From 54fd9b14b5d857307c7e78acf47c201a22bb7470 Mon Sep 17 00:00:00 2001
From: berserker111 <11058055+liu-jing110@user.noreply.gitee.com>
Date: Fri, 7 Feb 2025 15:15:54 +0800
Subject: [PATCH 1/3] =?UTF-8?q?=E6=96=B0=E5=A2=9Ehpckit12.30=E7=89=88?=
 =?UTF-8?q?=E6=9C=AC?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 package/hpckit/2024.12.30/install.sh | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 package/hpckit/2024.12.30/install.sh

diff --git a/package/hpckit/2024.12.30/install.sh b/package/hpckit/2024.12.30/install.sh
new file mode 100644
index 00000000..cc4a66f5
--- /dev/null
+++ b/package/hpckit/2024.12.30/install.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+export hpckit_ver="24.0.0"
+../meta.sh $1
-- 
Gitee


From 51fc4b742751c66dc29cd0603c98c6ef5b6e712a Mon Sep 17 00:00:00 2001
From: wanghanwen <1564586847@qq.com>
Date: Fri, 7 Feb 2025 09:56:55 +0000
Subject: [PATCH 2/3] =?UTF-8?q?Revert=20"=E6=96=B0=E5=A2=9Ehpckit12.30?=
 =?UTF-8?q?=E7=89=88=E6=9C=AC"?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This reverts commit 54fd9b14b5d857307c7e78acf47c201a22bb7470.
---
 package/hpckit/2024.12.30/install.sh | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 package/hpckit/2024.12.30/install.sh

diff --git a/package/hpckit/2024.12.30/install.sh b/package/hpckit/2024.12.30/install.sh
deleted file mode 100644
index cc4a66f5..00000000
--- a/package/hpckit/2024.12.30/install.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-set -e
-export hpckit_ver="24.0.0"
-../meta.sh $1
-- 
Gitee


From bd35fc2fa509d5963b7501572c57a6c17eb4caff Mon Sep 17 00:00:00 2001
From: berserker111 <604593208@qq.com>
Date: Sat, 11 Oct 2025 09:26:09 +0800
Subject: [PATCH 3/3] =?UTF-8?q?=E6=9B=B4=E6=96=B0hpckit=E5=AE=89=E8=A3=85r?=
 =?UTF-8?q?elion=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.arm.hpckit.cpu.config   | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 templates/relion/3.1.2/data.relion.arm.hpckit.cpu.config

diff --git a/templates/relion/3.1.2/data.relion.arm.hpckit.cpu.config b/templates/relion/3.1.2/data.relion.arm.hpckit.cpu.config
new file mode 100644
index 00000000..4b4261ee
--- /dev/null
+++ b/templates/relion/3.1.2/data.relion.arm.hpckit.cpu.config
@@ -0,0 +1,60 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+relion/3.1.2 $JARVIS_PROXY/3dem/relion/archive/refs/tags/3.1.2.tar.gz relion-3.1.2.tar.gz 
+
+[DEPENDENCY]
+yum install -y libtiff-* fltk* fltk-devel*
+module use ./software/modulefiles
+module purge
+./jarvis -install package/hpckit/25.1.0  any
+module use ${JARVIS_ROOT}/software/module*
+module add hpckit25.1.0/bisheng/compiler4.2.0.2/bishengmodule
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install wxWidgets/3.0.5 clang
+module load bisheng4.2.0.2/wxWidgets/3.0.5
+./jarvis -install ctffind/4.1.14/clang clang
+
+[ENV]
+module purge
+module use ${JARVIS_ROOT}/software/module*
+module add hpckit25.1.0/bisheng/compiler4.2.0.2/bishengmodule hpckit25.1.0/bisheng/hmpi25.1.0/release 
+module load bisheng4.2.0.2/wxWidgets/3.0.5 bisheng4.2.0.2/ctffind-clang/4.1.14
+export CC=clang CXX=clang++ FC=flang
+
+export np_per_node=128
+
+export install_path=$JARVIS_ROOT/software/apps/relion/3.1.2
+export bin_path=${install_path}/bin
+export case_path=/nfs02/home/whw/new/hpcrunner/case/relion_benchmark
+export case_name="relion_benchmark"
+export PATH=${PATH}:${bin_path}
+
+
+[APP]
+app_name = relion
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = 
+
+[BUILD]
+cd ${JARVIS_TMP}
+rm -rf relion-3.1.2
+tar -xvf ${JARVIS_DOWNLOAD}/relion-3.1.2.tar.gz
+cd relion-3.1.2
+mkdir build && cd build
+cmake -DCUDA=OFF  -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=release  -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/relion/3.1.2  ..
+make -j
+make install
+
+
+[RUN]
+run = 
+binary = 
+nodes = 1
+
+[BATCH]
+cd ${case_path}
+mkdir -p class3d
+time -p mpirun --allow-run-as-root -N $((np_per_node/4)) numactl --localalloc --cpunodebind=0,1,2,3 relion_refine_mpi --j 4  --cpu --pool 100 --dont_combine_weights_via_disc --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --maxsig 500 --fast_subsets --o class3d/test01
-- 
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