From 1542dc4d9a372e6af38e590ba330a99a629dd0db Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Wed, 17 Dec 2025 15:38:32 +0800
Subject: [PATCH 01/15] update
 templates\alphafold2\1.0\data.alphafold2.cpu.config

---
 .../alphafold2/1.0/data.alphafold2.cpu.config | 22 ++++++++++++++-----
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/templates/alphafold2/1.0/data.alphafold2.cpu.config b/templates/alphafold2/1.0/data.alphafold2.cpu.config
index 6225cc79..eb3eecd6 100644
--- a/templates/alphafold2/1.0/data.alphafold2.cpu.config
+++ b/templates/alphafold2/1.0/data.alphafold2.cpu.config
@@ -2,10 +2,10 @@
 11.11.11.11
 
 [DOWNLOAD]
-#Note:alphafold should be download of git clone
-#git clone https://github.com/IntelLabs/open-omics-alphafold.git -b v1.0
-#cd open-omics-alphafold
-#git submodule update --init --recursive 
+# Note:alphafold should be download of git clone
+# git clone https://github.com/IntelLabs/open-omics-alphafold.git -b v1.0
+# cd open-omics-alphafold
+# git submodule update --init --recursive 
 
 pytorch/2.5.0 https://github.com/pytorch/pytorch/releases/download/v2.5.0/pytorch-v2.5.0.tar.gz
 sse2neon/1.7.0 https://github.com/DLTcollab/sse2neon/archive/refs/tags/v1.7.0.tar.gz sse2neon-v1.7.0.tar.gz
@@ -33,8 +33,17 @@ case_dir = ${JARVIS_TMP}/open-omics-alphafold
 
 [BUILD]
 yum install numactl -y
+rm -rf ${JARVIS_TMP}/sse2neon-v1.7.0
+rm -rf ${JARVIS_TMP}/open-omics-alphafold
+rm -rf ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/envs/af2
+
+cd ${JARVIS_TMP}
+git clone https://github.com/IntelLabs/open-omics-alphafold.git -b v1.0
+cd open-omics-alphafold
+git submodule update --init --recursive
+
 
-if [ ! -d open-omics-alphafold ];then
+if [ ! -d ${JARVIS_TMP}/open-omics-alphafold ];then
  echo "open-omics-alphafold directory does not exists. Execute the following command to download."
  echo "git clone https://github.com/IntelLabs/open-omics-alphafold.git -b v1.0 && cd open-omics-alphafold && git submodule update --init --recursive"
  exit 1
@@ -68,6 +77,7 @@ export CFLAGS="-L$KML_LIB-lkblas"
 export CXXFLAGS="$CXXFLAGS -Wno-nonnull"
 python3 setup.py install
 
+cd ${JARVIS_TMP}
 if [ ! -d sse2neon-1.7.0 ];then
  tar xvf ${JARVIS_DOWNLOAD}/sse2neon-v1.7.0.tar.gz
 fi
@@ -90,7 +100,7 @@ rm -rf ${JARVIS_TMP}/sse2neon-1.7.0
 rm -rf ${JARVIS_TMP}/open-omics-alphafold
 
 [RUN]
-run =
+run = time
 binary =
 nodes = 1
 
-- 
Gitee


From 1d56ede73f26e672962f4a9b1625a9b05fc3fa5a Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Wed, 17 Dec 2025 15:44:20 +0800
Subject: [PATCH 02/15] update
 templates\chaste\2019.1\data.chaste.arm.cpu.config

---
 templates/chaste/2019.1/data.chaste.arm.cpu.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/chaste/2019.1/data.chaste.arm.cpu.config b/templates/chaste/2019.1/data.chaste.arm.cpu.config
index 14ad2d8f..d099db9c 100644
--- a/templates/chaste/2019.1/data.chaste.arm.cpu.config
+++ b/templates/chaste/2019.1/data.chaste.arm.cpu.config
@@ -100,7 +100,7 @@ tar -xvzf ${JARVIS_DOWNLOAD}/Propagation3d.tgz
 make clean
 
 [RUN]
-run = time -p mpirun -np 32 --allow-run-as-root -x OMP_NUM_THREADS=1
+run = time -p mpirun -np $(nproc) --allow-run-as-root -x OMP_NUM_THREADS=1
 binary = Chaste ChasteParameters.xml
 nodes = 1
 
-- 
Gitee


From d26438f6480ebb0f8f2bb8850532bd7ad4d88d0e Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Wed, 17 Dec 2025 15:51:13 +0800
Subject: [PATCH 03/15] update
 templates\deepmd-kit\2.2.10\deepmdkit.arm.cpu.kgcc.hmpi.config

---
 .../deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config
index ceedcdb1..b2b342a3 100644
--- a/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config
+++ b/templates/deepmd-kit/2.2.10/deepmdkit.arm.cpu.kgcc.hmpi.config
@@ -14,7 +14,7 @@ module use ./software/modulefiles
 source ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/etc/profile.d/conda.sh
 ./jarvis -install hpckit/${HPCKIT_VERSION} any
 module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
-module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi${HPCKIT_VERSION}/release
 export CC=`which gcc`
 export CXX=`which g++`
 export FC=`which gfortran`
@@ -26,7 +26,7 @@ module purge
 module use ./software/modulefiles
 source ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/etc/profile.d/conda.sh
 module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
-module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi${HPCKIT_VERSION}/release
 export CC=`which gcc`
 export CXX=`which g++`
 export FC=`which gfortran`
-- 
Gitee


From afd4ace8da9a3f675a2d0e56d254741eba2b57e5 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Wed, 17 Dec 2025 17:09:24 +0800
Subject: [PATCH 04/15] update
 templates\gromacs\2022.5\data.gromacs.arm.cpu.config

---
 .../gromacs/2022.5/data.gromacs.arm.cpu.config  | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
index 38672573..420270e3 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
@@ -3,6 +3,7 @@
 
 [DOWNLOAD]
 gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
+water_GMX50_bare https://ftp.gromacs.org/pub/benchmarks/water_GMX50_bare.tar.gz
 
 [DEPENDENCY]
 module purge
@@ -40,13 +41,13 @@ module load fftw/3.3.8
 export CC=mpicc CXX=mpicxx FC=mpifort
 export PATH=${JARVIS_ROOT}/gromacs-2022.5-kml/bin:$PATH
 openblas_path=$JARVIS_LIBS/bisheng2.1.0/openblas/0.3.18
-fftw_path=$JARVIS_LIBS/bisheng2.1.0/fftw/3.3.8/
+fftw_path=$JARVIS_LIBS/bisheng2.1.0-hmpi1.1.1/fftw/3.3.8/
 
 [APP]
 app_name = gromacs
 build_dir = ${JARVIS_ROOT}/gromacs-2022.5
-binary_dir = ${JARVIS_ROOT}/gromacs-2022.5-kml/bin 
-case_dir =
+binary_dir =  
+case_dir = ${JARVIS_ROOT}/water-cut1.0_GMX50_bare/0768/
 
 [BUILD]
 
@@ -55,7 +56,7 @@ mkdir -p build
 cd build
 
 openblas_path=$JARVIS_LIBS/bisheng2.1.0/openblas/0.3.18
-fftw_path=$JARVIS_LIBS/bisheng2.1.0/fftw/3.3.8/
+fftw_path=$JARVIS_LIBS/bisheng2.1.0-hmpi1.1.1/fftw/3.3.8/
 
 FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang -fuse-ld=lld" CC=mpicc CXX=mpicxx \
 cmake \
@@ -82,12 +83,18 @@ cmake \
 make -j
 make install
 
+cd $JARVIS_ROOT
+export PATH=$JARVIS_ROOT/gromacs-2022.5-kml/bin:$PATH
+tar xvf downloads/water_GMX50_bare.tar.gz
+cd water-cut1.0_GMX50_bare/0768
+$JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi grompp -f pme.mdp
+
 
 [CLEAN]
 ./clean_build
 
 [RUN]
-run =
+run = mpirun --allow-run-as-root --mca btl ^openib -np $(nproc) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
 binary =
 nodes = 1
 
-- 
Gitee


From 28903f97071c3f178e9f8920f5786b547d21dff9 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Wed, 17 Dec 2025 17:36:16 +0800
Subject: [PATCH 05/15] udpate
 templates\gromacs\2024.2\data.gromacs.arm.cpu.openblas.config

---
 .../2024.2/data.gromacs.arm.cpu.openblas.config     | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/templates/gromacs/2024.2/data.gromacs.arm.cpu.openblas.config b/templates/gromacs/2024.2/data.gromacs.arm.cpu.openblas.config
index b58cae74..671c9923 100644
--- a/templates/gromacs/2024.2/data.gromacs.arm.cpu.openblas.config
+++ b/templates/gromacs/2024.2/data.gromacs.arm.cpu.openblas.config
@@ -3,6 +3,7 @@
  
 [DOWNLOAD]
 gromacs/2024.2 http://ftp.gromacs.org/gromacs/gromacs-2024.2.tar.gz
+Testcase https://repository.prace-ri.eu/ueabs/GROMACS/2.2/GROMACS_TestCaseC.tar.xz
  
 [DEPENDENCY]
 module purge
@@ -41,12 +42,14 @@ export FFTW_PATH=$JARVIS_ROOT/software/libs/bisheng${BISHENG_VERSION}-hmpi${HMPI
 [APP]
 app_name = gromacs
 build_dir = $JARVIS_TMP 
-binary_dir = $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HPCKIT_VERSION}/gromacs-2024.2/bin
-case_dir = $JARVIS_TMP 
+binary_dir = 
+case_dir = $JARVIS_TMP/GROMACS_TestCaseC 
  
 [BUILD]
-rm -rf $JARVIS_TMP/gromacs-2024.2
 cd $JARVIS_TMP
+rm -rf gromacs-2024.2 GROMACS_TestCaseC
+tar -xf ${JARVIS_DOWNLOAD}/GROMACS_TestCaseC.tar.xz
+rm -rf $JARVIS_TMP/gromacs-2024.2
 tar -xf ${JARVIS_DOWNLOAD}/gromacs-2024.2.tar.gz
 cd gromacs-2024.2
 mkdir -p build
@@ -62,8 +65,8 @@ make install
 rm -rf $JARVIS_TMP/gromacs-2024.2/build/*
  
 [RUN]
-run =
-binary = mpirun -np 128 --allow-run-as-root -x UCX_TLS=sm --bind-to cpulist:ordered -mca pml ucx -mca btl ^vader,tcp,openib,uct $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HPCKIT_VERSION}/gromacs-2024.2/bin/gmx_mpi mdrun -dlb yes -v -nsteps 4000 -noconfout -pin on -pinoffset 0 -ntomp 1 -npme 40 -g md_sve_0229-ucpg-bisheng.log -s stmv.28M.tpr
+run = mpirun -np $(( $(nproc) / 2 )) --allow-run-as-root -x UCX_TLS=sm --bind-to cpulist:ordered -mca pml ucx -mca btl ^vader,tcp,openib,uct $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HPCKIT_VERSION}/gromacs-2024.2/bin/gmx_mpi mdrun -dlb yes -v -nsteps 4000 -noconfout -pin on -pinoffset 0 -ntomp 1 -g md_sve_0229-ucpg-bisheng.log -s stmv.28M.tpr
+binary = 
 nodes = 1
 
 
-- 
Gitee


From 657f9fe426181f7e3741c9c4d73e2086a3c4eb44 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 09:30:05 +0800
Subject: [PATCH 06/15] update templates\gromacs\2023.3\gromacs.2023.3.config

---
 templates/gromacs/2023.3/gromacs.2023.3.config | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/templates/gromacs/2023.3/gromacs.2023.3.config b/templates/gromacs/2023.3/gromacs.2023.3.config
index 0ef5ce13..7ec51304 100644
--- a/templates/gromacs/2023.3/gromacs.2023.3.config
+++ b/templates/gromacs/2023.3/gromacs.2023.3.config
@@ -18,6 +18,12 @@ export CC=mpicc CXX=mpicxx FC=mpifort
 if [ ! -d gromacs-2023.3 ]; then
 tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2023.3.tar.gz
 fi
+
+if [ ! -d GROMACS_TestCaseC ]; then
+tar -xvf ${JARVIS_DOWNLOAD}/GROMACS_TestCaseC.tar.xz
+fi
+
+
  
 [ENV]
 module purge
@@ -35,7 +41,7 @@ export gromacs_dir=$JARVIS_ROOT/gromacs-2023.3
 app_name = gromacs
 build_dir = $gromacs_dir
 binary_dir =
-case_dir = $JARVIS_ROOT/workloads/Gromacs/GROMACS_TestCaseC
+case_dir = $JARVIS_ROOT/GROMACS_TestCaseC
  
 [BUILD]
 #rm -rf build
@@ -56,8 +62,8 @@ make install
 ./clean_build
  
 [RUN]
-run =
-binary = mpirun -np 574 --allow-run-as-root -x UCX_TLS=sm --bind-to cpulist:ordered -mca pml ucx -mca btl ^vader,tcp,openib,uct ${gromacs_dir}/build/bin/gmx_mpi mdrun -dlb yes -v -nsteps 4000 -noconfout -pin on -pinoffset 0 -ntomp 1 -npme 112 -g md_sve_0229-ucpg-bisheng-2P.log -s stmv.28M.tpr
+run = mpirun -np $(( $(nproc) / 2 )) --allow-run-as-root -x UCX_TLS=sm --bind-to cpulist:ordered -mca pml ucx -mca btl ^vader,tcp,openib,uct ${gromacs_dir}/build/bin/gmx_mpi mdrun -dlb yes -v -nsteps 4000 -noconfout -pin on -pinoffset 0 -ntomp 1  -s stmv.28M.tpr
+binary = 
 nodes = 1
 
 [JOB]
-- 
Gitee


From f57afec554d40debcd03d2c34b0fd733c79ebde5 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 09:36:55 +0800
Subject: [PATCH 07/15] update
 templates\gromacs\2022.5\data.gromacs.arm.cpu.config

---
 templates/gromacs/2022.5/data.gromacs.arm.cpu.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
index 420270e3..6d55769c 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
@@ -94,7 +94,7 @@ $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi grompp -f pme.mdp
 ./clean_build
 
 [RUN]
-run = mpirun --allow-run-as-root --mca btl ^openib -np $(nproc) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
+run = mpirun --allow-run-as-root --mca btl ^openib -np $(( $(nproc) / 2 )) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
 binary =
 nodes = 1
 
-- 
Gitee


From 622c3c99dd4d8ddbf96642d66ac57b1269d8ff0a Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 11:47:09 +0800
Subject: [PATCH 08/15] udpate
 templates\gromacs\2019.3\bisheng\data.gromacs.arm.cpu.config

---
 .../2019.3/bisheng/data.gromacs.arm.cpu.config    | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/templates/gromacs/2019.3/bisheng/data.gromacs.arm.cpu.config b/templates/gromacs/2019.3/bisheng/data.gromacs.arm.cpu.config
index 1105f2df..0553c5ce 100644
--- a/templates/gromacs/2019.3/bisheng/data.gromacs.arm.cpu.config
+++ b/templates/gromacs/2019.3/bisheng/data.gromacs.arm.cpu.config
@@ -37,22 +37,23 @@ module load fftw/3.3.8
 
 [APP]
 app_name = gromacs
-build_dir = $JARVIS_ROOT
-binary_dir = $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/gromacs
-case_dir = $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/gromacs
+build_dir = ${JARVIS_TMP}
+binary_dir = 
+case_dir = 
 
 [BUILD]
 cd ${JARVIS_TMP}
-rm -rf gromacs-2019.3
+rm -rf gromacs-2019.3 
+tar -xf ${JARVIS_DOWNLOAD}/gromacs-2019.3.tar.gz
+
 rm -rf gromacs
 mkdir -p gromacs
-tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2019.3.tar.gz
 cd gromacs-2019.3
 mkdir build
 cd build
 
 openblas_path=$JARVIS_LIBS/bisheng2.1.0/openblas/0.3.18
-fftw_path=$JARVIS_LIBS/bisheng2.1.0/hmpi1.1.1/fftw/3.3.8
+fftw_path=$JARVIS_LIBS/bisheng2.1.0-hmpi1.1.1/fftw/3.3.8
 
 FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang -fuse-ld=lld" CC=mpicc CXX=mpicxx \
 cmake \
@@ -85,7 +86,7 @@ make install
 ./clean_build
 
 [RUN]
-run =
+run = $JARVIS_TMP/gromacs/bin/gmx_mpi --version
 binary =
 nodes = 1
 
-- 
Gitee


From 4f8a9fcdeef593b5a94b7c1931f10d90fb6fc305 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 12:12:32 +0800
Subject: [PATCH 09/15] update templates\namd\2.13\data.namd.arm.cpu.config

---
 templates/namd/2.13/data.namd.arm.cpu.config | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/templates/namd/2.13/data.namd.arm.cpu.config b/templates/namd/2.13/data.namd.arm.cpu.config
index e383c9bf..f4eca1b2 100644
--- a/templates/namd/2.13/data.namd.arm.cpu.config
+++ b/templates/namd/2.13/data.namd.arm.cpu.config
@@ -9,7 +9,7 @@ tcl/8.5   http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-arm64-th
 ./jarvis -install hpckit/${HPCKIT_VERSION} any
 module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
 module purge
-module load bisheng/compiler${BISHENG_VERSION}/bishengmodule bisheng/hmpi${HMPI_VERSION}/hmpi
+module load bisheng/compiler${BISHENG_VERSION}/bishengmodule bisheng/hmpi${HMPI_VERSION}/release
 
 export CC=mpicc FC=mpifort CXX=mpicxx
 
@@ -20,7 +20,7 @@ module load fftw/3.3.8
 [ENV]
 module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
 module purge
-module load bisheng/compiler${BISHENG_VERSION}/bishengmodule bisheng/hmpi${HMPI_VERSION}/hmpi
+module load bisheng/compiler${BISHENG_VERSION}/bishengmodule bisheng/hmpi${HMPI_VERSION}/release
 module use ${JARVIS_ROOT}/software/moduledeps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERSION}/
 module load fftw/3.3.8
 export PATH=$JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERSION}/namd/Linux-ARM64-clang:$PATH
@@ -28,8 +28,9 @@ export PATH=$JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERS
 [APP]
 app_name = namd
 build_dir = $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERSION}/namd
-binary_dir = $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERSION}/namd/Linux-ARM64-${CXX}
-case_dir = ${JARVIS_TMP}/stmv
+#binary_dir = $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERSION}/namd/NAMD_2.13_Source/Linux-ARM64-${CXX}
+binary_dir =
+case_dir = 
 
 [BUILD]
 set -x
@@ -125,9 +126,9 @@ echo "Install is success install_dir: $installdir"
 rm -rf $JARVIS_ROOT/software/apps/bisheng${BISHENG_VERSION}-hmpi${HMPI_VERSION}/namd
 
 [RUN]
-run =   
+run = time  
 binary = 
-nodes = 
+nodes = 1
 
 [BATCH]
 #定义日志文件
-- 
Gitee


From 482bec90708c1d818678a36c6dc91388a3d785b3 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 16:32:13 +0800
Subject: [PATCH 10/15] update
 templates\octopus\10.3\data.octopus.arm.kpgcc.cpu.config

---
 templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config b/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config
index 1ac73316..d9868545 100644
--- a/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config
+++ b/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config
@@ -53,7 +53,8 @@ module load fftw/3.3.8
 [APP]
 app_name = octopus
 build_dir = ${JARVIS_ROOT}/octopus-10.3
-binary_dir = ./software/apps/kgcc9.3.1/octopus/10.3
+#binary_dir = ${JARVIS_ROOT}/OCTOPUS
+binary_dir =
 case_dir =
 
 [BUILD]
@@ -71,7 +72,7 @@ make -j
 make install
 
 [RUN]
-run =
+run = time
 binary =
 nodes = 1
 
-- 
Gitee


From 31e86fe0aec23c278684981a0c74bc1c7931abf8 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 17:32:07 +0800
Subject: [PATCH 11/15] update
 templates\octopus\11.4\data.octopus.arm.bs-sve.cpu.config

---
 .../octopus/11.4/data.octopus.arm.bs-sve.cpu.config | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config b/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config
index 716bdc00..354b6852 100644
--- a/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config
+++ b/templates/octopus/11.4/data.octopus.arm.bs-sve.cpu.config
@@ -40,20 +40,21 @@ export PATH=/hpcrunner/software/apps/bisheng3.2.0/octopus/11.4/bin:$PATH
 [APP]
 app_name = octopus
 build_dir = ${JARVIS_ROOT}/octopus-11.4
-binary_dir = ${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4
+#binary_dir = ${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4
+binary_dir =
 case_dir =
 
 [BUILD]
-./configure  --prefix=${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4  CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true'  FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true'  --with-gsl-prefix=${JARVIS_LIBS}/bisheng3.2.0/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/bisheng3.2.0/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/bisheng3.2.0/hmpi2.3.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/liblapack.so  --enable-mpi
+./configure  --prefix=${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4  CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true'  FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -mcpu=linxicore9100 -mllvm -force-customized-pipeline=true'  --with-gsl-prefix=${JARVIS_LIBS}/bisheng3.2.0/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/bisheng3.2.0/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/bisheng3.2.0-hmpi2.3.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/liblapack.so  --enable-mpi
 
-patch -p0 < /hpcrunner/templates/octopus/11.4/cuda.F90.patch
-patch -p0 < /hpcrunner/templates/octopus/11.4/run.F90.patch
-patch -p0 < /hpcrunner/templates/octopus/11.4/accel_inc.F90.patch
+patch -p0 < ${JARVIS_ROOT}/templates/octopus/11.4/cuda.F90.patch
+patch -p0 < ${JARVIS_ROOT}/templates/octopus/11.4/run.F90.patch
+patch -p0 < ${JARVIS_ROOT}/templates/octopus/11.4/accel_inc.F90.patch
 make -j
 make install
 
 [RUN]
-run =
+run = time
 binary =
 nodes = 1
 
-- 
Gitee


From e8d10cf3011f9b2efa2159a8b991a62a5a1e5e65 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Thu, 18 Dec 2025 17:43:34 +0800
Subject: [PATCH 12/15] update data.gromacs.arm-sve.cpu.config
 data.gromacs.arm.cpu.config

---
 templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config | 2 +-
 templates/gromacs/2022.5/data.gromacs.arm.cpu.config     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config b/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
index a5625c26..34c03c97 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
@@ -87,7 +87,7 @@ $JARVIS_ROOT/gromacs/bin/gmx_mpi grompp -f pme.mdp
 ./clean_build
 
 [RUN]
-run = mpirun --allow-run-as-root --mca btl ^openib -np $(nproc) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
+run = mpirun --allow-run-as-root --mca btl ^openib -np $(( $(nproc) / 4 )) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
 binary =
 nodes = 1
 
diff --git a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
index 6d55769c..98cef228 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
@@ -94,7 +94,7 @@ $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi grompp -f pme.mdp
 ./clean_build
 
 [RUN]
-run = mpirun --allow-run-as-root --mca btl ^openib -np $(( $(nproc) / 2 )) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
+run = mpirun --allow-run-as-root --mca btl ^openib -np $(( $(nproc) / 4 )) -x OMP_NUM_THREADS=4 $JARVIS_ROOT/gromacs-2022.5-kml/bin/gmx_mpi mdrun -dlb yes -v -nsteps 10000 -resethway -noconfout -pin on -ntomp 4 -s topol.tpr
 binary =
 nodes = 1
 
-- 
Gitee


From 6e8cbc61ac5494e6a0d1488f855c5f2a16c1ff2a Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Fri, 19 Dec 2025 10:43:18 +0800
Subject: [PATCH 13/15] update
 hpcrunner\templates\octopus\11.4\data.octopus.arm.bs.cpu.config

---
 .../octopus/11.4/data.octopus.arm.bs.cpu.config     | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/templates/octopus/11.4/data.octopus.arm.bs.cpu.config b/templates/octopus/11.4/data.octopus.arm.bs.cpu.config
index b7cca51c..0f7bf84f 100644
--- a/templates/octopus/11.4/data.octopus.arm.bs.cpu.config
+++ b/templates/octopus/11.4/data.octopus.arm.bs.cpu.config
@@ -41,21 +41,22 @@ export PATH=/hpcrunner/software/apps/bisheng3.2.0/octopus/11.4/bin:$PATH
 [APP]
 app_name = octopus
 build_dir = ${JARVIS_ROOT}/octopus-11.4
-binary_dir = ${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4
+#binary_dir = ${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4
+binary_dir =
 case_dir =
 
 [BUILD]
-./configure  --prefix=${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4  CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  --with-gsl-prefix=${JARVIS_LIBS}/bisheng3.2.0/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/bisheng3.2.0/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/bisheng3.2.0/hmpi2.3.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/liblapack.so  --enable-mpi
+./configure  --prefix=${JARVIS_ROOT}/software/apps/bisheng3.2.0/octopus/11.4  CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  --with-gsl-prefix=${JARVIS_LIBS}/bisheng3.2.0/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/bisheng3.2.0/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/bisheng3.2.0-hmpi2.3.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/bisheng3.2.0/lapack/3.8.0/lib/liblapack.so  --enable-mpi
 
-patch -p0 < /hpcrunner/templates/octopus/11.4/cuda.F90.patch
-patch -p0 < /hpcrunner/templates/octopus/11.4/run.F90.patch
-patch -p0 < /hpcrunner/templates/octopus/11.4/accel_inc.F90.patch
+patch -p0 < ${JARVIS_ROOT}/templates/octopus/11.4/cuda.F90.patch
+patch -p0 < ${JARVIS_ROOT}/templates/octopus/11.4/run.F90.patch
+patch -p0 < ${JARVIS_ROOT}/templates/octopus/11.4/accel_inc.F90.patch
 
 make -j
 make install
 
 [RUN]
-run =
+run = time
 binary =
 nodes = 1
 
-- 
Gitee


From ee7fe0aaddc0439541cb3002f86319737abb00b6 Mon Sep 17 00:00:00 2001
From: wmr <1824643752@qq.com>
Date: Fri, 19 Dec 2025 14:15:33 +0800
Subject: [PATCH 14/15] update
 templates/octopus/11.4/data.octopus.arm.gcc.cpu.config

---
 templates/octopus/11.4/data.octopus.arm.gcc.cpu.config | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/templates/octopus/11.4/data.octopus.arm.gcc.cpu.config b/templates/octopus/11.4/data.octopus.arm.gcc.cpu.config
index 5875cf51..a4c66608 100644
--- a/templates/octopus/11.4/data.octopus.arm.gcc.cpu.config
+++ b/templates/octopus/11.4/data.octopus.arm.gcc.cpu.config
@@ -39,16 +39,17 @@ export PATH=/hpcrunner/software/apps/kgcc9.3.1/octopus/11.4/bin:$PATH
 [APP]
 app_name = octopus
 build_dir = ${JARVIS_ROOT}/octopus-11.4
-binary_dir = ${JARVIS_ROOT}/software/apps/kgcc9.3.1/octopus/11.4
+#binary_dir = ${JARVIS_ROOT}/software/apps/kgcc9.3.1/octopus/11.4
+binary_dir =
 case_dir =
 
 [BUILD]
-./configure  --prefix=${JARVIS_ROOT}/software/apps/kgcc9.3.1/octopus/11.4  CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  --with-gsl-prefix=${JARVIS_LIBS}/kgcc9.3.1/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/kgcc9.3.1/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/kgcc9.3.1/hmpi1.2.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/kgcc9.3.1/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/kgcc9.3.1/lapack/3.8.0/lib/liblapack.so  --enable-mpi
+./configure  --prefix=${JARVIS_ROOT}/software/apps/kgcc9.3.1/octopus/11.4  CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  FCFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 '  --with-gsl-prefix=${JARVIS_LIBS}/kgcc9.3.1/gsl/2.6 --with-libxc-prefix=${JARVIS_LIBS}/kgcc9.3.1/libxc/4.3.4 --with-fftw-prefix=${JARVIS_LIBS}/kgcc9.3.1-hmpi1.2.0/fftw/3.3.8 --with-blas=${JARVIS_LIBS}/kgcc9.3.1/lapack/3.8.0/lib/libblas.so --with-lapack=${JARVIS_LIBS}/kgcc9.3.1/lapack/3.8.0/lib/liblapack.so  --enable-mpi
 make -j
 make install
 
 [RUN]
-run =
+run = time
 binary =
 nodes = 1
 
-- 
Gitee


From c715533d488ae69cd3ef58a51f9ac81ff7156f01 Mon Sep 17 00:00:00 2001
From: wuhuajian <1824643752@qq.com>
Date: Mon, 22 Dec 2025 16:47:44 +0800
Subject: [PATCH 15/15] update
 templates/abinit/8.10.3/data.abinit.arm.cpu.config,templates/alphafold2/1.0/data.alphafold2.cpu.config

---
 .../abinit/8.10.3/data.abinit.arm.cpu.config  | 42 ++++++++++++-------
 .../alphafold2/1.0/data.alphafold2.cpu.config |  4 +-
 2 files changed, 30 insertions(+), 16 deletions(-)

diff --git a/templates/abinit/8.10.3/data.abinit.arm.cpu.config b/templates/abinit/8.10.3/data.abinit.arm.cpu.config
index 12af84ec..19e1dc2f 100644
--- a/templates/abinit/8.10.3/data.abinit.arm.cpu.config
+++ b/templates/abinit/8.10.3/data.abinit.arm.cpu.config
@@ -2,7 +2,8 @@
 11.11.11.11
 
 [DOWNLOAD]
-abinit/8.10.3 https://www.abinit.org/sites/default/files/packages/abinit-8.10.3.tar.gz
+#abinit/8.10.3 https://www.abinit.org/sites/default/files/packages/abinit-8.10.3.tar.gz
+abinit/8.10.3 $JARVIS_PROXY/abinit/abinit/archive/refs/tags/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
@@ -22,7 +23,8 @@ module load ./software/moduledeps/kgcc10.3.1/hmpi/1.1.1
 export CC=mpicc CXX=mpicxx FC=mpifort
 ./jarvis -install hdf5/1.10.1 gcc+mpi
 ./jarvis -install package/pnetcdf/1.9.0 gcc+mpi
-module load ./software/moduledeps/gcc10.3.1-hmpi1.1.1/pnetcdf/1.9.0
+module load ./software/moduledeps/kgcc10.3.1-hmpi1.1.1/pnetcdf/1.9.0
+module load ./software/moduledeps/kgcc10.3.1-hmpi1.1.1/hdf5/1.10.1
 ./jarvis -install package/netcdf/4.7.0 gcc+mpi
 ./jarvis -install package/openblas/0.3.18 gcc
 
@@ -42,8 +44,10 @@ export CC=mpicc CXX=mpicxx FC=mpifort
 [APP]
 app_name = abinit
 build_dir = $JARVIS_ROOT
-binary_dir = $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/abinit
-case_dir = $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/abinit
+binary_dir = $JARVIS_ROOT/abinit/bin
+#binary_dir = 
+#case_dir = $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/abinit
+case_dir = 
 
 [BUILD]
 set -x
@@ -54,16 +58,20 @@ set -e
 #cd $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/abinit
 
 cd ${JARVIS_TMP}
-ABINIT_INSTALL_DIR="$JARVIS_ROOT/software/apps/kgcc9.3.1/hmpi1.1.1/abinit/"
+ABINIT_INSTALL_DIR="$JARVIS_ROOT"
 
 MPI_HOME=`which mpicc`
 MPI_HOME=${MPI_HOME%/*/*}
 
 
-hdf5_path=`which h5diff`
-hdf5_path=${hdf5_path%/*/*}
-netcdf_path=`nc-config --prefix`
-pnetcdf_path=`pnetcdf-config --prefix`
+#hdf5_path=`which h5diff`
+#hdf5_path=${hdf5_path%/*/*}
+#netcdf_path=`nc-config --prefix`
+#pnetcdf_path=`pnetcdf-config --prefix`
+
+hdf5_path=$JARVIS_LIBS/kgcc10.3.1-hmpi1.1.1/hdf5/1.10.1
+pnetcdf_path=$JARVIS_LIBS/kgcc10.3.1-hmpi1.1.1/pnetcdf/1.9.0
+netcdf_path=$JARVIS_LIBS/kgcc10.3.1-hmpi1.1.1/netcdf/4.7.0
 
 array=(${LD_LIBRARY_PATH//:/ })
 for var in ${array[@]}
@@ -87,10 +95,12 @@ export FFLAGS=" -I${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
+#tar -zxvf $JARVIS_DOWNLOAD/abinit-8.10.3.tar.gz
+tar -zxvf $JARVIS_DOWNLOAD/8.10.3.tar.gz
 cd abinit-8.10.3
 temp_path=`pwd`
-
+bash autogen.sh
+sed -i '5295i\  : # IBM compiler case - do nothing' fallbacks/configure
 cp $JARVIS_DOWNLOAD/abinit_patch-8.10.3.patch  ./
 cd ./src
 patch -p2 < ../abinit_patch-8.10.3.patch
@@ -105,15 +115,19 @@ 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${openblas_path}/ -lblas -llapack"  --prefix=$ABINIT_INSTALL_DIR 
+../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 -lnetcdff" FLDFLAGS="-L${netcdf_path}/lib -Wl,-rpath,${netcdf_path}/lib" FCFLAGS="-g -O2 -ffree-line-length-none -fallow-argument-mismatch" --with-linalg-libs="-L${openblas_path}/ -lblas -llapack"  --prefix=$ABINIT_INSTALL_DIR/abinit 
+
 
-FC=mpif90 CC=mpicc CXX=mpicxx make multi multi_nprocs=96
+FC=mpif90 CC=mpicc CXX=mpicxx make multi multi_nprocs=4
 
+rm -rf $ABINIT_INSTALL_DIR/abinit
+make -j
+make install
 
 [CLEAN]
 ./clean_build
 
 [RUN]
-run =
+run = $JARVIS_ROOT/abinit/bin/abinit --version
 binary =
 nodes = 1
diff --git a/templates/alphafold2/1.0/data.alphafold2.cpu.config b/templates/alphafold2/1.0/data.alphafold2.cpu.config
index eb3eecd6..f0ae8e7b 100644
--- a/templates/alphafold2/1.0/data.alphafold2.cpu.config
+++ b/templates/alphafold2/1.0/data.alphafold2.cpu.config
@@ -35,8 +35,8 @@ case_dir = ${JARVIS_TMP}/open-omics-alphafold
 yum install numactl -y
 rm -rf ${JARVIS_TMP}/sse2neon-v1.7.0
 rm -rf ${JARVIS_TMP}/open-omics-alphafold
-rm -rf ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/envs/af2
-
+#rm -rf ${JARVIS_ROOT}/software/utils/anaconda3/2024.10/envs/af2
+conda env remove --name af2 -y
 cd ${JARVIS_TMP}
 git clone https://github.com/IntelLabs/open-omics-alphafold.git -b v1.0
 cd open-omics-alphafold
-- 
Gitee