From 3a2bb5997ace85b87966bd9ec17b7cc50e503936 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Tue, 13 May 2025 16:42:23 +0800
Subject: [PATCH 01/12] hmmer

---
 .../3.3.2/hmmer.arm.cpu.bisheng.hmpi.config   | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config

diff --git a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
new file mode 100644
index 0000000..971b6f5
--- /dev/null
+++ b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
@@ -0,0 +1,67 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+hmmer/3.3.2 $JARVIS_PROXY/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
+master $JARVIS_PROXY/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
+
+[DEPENDENCY]
+set -e
+set -x
+module purge
+./jarvis -install bisheng/4.1.0 com
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+./jarvis -install hmpi/2.4.2 clang
+module use ./software/moduledeps/bisheng4.1.0
+module load hmpi/2.4.2
+yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget
+mkdir -p hmmer
+unzip ${JARVIS_DOWNLOAD}/hmmer-h3-arm.zip
+mv hmmer-h3-arm/ hmmer-3.3.2/
+cd hmmer-3.3.2/
+#wget https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip
+unzip ${JARVIS_DOWNLOAD}/master.zip
+mv easel-master/ easel/
+cd ..
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+module use ./software/moduledeps/bisheng4.1.0
+module load hmpi/2.4.2
+
+[APP]
+app_name = diamond
+build_dir = ${JARVIS_ROOT}/hmmer-3.3.2/
+binary_dir = ${JARVIS_ROOT}/hmmer/bin/
+case_dir = ${JARVIS_ROOT}/hmmer-3.3.2/tutorial/
+
+[BUILD]
+autoconf
+./configure --prefix=${JARVIS_ROOT}/hmmer --enable-mpi --enable-neon CC=$MPICC CXX=$MPICXX FC=$MPIFC F77=$MPIFC
+make -j
+make check
+make -j install
+cd easel/
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run =
+binary = hmmbuild globins4.hmm globins4.sto
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From e399352ea6974d4d8c32b6676c6dd23966b1a414 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Tue, 13 May 2025 17:31:23 +0800
Subject: [PATCH 02/12] hmmer

---
 templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
index 971b6f5..52510f1 100644
--- a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
+++ b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
@@ -2,8 +2,8 @@
 11.11.11.11
 
 [DOWNLOAD]
-hmmer/3.3.2 $JARVIS_PROXY/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
-master $JARVIS_PROXY/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
+hmmer/3.3.2 https://github.com/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
+master https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
 
 [DEPENDENCY]
 set -e
@@ -18,7 +18,7 @@ export FC=`which flang`
 ./jarvis -install hmpi/2.4.2 clang
 module use ./software/moduledeps/bisheng4.1.0
 module load hmpi/2.4.2
-yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget
+yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget cmake make
 mkdir -p hmmer
 unzip ${JARVIS_DOWNLOAD}/hmmer-h3-arm.zip
 mv hmmer-h3-arm/ hmmer-3.3.2/
-- 
Gitee


From aa9ca959489e3f5881a3680f70e6d19810c03efc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Tue, 13 May 2025 20:06:26 +0800
Subject: [PATCH 03/12] minighost

---
 ...data.minighost.arm.cpu.bisheng.hmpi.config | 84 +++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
new file mode 100644
index 0000000..3e20793
--- /dev/null
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -0,0 +1,84 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+miniGhost/v1.0 https://github.com/Mantevo/miniGhost/archive/refs/heads/master.zip miniGhost-master.zip
+
+[DEPENDENCY]
+set -e
+set -x
+
+./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
+unzip ${JARVIS_DOWNLOAD}/miniGhost-master.zip
+cd ./miniGhost-master/ref
+mv Makefile Makefile.bak
+cp makefile.mpi.gnu Makefile
+sed -i '$d' Makefile
+
+echo '
+
+PROTOCOL = -D_MG_MPI
+MPI_LOC = ${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/bisheng/hmpi
+MPI_INCLUDE = -I$(MPI_LOC)/include
+# State precision: -D_REAL4 and/or -D_REAL8.
+REAL_PRECISION = -D_MG_REAL8
+# Integer precision: -D_INT4 and/or -D_INT8.
+INT_PRECISION = -D_MG_INT4
+# Compilers
+FC=$(MPI_LOC)/bin/mpif90
+CC=$(MPI_LOC)/bin/mpicc
+CFLAGS = $(PROTOCOL) $(REAL_PRECISION) $(INT_PRECISION)
+# C main calling Fortran subroutine:
+CFLAGS += -Df2c_ -fsigned-char
+CFLAGS += $(MPI_INCLUDE)
+FFLAGS = $(PROTOCOL) $(REAL_PRECISION) $(INT_PRECISION) -fallow-argument-mismatch
+# Optimization
+OPT_F =-O3
+FFLAGS += $(OPT_F)
+#FFLAGS += $(MPI_INCLUDE)
+# Free-form Fortran source code:
+FFLAGS += -ffree-form -ffree-line-length-none
+# Array bounds checking: (expensive!)
+#FFLAGS += -fbounds-check
+# Compile to include checkpointing capability.
+FFLAGS += -D_MG_CHECKPT
+NCPATH=
+LNCDF=-L$(NCPATH)/lib
+LD=$(FC)
+LDFLAGS=$(CFLAGS) $(FFLAGS) -L/${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/bisheng/hmpi -lmpi_mpifh
+#LDFLAGS=$(CFLAGS) $(FFLAGS)
+#LDFLAGS=$(FFLAGS)
+LIBS=
+include make_targets
+
+' >> Makefile
+
+[ENV]
+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
+
+[APP]
+app_name = miniGhost
+build_dir = ${JARVIS_ROOT}/miniGhost-master/ref
+binary_dir = ${JARVIS_ROOT}/miniGhost-master/ref
+case_dir = ${JARVIS_ROOT}/miniGhost-master/ref
+
+[BUILD]
+make
+
+[CLEAN]
+make clean
+
+[RUN]
+run = 
+binary = 
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From de0a4946cff24260173d3e631ae6aa2b36bfff55 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Wed, 14 May 2025 15:00:42 +0800
Subject: [PATCH 04/12] minighost

---
 .../1.0/data.minighost.arm.cpu.bisheng.hmpi.config   | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
index 3e20793..fed3fe6 100644
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -11,17 +11,17 @@ set -x
 ./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
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
 unzip ${JARVIS_DOWNLOAD}/miniGhost-master.zip
 cd ./miniGhost-master/ref
 mv Makefile Makefile.bak
 cp makefile.mpi.gnu Makefile
 sed -i '$d' Makefile
 
-echo '
+echo "
 
 PROTOCOL = -D_MG_MPI
-MPI_LOC = ${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/bisheng/hmpi
+MPI_LOC = ${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi
 MPI_INCLUDE = -I$(MPI_LOC)/include
 # State precision: -D_REAL4 and/or -D_REAL8.
 REAL_PRECISION = -D_MG_REAL8
@@ -48,13 +48,13 @@ FFLAGS += -D_MG_CHECKPT
 NCPATH=
 LNCDF=-L$(NCPATH)/lib
 LD=$(FC)
-LDFLAGS=$(CFLAGS) $(FFLAGS) -L/${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/bisheng/hmpi -lmpi_mpifh
+LDFLAGS=$(CFLAGS) $(FFLAGS) -L/${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
 #LDFLAGS=$(CFLAGS) $(FFLAGS)
 #LDFLAGS=$(FFLAGS)
 LIBS=
 include make_targets
 
-' >> Makefile
+" >> Makefile
 
 [ENV]
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
@@ -74,7 +74,7 @@ make
 make clean
 
 [RUN]
-run = 
+run = mpirun -mca btl ^openib -x LD_LIBRARY_PATH --allow-run-as-root -np 96 ./miniGhost.x
 binary = 
 nodes = 1
 
-- 
Gitee


From 44a1126ec2c9b81bb5c48b4a252bfc06f3567ef4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Wed, 14 May 2025 15:15:33 +0800
Subject: [PATCH 05/12] minighost

---
 .../minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
index fed3fe6..356d52e 100644
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -59,7 +59,7 @@ include make_targets
 [ENV]
 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
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
 
 [APP]
 app_name = miniGhost
-- 
Gitee


From fdfe0b8e6a037a813aa3b922f28d98be82b459b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Wed, 14 May 2025 15:38:47 +0800
Subject: [PATCH 06/12] minighost

---
 .../minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
index 356d52e..18d6296 100644
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -48,7 +48,7 @@ FFLAGS += -D_MG_CHECKPT
 NCPATH=
 LNCDF=-L$(NCPATH)/lib
 LD=$(FC)
-LDFLAGS=$(CFLAGS) $(FFLAGS) -L/${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
+LDFLAGS=$(CFLAGS) $(FFLAGS) -L${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
 #LDFLAGS=$(CFLAGS) $(FFLAGS)
 #LDFLAGS=$(FFLAGS)
 LIBS=
-- 
Gitee


From a9099baaeb96a0eb90e264f97926aca70c8145d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Wed, 14 May 2025 15:52:31 +0800
Subject: [PATCH 07/12] minighost

---
 .../minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
index 18d6296..10656ff 100644
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -16,7 +16,7 @@ unzip ${JARVIS_DOWNLOAD}/miniGhost-master.zip
 cd ./miniGhost-master/ref
 mv Makefile Makefile.bak
 cp makefile.mpi.gnu Makefile
-sed -i '$d' Makefile
+sed -i '36,$d' Makefile
 
 echo "
 
-- 
Gitee


From 3a00095bb95f64f8f726e53eb5239ec32df886e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Wed, 14 May 2025 16:20:32 +0800
Subject: [PATCH 08/12] minighost

---
 .../1.0/data.minighost.arm.cpu.bisheng.hmpi.config        | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
index 10656ff..106ce0c 100644
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -18,10 +18,10 @@ mv Makefile Makefile.bak
 cp makefile.mpi.gnu Makefile
 sed -i '36,$d' Makefile
 
-echo "
+echo ' 
 
 PROTOCOL = -D_MG_MPI
-MPI_LOC = ${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi
+MPI_LOC = '"${JARVIS_ROOT}"'/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi
 MPI_INCLUDE = -I$(MPI_LOC)/include
 # State precision: -D_REAL4 and/or -D_REAL8.
 REAL_PRECISION = -D_MG_REAL8
@@ -48,13 +48,13 @@ FFLAGS += -D_MG_CHECKPT
 NCPATH=
 LNCDF=-L$(NCPATH)/lib
 LD=$(FC)
-LDFLAGS=$(CFLAGS) $(FFLAGS) -L${JARVIS_ROOT}/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
+LDFLAGS=$(CFLAGS) $(FFLAGS) -L'"${JARVIS_ROOT}"'/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
 #LDFLAGS=$(CFLAGS) $(FFLAGS)
 #LDFLAGS=$(FFLAGS)
 LIBS=
 include make_targets
 
-" >> Makefile
+' >> Makefile
 
 [ENV]
 module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
-- 
Gitee


From c13919fcad02838488a84fb764951d9ee7489c50 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 10:25:03 +0800
Subject: [PATCH 09/12] minighost

---
 .../minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
index 106ce0c..d7d9858 100644
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
@@ -74,7 +74,7 @@ make
 make clean
 
 [RUN]
-run = mpirun -mca btl ^openib -x LD_LIBRARY_PATH --allow-run-as-root -np 96 ./miniGhost.x
+run = mpirun -mca btl ^openib -x LD_LIBRARY_PATH --allow-run-as-root -np 8 ./miniGhost.x
 binary = 
 nodes = 1
 
-- 
Gitee


From a713cc01324679b255aadf43830ced102c3176bc 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 10:32:09 +0800
Subject: [PATCH 10/12] minighost

---
 .../data.minighost.arm.cpu.gcc.hmpi.config    | 84 +++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 templates/minighost/1.0/data.minighost.arm.cpu.gcc.hmpi.config

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.gcc.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.gcc.hmpi.config
new file mode 100644
index 0000000..d7d9858
--- /dev/null
+++ b/templates/minighost/1.0/data.minighost.arm.cpu.gcc.hmpi.config
@@ -0,0 +1,84 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+miniGhost/v1.0 https://github.com/Mantevo/miniGhost/archive/refs/heads/master.zip miniGhost-master.zip
+
+[DEPENDENCY]
+set -e
+set -x
+
+./jarvis -install hpckit/2024.12.30 any
+module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
+module purge
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
+unzip ${JARVIS_DOWNLOAD}/miniGhost-master.zip
+cd ./miniGhost-master/ref
+mv Makefile Makefile.bak
+cp makefile.mpi.gnu Makefile
+sed -i '36,$d' Makefile
+
+echo ' 
+
+PROTOCOL = -D_MG_MPI
+MPI_LOC = '"${JARVIS_ROOT}"'/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi
+MPI_INCLUDE = -I$(MPI_LOC)/include
+# State precision: -D_REAL4 and/or -D_REAL8.
+REAL_PRECISION = -D_MG_REAL8
+# Integer precision: -D_INT4 and/or -D_INT8.
+INT_PRECISION = -D_MG_INT4
+# Compilers
+FC=$(MPI_LOC)/bin/mpif90
+CC=$(MPI_LOC)/bin/mpicc
+CFLAGS = $(PROTOCOL) $(REAL_PRECISION) $(INT_PRECISION)
+# C main calling Fortran subroutine:
+CFLAGS += -Df2c_ -fsigned-char
+CFLAGS += $(MPI_INCLUDE)
+FFLAGS = $(PROTOCOL) $(REAL_PRECISION) $(INT_PRECISION) -fallow-argument-mismatch
+# Optimization
+OPT_F =-O3
+FFLAGS += $(OPT_F)
+#FFLAGS += $(MPI_INCLUDE)
+# Free-form Fortran source code:
+FFLAGS += -ffree-form -ffree-line-length-none
+# Array bounds checking: (expensive!)
+#FFLAGS += -fbounds-check
+# Compile to include checkpointing capability.
+FFLAGS += -D_MG_CHECKPT
+NCPATH=
+LNCDF=-L$(NCPATH)/lib
+LD=$(FC)
+LDFLAGS=$(CFLAGS) $(FFLAGS) -L'"${JARVIS_ROOT}"'/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
+#LDFLAGS=$(CFLAGS) $(FFLAGS)
+#LDFLAGS=$(FFLAGS)
+LIBS=
+include make_targets
+
+' >> Makefile
+
+[ENV]
+module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
+module purge
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
+
+[APP]
+app_name = miniGhost
+build_dir = ${JARVIS_ROOT}/miniGhost-master/ref
+binary_dir = ${JARVIS_ROOT}/miniGhost-master/ref
+case_dir = ${JARVIS_ROOT}/miniGhost-master/ref
+
+[BUILD]
+make
+
+[CLEAN]
+make clean
+
+[RUN]
+run = mpirun -mca btl ^openib -x LD_LIBRARY_PATH --allow-run-as-root -np 8 ./miniGhost.x
+binary = 
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From 33c4c8dd1ce5fb9852da7ea9604784b194de9282 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 10:34:03 +0800
Subject: [PATCH 11/12] minighost

---
 ...data.minighost.arm.cpu.bisheng.hmpi.config | 84 -------------------
 1 file changed, 84 deletions(-)
 delete mode 100644 templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config

diff --git a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config b/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
deleted file mode 100644
index d7d9858..0000000
--- a/templates/minighost/1.0/data.minighost.arm.cpu.bisheng.hmpi.config
+++ /dev/null
@@ -1,84 +0,0 @@
-[SERVER]
-11.11.11.11
-
-[DOWNLOAD]
-miniGhost/v1.0 https://github.com/Mantevo/miniGhost/archive/refs/heads/master.zip miniGhost-master.zip
-
-[DEPENDENCY]
-set -e
-set -x
-
-./jarvis -install hpckit/2024.12.30 any
-module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
-module purge
-module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
-unzip ${JARVIS_DOWNLOAD}/miniGhost-master.zip
-cd ./miniGhost-master/ref
-mv Makefile Makefile.bak
-cp makefile.mpi.gnu Makefile
-sed -i '36,$d' Makefile
-
-echo ' 
-
-PROTOCOL = -D_MG_MPI
-MPI_LOC = '"${JARVIS_ROOT}"'/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi
-MPI_INCLUDE = -I$(MPI_LOC)/include
-# State precision: -D_REAL4 and/or -D_REAL8.
-REAL_PRECISION = -D_MG_REAL8
-# Integer precision: -D_INT4 and/or -D_INT8.
-INT_PRECISION = -D_MG_INT4
-# Compilers
-FC=$(MPI_LOC)/bin/mpif90
-CC=$(MPI_LOC)/bin/mpicc
-CFLAGS = $(PROTOCOL) $(REAL_PRECISION) $(INT_PRECISION)
-# C main calling Fortran subroutine:
-CFLAGS += -Df2c_ -fsigned-char
-CFLAGS += $(MPI_INCLUDE)
-FFLAGS = $(PROTOCOL) $(REAL_PRECISION) $(INT_PRECISION) -fallow-argument-mismatch
-# Optimization
-OPT_F =-O3
-FFLAGS += $(OPT_F)
-#FFLAGS += $(MPI_INCLUDE)
-# Free-form Fortran source code:
-FFLAGS += -ffree-form -ffree-line-length-none
-# Array bounds checking: (expensive!)
-#FFLAGS += -fbounds-check
-# Compile to include checkpointing capability.
-FFLAGS += -D_MG_CHECKPT
-NCPATH=
-LNCDF=-L$(NCPATH)/lib
-LD=$(FC)
-LDFLAGS=$(CFLAGS) $(FFLAGS) -L'"${JARVIS_ROOT}"'/software/utils/hpckit/2024.12.30/HPCKit/24.12.30/hmpi/gcc/hmpi -lmpi_mpifh
-#LDFLAGS=$(CFLAGS) $(FFLAGS)
-#LDFLAGS=$(FFLAGS)
-LIBS=
-include make_targets
-
-' >> Makefile
-
-[ENV]
-module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
-module purge
-module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
-
-[APP]
-app_name = miniGhost
-build_dir = ${JARVIS_ROOT}/miniGhost-master/ref
-binary_dir = ${JARVIS_ROOT}/miniGhost-master/ref
-case_dir = ${JARVIS_ROOT}/miniGhost-master/ref
-
-[BUILD]
-make
-
-[CLEAN]
-make clean
-
-[RUN]
-run = mpirun -mca btl ^openib -x LD_LIBRARY_PATH --allow-run-as-root -np 8 ./miniGhost.x
-binary = 
-nodes = 1
-
-[PERF]
-perf= 
-nsys=
-ncu=--target-processes all
-- 
Gitee


From 643d7376d4da7c32eb43ba36fcf64f5f31a1f626 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 10:35:15 +0800
Subject: [PATCH 12/12] hmmer

---
 .../3.3.2/hmmer.arm.cpu.bisheng.hmpi.config   | 67 -------------------
 1 file changed, 67 deletions(-)
 delete mode 100644 templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config

diff --git a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
deleted file mode 100644
index 52510f1..0000000
--- a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
+++ /dev/null
@@ -1,67 +0,0 @@
-[SERVER]
-11.11.11.11
-
-[DOWNLOAD]
-hmmer/3.3.2 https://github.com/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
-master https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
-
-[DEPENDENCY]
-set -e
-set -x
-module purge
-./jarvis -install bisheng/4.1.0 com
-module use ./software/modulefiles
-module load bisheng/4.1.0
-export CC=`which clang`
-export CXX=`which clang++`
-export FC=`which flang`
-./jarvis -install hmpi/2.4.2 clang
-module use ./software/moduledeps/bisheng4.1.0
-module load hmpi/2.4.2
-yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget cmake make
-mkdir -p hmmer
-unzip ${JARVIS_DOWNLOAD}/hmmer-h3-arm.zip
-mv hmmer-h3-arm/ hmmer-3.3.2/
-cd hmmer-3.3.2/
-#wget https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip
-unzip ${JARVIS_DOWNLOAD}/master.zip
-mv easel-master/ easel/
-cd ..
-
-[ENV]
-module purge
-module use ./software/modulefiles
-module load bisheng/4.1.0
-export CC=`which clang`
-export CXX=`which clang++`
-export FC=`which flang`
-module use ./software/moduledeps/bisheng4.1.0
-module load hmpi/2.4.2
-
-[APP]
-app_name = diamond
-build_dir = ${JARVIS_ROOT}/hmmer-3.3.2/
-binary_dir = ${JARVIS_ROOT}/hmmer/bin/
-case_dir = ${JARVIS_ROOT}/hmmer-3.3.2/tutorial/
-
-[BUILD]
-autoconf
-./configure --prefix=${JARVIS_ROOT}/hmmer --enable-mpi --enable-neon CC=$MPICC CXX=$MPICXX FC=$MPIFC F77=$MPIFC
-make -j
-make check
-make -j install
-cd easel/
-make install
-
-[CLEAN]
-make clean
-
-[RUN]
-run =
-binary = hmmbuild globins4.hmm globins4.sto
-nodes = 1
-
-[PERF]
-perf= 
-nsys=
-ncu=--target-processes all
-- 
Gitee