From 6a0636cc840bcea30570ef55e407c1fc29e1ae55 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Thu, 26 Jun 2025 09:57:21 +0800
Subject: [PATCH 1/9] gromacs

---
 .../bisheng/data.gromacs.arm.gpu.config       | 22 ++++++++++++++-----
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config b/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config
index 96ea9ab..be7ef32 100644
--- a/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config
+++ b/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config
@@ -5,25 +5,34 @@
 gromacs/2019.3 http://ftp.gromacs.org/pub/gromacs/gromacs-2019.3.tar.gz
 
 [DEPENDENCY]
-module use ./software/modulefiles
 module purge
+module use ./software/modulefiles
 ./jarvis -install bisheng/2.1.0 com
 module load bisheng/2.1.0
 export CC=clang CXX=clang++ FC=flang
-./jarvis -install hmpi/1.1.1 clang
-./jarvis -install openblas/0.3.18 clang
-./jarvis -install cmake/3.23.1 clang
+./jarvis -install hmpi/1.1.1 bisheng
+module use software/moduledeps/bisheng2.1.0
 module load hmpi/1.1.1
 export CC=mpicc CXX=mpicxx FC=mpifort
+./jarvis -install openblas/0.3.18 bisheng
+module load openblas/0.3.18
+./jarvis -install cmake/3.23.1 bisheng
+module load cmake/3.23.1
 ./jarvis -install fftw/3.3.8 clang+mpi
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
 
 [ENV]
-module use ./software/modulefiles
 module purge
+module use ./software/modulefiles
 module load bisheng/2.1.0
+module use software/moduledeps/bisheng2.1.0
 module load hmpi/1.1.1
-module load fftw/3.3.8 cmake/3.23.1 openblas/0.3.18
 export CC=mpicc CXX=mpicxx FC=mpifort
+module load openblas/0.3.18
+module load cmake/3.23.1
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
 
 [APP]
 app_name = gromacs
@@ -76,3 +85,4 @@ make install
 run =
 binary =
 nodes = 1
+
-- 
Gitee


From a786bdf1e35b6986374923f1f34287845578dafb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Thu, 26 Jun 2025 11:09:05 +0800
Subject: [PATCH 2/9] gromacs

---
 .../2019.3/bisheng/data.gromacs.arm.gpu.config    | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config b/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config
index be7ef32..1105f2d 100644
--- a/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config
+++ b/templates/gromacs/2019.3/bisheng/data.gromacs.arm.gpu.config
@@ -10,14 +10,15 @@ module use ./software/modulefiles
 ./jarvis -install bisheng/2.1.0 com
 module load bisheng/2.1.0
 export CC=clang CXX=clang++ FC=flang
-./jarvis -install hmpi/1.1.1 bisheng
-module use software/moduledeps/bisheng2.1.0
-module load hmpi/1.1.1
-export CC=mpicc CXX=mpicxx FC=mpifort
 ./jarvis -install openblas/0.3.18 bisheng
+module use software/moduledeps/bisheng2.1.0
 module load openblas/0.3.18
 ./jarvis -install cmake/3.23.1 bisheng
 module load cmake/3.23.1
+./jarvis -install hmpi/1.1.1 bisheng
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
 ./jarvis -install fftw/3.3.8 clang+mpi
 module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
 module load fftw/3.3.8
@@ -43,17 +44,19 @@ case_dir = $JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/gromacs
 [BUILD]
 cd ${JARVIS_TMP}
 rm -rf gromacs-2019.3
+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=$JARVIS_LIBS/bisheng/openblas/0.3.18
+openblas_path=$JARVIS_LIBS/bisheng2.1.0/openblas/0.3.18
 fftw_path=$JARVIS_LIBS/bisheng2.1.0/hmpi1.1.1/fftw/3.3.8
 
 FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang -fuse-ld=lld" CC=mpicc CXX=mpicxx \
 cmake \
--DCMAKE_INSTALL_PREFIX=$JARVIS_ROOT/software/apps/bisheng2.1.0/hmpi1.1.1/gromacs \
+-DCMAKE_INSTALL_PREFIX=$JARVIS_TMP/gromacs \
 -DBUILD_SHARED_LIBS=on \
 -DBUILD_TESTING=on \
 -DREGRESSIONTEST_DOWNLOAD=off \
-- 
Gitee


From c5caf4538ee8031c0a4d19973d326114c9c20543 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Thu, 26 Jun 2025 18:07:03 +0800
Subject: [PATCH 3/9] data.gromacs.arm.gpu.config

---
 .../gromacs/2021.3/data.gromacs.arm.gpu.config  | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config
index c931b2b..140e870 100644
--- a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config
+++ b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config
@@ -3,10 +3,12 @@
 
 [DOWNLOAD]
 gromacs/2021.3 http://ftp.gromacs.org/pub/gromacs/gromacs-2021.3.tar.gz
+cuda/11.4.0 https://developer.download.nvidia.com/compute/cuda/11.4.0/local_installers/cuda_11.4.0_470.42.01_linux_sbsa.run
 
 [DEPENDENCY]
 set -e
 set -x
+yum install -y cmake make
 module use ./software/modulefiles
 module purge
 ./jarvis -install kgcc/9.3.1 com
@@ -17,6 +19,21 @@ module load hmpi/1.1.1
 export CC=mpicc CXX=mpicxx FC=mpifort
 ./jarvis -install fftw/3.3.8 gcc+mpi
 tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2021.3.tar.gz
+# 1. 添加执行权限
+sudo chmod +x ${JARVIS_DOWNLOAD}/cuda_11.4.0_470.42.01_linux_sbsa.run
+# 2. 静默安装
+sudo sh ${JARVIS_DOWNLOAD}/cuda_11.4.0_470.42.01_linux_sbsa.run \
+  --silent \
+  --toolkit \
+  --override \
+  --no-opengl-libs \
+  --no-man-page \
+  --no-drm \
+  --installpath=/usr/local/cuda \
+  --toolkitpath=/usr/local/cuda \
+  --samplespath=/usr/local/cuda/samples \
+
+tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2021.3.tar.gz
 
 [ENV]
 module use ./software/modulefiles
-- 
Gitee


From 99c91d68cfd25f83f3847dbbc8afd28fff96929d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Thu, 26 Jun 2025 20:38:38 +0800
Subject: [PATCH 4/9] gromacs

---
 templates/gromacs/2021.3/data.gromacs.arm.gpu.config | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config
index 140e870..95b22f5 100644
--- a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config
+++ b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config
@@ -31,9 +31,7 @@ sudo sh ${JARVIS_DOWNLOAD}/cuda_11.4.0_470.42.01_linux_sbsa.run \
   --no-drm \
   --installpath=/usr/local/cuda \
   --toolkitpath=/usr/local/cuda \
-  --samplespath=/usr/local/cuda/samples \
-
-tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2021.3.tar.gz
+  --samplespath=/usr/local/cuda/samples 
 
 [ENV]
 module use ./software/modulefiles
-- 
Gitee


From b2f4938548f5f3096c044f221b49c251c42f1e90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Fri, 27 Jun 2025 14:24:21 +0800
Subject: [PATCH 5/9] data.gromacs.arm.cpu.config

---
 .../2022.5/data.gromacs.arm.cpu.config        | 84 ++++++++++++-------
 1 file changed, 56 insertions(+), 28 deletions(-)

diff --git a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
index efeeb8a..3c8af09 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm.cpu.config
@@ -6,55 +6,83 @@ gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
 
 [DEPENDENCY]
 module purge
-./jarvis -install bisheng/3.2.0-mini com
 module use ./software/modulefiles
-module load bisheng/3.2.0-mini
+./jarvis -install bisheng/2.1.0 com
+module load bisheng/2.1.0
 export CC=clang CXX=clang++ FC=flang
-./jarvis -install hmpi/2.3.0 clang
-module use ./software/moduledeps/bisheng3.2.0
-module load hmpi/2.3.0
-./jarvis -install kml/2.2.0/bisheng bisheng
-module load kml-bisheng/2.2.0
+./jarvis -install openblas/0.3.18 bisheng
+module use software/moduledeps/bisheng2.1.0
+module load openblas/0.3.18
+./jarvis -install cmake/3.23.1 bisheng
+module load cmake/3.23.1
+./jarvis -install hmpi/1.1.1 bisheng
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+./jarvis -install fftw/3.3.8 clang+mpi
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
+rm -rf gromacs-2022.5-kml
+mkdir -p gromacs-2022.5-kml
+rm -rf gromacs-2022.5
+tar -xf ${JARVIS_DOWNLOAD}/gromacs-2022.5.tar.gz
 
 [ENV]
 module purge
 module use ./software/modulefiles
-module purge
-module load bisheng/3.2.0-mini
-module use ./software/moduledeps/bisheng3.2.0
-module load kml-bisheng/2.2.0
-module load hmpi/2.3.0
+module load bisheng/2.1.0
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
+module load openblas/0.3.18
+module load cmake/3.23.1
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
 export CC=mpicc CXX=mpicxx FC=mpifort
-export PMIX_INSTALL_PREFIX=${OPAL_PREFIX}
-cd /hpcrunner
-CUR_PATH=$(pwd)
-export JARVIS_ROOT=${CUR_PATH}
-export JARVIS_TMP=${CUR_PATH}/tmp
 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/hmpi1.1.1/fftw/3.3.8
 
 [APP]
 app_name = gromacs
-build_dir = $JARVIS_TMP/gromacs-2022.5
-binary_dir = $JARVIS_ROOT/gromacs-2022.5-kml/bin 
+build_dir = ${JARVIS_ROOT}/gromacs-2022.5
+binary_dir = ${JARVIS_ROOT}/gromacs-2022.5-kml/bin 
 case_dir =
 
 [BUILD]
-cd ${JARVIS_TMP}
-rm -rf gromacs-2022.5
-tar -xf ${JARVIS_DOWNLOAD}/gromacs-2022.5.tar.gz
-cd gromacs-2022.5
 
-sed -i '204s/return fftw_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
-sed -i '206s/return fftwf_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
-sed -i '505s/int fftwflags = FFTW_DESTROY_INPUT;/int fftwflags = 0;/g' src/gromacs/fft/fft5d.cpp
 rm -rf build
 mkdir -p build
 cd build
-FLAGS="-mcpu=tsv110 -O3 -lgfortran"; CFLAGS=$FLAGS CXXFLAGS="-mcpu=tsv110 -O3 -lgfortran" CC=mpicc CXX=mpicxx FC=mpifort cmake -DCMAKE_INSTALL_PREFIX=$JARVIS_ROOT/gromacs-2022.5-kml -DBUILD_SHARED_LIBS=on -DBUILD_TESTING=on -DREGRESSIONTEST_DOWNLOAD=off -DGMX_BUILD_OWN_FFTW=off -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_DOUBLE=off -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DGMX_FFT_LIBRARY=fftw3 -DGMX_BLAS_USER=${KML_BISHENG_PATH}/lib/kblas/omp/libkblas.so -DGMX_LAPACK_USER=${KML_BISHENG_PATH}/lib/libklapack_full.so -DFFTWF_LIBRARY=${KML_BISHENG_PATH}/lib/libkfftf.so -DFFTWF_INCLUDE_DIR=${KML_BISHENG_PATH}/include -DGMX_GPU=off -DGMX_MPI=on -DGMX_OPENMP=on -DGMX_X11=off ../
 
-make -j40 V=1
+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
+
+FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang -fuse-ld=lld" CC=mpicc CXX=mpicxx \
+cmake \
+-DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/gromacs-2022.5-kml \
+-DBUILD_SHARED_LIBS=on \
+-DBUILD_TESTING=on \
+-DREGRESSIONTEST_DOWNLOAD=off \
+-DGMX_BUILD_OWN_FFTW=off \
+-DGMX_SIMD=ARM_NEON_ASIMD \
+-DGMX_DOUBLE=off \
+-DGMX_EXTERNAL_BLAS=on \
+-DGMX_EXTERNAL_LAPACK=on \
+-DGMX_FFT_LIBRARY=fftw3 \
+-DGMX_BLAS_USER=$openblas_path/lib/libopenblas.a \
+-DGMX_LAPACK_USER=$openblas_path/lib/libopenblas.a \
+-DFFTWF_LIBRARY=$fftw_path/lib/libfftw3f.so \
+-DFFTWF_INCLUDE_DIR=$fftw_path/include \
+-DGMX_GPU=off \
+-DGMX_MPI=on \
+-DGMX_OPENMP=on \
+-DGMX_X11=off \
+../
+
+make -j
 make install
 
+
 [CLEAN]
 ./clean_build
 
-- 
Gitee


From 6054ae0bbea3d2acb2d6579a0cf9a39a37f7f2b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Mon, 30 Jun 2025 12:01:10 +0800
Subject: [PATCH 6/9] gromacs

---
 .../2022.5/data.gromacs.arm.gpu.config        | 68 ++++++++++++-------
 1 file changed, 45 insertions(+), 23 deletions(-)

diff --git a/templates/gromacs/2022.5/data.gromacs.arm.gpu.config b/templates/gromacs/2022.5/data.gromacs.arm.gpu.config
index b27c28e..70afb09 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm.gpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm.gpu.config
@@ -2,58 +2,80 @@
 11.11.11.11
 
 [DOWNLOAD]
-gromacs/2022.3 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
+gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
 
 [DEPENDENCY]
 #set -e
 #set -x
 module purge
 module use ./software/modulefiles
-./jarvis -install bisheng/2.5.0 com
-module load bisheng/2.5.0
-./jarvis -install openblas/0.3.18 clang
-./jarvis -install hmpi/1.2.0 clang
-module load hmpi/1.2.0
+./jarvis -install bisheng/2.1.0 com
+module load bisheng/2.1.0
+export CC=clang CXX=clang++ FC=flang
+./jarvis -install openblas/0.3.18 bisheng
+module load openblas/0.3.18
+./jarvis -install hmpi/1.1.1 bisheng
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
 export CC=mpicc CXX=mpicxx FC=mpifort
 ./jarvis -install fftw/3.3.8 clang+mpi
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
+mkdir -p gromacs
 if [ ! -d gromacs-2022.5 ]; then
+ rm -rf gromacs-2022.5
  tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2022.5.tar.gz
 fi
 
 [ENV]
 module purge
 module use ./software/modulefiles
-module use ./software/moduledeps
-module load bisheng/2.5.0
-module load hmpi/1.2.0
-module load fftw/3.3.8
+module load bisheng/2.1.0
 module load openblas/0.3.18
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
 export CC=mpicc CXX=mpicxx FC=mpifort
-export GMX_FORCE_UPDATE_DEFAULT_GPU=true
-export GMX_GPU_PME_PP_COMMS=true
-export GMX_GPU_DD_COMMS=true
-export PATH=/usr/local/cuda/bin:$PATH
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
 
 [APP]
 app_name = gromacs
-build_dir = $JARVIS_ROOT/gromacs-2022.5
+build_dir = ${JARVIS_ROOT}/gromacs-2022.5
 binary_dir = 
-case_dir = $JARVIS_ROOT/workloads/gromacs/water-cut1.0_GMX50_bare/0768/
+case_dir = ${JARVIS_ROOT}/workloads/gromacs/water-cut1.0_GMX50_bare/0768/
 
 [BUILD]
-sed -i '204s/return fftw_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
-sed -i '206s/return fftwf_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
-sed -i '505s/int fftwflags = FFTW_DESTROY_INPUT;/int fftwflags = 0;/g' src/gromacs/fft/fft5d.cpp
 rm -rf build
 mkdir -p build
 cd build
-FLAGS="-mcpu=tsv110 -O3 -lgfortran"; CFLAGS=$FLAGS CXXFLAGS="-mcpu=tsv110 -O3 -lgfortran" CC=mpicc CXX=mpicxx FC=mpifort cmake -DCMAKE_INSTALL_PREFIX=$JARVIS_ROOT/gromacs-kml -DBUILD_SHARED_LIBS=on -DBUILD_TESTING=on -DREGRESSIONTEST_DOWNLOAD=off -DGMX_BUILD_OWN_FFTW=off -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_DOUBLE=off -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DGMX_FFT_LIBRARY=fftw3 -DGMX_BLAS_USER=${OPEBLAS_PATH}/lib/libopenblas.a -DGMX_LAPACK_USER=${OPEBLAS_PATH}/lib/libopenblas.a -DFFTWF_LIBRARY=$FFTW_PATH/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=$FFTW_PATH/include -DGMX_GPU=CUDA -DGMX_MPI=off -DGMX_OPENMP=on -DGMX_X11=off -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda ../
+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
+
+FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang -fuse-ld=lld" CC=mpicc CXX=mpicxx \
+cmake \
+-DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/gromacs \
+-DBUILD_SHARED_LIBS=on \
+-DBUILD_TESTING=on \
+-DREGRESSIONTEST_DOWNLOAD=off \
+-DGMX_BUILD_OWN_FFTW=off \
+-DGMX_SIMD=ARM_NEON_ASIMD \
+-DGMX_DOUBLE=off \
+-DGMX_EXTERNAL_BLAS=on \
+-DGMX_EXTERNAL_LAPACK=on \
+-DGMX_FFT_LIBRARY=fftw3 \
+-DGMX_BLAS_USER=$openblas_path/lib/libopenblas.a \
+-DGMX_LAPACK_USER=$openblas_path/lib/libopenblas.a \
+-DFFTWF_LIBRARY=$fftw_path/lib/libfftw3f.so \
+-DFFTWF_INCLUDE_DIR=$fftw_path/include \
+-DGMX_GPU=off \
+-DGMX_MPI=on \
+-DGMX_OPENMP=on \
+-DGMX_X11=off \
+../
 
-make -j40 V=1
+make -j
 make install
 
-#-DGMX_BLAS_USER=$openblas_path/lib/libopenblas.a #-DGMX_LAPACK_USER=$openblas_path/lib/libopenblas.a 
-#-DGMX_BLAS_USER=${KML_GCC_PATH}/lib/kblas/omp/libkblas.so -DGMX_LAPACK_USER=${KML_GCC_PATH}/lib/libklapack_full.so -DFFTWF_LIBRARY=$KFFT_PATH/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=$KFFT_PATH/include
 
 [CLEAN]
 ./clean_build
-- 
Gitee


From cbf1f5e788e40735af5f84d2bfd5bb70c8dc38bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Tue, 1 Jul 2025 10:43:26 +0800
Subject: [PATCH 7/9] data.gromacs.arm-sve.cpu.config

---
 .../2022.5/data.gromacs.arm-sve.cpu.config    | 83 ++++++++++++-------
 1 file changed, 52 insertions(+), 31 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 56c4899..35258f4 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
@@ -5,54 +5,75 @@
 gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
 
 [DEPENDENCY]
+#set -e
+#set -x
 module purge
-./jarvis -install bisheng/3.2.0-mini com
 module use ./software/modulefiles
-module load bisheng/3.2.0-mini
+./jarvis -install bisheng/2.1.0 com
+module load bisheng/2.1.0
 export CC=clang CXX=clang++ FC=flang
-./jarvis -install hmpi/2.3.0 clang
-module use ./software/moduledeps/bisheng3.2.0
-module load hmpi/2.3.0
-./jarvis -install kml/2.2.0/bisheng bisheng
-module load kml-bisheng/2.2.0
+./jarvis -install openblas/0.3.18 bisheng
+module load openblas/0.3.18
+./jarvis -install hmpi/1.1.1 bisheng
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
+export CC=mpicc CXX=mpicxx FC=mpifort
+./jarvis -install fftw/3.3.8 clang+mpi
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
+mkdir -p gromacs
+if [ ! -d gromacs-2022.5 ]; then
+ rm -rf gromacs-2022.5
+ tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2022.5.tar.gz
+fi
 
 [ENV]
 module purge
 module use ./software/modulefiles
-module purge
-module load bisheng/3.2.0-mini
-module use ./software/moduledeps/bisheng3.2.0
-module load kml-bisheng/2.2.0
-module load hmpi/2.3.0
+module load bisheng/2.1.0
+module load openblas/0.3.18
+module use software/moduledeps/bisheng2.1.0
+module load hmpi/1.1.1
 export CC=mpicc CXX=mpicxx FC=mpifort
-export PMIX_INSTALL_PREFIX=${OPAL_PREFIX}
-cd /hpcrunner
-CUR_PATH=$(pwd)
-export JARVIS_ROOT=${CUR_PATH}
-export JARVIS_TMP=${CUR_PATH}/tmp
-export PATH=${JARVIS_ROOT}/gromacs-2022.5-kml/bin:$PATH
+module use software/moduledeps/bisheng2.1.0-hmpi1.1.1
+module load fftw/3.3.8
 
 [APP]
 app_name = gromacs
-build_dir = $JARVIS_TMP/gromacs-2022.5
-binary_dir = $JARVIS_ROOT/gromacs-2022.5-kml/bin 
-case_dir =
+build_dir = ${JARVIS_ROOT}/gromacs-2022.5/
+binary_dir = 
+case_dir = ${JARVIS_ROOT}/workloads/gromacs/water-cut1.0_GMX50_bare/0768/
 
 [BUILD]
-cd ${JARVIS_TMP}
-rm -rf gromacs-2022.5
-tar -xf ${JARVIS_DOWNLOAD}/gromacs-2022.5.tar.gz
-cd gromacs-2022.5
-
-sed -i '204s/return fftw_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
-sed -i '206s/return fftwf_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp
-sed -i '505s/int fftwflags = FFTW_DESTROY_INPUT;/int fftwflags = 0;/g' src/gromacs/fft/fft5d.cpp
 rm -rf build
 mkdir -p build
 cd build
-FLAGS="-mcpu=linxicore9100 -mllvm -force-customized-pipeline=true -O3 -lgfortran"; CFLAGS=$FLAGS CXXFLAGS="-mcpu=linxicore9100 -mllvm -force-customized-pipeline=true -O3 -lgfortran" CC=mpicc CXX=mpicxx FC=mpifort cmake -DCMAKE_INSTALL_PREFIX=$JARVIS_ROOT/gromacs-2022.5-kml -DBUILD_SHARED_LIBS=on -DBUILD_TESTING=on -DREGRESSIONTEST_DOWNLOAD=off -DGMX_BUILD_OWN_FFTW=off -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_DOUBLE=off -DGMX_EXTERNAL_BLAS=on -DGMX_EXTERNAL_LAPACK=on -DGMX_FFT_LIBRARY=fftw3 -DGMX_BLAS_USER=${KML_BISHENG_PATH}/lib/kblas/omp/libkblas.so -DGMX_LAPACK_USER=${KML_BISHENG_PATH}/lib/libklapack_full.so -DFFTWF_LIBRARY=${KML_BISHENG_PATH}/lib/libkfftf.so -DFFTWF_INCLUDE_DIR=${KML_BISHENG_PATH}/include -DGMX_GPU=off -DGMX_MPI=on -DGMX_OPENMP=on -DGMX_X11=off ../
+openblas_path=$JARVIS_LIBS/bisheng2.1.0/openblas/0.3.18
+fftw_path=$JARVIS_LIBS/bisheng2.1.0/hmpi1.1.1/fftw/3.3.8
+
+FLAGS="-mcpu=tsv110"; CFLAGS=$FLAGS CXXFLAGS=$FLAGS LDFLAGS="-lflang -fuse-ld=lld" CC=mpicc CXX=mpicxx \
+cmake \
+-DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/gromacs \
+-DBUILD_SHARED_LIBS=on \
+-DBUILD_TESTING=on \
+-DREGRESSIONTEST_DOWNLOAD=off \
+-DGMX_BUILD_OWN_FFTW=off \
+-DGMX_SIMD=ARM_NEON_ASIMD \
+-DGMX_DOUBLE=off \
+-DGMX_EXTERNAL_BLAS=on \
+-DGMX_EXTERNAL_LAPACK=on \
+-DGMX_FFT_LIBRARY=fftw3 \
+-DGMX_BLAS_USER=$openblas_path/lib/libopenblas.a \
+-DGMX_LAPACK_USER=$openblas_path/lib/libopenblas.a \
+-DFFTWF_LIBRARY=$fftw_path/lib/libfftw3f.so \
+-DFFTWF_INCLUDE_DIR=$fftw_path/include \
+-DGMX_GPU=off \
+-DGMX_MPI=on \
+-DGMX_OPENMP=on \
+-DGMX_X11=off \
+../
 
-make -j40 V=1
+make -j
 make install
 
 [CLEAN]
-- 
Gitee


From 7088e3c49d4c38f533a5cdb159d80501f96b79a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Tue, 1 Jul 2025 10:57:23 +0800
Subject: [PATCH 8/9] data.gromacs.arm-sve.cpu.config

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

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 35258f4..8024d8b 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm-sve.cpu.config
@@ -7,6 +7,7 @@ gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
 [DEPENDENCY]
 #set -e
 #set -x
+yum install -y cmake make
 module purge
 module use ./software/modulefiles
 ./jarvis -install bisheng/2.1.0 com
-- 
Gitee


From 3c7567cb61b3fe84010bef676c6af90de98708a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?=
 <12963281+gao-wenyao123@user.noreply.gitee.com>
Date: Tue, 1 Jul 2025 10:58:43 +0800
Subject: [PATCH 9/9] data.gromacs.arm.gpu.config

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

diff --git a/templates/gromacs/2022.5/data.gromacs.arm.gpu.config b/templates/gromacs/2022.5/data.gromacs.arm.gpu.config
index 70afb09..e40fc62 100644
--- a/templates/gromacs/2022.5/data.gromacs.arm.gpu.config
+++ b/templates/gromacs/2022.5/data.gromacs.arm.gpu.config
@@ -7,6 +7,7 @@ gromacs/2022.5 http://ftp.gromacs.org/pub/gromacs/gromacs-2022.5.tar.gz
 [DEPENDENCY]
 #set -e
 #set -x
+yum install -y cmake make
 module purge
 module use ./software/modulefiles
 ./jarvis -install bisheng/2.1.0 com
-- 
Gitee