From 1f8c20b338e73449feb09a485a30a3fc6112bd69 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 12:02:04 +0800 Subject: [PATCH 1/4] mrbayes --- .../3.2.7a/mrbayes.arm.cpu.kgcc.config | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config diff --git a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config new file mode 100644 index 0000000..68ef22c --- /dev/null +++ b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config @@ -0,0 +1,47 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] + +[DEPENDENCY] +set -e +set -x +module purge +./jarvis -install kgcc/10.3.1 com +module use software/modulefiles +module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +git clone --depth=1 https://github.com/NBISweden/MrBayes.git +mkdir -p mybayes + + +[ENV] +module purge +module use software/modulefiles +module load kgcc/10.3.1 + +[APP] +app_name = diamond +build_dir = ${JARVIS_ROOT}/MrBayes/ +binary_dir = ${JARVIS_ROOT}/mybayes/bin/ +case_dir = ${JARVIS_ROOT}/mybayes/bin/ + +[BUILD] +./configure --prefix=${JARVIS_ROOT}/mybayes +make +make install + +[CLEAN] +make clean + +[RUN] +run = +binary = mb +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all -- Gitee From 013de6d50d342a2501ead1d24eb87ac4c18e45f4 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 16:40:38 +0800 Subject: [PATCH 2/4] mrbayes --- templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config index 68ef22c..9b8809c 100644 --- a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config +++ b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config @@ -2,6 +2,7 @@ 11.11.11.11 [DOWNLOAD] +mybayes/3.2.7a https://github.com/NBISweden/MrBayes/archive/refs/heads/develop.zip [DEPENDENCY] set -e @@ -13,9 +14,8 @@ module load kgcc/10.3.1 export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` -git clone --depth=1 https://github.com/NBISweden/MrBayes.git mkdir -p mybayes - +unzip ${JARVIS_DOWNLOAD}/develop.zip [ENV] module purge @@ -24,7 +24,7 @@ module load kgcc/10.3.1 [APP] app_name = diamond -build_dir = ${JARVIS_ROOT}/MrBayes/ +build_dir = ${JARVIS_ROOT}/MrBayes-develop/ binary_dir = ${JARVIS_ROOT}/mybayes/bin/ case_dir = ${JARVIS_ROOT}/mybayes/bin/ @@ -42,6 +42,7 @@ binary = mb nodes = 1 [PERF] -perf= +perf= nsys= ncu=--target-processes all + -- Gitee From 28c99b269e7a7f72f2e64d6592579e9e43c96ee9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com> Date: Thu, 12 Jun 2025 17:37:55 +0800 Subject: [PATCH 3/4] mrbayes --- templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config index 9b8809c..d1b6768 100644 --- a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config +++ b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config @@ -2,7 +2,7 @@ 11.11.11.11 [DOWNLOAD] -mybayes/3.2.7a https://github.com/NBISweden/MrBayes/archive/refs/heads/develop.zip +mybayes/3.2.7 https://github.com/NBISweden/MrBayes/archive/refs/heads/develop.zip [DEPENDENCY] set -e @@ -23,7 +23,7 @@ module use software/modulefiles module load kgcc/10.3.1 [APP] -app_name = diamond +app_name = mybayes build_dir = ${JARVIS_ROOT}/MrBayes-develop/ binary_dir = ${JARVIS_ROOT}/mybayes/bin/ case_dir = ${JARVIS_ROOT}/mybayes/bin/ -- Gitee From 4312c71d7f338f78d538ef9c7baaf63e1f386082 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, 13 Jun 2025 10:48:35 +0800 Subject: [PATCH 4/4] mrbayes --- .../mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config index d1b6768..020178f 100644 --- a/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config +++ b/templates/mrbayes/3.2.7a/mrbayes.arm.cpu.kgcc.config @@ -2,11 +2,12 @@ 11.11.11.11 [DOWNLOAD] -mybayes/3.2.7 https://github.com/NBISweden/MrBayes/archive/refs/heads/develop.zip +mybayes/3.2.7 https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz develop.zip [DEPENDENCY] set -e set -x +yum install readline-devel make cmake -y module purge ./jarvis -install kgcc/10.3.1 com module use software/modulefiles @@ -15,21 +16,25 @@ export CC=`which gcc` export CXX=`which g++` export FC=`which gfortran` mkdir -p mybayes -unzip ${JARVIS_DOWNLOAD}/develop.zip +tar -vzxf ${JARVIS_DOWNLOAD}/develop.zip [ENV] module purge module use software/modulefiles module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` [APP] -app_name = mybayes -build_dir = ${JARVIS_ROOT}/MrBayes-develop/ +app_name = mybayes +build_dir = ${JARVIS_ROOT}/mrbayes-3.2.7/ binary_dir = ${JARVIS_ROOT}/mybayes/bin/ case_dir = ${JARVIS_ROOT}/mybayes/bin/ [BUILD] -./configure --prefix=${JARVIS_ROOT}/mybayes +sed -i '43i#include \n#include ' ./src/bayes.c +./configure --prefix=${JARVIS_ROOT}/mybayes --with-readline make make install @@ -45,4 +50,3 @@ nodes = 1 perf= nsys= ncu=--target-processes all - -- Gitee