9b Mon Sep 17 00:00:00 2001
From: berserker111 <2162443403@qq.com>
Date: Mon, 22 Apr 2024 10:55:05 +0800
Subject: [PATCH 7/9] =?UTF-8?q?relion=20sve=E4=BC=98=E5=8C=96?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../data.relion.mini.all.sve.arm.cpu.config   | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config

diff --git a/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config b/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config
new file mode 100644
index 0000000..3f15f01
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.mini.all.sve.arm.cpu.config
@@ -0,0 +1,56 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 https://github.com/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+module use ./software/modulefiles
+module purge
+./jarvis -install bisheng/3.2.0-mini com
+module add bisheng/3.2.0-mini
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module use ./software/moduledeps/bisheng3.2.0
+module add wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+./jarvis -install hmpi/2.3.0 clang
+
+[ENV]
+module purge
+module use software/modulefiles
+module use software/moduledeps/bisheng3.2.0
+module add bisheng/3.2.0-mini
+module add wxWidgets/3.0.5
+module add ctffind-clang/4.1.14
+module add hmpi/2.3.0
+export CC=clang CXX=clang++ FC=flang
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+cd relion-3.1.2
+
+sed -i "12i set(CMAKE_CXX_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+sed -i "12i set(CMAKE_C_FLAGS \"-O3 -ffast-math -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true -march=armv8.2-a -mcpu=tsv110 -ffast-math -g -mllvm -check-trivial-remat-reg-pressure=false -mllvm -enable-prefetch-barrier=false -mllvm -replace-sqrt-compare-by-square=true \")" CMakeLists.txt
+sed -i "14i set(CMAKE_CXX_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+sed -i "14i set(CMAKE_C_FLAGS_RELEASE \"-O3 -DNDEBUG\")" CMakeLists.txt
+mkdir build && cd build
+yum install -y libtiff-* fltk* fltk-devel* tbb-devel
+yum -y install xorg-x11-xauth
+cmake -DCUDA=OFF -DGUI=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release -DALTCPU=ON  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
-- 
Gitee


From 0aaaa20fc5039d4d2e4cb00d2d8aa71506768e21 Mon Sep 17 00:00:00 2001
From: berserker111 <2162443403@qq.com>
Date: Tue, 21 May 2024 16:57:11 +0800
Subject: [PATCH 8/9] =?UTF-8?q?=E6=96=B0=E5=A2=9Eopar2=E3=80=81otf2?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 package/opari2/2.0.7/install.sh | 11 +++++++++++
 package/otf2/3.0.3/install.sh   | 11 +++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 package/opari2/2.0.7/install.sh
 create mode 100644 package/otf2/3.0.3/install.sh

diff --git a/package/opari2/2.0.7/install.sh b/package/opari2/2.0.7/install.sh
new file mode 100644
index 0000000..a818e3c
--- /dev/null
+++ b/package/opari2/2.0.7/install.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+set -x
+set -e
+szip_ver='2.0.7'
+. ${DOWNLOAD_TOOL} -u https://perftools.pages.jsc.fz-juelich.de/cicd/opari2/tags/opari2-2.0.7/opari2-${szip_ver}.tar.gz 
+cd ${JARVIS_TMP}
+tar xvf ${JARVIS_DOWNLOAD}/opari2-${szip_ver}.tar.gz
+cd opari2-${szip_ver}
+./configure --prefix=$1
+make -j
+make install
diff --git a/package/otf2/3.0.3/install.sh b/package/otf2/3.0.3/install.sh
new file mode 100644
index 0000000..c407a46
--- /dev/null
+++ b/package/otf2/3.0.3/install.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+set -x
+set -e
+szip_ver='3.0.3'
+. ${DOWNLOAD_TOOL} -u https://perftools.pages.jsc.fz-juelich.de/cicd/otf2/tags/otf2-3.0.3/otf2-${szip_ver}.tar.gz 
+cd ${JARVIS_TMP}
+tar xvf ${JARVIS_DOWNLOAD}/otf2-${szip_ver}.tar.gz
+cd otf2-${szip_ver}
+./configure --prefix=$1
+make -j
+make install
-- 
Gitee


From c6cdea94510130d44619f0363b79f2a95ce3ad36 Mon Sep 17 00:00:00 2001
From: berserker111 <2162443403@qq.com>
Date: Thu, 19 Sep 2024 16:18:53 +0800
Subject: [PATCH 9/9] =?UTF-8?q?=E6=96=B0=E5=A2=9Ehpckit=E9=80=9A=E7=94=A8?=
 =?UTF-8?q?=E5=AE=89=E8=A3=85=E8=84=9A=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 package/hpckit/2024.6.30/install.sh |  4 ++++
 package/hpckit/meta.sh              | 18 ++++++++++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 package/hpckit/2024.6.30/install.sh
 create mode 100644 package/hpckit/meta.sh

diff --git a/package/hpckit/2024.6.30/install.sh b/package/hpckit/2024.6.30/install.sh
new file mode 100644
index 0000000..08a9bf6
--- /dev/null
+++ b/package/hpckit/2024.6.30/install.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+export hpckit_ver="24.0.RC2"
+../meta.sh $1
diff --git a/package/hpckit/meta.sh b/package/hpckit/meta.sh
new file mode 100644
index 0000000..cf613e9
--- /dev/null
+++ b/package/hpckit/meta.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -x
+set -e
+#hpckit_ver="24.0.RC1"
+. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/HPC/HPCKit/HPCKit_${hpckit_ver}_Linux-aarch64.tar.gz
+
+cd $JARVIS_TMP
+if [ ! -d HPCKit_${hpckit_ver}_Linux-aarch64 ];then
+   tar xvf $JARVIS_DOWNLOAD/HPCKit_${hpckit_ver}_Linux-aarch64.tar.gz
+fi
+cd HPCKit_${hpckit_ver}_Linux-aarch64
+sh install.sh -y --prefix=$1
+echo -e "HPCKit has installed in your environment."
+#useage:
+#1.source software/utils/hpckit/2024.3.30/HPCKit/latest/setvars.sh --use-bisheng
+#2.module purge
+#module use software/utils/hpckit/2024.3.30/HPCKit/24.3.30/modulefiles
+#module load bisheng/compiler/bishengmodule bisheng/kml/omp
-- 
Gitee