diff --git "a/doc/bowtie2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204bowtie2\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/bowtie2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204bowtie2\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 6fa3ecebcb2582f330f6c3f684932931379db529..da7c0c0d6be1e74eaa50a6a62593ca8263de6d26 100644 --- "a/doc/bowtie2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204bowtie2\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/bowtie2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204bowtie2\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -8,7 +8,7 @@ - 官网地址：http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml -- GITHUB托管地址：$JARVIS_PROXY/BenLangmead/bowtie2 +- GITHUB托管地址：https://github.com/BenLangmead/bowtie2 - 特征： @@ -35,7 +35,7 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | +| CMake | 3.23.1 | | ### 3.2.创建文件夹 @@ -88,7 +88,7 @@ export CXX=`which g++` ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc ``` @@ -100,7 +100,7 @@ echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.ba 获取bowtie2软件源码并解压文件 ```bash # 下载源码文件 -wget $JARVIS_PROXY/BenLangmead/bowtie2/archive/refs/tags/v2.4.5.tar.gz +wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.4.5.tar.gz # 解压源码文件 tar -xvf $DEP_DOWNLOAD_DIR/v2.4.5.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/bowtie2-2.4.5 @@ -230,7 +230,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/duns/\343\200\212\345\237\272\344\272\216openEuler\347\232\204duns\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/duns/\343\200\212\345\237\272\344\272\216openEuler\347\232\204duns\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 501fbc232370f6a4ea131e388434ee2d754c455c..1fe257b75ac30641cd7a816d28301e4e533565e0 100644 --- "a/doc/duns/\343\200\212\345\237\272\344\272\216openEuler\347\232\204duns\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/duns/\343\200\212\345\237\272\344\272\216openEuler\347\232\204duns\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -229,7 +229,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/imb/2021.3/\343\200\212\345\237\272\344\272\216openEuler\347\232\204imb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/imb/2021.3/\343\200\212\345\237\272\344\272\216openEuler\347\232\204imb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index b8370613a52ecb545397e500f7b121060569fb59..4111e31ad190c1d9417f675bb7fb969a4fe7347a 100644 --- "a/doc/imb/2021.3/\343\200\212\345\237\272\344\272\216openEuler\347\232\204imb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/imb/2021.3/\343\200\212\345\237\272\344\272\216openEuler\347\232\204imb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -8,7 +8,7 @@ - 官网地址： -- GITHUB托管地址：<$JARVIS_PROXY/intel/mpi-benchmarks.git> +- GITHUB托管地址： ## 2.环境要求 @@ -28,7 +28,7 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.1.1 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip> | +| hmpi | 1.1.1 | | | gcc | 9.3.0 | | ### 3.2.创建文件夹 @@ -84,9 +84,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip @@ -124,7 +124,7 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载源码文件 -wget $JARVIS_PROXY/intel/mpi-benchmarks/archive/refs/tags/IMB-v2021.3.tar.gz -O $DEP_DOWNLOAD_DIR/IMB-v2021.3.tar.gz +wget https://github.com/intel/mpi-benchmarks/archive/refs/tags/IMB-v2021.3.tar.gz -O $DEP_DOWNLOAD_DIR/IMB-v2021.3.tar.gz # 解压源码文件 tar -xvf $DEP_DOWNLOAD_DIR/IMB-v2021.3.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/IMB-v2021.3 @@ -256,7 +256,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/mfem/4.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mfem\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/mfem/4.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mfem\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index b5069e39681ccf08fd689f6e3cf56b6c5908d9c5..f397a1eeff1fa43e5222908c04bbf6abd139a610 100644 --- "a/doc/mfem/4.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mfem\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/mfem/4.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mfem\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -8,7 +8,7 @@ - 官网地址：https://mfem.org/ -- GITHUB托管地址：$JARVIS_PROXY/mfem/mfem +- GITHUB托管地址：https://github.com/mfem/mfem - 特性： @@ -38,8 +38,8 @@ | 名称 | 版本 | 软件下载地址 | | ------- | ------ | ------------------------------------------------------------ | -| hmpi | 1.1.1 | $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip | -| hypre | 2.25.0 | $JARVIS_PROXY/hypre-space/hypre/archive/refs/tags/v2.25.0.tar.gz | +| hmpi | 1.1.1 | https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip | +| hypre | 2.25.0 | https://github.com/hypre-space/hypre/archive/refs/tags/v2.25.0.tar.gz | | metis | 4.0.3 | http://coin-or-tools.github.io/ThirdParty-Metis/metis-4.0.3.tar.gz | | bisheng | 2.1.0 | https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz | @@ -94,9 +94,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip @@ -129,7 +129,7 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载并编译hypre -wget $JARVIS_PROXY/hypre-space/hypre/archive/refs/tags/v2.25.0.tar.gz -O $DEP_DOWNLOAD_DIR/hypre-2.25.0.tar.gz +wget https://github.com/hypre-space/hypre/archive/refs/tags/v2.25.0.tar.gz -O $DEP_DOWNLOAD_DIR/hypre-2.25.0.tar.gz tar -xf $DEP_DOWNLOAD_DIR/hypre-2.25.0.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/hypre-2.25.0/src ./configure --disable-fortran @@ -157,7 +157,7 @@ ln -sf metis-4.0.3 metis-4.0 # 下载源码文件 cd /root/build -wget $JARVIS_PROXY/mfem/mfem/archive/refs/tags/v4.4.tar.gz -O $DEP_DOWNLOAD_DIR/mfem-4.4.tar.gz +wget https://github.com/mfem/mfem/archive/refs/tags/v4.4.tar.gz -O $DEP_DOWNLOAD_DIR/mfem-4.4.tar.gz # 解压源码文件 tar -xf $DEP_DOWNLOAD_DIR/mfem-4.4.tar.gz -C $DEP_BUILD_DIR # 修改测试代码，适配openeuler本地环境 @@ -287,7 +287,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/mumps/5.1.2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mumps\350\275\257\344\273\266\346\265\213\350\257\225\346\212\245\345\221\212\343\200\213.md" "b/doc/mumps/5.1.2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mumps\350\275\257\344\273\266\346\265\213\350\257\225\346\212\245\345\221\212\343\200\213.md" new file mode 100644 index 0000000000000000000000000000000000000000..d030c0920e1db4f144b3f96afdaa527093db9bbb --- /dev/null +++ "b/doc/mumps/5.1.2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mumps\350\275\257\344\273\266\346\265\213\350\257\225\346\212\245\345\221\212\343\200\213.md" @@ -0,0 +1,845 @@ +# 《基于openEuler的mumps软件测试报告》 + +## 1. 规范性自检 + +对项目使用fprettify对文件进行格式化 + +fprettify是一个现代Fortran代码的自动格式化程序，它采用严格的空白格式，用Python编写。 + +对于当前项目，检查代码规范性，可以通过使用fprettify对所有源码进行重新格式化，然后使用git工具查看文件修改。 + +### 1.1 选择统计文件类型 + +统计项目文件类型及其文件数量，通过Python脚本自动进行统计并进行排序： + +```python +# -*- coding: utf-8 -*- + +import os + +me = __file__ +print("分析文件夹：" + os.getcwd()) + +def getAllFiles(targetDir): + files = [] + listFiles = os.listdir(targetDir) + for file in listFiles: + path = os.path.join(targetDir, file) + if os.path.isdir(path): + files.extend(getAllFiles(path)) + elif os.path.isfile(path) and path != me: + files.append(path) + return files + +all_files=getAllFiles(os.curdir) +type_dict=dict() + +for file in all_files: + if os.path.isdir(file): + type_dict.setdefault("文件夹", 0) + type_dict["文件夹"]+=1 + else: + ext=os.path.splitext(file)[1] + type_dict.setdefault(ext, 0) + type_dict[ext]+=1 + +type_dict["空"] = type_dict.pop("") +sort_dict = sorted(type_dict.items(), key = lambda a: a[1], reverse = True) + +for each_type in sort_dict: + print("当前文件夹下共有后缀名为[%s]的文件%d个" %(each_type[0], each_type[1])) +``` + +在mumps项目根目录下运行，得到统计结果如下（排除自身）： + +```shell +/root/MUMPS_5.1.2 +当前文件夹下共有[]的文件579个 +当前文件夹下共有[.F]的文件385个 +当前文件夹下共有[.h]的文件40个 +当前文件夹下共有[.c]的文件36个 +当前文件夹下共有[.sample]的文件13个 +当前文件夹下共有[.SEQ]的文件12个 +当前文件夹下共有[.m]的文件11个 +当前文件夹下共有[.PAR]的文件9个 +当前文件夹下共有[.sce]的文件6个 +当前文件夹下共有[.sci]的文件5个 +当前文件夹下共有[.xml]的文件3个 +当前文件夹下共有[.html]的文件3个 +当前文件夹下共有[.pdf]的文件1个 +当前文件夹下共有[.f]的文件1个 +当前文件夹下共有[.dtd]的文件1个 +当前文件夹下共有[.htm]的文件1个 +当前文件夹下共有[.generic]的文件1个 +当前文件夹下共有[.inc]的文件1个 +当前文件夹下共有[.mat]的文件1个 +``` + +主要源码文件后缀名为`F`，`h`，`c`以及部分C语言文件。由此判断该项目主要语言为C++/C。 + +### 1.2 统计源码代码量 + +统计行数： + +```shell +find ./ -regex ".*\.F\|.*\.cpp|.*\.c" | xargs wc -l +``` + +行数统计后结果输出如下： + +```shell +350231 total +``` + +### 1.3 统计不符合要求的总行数 + +对源代码文件（后缀名为`F`，`h`，`c`）进行fprettify代码样式格式化，格式化结果如下： + +```shell +[root@host- src]# fprettify -r src/ +[root@host- src]# git commit -m "fomat update" +[master b0a0ea8] fomat update + 44 files changed, 1044 insertions(+), 1044 deletions(-) + rewrite src/ana_omp_m.F (97%) + rewrite src/cfac_omp_m.F (97%) + rewrite src/cfac_process_bf.F (97%) + rewrite src/clr_type.F (94%) + rewrite src/cmumps_iXamax.F (99%) + rewrite src/cmumps_save_restore.F (97%) + rewrite src/cmumps_save_restore_files.F (97%) + rewrite src/cmumps_struc_def.F (97%) + rewrite src/comp_tps_m.F (97%) + rewrite src/cstatic_ptr_m.F (71%) + rewrite src/dfac_omp_m.F (97%) + rewrite src/dfac_process_bf.F (97%) + rewrite src/dlr_type.F (94%) + rewrite src/dmumps_iXamax.F (98%) + rewrite src/dmumps_save_restore.F (97%) + rewrite src/dmumps_save_restore_files.F (97%) + rewrite src/dmumps_struc_def.F (97%) + rewrite src/domp_tps_m.F (97%) + rewrite src/dstatic_ptr_m.F (70%) + rewrite src/fac_future_niv2_mod.F (97%) + rewrite src/fac_ibct_data_m.F (97%) + rewrite src/mumps_comm_ibcast.F (97%) + rewrite src/mumps_l0_omp_m.F (90%) + rewrite src/mumps_type_size.F (92%) + rewrite src/mumps_version.F (98%) + rewrite src/omp_tps_common_m.F (97%) + rewrite src/sfac_omp_m.F (97%) + rewrite src/sfac_process_bf.F (97%) + rewrite src/slr_type.F (94%) + rewrite src/smumps_iXamax.F (98%) + rewrite src/smumps_save_restore.F (97%) + rewrite src/smumps_save_restore_files.F (97%) + rewrite src/smumps_struc_def.F (97%) + rewrite src/somp_tps_m.F (97%) + rewrite src/sstatic_ptr_m.F (72%) + rewrite src/zfac_omp_m.F (97%) + rewrite src/zfac_process_bf.F (97%) + rewrite src/zlr_type.F (94%) + rewrite src/zmumps_iXamax.F (99%) + rewrite src/zmumps_save_restore.F (97%) + rewrite src/zmumps_save_restore_files.F (97%) + rewrite src/zmumps_struc_def.F (97%) + rewrite src/zomp_tps_m.F (97%) + rewrite src/zstatic_ptr_m.F (70%) +``` + +### 1.4.统计结果 + +综上信息，项目中代码规范性自检检查结果为 + +通过率 : 99.702% 1-1044/350231*100% + +不通过率 : 0.628% 1044/166350*100% + +## 2. 功能性测试 + +### 2.1 测试案例 + +mumps提供了运行的不同example，需要用户在编译后自行进入各个测试案例目录运行。部分测试程序需要外部输入文件，mumps已在对应目录提供。 + +example文件如下： + +```shell +~/MUMPS_5.1.2 |master ✓| → tree examples/ +examples/ +├── c_example.c +├── csimpletest.F +├── dsimpletest.F +├── input_simpletest_cmplx +├── input_simpletest_real +├── Makefile +├── multiple_arithmetics_example.F +├── README +├── ssimpletest.F +└── zsimpletest.F +``` + +案例测试程序对应程序如下： + +```fortran +C +C This file is part of MUMPS 5.1.2, released +C on Mon Oct 2 07:37:01 UTC 2017 +C + PROGRAM MUMPS_TEST + IMPLICIT NONE + INCLUDE 'mpif.h' + INCLUDE 'smumps_struc.h' + TYPE (SMUMPS_STRUC) mumps_par + INTEGER IERR, I + INTEGER(8) I8 + CALL MPI_INIT(IERR) +C Define a communicator for the package. + mumps_par%COMM = MPI_COMM_WORLD +C Initialize an instance of the package +C for L U factorization (sym = 0, with working host) + mumps_par%JOB = -1 + mumps_par%SYM = 0 + mumps_par%PAR = 1 + CALL SMUMPS(mumps_par) + IF (mumps_par%INFOG(1).LT.0) THEN + WRITE(6,'(A,A,I6,A,I9)') " ERROR RETURN: ", + & " mumps_par%INFOG(1)= ", mumps_par%INFOG(1), + & " mumps_par%INFOG(2)= ", mumps_par%INFOG(2) + GOTO 500 + END IF +C Define problem on the host (processor 0) + IF ( mumps_par%MYID .eq. 0 ) THEN + READ(5,*) mumps_par%N + READ(5,*) mumps_par%NNZ + ALLOCATE( mumps_par%IRN ( mumps_par%NNZ ) ) + ALLOCATE( mumps_par%JCN ( mumps_par%NNZ ) ) + ALLOCATE( mumps_par%A( mumps_par%NNZ ) ) + ALLOCATE( mumps_par%RHS ( mumps_par%N ) ) + DO I8 = 1, mumps_par%NNZ + READ(5,*) mumps_par%IRN(I8),mumps_par%JCN(I8),mumps_par%A(I8) + END DO + DO I = 1, mumps_par%N + READ(5,*) mumps_par%RHS(I) + END DO + END IF +C Call package for solution + mumps_par%JOB = 6 + CALL SMUMPS(mumps_par) + IF (mumps_par%INFOG(1).LT.0) THEN + WRITE(6,'(A,A,I6,A,I9)') " ERROR RETURN: ", + & " mumps_par%INFOG(1)= ", mumps_par%INFOG(1), + & " mumps_par%INFOG(2)= ", mumps_par%INFOG(2) + GOTO 500 + END IF +C Solution has been assembled on the host + IF ( mumps_par%MYID .eq. 0 ) THEN + WRITE( 6, * ) ' Solution is ',(mumps_par%RHS(I),I=1,mumps_par%N) + END IF +C Deallocate user data + IF ( mumps_par%MYID .eq. 0 )THEN + DEALLOCATE( mumps_par%IRN ) + DEALLOCATE( mumps_par%JCN ) + DEALLOCATE( mumps_par%A ) + DEALLOCATE( mumps_par%RHS ) + END IF +C Destroy the instance (deallocate internal data structures) + mumps_par%JOB = -2 + CALL SMUMPS(mumps_par) + IF (mumps_par%INFOG(1).LT.0) THEN + WRITE(6,'(A,A,I6,A,I9)') " ERROR RETURN: ", + & " mumps_par%INFOG(1)= ", mumps_par%INFOG(1), + & " mumps_par%INFOG(2)= ", mumps_par%INFOG(2) + GOTO 500 + END IF + 500 CALL MPI_FINALIZE(IERR) + STOP + END +``` + +输入文件： + +```shell +5 :N +12 :NZ +1 2 3.0 +2 3 -3.0 +4 3 2.0 +5 5 1.0 +2 1 3.0 +1 1 2.0 +5 2 4.0 +3 4 2.0 +2 5 6.0 +3 2 -1.0 +1 3 4.0 +3 3 1.0 :values +20.0 +24.0 +9.0 +6.0 +13.0 :RHS +``` + +### 2.2 功能测试 + +mumps仅作为一个框架，只生成对应的库文件和头文件，而在examples目录中提供了各种方向的测试程序，需要用户在编译后自行进入各个测试案例目录运行。部分测试程序需要外部输入文件，mumps已在对应目录提供。 + +```shell +make all +``` + +- 进行测试 + +```shell +# 测试命令 +#!/bin/bash + +export OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 +MPIRUN="mpirun -np 3 --mca plm_rsh_agent sh --mca opal_warn_on_missing_libcuda 0 --oversubscribe" +${MPIRUN} ./ssimpletest < input_simpletest_real +``` + +- 测试结果 + +```shell +Entering SMUMPS 5.1.2 with JOB, N, NNZ = 6 5 12 + executing #MPI = 3, without OMP + + ================================================= + ================================================= +L U Solver for unsymmetric matrices +Type of parallelism: Working host + + ****** ANALYSIS STEP ******** + + ... Structural symmetry (in percent)= 92 + Average density of rows/columns = 2 + ... No column permutation + Ordering based on AMF + +Leaving analysis phase with ... +INFOG(1) = 0 +INFOG(2) = 0 + -- (20) Number of entries in factors (estim.) = 15 + -- (3) Storage of factors (REAL, estimated) = 15 + -- (4) Storage of factors (INT , estimated) = 65 + -- (5) Maximum frontal size (estimated) = 3 + -- (6) Number of nodes in the tree = 3 + -- (32) Type of analysis effectively used = 1 + -- (7) Ordering option effectively used = 2 +ICNTL(6) Maximum transversal option = 0 +ICNTL(7) Pivot order option = 7 +Percentage of memory relaxation (effective) = 20 +Number of level 2 nodes = 0 +Number of split nodes = 0 +RINFOG(1) Operations during elimination (estim)= 1.900D+01 + ** Rank of proc needing largest memory in IC facto : 0 + ** Estimated corresponding MBYTES for IC facto : 1 + ** Estimated avg. MBYTES per work. proc at facto (IC) : 1 + ** TOTAL space in MBYTES for IC factorization : 3 + ** Rank of proc needing largest memory for OOC facto : 0 + ** Estimated corresponding MBYTES for OOC facto : 1 + ** Estimated avg. MBYTES per work. proc at facto (OOC) : 1 + ** TOTAL space in MBYTES for OOC factorization : 3 + ELAPSED TIME IN ANALYSIS DRIVER= 0.0022 + + ****** FACTORIZATION STEP ******** + + + GLOBAL STATISTICS PRIOR NUMERICAL FACTORIZATION ... + NUMBER OF WORKING PROCESSES = 3 + OUT-OF-CORE OPTION (ICNTL(22)) = 0 + REAL SPACE FOR FACTORS = 15 + INTEGER SPACE FOR FACTORS = 65 + MAXIMUM FRONTAL SIZE (ESTIMATED) = 3 + NUMBER OF NODES IN THE TREE = 3 + MEMORY ALLOWED (MB -- 0: N/A ) = 0 + RELATIVE THRESHOLD FOR PIVOTING, CNTL(1) = 0.1000D-01 + Convergence error after scaling for ONE-NORM (option 7/8) = 0.38D+00 + Maximum effective relaxed size of S = 475 + Average effective relaxed size of S = 469 + ELAPSED TIME FOR MATRIX DISTRIBUTION = 0.0000 + ** Memory relaxation parameter ( ICNTL(14) ) : 20 + ** Rank of processor needing largest memory in facto : 0 + ** Space in MBYTES used by this processor for facto : 1 + ** Avg. Space in MBYTES per working proc during facto : 1 + + ELAPSED TIME FOR FACTORIZATION = 0.0023 + Maximum effective space used in S (KEEP8(67)) 12 + Average effective space used in S (KEEP8(67)) 5 + ** EFF Min: Rank of processor needing largest memory : 0 + ** EFF Min: Space in MBYTES used by this processor : 1 + ** EFF Min: Avg. Space in MBYTES per working proc : 1 + + GLOBAL STATISTICS + RINFOG(2) OPERATIONS IN NODE ASSEMBLY = 2.000D+00 + ------(3) OPERATIONS IN NODE ELIMINATION= 1.900D+01 + INFOG (9) REAL SPACE FOR FACTORS = 15 + INFOG(10) INTEGER SPACE FOR FACTORS = 65 + INFOG(11) MAXIMUM FRONT SIZE = 3 + INFOG(29) NUMBER OF ENTRIES IN FACTORS = 15 + INFOG(12) NUMBER OF OFF DIAGONAL PIVOTS = 0 + INFOG(13) NUMBER OF DELAYED PIVOTS = 0 + INFOG(14) NUMBER OF MEMORY COMPRESS = 0 + ELAPSED TIME IN FACTORIZATION DRIVER= 0.0031 + + + ****** SOLVE & CHECK STEP ******** + + + STATISTICS PRIOR SOLVE PHASE ........... + NUMBER OF RIGHT-HAND-SIDES = 1 + BLOCKING FACTOR FOR MULTIPLE RHS = 1 + ICNTL (9) = 1 + --- (10) = 0 + --- (11) = 0 + --- (20) = 0 + --- (21) = 0 + --- (30) = 0 + ** Rank of processor needing largest memory in solve : 0 + ** Space in MBYTES used by this processor for solve : 0 + ** Avg. Space in MBYTES per working proc during solve : 0 + + Global statistics + TIME to build/scatter RHS = 0.000093 + TIME in solution step (fwd/bwd) = 0.000231 + .. TIME in forward (fwd) step = 0.000133 + .. TIME in backward (bwd) step = 0.000090 + TIME to gather solution(cent.sol)= 0.000005 + TIME to copy/scale RHS (dist.sol)= 0.000000 + ELAPSED TIME IN SOLVE DRIVER= 0.0010 + Solution is 1.00000048 2.00000024 3.00000000 4.00000000 4.99999952 + +Entering SMUMPS 5.1.2 with JOB = -2 + executing #MPI = 3, without OMP + +Entering DMUMPS 5.1.2 with JOB, N, NNZ = 6 5 12 + executing #MPI = 3, without OMP + + ================================================= + ================================================= +L U Solver for unsymmetric matrices +Type of parallelism: Working host + + ****** ANALYSIS STEP ******** + + ... Structural symmetry (in percent)= 92 + Average density of rows/columns = 2 + ... No column permutation + Ordering based on AMF + +Leaving analysis phase with ... +INFOG(1) = 0 +INFOG(2) = 0 + -- (20) Number of entries in factors (estim.) = 15 + -- (3) Storage of factors (REAL, estimated) = 15 + -- (4) Storage of factors (INT , estimated) = 65 + -- (5) Maximum frontal size (estimated) = 3 + -- (6) Number of nodes in the tree = 3 + -- (32) Type of analysis effectively used = 1 + -- (7) Ordering option effectively used = 2 +ICNTL(6) Maximum transversal option = 0 +ICNTL(7) Pivot order option = 7 +Percentage of memory relaxation (effective) = 20 +Number of level 2 nodes = 0 +Number of split nodes = 0 +RINFOG(1) Operations during elimination (estim)= 1.900D+01 + ** Rank of proc needing largest memory in IC facto : 0 + ** Estimated corresponding MBYTES for IC facto : 1 + ** Estimated avg. MBYTES per work. proc at facto (IC) : 1 + ** TOTAL space in MBYTES for IC factorization : 3 + ** Rank of proc needing largest memory for OOC facto : 0 + ** Estimated corresponding MBYTES for OOC facto : 1 + ** Estimated avg. MBYTES per work. proc at facto (OOC) : 1 + ** TOTAL space in MBYTES for OOC factorization : 3 + ELAPSED TIME IN ANALYSIS DRIVER= 0.0006 + + ****** FACTORIZATION STEP ******** + + + GLOBAL STATISTICS PRIOR NUMERICAL FACTORIZATION ... + NUMBER OF WORKING PROCESSES = 3 + OUT-OF-CORE OPTION (ICNTL(22)) = 0 + REAL SPACE FOR FACTORS = 15 + INTEGER SPACE FOR FACTORS = 65 + MAXIMUM FRONTAL SIZE (ESTIMATED) = 3 + NUMBER OF NODES IN THE TREE = 3 + MEMORY ALLOWED (MB -- 0: N/A ) = 0 + RELATIVE THRESHOLD FOR PIVOTING, CNTL(1) = 0.1000D-01 + Convergence error after scaling for ONE-NORM (option 7/8) = 0.38D+00 + Maximum effective relaxed size of S = 475 + Average effective relaxed size of S = 469 + ELAPSED TIME FOR MATRIX DISTRIBUTION = 0.0000 + ** Memory relaxation parameter ( ICNTL(14) ) : 20 + ** Rank of processor needing largest memory in facto : 0 + ** Space in MBYTES used by this processor for facto : 1 + ** Avg. Space in MBYTES per working proc during facto : 1 + + ELAPSED TIME FOR FACTORIZATION = 0.0012 + Maximum effective space used in S (KEEP8(67)) 12 + Average effective space used in S (KEEP8(67)) 5 + ** EFF Min: Rank of processor needing largest memory : 0 + ** EFF Min: Space in MBYTES used by this processor : 1 + ** EFF Min: Avg. Space in MBYTES per working proc : 1 + + GLOBAL STATISTICS + RINFOG(2) OPERATIONS IN NODE ASSEMBLY = 2.000D+00 + ------(3) OPERATIONS IN NODE ELIMINATION= 1.900D+01 + INFOG (9) REAL SPACE FOR FACTORS = 15 + INFOG(10) INTEGER SPACE FOR FACTORS = 65 + INFOG(11) MAXIMUM FRONT SIZE = 3 + INFOG(29) NUMBER OF ENTRIES IN FACTORS = 15 + INFOG(12) NUMBER OF OFF DIAGONAL PIVOTS = 0 + INFOG(13) NUMBER OF DELAYED PIVOTS = 0 + INFOG(14) NUMBER OF MEMORY COMPRESS = 0 + ELAPSED TIME IN FACTORIZATION DRIVER= 0.0019 + + + ****** SOLVE & CHECK STEP ******** + + + STATISTICS PRIOR SOLVE PHASE ........... + NUMBER OF RIGHT-HAND-SIDES = 1 + BLOCKING FACTOR FOR MULTIPLE RHS = 1 + ICNTL (9) = 1 + --- (10) = 0 + --- (11) = 0 + --- (20) = 0 + --- (21) = 0 + --- (30) = 0 + ** Rank of processor needing largest memory in solve : 0 + ** Space in MBYTES used by this processor for solve : 0 + ** Avg. Space in MBYTES per working proc during solve : 0 + + Global statistics + TIME to build/scatter RHS = 0.000062 + TIME in solution step (fwd/bwd) = 0.000247 + .. TIME in forward (fwd) step = 0.000170 + .. TIME in backward (bwd) step = 0.000055 + TIME to gather solution(cent.sol)= 0.000004 + TIME to copy/scale RHS (dist.sol)= 0.000000 + ELAPSED TIME IN SOLVE DRIVER= 0.0006 + Solution is 0.99999999999999989 2.0000000000000000 3.0000000000000004 3.9999999999999996 4.9999999999999991 + +Entering DMUMPS 5.1.2 with JOB = -2 + executing #MPI = 3, without OMP +``` + +模型验证且运行成功，测试通过。 + +## 3.性能测试 + +### 3.1.测试平台信息对比 + +| | arm信息 | x86信息 | +| -------- | -------------------------------- | --------------------- | +| 操作系统 | openEuler 22.03 (LTS) | openEuler 22.03 (LTS) | +| 内核版本 | 5.10.0-60.18.0.50.oe2203.aarch64 | 5.15.79.1.oe1.x86_64 | + +### 3.2.测试软件环境信息对比 + +| | arm信息 | x86信息 | +| --------- | ------------- | --------- | +| gcc | bisheng 2.1.0 | gcc 9.3.0 | +| mpi | hmpi1.1.1 | hmpi1.1.1 | +| CMake | 3.23.1 | 3.23.1 | +| OpenBLAS | 0.3.18 | 0.3.18 | +| lapack | 3.8.0 | 3.8.0 | +| scalapack | 2.1.0 | 2.1.0 | + +### 3.3.测试硬件性能信息对比 + +| | arm信息 | x86信息 | +| ------ | ----------- | -------- | +| cpu | Kunpeng 920 | | +| 核心数 | 16 | 4 | +| 内存 | 32 GB | 8 GB | +| 磁盘io | 1.3 GB/s | 400 MB/s | +| 虚拟化 | KVM | KVM | + +### 3.4.测试选择的案例 + +example/ 目录下的文件 csimpletest + +测试文件如下 + +```fortran +C +C This file is part of MUMPS 5.1.2, released +C on Mon Oct 2 07:37:01 UTC 2017 +C + PROGRAM MUMPS_TEST + IMPLICIT NONE + INCLUDE 'mpif.h' + INCLUDE 'cmumps_struc.h' + TYPE (CMUMPS_STRUC) mumps_par + INTEGER IERR, I + INTEGER(8) I8 + CALL MPI_INIT(IERR) +C Define a communicator for the package. + mumps_par%COMM = MPI_COMM_WORLD +C Initialize an instance of the package +C for L U factorization (sym = 0, with working host) + mumps_par%JOB = -1 + mumps_par%SYM = 0 + mumps_par%PAR = 1 + CALL CMUMPS(mumps_par) + IF (mumps_par%INFOG(1).LT.0) THEN + WRITE(6,'(A,A,I6,A,I9)') " ERROR RETURN: ", + & " mumps_par%INFOG(1)= ", mumps_par%INFOG(1), + & " mumps_par%INFOG(2)= ", mumps_par%INFOG(2) + GOTO 500 + END IF +C Define problem on the host (processor 0) + IF ( mumps_par%MYID .eq. 0 ) THEN + READ(5,*) mumps_par%N + READ(5,*) mumps_par%NNZ + ALLOCATE( mumps_par%IRN ( mumps_par%NNZ ) ) + ALLOCATE( mumps_par%JCN ( mumps_par%NNZ ) ) + ALLOCATE( mumps_par%A( mumps_par%NNZ ) ) + ALLOCATE( mumps_par%RHS ( mumps_par%N ) ) + DO I8 = 1, mumps_par%NNZ + READ(5,*) mumps_par%IRN(I8),mumps_par%JCN(I8),mumps_par%A(I8) + END DO + DO I = 1, mumps_par%N + READ(5,*) mumps_par%RHS(I) + END DO + END IF +C Call package for solution + mumps_par%JOB = 6 + CALL CMUMPS(mumps_par) + IF (mumps_par%INFOG(1).LT.0) THEN + WRITE(6,'(A,A,I6,A,I9)') " ERROR RETURN: ", + & " mumps_par%INFOG(1)= ", mumps_par%INFOG(1), + & " mumps_par%INFOG(2)= ", mumps_par%INFOG(2) + GOTO 500 + END IF +C Solution has been assembled on the host + IF ( mumps_par%MYID .eq. 0 ) THEN + WRITE( 6, * ) ' Solution is ',(mumps_par%RHS(I),I=1,mumps_par%N) + END IF +C Deallocate user data + IF ( mumps_par%MYID .eq. 0 )THEN + DEALLOCATE( mumps_par%IRN ) + DEALLOCATE( mumps_par%JCN ) + DEALLOCATE( mumps_par%A ) + DEALLOCATE( mumps_par%RHS ) + END IF +C Destroy the instance (deallocate internal data structures) + mumps_par%JOB = -2 + CALL CMUMPS(mumps_par) + IF (mumps_par%INFOG(1).LT.0) THEN + WRITE(6,'(A,A,I6,A,I9)') " ERROR RETURN: ", + & " mumps_par%INFOG(1)= ", mumps_par%INFOG(1), + & " mumps_par%INFOG(2)= ", mumps_par%INFOG(2) + GOTO 500 + END IF + 500 CALL MPI_FINALIZE(IERR) + STOP + END +``` + +输入文件 + +```shell +5 : N +12 : NZ +1 2 (3.0,0.0) +2 3 (-3.0,0.0) +4 3 (2.0,0.0) +5 5 (1.0,0.0) +2 1 (3.0,0.0) +1 1 (2.0,0.0) +5 2 (4.0,0.0) +3 4 (2.0,0.0) +2 5 (6.0,0.0) +3 2 (-1.0,0.0) +1 3 (4.0,0.0) +3 3 (1.0,0.0) +(20.0,0.0) +(24.0,0.0) +(9.0,0.0) +(6.0,0.0) +(13.0,0.0) : RHS + +``` + +### 3.5.单线程 + +单线程运行测试时间对比（五次运行取平均值） + +| | arm | x86 | +| ----------- | ------ | ------ | +| 实际CPU时间 | 0.160s | 0.188s | +| 用户时间 | 0.064s | 0.063s | + +### 3.6.多线程 + +多线程运行测试时间对比（五次运行取平均值） + +| | arm | x86 | +| ----------- | ------ | ----- | +| 线程数 | 4 | 4 | +| 实际CPU时间 | 0.159s | 0.204 | +| 用户时间 | 0.197s | 0.168 | + +arm多线程时间耗费数据表： + +| 线程 | 1 | 2 | 4 | 8 | +| :------------ | ----- | ----- | ----- | ----- | +| 用户时间(s) | 0.160 | 0.155 | 0.159 | 0.174 | +| 用户态时间(s) | 0.064 | 0.099 | 0.197 | 0.407 | +| 内核态时间(s) | 0.053 | 0.082 | 0.127 | 0.257 | + +x86多线程时间耗费数据表： + +| 线程 | 1 | 2 | 3 | 4 | +| --------------- | ----- | ----- | ----- | ----- | +| 用户时间 （s） | 0.188 | 0.195 | 0.216 | 0.204 | +| 用户态时间（s） | 0.063 | 0.079 | 0.150 | 0.168 | +| 内核态时间（s） | 0.163 | 0.281 | 0.424 | 0.520 | + +由上表可知，在线程逐渐增加的情况下，所减少的用户时间并非线性关系，线程数增加后，运算用时并未显著下降，且系统调用的时间有较为明显的上升趋势。 + +### 3.7.测试总结 + +性能测试arm平台均在x86平台50%以上,且随着线程数的增加，两个平台的对于同一个应用的所耗费的时间差距逐渐减少。 + +且线程增加并不会无限制减少应用的实际耗费时间，在合理的范围内分配线程数才能更好的利用算力资源。 + +## 4.精度测试 + +### 4.1.所选测试案例 + +example/ 目录下的文件 c_example.c + +使用 C 接口的示例程序 + +- MUMPS 的双实数算术版本，dmumps_c。 +- 我们解决系统 A x = RHS 与 +- A = diag(1 2) 和 RHS = [1 4]^T +- 解是 [1 2]^T */ + +测试文件如下 + +```c +/* + * + * This file is part of MUMPS 5.1.2, released + * on Mon Oct 2 07:37:01 UTC 2017 + * + */ +/* Example program using the C interface to the + * double real arithmetic version of MUMPS, dmumps_c. + * We solve the system A x = RHS with + * A = diag(1 2) and RHS = [1 4]^T + * Solution is [1 2]^T */ +#include +#include +#include "mpi.h" +#include "dmumps_c.h" +#define JOB_INIT -1 +#define JOB_END -2 +#define USE_COMM_WORLD -987654 + +#if defined(MAIN_COMP) +/* + * Some Fortran compilers (COMPAQ fort) define main inside + * their runtime library while a Fortran program translates + * to MAIN_ or MAIN__ which is then called from "main". This + * is annoying because MAIN__ has no arguments and we must + * define argc/argv arbitrarily !! + */ +int MAIN__(); +int MAIN_() + { + return MAIN__(); + } + +int MAIN__() +{ + int argc=1; + char * name = "c_example"; + char ** argv ; +#else +int main(int argc, char ** argv) +{ +#endif + DMUMPS_STRUC_C id; + MUMPS_INT n = 2; + MUMPS_INT8 nnz = 2; + MUMPS_INT irn[] = {1,2}; + MUMPS_INT jcn[] = {1,2}; + double a[2]; + double rhs[2]; + + MUMPS_INT myid, ierr; + + int error = 0; +#if defined(MAIN_COMP) + argv = &name; +#endif + ierr = MPI_Init(&argc, &argv); + ierr = MPI_Comm_rank(MPI_COMM_WORLD, &myid); + /* Define A and rhs */ + rhs[0]=1.0;rhs[1]=4.0; + a[0]=1.0;a[1]=2.0; + + /* Initialize a MUMPS instance. Use MPI_COMM_WORLD */ + id.comm_fortran=USE_COMM_WORLD; + id.par=1; id.sym=0; + id.job=JOB_INIT; + dmumps_c(&id); + + /* Define the problem on the host */ + if (myid == 0) { + id.n = n; id.nnz =nnz; id.irn=irn; id.jcn=jcn; + id.a = a; id.rhs = rhs; + } +#define ICNTL(I) icntl[(I)-1] /* macro s.t. indices match documentation */ + /* No outputs */ + id.ICNTL(1)=-1; id.ICNTL(2)=-1; id.ICNTL(3)=-1; id.ICNTL(4)=0; + + /* Call the MUMPS package (analyse, factorization and solve). */ + id.job=6; + dmumps_c(&id); + if (id.infog[0]<0) { + printf(" (PROC %d) ERROR RETURN: \tINFOG(1)= %d\n\t\t\t\tINFOG(2)= %d\n", + myid, id.infog[0], id.infog[1]); + error = 1; + } + + /* Terminate instance. */ + id.job=JOB_END; + dmumps_c(&id); + if (myid == 0) { + if (!error) { + printf("Solution is : (%8.2f %8.2f)\n", rhs[0],rhs[1]); + } else { + printf("An error has occured, please check error code returned by MUMPS.\n"); + } + } + ierr = MPI_Finalize(); + return 0; +} +``` + +通过Makefile进行编译 +运行选项如下： + +```bash +make clean all +MPIRUN="mpirun -np 3 --mca plm_rsh_agent sh --mca opal_warn_on_missing_libcuda 0 --oversubscribe" +${MPIRUN} ./c_example +``` + +### 4.2.获取对比数据 + +arm 运行结果 + +```bash +Solution is : ( 1.00 2.00) +``` + +### 4.3.测试总结 + +从arm输出结果可以看出测试通过，满足example/README中的结果。 diff --git "a/doc/mumps/5.1.2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mumps\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/mumps/5.1.2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mumps\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" new file mode 100644 index 0000000000000000000000000000000000000000..0bf05d1d47a544e46fc98bd5af03bf59f5d926f7 --- /dev/null +++ "b/doc/mumps/5.1.2/\343\200\212\345\237\272\344\272\216openEuler\347\232\204mumps\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -0,0 +1,375 @@ +# 《基于openEuler的MUMPS软件移植指南》 + +## 1.介绍 + +- MUMPS（"MUltifrontal Massively Parallel Solver"）是一个用于求解线性方程组的软件包。 + +- 官网地址： + +- 特性： + + - 实数或复数算术（单精度或双精度） + - 平行因式分解和求解阶段 + - (也可使用单处理器版本) + - 脱离核心的数值阶段 + - 迭代细化和逆向误差分析 + - 各种矩阵输入格式集合式、分布式、元素式格式 + - 部分因式分解和Schur互补矩阵（集中式或二维块状循环式），具有减少/压缩的右手边 + +## 2.环境要求 + +- 操作系统：OpenEuler arm/x86 (本文档以 x86 架构为例) + +## 3.配置编译环境 + +配置环境指导，手动进行配置依赖环境。 + +### 3.1.环境总览 + +- 编译器： gcc + +- MPI：hmpi + +- 其他类库：`CMake`, `OpenBLAS`, `zlib`, `lapack`, `scalapack` + + 具体版本和下载地址如下 + +| 名称 | 版本 | 软件下载地址 | +| --------- | ------ | ---------------------------------------------------------------------------------------------- | +| hmpi | 1.1.1 | | +| gcc | 9.3.0 | | +| CMake | 3.23.1 | | +| OpenBLAS | 0.3.18 | | +| zlib | 1.2.12 | | +| lapack | 3.8.0 | | +| scalapack | 2.1.0 | | + +### 3.2.创建文件夹 + +```bash +mkdir -p $HOME/build +mkdir -p $HOME/install +mkdir -p $HOME/tmp +``` + +### 3.3.安装预设 + +设置环境变量，方便修改自定义安装目录 + +- 编译目录为 $HOME/build , 根据实际情况进行修改 +- 软件安装目录为 $HOME/install , 根据实际情况进行修改 +- 下载目录为 $HOME/tmp , 根据实际情况进行修改 + +```bash +#为了方便自定义软件安装目录 +#环境变量DEP_INSTALL_DIR将在后文中作为软件安装目录的根目录 +export DEP_INSTALL_DIR=$HOME/install +#环境变量DEP_BUILD_DIR将在后文中作为编译的根目录 +export DEP_BUILD_DIR=$HOME/build +#环境变量DEP_DOWNLOAD_DIR将在后文中作为下载文件的保存目录 +export DEP_DOWNLOAD_DIR=$HOME/tmp + +#注： 以上变量只在一次会话中有效。如果中途断开ssh会话，则在后续的安装过程中不会生效，需要重新运行 +``` + +### 3.4.安装环境依赖和gcc编译器 + +```bash +#环境依赖 +yum -y install wget tar libatomic + +#安装bisheng编译器 +wget -P $DEP_DOWNLOAD_DIR https://ftp.gnu.org/gnu/gcc/gcc-9.3.0/gcc-9.3.0.tar.gz +tar -xf $DEP_DOWNLOAD_DIR/gcc-9.3.0.tar.gz -C $DEP_INSTALL_DIR +sed -i "35s/ftp/http/g" ./contrib/download_prerequisites +./contrib/download_prerequisites +./configure --disable-multilib --enable-languages="c,c++,fortran" --prefix=$1 --disable-static --enable-shared +make -j && make install +#设置环境变量 +echo "export PATH=$DEP_INSTALL_DIR/gcc-9.3.0/bin:$PATH" >> ~/.bashrc && source ~/.bashrc +export CC=`which clang` +export CXX=`which clang++` +``` + +## 3.5.下载并编译hmpi + +```bash +yum -y install libstdc++ libstdc++-devel +yum -y install unzip make autoconf automake git libtool +#下载解压源码文件 +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip + +cd $DEP_BUILD_DIR +unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +unzip -q $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +unzip -q $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +cp -rf xucg-1.1.1-huawei/* hucx-1.1.1-huawei/src/ucg/ + +#编译hucx +cd $DEP_BUILD_DIR/hucx-1.1.1-huawei +./autogen.sh +./contrib/configure-opt --prefix=$DEP_INSTALL_DIR/hmpi/hucx CFLAGS="-DHAVE___CLEAR_CACHE=1" --disable-numa --without-java +for file in `find . -name Makefile`;do sed -i "s/-Werror//g" $file;done +for file in `find . -name Makefile`;do sed -i "s/-implicit-function-declaration//g" $file;done +make -j +make install + +yum -y install flex +#编译hmpi +cd $DEP_BUILD_DIR/hmpi-1.1.1-huawei +./autogen.pl +./configure --prefix=$DEP_INSTALL_DIR/hmpi --with-platform=contrib/platform/mellanox/optimized --enable-mpi1-compatibility --with-ucx=$DEP_INSTALL_DIR/hmpi/hucx +make -j +make install + +echo "export PATH=$DEP_INSTALL_DIR/hmpi/bin:$PATH" >> ~/.bashrc && source ~/.bashrc +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort +``` + +## 3.6.下载并编译`CMake`, `OpenBLAS`, `zlib`, `lapack`, `scalapack` + +```bash +# 下载CMake +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 +echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc + +# 下载并编译OpenBLAS +wget https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz +tar -xzvf $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz -C $DEP_BUILD_DIR +cd $DEP_BUILD_DIR/OpenBLAS-0.3.18 +make -j +make PREFIX=$DEP_INSTALL_DIR/OpenBLAS install +echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/OpenBLAS/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc + +# 下载并编译zlib +wget https://zlib.net/fossils/zlib-1.2.12.tar.gz -O $DEP_DOWNLOAD_DIR/zlib-1.2.12.tar.gz +tar -xvf $DEP_DOWNLOAD_DIR/zlib-1.2.12.tar.gz -C $DEP_BUILD_DIR +cd $DEP_BUILD_DIR/zlib-1.2.12 +CC= CXX= ./configure --prefix=$DEP_INSTALL_DIR/zlib +make -j +make install +echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/zlib/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc + +# 下载并编译lapack +wget https://www.cp2k.org/static/downloads/lapack-3.8.0.tgz -O $DEP_DOWNLOAD_DIR/lapack-3.8.0.tgz +tar -xvf $DEP_DOWNLOAD_DIR/lapack-3.8.0.tgz -C $DEP_BUILD_DIR +cd $DEP_BUILD_DIR/lapack-3.8.0 +./bootstrap.sh +mkdir build && cd build +cmake .. -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_LIBDIR=$DEP_INSTALL_DIR/lapack +make -j +make install -j +echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/lapack/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc + +# 下载并编译scalapack +wget http://www.netlib.org/scalapack/scalapack-2.1.0.tgz -O $DEP_DOWNLOAD_DIR/scalapack-2.1.0.tgz +tar -xvf $DEP_DOWNLOAD_DIR/scalapack-2.1.0.tgz -C $DEP_BUILD_DIR +cd $DEP_BUILD_DIR/scalapack-2.1.0 +mkdir build && cd build +cmake \ +-DCMAKE_INSTALL_PREFIX=$DEP_INSTALL_DIR/scalapack \ +-DBUILD_SHARED_LIBS=ON \ +-DBLAS_LIBRARIES=$DEP_INSTALL_DIR/OpenBLAS/lib/libopenblas.so \ +-DLAPACK_LIBRARIES=$DEP_INSTALL_DIR/lapack/lib/liblapack.so \ +-DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 \ +.. / +make -j +make install +echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/scalapack/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc + +``` + +## 4.编译MUMPS + +### 4.1.下载并编译 MUMPS + +获取 MUMPS软件源码并解压文件 + +```bash + +# 下载源码文件 +wget http://graal.ens-lyon.fr/MUMPS/MUMPS_5.1.2.tar.gz -O $DEP_DOWNLOAD_DIR/MUMPS_5.1.2.tar.gz +# 解压源码文件 +tar -xvf $DEP_DOWNLOAD_DIR/MUMPS_5.1.2.tar.gz -C $DEP_BUILD_DIR +cd $DEP_BUILD_DIR/MUMPS_5.1.2 +#编译源码 +mkdir -p lib +cp Make.inc/Makefile.inc.generic ./Makefile.inc +sed -i 's/f90/mpifort/g' ./Makefile.inc +sed -i 's/CC = cc/CC = mpicc/g' ./Makefile.inc +sed -i '94c LIBEXT = .so' ./Makefile.inc +sed -i '107c AR = $(CC) -shared $(OPTC) -o' ./Makefile.inc +sed -i '115c LAPACK = -Wl,-rpath,$DEP_INSTALL_DIR/lapack/ -L$DEP_INSTALL_DIR/lapack/ -llapack' ./Makefile.inc +sed -i '118c SCALAP = -Wl,-rpath,$DEP_INSTALL_DIR/scalapack/lib/ -L$DEP_INSTALL_DIR/scalapack/lib/ -lscalapack' ./Makefile.inc +sed -i '121c INCPAR = -I$DEP_INSTALL_DIR/hmpi/include' ./Makefile.inc +sed -i '124c LIBPAR = $(SCALAP) $(LAPACK) -L$DEP_INSTALL_DIR/hmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi' ./Makefile.inc +sed -i '134c LIBBLAS = -Wl,-rpath,$DEP_INSTALL_DIR/openblas/lib -L$DEP_INSTALL_DIR/openblas/lib -lopenblas' ./Makefile.inc +sed -i '153c OPTF = -DALLOW_NON_INIT ${CFLAGS} -fPIC -Wno-argument-mismatch' ./Makefile.inc +sed -i '154c OPTC = ${CFLAGS} -fPIC' ./Makefile.inc +sed -i '155c OPTL = ${CFLAGS} -fPIC' ./Makefile.inc +sed -i '71c cp $(LPORDDIR)/libpord$(LIBEXT) `pwd`/lib; \\' ./Makefile +make alllib all +``` + +### 4.2. 运行测试文件 + +运行MUMPS项目测试文件 + +```bash +cd $DEP_BUILD_DIR/MUMPS_5.1.2/example +export OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 +make clean all +export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$DEP_BUILD_DIR/MUMPS_5.1.2/lib +${MPIRUN} ./ssimpletest < input_simpletest_real +${MPIRUN} ./dsimpletest < input_simpletest_real +${MPIRUN} ./csimpletest < input_simpletest_cmplx +${MPIRUN} ./zsimpletest < input_simpletest_cmplx +${MPIRUN} ./c_example +${MPIRUN} ./multiple_arithmetics_example +``` + +## 附A：使用hpcrunner进行一键安装MUMPS + +推荐使用hpcrunner进行安装MUMPS + +### 1.克隆仓库 + +```bash +git clone https://gitee.com/openeuler/hpcrunner.git +``` + +## 2.初始化hpcrunner 和 安装必要软件包 + +初始化项目助手 + +```bash +cd hpcrunner +source init.sh +``` + +安装必要软件包 + +**arm / x86 需要的软件包不同，根据实际环境进行选择** + +```bash +# arm +yum install -y environment-modules git wget unzip make flex tar +# x86 +yum install -y environment-modules git wget unzip make flex tar +yum install -y gcc gcc-c++ gcc-gfortran glibc-devel libgfortran +yum install -y tcsh tcl lsof tk bc +``` + +### 3.选择平台对应配置文件 + +- arm平台的配置文件为 `templates/mumps/5.1.2/data.mumps.arm.cpu.config` + + ```bash + ./jarvis -use templates/mumps/5.1.2/data.mumps.arm.cpu.config + ``` + +- x86 平台的配置文件为 `templates/mumps/5.1.2/data.mumps.amd.cpu.config` + + ```bash + ./jarvis -use templates/mumps/5.1.2/data.mumps.amd.cpu.config + ``` + +### 4.下载mumps源码 + +```bash +./jarvis -d +``` + +### 5.一键配置依赖环境 + +```bash +./jarvis -dp +``` + +### 6.一键进行编译 + +```bash +./jarvis -b +``` + +### 7.一键进行运行测试 + +```bash +./jarvis -r +``` + +## 附B：使用singularity运行容器 + +### 使用教程 + +### 下载容器镜像 + +通过链接下载： + +[百度云盘](https://pan.baidu.com/s/1UjHiv6DN_oOVXcuohP5Uqg?pwd=vxit) + +或者扫码下载： + +![百度云](data:image/png;base64,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) + +#### 1.安装singularity + +安装singularity， + +具体步骤如下 + +```bash +mkdir -p ~/install +mkdir -p ~/build + +#安装编译所需依赖 +yum -y install libatomic libstdc++ libstdc++-devel libseccomp-devel glib2-devel gcc squashfs-tools tar + +#安装bisheng编译器 +cd ~/build +wget https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +tar -C ~/install -xf bisheng-compiler-2.1.0-aarch64-linux.tar.gz +echo "export PATH=$HOME/install/bisheng-compiler-2.1.0-aarch64-linux/bin:$PATH" >> ~/.bashrc && source ~/.bashrc +export CC=`which clang` +export CXX=`which clang++` + +#安装go编译器 +cd ~/build +wget https://go.dev/dl/go1.19.linux-arm64.tar.gz +tar -C ~/install -xf go1.19.linux-arm64.tar.gz +echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc + +#安装singularity +cd ~/build +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +tar -xf singularity-ce-3.10.2.tar.gz +cd singularity-ce-3.10.2 +./mconfig --prefix=$HOME/install/singularity +make -C ./builddir +make -C ./builddir install +echo "export PATH=$HOME/install/singularity/bin:$PATH" >> ~/.bashrc && source ~/.bashrc +``` + +#### 2.构建镜像 + +```shell +# x86 +singularity build ./name-of-image.sif openeuler-gcc-9.3.0-hmpi1-mumps-5.1.2.def +# arm +singularity build ./name-of-image.sif openeuler-bisheng2-hmpi1-mumps-5.1.2.def +# 转换为沙盒 +singularity build --sandbox image-sandbox name-of-image.sif +``` + +#### 3.在沙盒中运行 + +```shell +#进入沙盒 +singularity shell -w image-sandbox +#在沙盒中运行内置的测试案例 +cd /hpcrunner +./jarvis -r +``` diff --git "a/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index de5c3bd3d3e668b9e7ee23b744fb50496084cd48..0eaa9e94f08baab5a7d11f125adb8a41712ece44 100644 --- "a/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -14,7 +14,7 @@ ## NCO - netCDF Operators (NCO) 工具用来操作和分析 netCDF 自描述数据存储格式 -- 官网地址：<$JARVIS_PROXY/nco/nco> +- 官网地址： - 特性： @@ -48,7 +48,7 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| openmpi | 4.1.2 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip> | +| openmpi | 4.1.2 | | | gcc | 10.3.0 | | | antlr | 2.7.7 | | | cairo | 1.16.0 | | @@ -386,7 +386,7 @@ ncview依赖为 hdf5 pnetcdf netcdf udunits # 下载源码文件 cd $DEP_DOWNLOAD_DIR -git clone $JARVIS_PROXY/wannier-developers/wannier90.git +git clone https://github.com/wannier-developers/wannier90.git # 解压源码文件 cd $DEP_BUILD_DIR/wannier90 #编译源码 @@ -543,7 +543,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/opencoarrays/\343\200\212\345\237\272\344\272\216openEuler\347\232\204opencoarrays\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/opencoarrays/\343\200\212\345\237\272\344\272\216openEuler\347\232\204opencoarrays\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 6446ea2878aed3a8a1168e41cf65ecb9352a122f..524f6cbe801e71d3b1e14b30cee8040cc82e06e5 100644 --- "a/doc/opencoarrays/\343\200\212\345\237\272\344\272\216openEuler\347\232\204opencoarrays\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/opencoarrays/\343\200\212\345\237\272\344\272\216openEuler\347\232\204opencoarrays\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -6,7 +6,7 @@ - 官网地址： -- GITHUB托管地址：<$JARVIS_PROXY/opencoarrays/opencoarrays> +- GITHUB托管地址： ## 2.环境要求 @@ -28,15 +28,15 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.1.1 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip> | +| hmpi | 1.1.1 | | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | -| OpenBLAS | 0.3.18 | <$JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz> | +| CMake | 3.23.1 | | +| OpenBLAS | 0.3.18 | | | HDF5 | 1.10.1 | | | BOOST | 1.72.0 | | | FFTW | 3.3.10 | | | Python3 | 3.7.10 | | -| LibXml2 | 2.10.1 | <$JARVIS_PROXY/GNOME/libxml2/archive/v2.10.1.tar.gz> | +| LibXml2 | 2.10.1 | | ### 3.2.创建文件夹 @@ -91,9 +91,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip @@ -126,12 +126,12 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译OpenBLAS -wget $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz +wget https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz tar -xzvf $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/OpenBLAS-0.3.18 make -j @@ -179,7 +179,7 @@ echo "export PATH=$DEP_INSTALL_DIR/python3/bin:$PATH" >> ~/.bashrc && source ~/. echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/python3/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译LibXml2 -wget $JARVIS_PROXY/GNOME/libxml2/archive/v2.10.1.tar.gz -O $DEP_DOWNLOAD_DIR/libxml2-2.10.1.tar.gz +wget https://github.com/GNOME/libxml2/archive/v2.10.1.tar.gz -O $DEP_DOWNLOAD_DIR/libxml2-2.10.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/libxml2-2.10.1.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/libxml2-2.10.1 ./autogen.sh @@ -198,7 +198,7 @@ make install ```bash # 下载源码文件 -wget $JARVIS_PROXY/opencoarrays/opencoarrays/archive/refs/tags/v3.13.0.tar.gz -O $DEP_DOWNLOAD_DIR/opencoarrays-2.10.1.tar.gz +wget https://github.com/opencoarrays/opencoarrays/archive/refs/tags/v3.13.0.tar.gz -O $DEP_DOWNLOAD_DIR/opencoarrays-2.10.1.tar.gz # 解压源码文件 tar -xvf $DEP_DOWNLOAD_DIR/opencoarrays-2.10.1.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/opencoarrays-2.10.1/build @@ -338,7 +338,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/openlb/1.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204openlb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/openlb/1.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204openlb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 17329729dc36ab4bdb17144757eb2d0605552e11..6383b7dcdd6849ca6174753182285c25f14df6eb 100644 --- "a/doc/openlb/1.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204openlb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/openlb/1.4/\343\200\212\345\237\272\344\272\216openEuler\347\232\204openlb\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -61,10 +61,10 @@ | :--------------- | :---------------------- | :------------------------------------------------------------------------------------------------------------------------------------ | | Bisheng Compiler | 1.3.3 | https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-1.3.3-aarch64-linux.tar.gz | | Hyper MPI | 1.1.1（二进制包） | https://mirrors.huaweicloud.com/kunpeng/archive/HyperMPI/1.1.1/Hyper-MPI_1.1.1_aarch64_OpenEuler20.03-LTS_Bisheng2.1.0_MLNX-OFED5.4.tar.gz | -| | 1.1.1（源码） | $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.tar.gz | +| | 1.1.1（源码） | https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.tar.gz | | KML | 1.6.0（毕昇编译器版本） | https://kunpeng-repo.obs.cn-north-4.myhuaweicloud.com/Kunpeng%20BoostKit/Kunpeng%20BoostKit%2022.0.RC3/BoostKit-kml_1.6.0_bisheng.zip | | | 1.6.0（GCC编译器版本） | https://kunpeng-repo.obs.cn-north-4.myhuaweicloud.com/Kunpeng%20BoostKit/Kunpeng%20BoostKit%2022.0.RC3/BoostKit-kml_1.6.0.zip | -| OpenBlas | 0.3.21 | $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.21.tar.gz | +| OpenBlas | 0.3.21 | https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.21.tar.gz | | OpenLB | 1.4r0 | https://www.openlb.net/wp-content/uploads/2020/11/olb-1.4r0.tgz | ### 2.3 环境管理 @@ -119,9 +119,9 @@ - 下载解压源码文件 ```shell - wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $OLB_PACKAGE_DIR/hucx-1.1.1-huawei.zip - wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $OLB_PACKAGE_DIR/xucg-1.1.1-huawei.zip - wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $OLB_PACKAGE_DIR/hmpi-1.1.1-huawei.zip + wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $OLB_PACKAGE_DIR/hucx-1.1.1-huawei.zip + wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $OLB_PACKAGE_DIR/xucg-1.1.1-huawei.zip + wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $OLB_PACKAGE_DIR/hmpi-1.1.1-huawei.zip cd $OLB_BUILD_DIR unzip -q $OLB_PACKAGE_DIR/hucx-1.1.1-huawei.zip @@ -194,7 +194,7 @@ ```shell cd ${OLB_PACKAGE_DIR} - wget -c $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.21.tar.gz -O openblas-0.3.21.tar.gz + wget -c https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.21.tar.gz -O openblas-0.3.21.tar.gz cd ${OLB_BUILD_DIR} tar -xvf ${OLB_PACKAGE_DIR}/openblas-0.3.21.tar.gz -C . cd openblas-0.3.21 diff --git "a/doc/petsc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204petsc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/petsc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204petsc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 9b596f43ccee1ed892f98ac758766f935f10659d..c65df18bb24e5a7cd127fab02994fa8b84e57bbe 100644 --- "a/doc/petsc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204petsc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/petsc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204petsc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -36,10 +36,10 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.2.0 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip> | +| hmpi | 1.2.0 | | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | -| OpenBLAS | 0.3.18 | <$JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz> | +| CMake | 3.23.1 | | +| OpenBLAS | 0.3.18 | | | lapack | 3.8.0 | | | Python3 | 3.7.10 | | | BOOST | 1.72.0 | | @@ -98,9 +98,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.2.0-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.2.0-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip @@ -133,12 +133,12 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译OpenBLAS -wget $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz +wget https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz tar -xzvf $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/OpenBLAS-0.3.18 make -j @@ -331,7 +331,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/qmcpack/3.13.0/\343\200\212\345\237\272\344\272\216openEuler\347\232\204QMCPACK\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/qmcpack/3.13.0/\343\200\212\345\237\272\344\272\216openEuler\347\232\204QMCPACK\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 15b2c4ed04fe5abd860b070701313989ead22ebc..42c06c4c856c7b4993a340df3d33e619cb3ffb90 100644 --- "a/doc/qmcpack/3.13.0/\343\200\212\345\237\272\344\272\216openEuler\347\232\204QMCPACK\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/qmcpack/3.13.0/\343\200\212\345\237\272\344\272\216openEuler\347\232\204QMCPACK\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -8,7 +8,7 @@ - 官网地址： -- GITHUB托管地址：<$JARVIS_PROXY/QMCPACK/qmcpack> +- GITHUB托管地址： - 特性： @@ -39,15 +39,15 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.1.1 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip> | +| hmpi | 1.1.1 | | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | -| OpenBLAS | 0.3.18 | <$JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz> | +| CMake | 3.23.1 | | +| OpenBLAS | 0.3.18 | | | HDF5 | 1.10.1 | | | BOOST | 1.72.0 | | | FFTW | 3.3.10 | | | Python3 | 3.7.10 | | -| LibXml2 | 2.10.1 | <$JARVIS_PROXY/GNOME/libxml2/archive/v2.10.1.tar.gz> | +| LibXml2 | 2.10.1 | | ### 3.2.创建文件夹 @@ -102,9 +102,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip @@ -137,12 +137,12 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译OpenBLAS -wget $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz +wget https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz tar -xzvf $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/OpenBLAS-0.3.18 make -j @@ -190,7 +190,7 @@ echo "export PATH=$DEP_INSTALL_DIR/python3/bin:$PATH" >> ~/.bashrc && source ~/. echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/python3/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译LibXml2 -wget $JARVIS_PROXY/GNOME/libxml2/archive/v2.10.1.tar.gz -O $DEP_DOWNLOAD_DIR/libxml2-2.10.1.tar.gz +wget https://github.com/GNOME/libxml2/archive/v2.10.1.tar.gz -O $DEP_DOWNLOAD_DIR/libxml2-2.10.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/libxml2-2.10.1.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/libxml2-2.10.1 ./autogen.sh @@ -209,7 +209,7 @@ make install ```bash # 下载源码文件 -wget $JARVIS_PROXY/QMCPACK/qmcpack/archive/refs/tags/v3.13.0.tar.gz -O $DEP_DOWNLOAD_DIR/qmcpack-3.13.0.tar.gz +wget https://github.com/QMCPACK/qmcpack/archive/refs/tags/v3.13.0.tar.gz -O $DEP_DOWNLOAD_DIR/qmcpack-3.13.0.tar.gz # 解压源码文件 tar -xvf $DEP_DOWNLOAD_DIR/qmcpack-3.13.0.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/qmcpack-3.13.0/build @@ -349,7 +349,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/scotch/7.0.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204scotch\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/scotch/7.0.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204scotch\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 8fdeb847d1e1b0be7f6a1a74addef8805c8001e5..ed2abf46f85dcd91dd599c4a2e9b4098a8658bff 100644 --- "a/doc/scotch/7.0.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204scotch\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/scotch/7.0.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204scotch\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -39,10 +39,10 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.1.1 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip> | +| hmpi | 1.1.1 | | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | -| OpenBLAS | 0.3.18 | <$JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz> | +| CMake | 3.23.1 | | +| OpenBLAS | 0.3.18 | | ### 3.2.创建文件夹 @@ -97,9 +97,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip @@ -132,12 +132,12 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译OpenBLAS -wget $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz +wget https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz tar -xzvf $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/OpenBLAS-0.3.18 make -j @@ -294,7 +294,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/slepc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204slepc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/slepc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204slepc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 0e59cff1b1569d2edb23a2c9342da492a4a945f4..82f29df9ec2ee23287003154cd97927b99143c8c 100644 --- "a/doc/slepc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204slepc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/slepc/3.18.1/\343\200\212\345\237\272\344\272\216openEuler\347\232\204slepc\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -35,10 +35,10 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.2.0 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip> | +| hmpi | 1.2.0 | | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | -| OpenBLAS | 0.3.18 | <$JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz> | +| CMake | 3.23.1 | | +| OpenBLAS | 0.3.18 | | | lapack | 3.8.0 | | | Python3 | 3.7.10 | | | BOOST | 1.72.0 | | @@ -98,9 +98,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.2.0-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.2.0-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip @@ -133,12 +133,12 @@ export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译OpenBLAS -wget $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz +wget https://github.com/xianyi/OpenBLAS/archive/refs/tags/v0.3.18.tar.gz -O $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz tar -xzvf $DEP_DOWNLOAD_DIR/OpenBLAS-0.3.18.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/OpenBLAS-0.3.18 make -j @@ -339,7 +339,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/stream/\343\200\212\345\237\272\344\272\216openEuler\347\232\204stream\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/stream/\343\200\212\345\237\272\344\272\216openEuler\347\232\204stream\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index c00548a940ee85a26b2acb1409d1cf48b8976c65..9808ba8f1976814a6ac2dfcdeb410a805b8436cc 100644 --- "a/doc/stream/\343\200\212\345\237\272\344\272\216openEuler\347\232\204stream\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/stream/\343\200\212\345\237\272\344\272\216openEuler\347\232\204stream\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -6,7 +6,7 @@ - 官网地址： -- GITHUB托管地址：<$JARVIS_PROXY/jeffhammond/stream> +- GITHUB托管地址： ## 2.环境要求 @@ -82,9 +82,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.1.1-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.1.1-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.1.1-huawei.zip @@ -244,7 +244,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/trinity/\343\200\212\345\237\272\344\272\216openEuler\347\232\204Trinity\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/trinity/\343\200\212\345\237\272\344\272\216openEuler\347\232\204Trinity\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 1c0bffd2d1b546752acf7fb56d4e4fd02d0ffd26..022ce982bad284970058c9f90444a67edb133e7c 100644 --- "a/doc/trinity/\343\200\212\345\237\272\344\272\216openEuler\347\232\204Trinity\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/trinity/\343\200\212\345\237\272\344\272\216openEuler\347\232\204Trinity\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -4,9 +4,9 @@ - 由布罗德研究所和耶路撒冷希伯来大学开发的Trinity代表了一种从RNA-seq数据高效、可靠地从头重建转录组的新方法。Trinity结合了三个独立的软件模块：Inchworm，Chrysalis和Butterfly，这些模块依次应用于处理大量RNA-seq读取。Trinity将序列数据划分为许多个独立的de Bruijn图，每个图代表给定基因或基因座的转录复杂性，然后独立处理每个图以提取全长剪接同工型，并挑出源自旁系基因的转录本。 -- 官网地址：$JARVIS_PROXY/trinityrnaseq/trinityrnaseq/wiki +- 官网地址：https://github.com/trinityrnaseq/trinityrnaseq/wiki -- GITHUB托管地址：$JARVIS_PROXY/trinityrnaseq/trinityrnaseq +- GITHUB托管地址：https://github.com/trinityrnaseq/trinityrnaseq # 2.环境要求 @@ -29,13 +29,13 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | | gcc | 9.3.0 | | -| CMake | 3.23.1 | <$JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-aarch64.tar.gz> | +| CMake | 3.23.1 | | | Zlib | 1.2.11 | | | BOOST | 1.72.0 | | -| Salmon | 1.9.0 | <$JARVIS_PROXY/COMBINE-lab/salmon/archive/refs/tags/v1.9.0.tar.gz> | -| Jellyfish| 2.3.0 | <$JARVIS_PROXY/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz> | -| Samtools | 1.15.0 | <$JARVIS_PROXY/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2> | -| Bowtie2 | 2.4.5 | <$JARVIS_PROXY/BenLangmead/bowtie2/archive/refs/tags/v2.4.5.tar.gz> | +| Salmon | 1.9.0 | | +| Jellyfish| 2.3.0 | | +| Samtools | 1.15.0 | | +| Bowtie2 | 2.4.5 | | ### 3.2.创建文件夹 @@ -87,7 +87,7 @@ export CXX=`which g++` ### 3.5.下载并编译`Cmake`, `Zlib`, `Boost`, `Salmon`, `Jellyfish`, `Samtools`, `Bowtie2` ```bash # 下载CMake -wget $JARVIS_PROXY/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz +wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz -O $DEP_DOWNLOAD_DIR/cmake-3.23.1.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/cmake-3.23.1-linux-x86_64.tar.gz -C $DEP_INSTALL_DIR/cmake --strip-components=1 echo "export PATH=$DEP_INSTALL_DIR/cmake/bin:$PATH" >> ~/.bashrc && source ~/.bashrc @@ -110,7 +110,7 @@ echo "export BOOST_ROOT=$DEP_INSTALL_DIR/boost/" >> ~/.bashrc && source ~/.bashr echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/boost/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译Salmon -wget $JARVIS_PROXY/COMBINE-lab/salmon/archive/refs/tags/v1.9.0.tar.gz -O $DEP_DOWNLOAD_DIR/v1.9.0.tar.gz +wget https://github.com/COMBINE-lab/salmon/archive/refs/tags/v1.9.0.tar.gz -O $DEP_DOWNLOAD_DIR/v1.9.0.tar.gz tar -xvf $DEP_DOWNLOAD_DIR/v1.9.0.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/salmon-1.9.0 CC=`which gcc` CXX=`which g++` cmake -DCMAKE_INSTALL_PREFIX=$DEP_INSTALL_DIR/salmon . @@ -120,7 +120,7 @@ echo "export PATH=$DEP_INSTALL_DIR/salmon/bin:$PATH" >> ~/.bashrc && source ~/.b echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/salmon/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译Jellyfish -wget $JARVIS_PROXY/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz -O $DEP_DOWNLOAD_DIR/jellyfish-2.3.0.tar.gz +wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz -O $DEP_DOWNLOAD_DIR/jellyfish-2.3.0.tar.gz tar -zxvf $DEP_DOWNLOAD_DIR/ellyfish-2.3.0.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/ellyfish-2.3.0 ./configure --prefix=$DEP_INSTALL_DIR/jellyfish @@ -130,7 +130,7 @@ echo "export PATH=$DEP_INSTALL_DIR/jellyfish/bin:$PATH" >> ~/.bashrc && source ~ echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/jellyfish/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译Samtools -wget $JARVIS_PROXY/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 -O $DEP_DOWNLOAD_DIR/samtools-1.15.tar.bz2 +wget https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 -O $DEP_DOWNLOAD_DIR/samtools-1.15.tar.bz2 tar -xJf $DEP_DOWNLOAD_DIR/samtools-1.15.tar.bz2 -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/samtools-1.15 ./configure --prefix=$DEP_INSTALL_DIR/samtools @@ -139,7 +139,7 @@ make install echo "export PATH=$DEP_INSTALL_DIR/samtools/bin:$PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译Bowtie2 -wget $JARVIS_PROXY/BenLangmead/bowtie2/archive/refs/tags/v2.4.5.tar.gz -O $DEP_DOWNLOAD_DIR/v2.4.5.tar.gz +wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.4.5.tar.gz -O $DEP_DOWNLOAD_DIR/v2.4.5.tar.gz tar -xzf $DEP_DOWNLOAD_DIR/v2.4.5.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/bowtie2-2.4.5 make -j @@ -158,7 +158,7 @@ echo "export PATH=$DEP_INSTALL_DIR/bowtie2/bin:$PATH" >> ~/.bashrc && source ~/. ```bash # 下载源码文件 -wget $JARVIS_PROXY/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.14.0/trinityrnaseq-v2.14.0.FULL_with_extendedTestData.tar.gz -O $DEP_DOWNLOAD_DIR/trinityrnaseq-v2.14.0.FULL_with_extendedTestData.tar.gz +wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.14.0/trinityrnaseq-v2.14.0.FULL_with_extendedTestData.tar.gz -O $DEP_DOWNLOAD_DIR/trinityrnaseq-v2.14.0.FULL_with_extendedTestData.tar.gz # 解压源码文件 tar -xvf $DEP_DOWNLOAD_DIR/trinityrnaseq-v2.14.0.FULL_with_extendedTestData.tar.gz -C $DEP_BUILD_DIR cd $DEP_BUILD_DIR/trinityrnaseq-v2.14.0 @@ -287,7 +287,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git "a/doc/wannier90/\343\200\212\345\237\272\344\272\216openEuler\347\232\204wannier90\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/wannier90/\343\200\212\345\237\272\344\272\216openEuler\347\232\204wannier90\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index 413d1286ca466cb287884e4b2aa353e6c24c67af..3b41af7e2e0c4569b51df224e06a3dfc0caf793c 100644 --- "a/doc/wannier90/\343\200\212\345\237\272\344\272\216openEuler\347\232\204wannier90\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/wannier90/\343\200\212\345\237\272\344\272\216openEuler\347\232\204wannier90\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -6,7 +6,7 @@ - 官网地址： -- GITHUB托管地址：<$JARVIS_PROXY/wannier-developers/wannier90> +- GITHUB托管地址： - 特性： @@ -36,11 +36,11 @@ | 名称 | 版本 | 软件下载地址 | | -------- | ------ | ---------------------------------------------------------------------------------------------- | -| hmpi | 1.2.0 | <$JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip> | +| hmpi | 1.2.0 | | | kgcc | 10.3.1 | | | BLAS | 3.10.1 | | | Python3 | 3.7.10 | | -| lapack | 3.10.1 | <$JARVIS_PROXY/Reference-LAPACK/lapack/archive/refs/tags/v3.10.1.tar.gz > | +| lapack | 3.10.1 | | ### 3.2.创建文件夹 @@ -94,9 +94,9 @@ export CXX=`which clang++` yum -y install libstdc++ libstdc++-devel yum -y install unzip make autoconf automake git libtool #下载解压源码文件 -wget $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.2.0-huawei.zip -wget $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/xucg-1.2.0-huawei.zip +wget https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.2.0-huawei.zip -O $DEP_DOWNLOAD_DIR/hmpi-1.2.0-huawei.zip cd $DEP_BUILD_DIR unzip -q $DEP_DOWNLOAD_DIR/hucx-1.2.0-huawei.zip @@ -151,7 +151,7 @@ echo "export PATH=$DEP_INSTALL_DIR/python3/bin:$PATH" >> ~/.bashrc && source ~/. echo "export LD_LIBRARY_PATH=$DEP_INSTALL_DIR/python3/lib:$LD_LIBRARY_PATH" >> ~/.bashrc && source ~/.bashrc # 下载并编译lapack -wget -u $JARVIS_PROXY/Reference-LAPACK/lapack/archive/refs/tags/v3.10.1.tar.gz -O $DEP_DOWNLOAD_DIR/lapack=3.10.1.tar.gz +wget -u https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.10.1.tar.gz -O $DEP_DOWNLOAD_DIR/lapack=3.10.1.tar.gz cd $DEP_DOWNLOAD_DIR tar -xvf $DEP_DOWNLOAD_DIR/lapack-3.10.1.tar.gz cd lapack-3.10.1 @@ -174,7 +174,7 @@ cp *.a /usr/local/lib # 下载源码文件 cd $DEP_DOWNLOAD_DIR -git clone $JARVIS_PROXY/wannier-developers/wannier90.git +git clone https://github.com/wannier-developers/wannier90.git # 解压源码文件 cd $DEP_BUILD_DIR/wannier90 #编译源码 @@ -314,7 +314,7 @@ echo "export PATH=$HOME/install/go/bin:$PATH" >> ~/.bashrc && source ~/.bashrc #安装singularity cd ~/build -wget $JARVIS_PROXY/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz +wget https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce-3.10.2.tar.gz tar -xf singularity-ce-3.10.2.tar.gz cd singularity-ce-3.10.2 ./mconfig --prefix=$HOME/install/singularity diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README.md index 5a2591289cbc6a6e1197ade62e9b6e1d33f4ba49..c8805bd3ec1627a872e59e1a806e93f800ed8db0 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README.md @@ -17,7 +17,7 @@ 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README_en.md index 6f4399491c9e10ffd38e1b59212bb2c89b8817b7..e6956d3159e639a7c69bb4b32c9e6ec81d7816d0 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/helloworld/README_en.md @@ -17,7 +17,7 @@ English | [简体中文](README.md) 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README.md index 2a714c8b1c889b0bd826b69760cc4e09411a2d0e..dbb641e3b3329ba574909dc2066aaaaee3cee25c 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README.md @@ -22,7 +22,7 @@ 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README_en.md index b118aff86a9478271796495a03215d56f0634bc6..78c05678d522e5945e440dc7562dae277c06122c 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/hmpi/bcast/README_en.md @@ -26,7 +26,7 @@ English | [简体中文](README.md) 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README.md index e6529707777a366a58dc37bdbddf57fb1eb0d561..cfc081bc26507c58cb564d633e91a4c22bc36c14 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README.md @@ -26,7 +26,7 @@ KML_BLAS有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README_en.md index 82ac60120dbe9ac17663b061f9c8b41c3b4cc346..fe2cf94ca1556f813ae39ecbbba42cb7af9cf717 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/blas/README_en.md @@ -27,7 +27,7 @@ There are multiple versions of KML_BLAS: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README.md index 6866c60c40af13acdf14646b758b35125027996c..a3a0b369483ddc645e795f53fda7ec0032231461 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README.md @@ -22,7 +22,7 @@ KML_FFT有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README_en.md index 6b0c64ef064bc7dc25caba94aac14333a8a01e94..a8f21baf14bbe2d4e26fd003ccebb8ed33e5b2e0 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/fft/README_en.md @@ -22,7 +22,7 @@ There are multiple versions of KML_FFT: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README.md index 7f332918fdeb4537e440953e1ade08e73d553bf9..42a050a28c9e7bf9cd9dc92363af66a37d600d33 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README.md @@ -17,7 +17,7 @@ 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README_en.md index abcd55a002ad0dff8dc6605f3e42aa64634da8f2..d066f97d9926b330285e73dcc14ab38753a41745 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/lapack/README_en.md @@ -18,7 +18,7 @@ English | [简体中文](README.md) 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README.md index c13ce96de52b0bbf4f95a1b385e5a6b9e17568b3..f59d2c197045d73ed3b0d40f826e70f990be3136 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README.md @@ -22,7 +22,7 @@ KML_MATH有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README_en.md index 5b52eb916511351033f4336accb8bed86daa2d32..0ab2178d3afece1d7ee136fd2b74ebce264d5127 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/math/README_en.md @@ -22,7 +22,7 @@ There are multiple versions of KML_MATH: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README.md index e6b1002397efb69a4c33d910f6e3ef03e539ed61..12f35e81e34caf834fd779f839c54068bcf806aa 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README.md @@ -22,7 +22,7 @@ KML_SPBLAS有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README_en.md b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README_en.md index 1e986fac4518a4fba292fabd2cf8689bc9d7ebbf..7273d3763fa0db152757d8e210066918638e340f 100644 --- a/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README_en.md +++ b/examples/mpi/devkitdemo-main/Development_framework/hpc-sdk/examples/kml/spblas/README_en.md @@ -24,7 +24,7 @@ There are multiple versions of KML_SPBLAS: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/Porting_advisor/testdemo/code_migration/code_mod/ksw.c b/examples/mpi/devkitdemo-main/Porting_advisor/testdemo/code_migration/code_mod/ksw.c index 339d397460ae647153c2407518eeee2c28f64066..aca564ea04cf71dd7f16c1c220991c2dc030accb 100644 --- a/examples/mpi/devkitdemo-main/Porting_advisor/testdemo/code_migration/code_mod/ksw.c +++ b/examples/mpi/devkitdemo-main/Porting_advisor/testdemo/code_migration/code_mod/ksw.c @@ -15,7 +15,7 @@ */ #if defined __aarch64__ #include "avx2neon.h" - //Suggestion: visit '$JARVIS_PROXY/kunpengcomputer/AvxToNeon' and obtain the 'avx2neon.h' source code according to the README.md file. + //Suggestion: visit 'https://github.com/kunpengcomputer/AvxToNeon' and obtain the 'avx2neon.h' source code according to the README.md file. #endif #include #include diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README.md index 2a714c8b1c889b0bd826b69760cc4e09411a2d0e..dbb641e3b3329ba574909dc2066aaaaee3cee25c 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README.md @@ -22,7 +22,7 @@ 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README_en.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README_en.md index b118aff86a9478271796495a03215d56f0634bc6..78c05678d522e5945e440dc7562dae277c06122c 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README_en.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/hmpi/bcast/README_en.md @@ -26,7 +26,7 @@ English | [简体中文](README.md) 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README.md index cbaa3162c35cfea50138e03af62f87c882279272..43d444163ede9d7994e1134ba05c0dfc5f9a0d98 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README.md @@ -28,7 +28,7 @@ KML_BLAS有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README_en.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README_en.md index 9ab53debb1e41179856ddc1f1373c3e15922b411..b45b5dc1c229f72d28e945f668bdaaaac40d5769 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README_en.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/blas/README_en.md @@ -29,7 +29,7 @@ There are multiple versions of KML_BLAS: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README.md index 00f1eac78fd3f3d52020574f0460db64d0dfe9a4..1eb55ebdc7764e52ceec70105b2c015748d1a45d 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README.md @@ -24,7 +24,7 @@ KML_FFT有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README_en.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README_en.md index 30a5b5bc2fd8f210421435f55008899f53fa649c..532c33fc024e72d93cd501fbc312b52824aab68c 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README_en.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/fft/README_en.md @@ -24,7 +24,7 @@ There are multiple versions of KML_FFT: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README.md index 9939a876546765661917e0b6c2d198aa878d8844..568231be973712bd44d3936caf19e437a7a7ea88 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README.md @@ -20,7 +20,7 @@ 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README_en.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README_en.md index a336e625fa342bdebfdda666e7804c982337b18d..bdc82ee12d1326b79dd540d9c09a714a3d236f1f 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README_en.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/lapack/README_en.md @@ -21,7 +21,7 @@ English | [简体中文](README.md) 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README.md index d354499b9e99266b742001db460634be78f1ca4d..81a5966652b1d118efb765d80e5177e36caf669e 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README.md @@ -24,7 +24,7 @@ KML_MATH有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README_en.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README_en.md index 4a1dacc68905d049f39119dce7ab2ca76cd76205..b8bad517a0241302618b0732910135940c14d5f8 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README_en.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/math/README_en.md @@ -24,7 +24,7 @@ There are multiple versions of KML_MATH: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README.md index c8d0ba618cf88cf0f392e89e4a38cdc4649c765e..12a5aa46385e26a5cc4478dcdc0eff6020b88937 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README.md @@ -24,7 +24,7 @@ KML_SPBLAS有多个版本： 1. 获取代码 ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. 切入到项目根路径 diff --git a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README_en.md b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README_en.md index bcb98b68d2ad8f334602798899bf18b980463f35..8a8de0fb20dcb96446390944f5b5b7da5706f83b 100644 --- a/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README_en.md +++ b/examples/mpi/devkitdemo-main/hpc-sdk/examples/kml/spblas/README_en.md @@ -28,7 +28,7 @@ There are multiple versions of KML_SPBLAS: 1. Obtain the code. ```shell - git clone $JARVIS_PROXY/kunpengcompute/devkitdemo.git + git clone https://github.com/kunpengcompute/devkitdemo.git ``` 2. Switch to the project root path. diff --git a/init.sh b/init.sh index c742945dbad8761cf3e557862622b2dbec7b5c64..bd7ec9205d1fcebe67aadcfd620d3d0708639c50 100644 --- a/init.sh +++ b/init.sh @@ -30,3 +30,9 @@ if ! type module >/dev/null 2>&1;then . $CHECK_ROOT && yum install -y environment-modules || apt install -y environment-modules source /etc/profile fi + +#yum װҪ +#echo "Install dep" +#dnf config-manager --add-repo http://10.0.0.101/iso/ +#yum -y --installroot=$JARVIS_EXE install curl curl-devel +#yum -y --installroot=$JARVIS_EXE install patch python3-devel \ No newline at end of file diff --git a/package/gsl/2.5/install.sh b/package/gsl/2.5/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..3850e409ef7da81ca4ab257d0c583050ce4219a2 --- /dev/null +++ b/package/gsl/2.5/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u http://mirrors.ustc.edu.cn/gnu/gsl/gsl-2.5.tar.gz +cd ${JARVIS_TMP} +rm -rf gsl-2.5 +tar -xvf ${JARVIS_DOWNLOAD}/gsl-2.5.tar.gz +cd gsl-2.5 +./configure --prefix=$1 +make -j +make install diff --git a/package/lapack/3.10.1/install.sh b/package/lapack/3.10.1/install.sh index d3ef54935fcdccdde8ab0c871224c3e36a213aaa..bef3538874fc7ba9c68a6fb4799d8d6eadf96e3d 100755 --- a/package/lapack/3.10.1/install.sh +++ b/package/lapack/3.10.1/install.sh @@ -5,10 +5,16 @@ set -e cd ${JARVIS_TMP} tar -xvf ${JARVIS_DOWNLOAD}/lapack-3.10.1.tar.gz cd lapack-3.10.1 +cp make.inc.example make.inc rm build -rf mkdir build cd build cmake ../ -DCMAKE_INSTALL_PREFIX=$1 -DBUILD_SHARED_LIBS=ON make -j $(nproc) make install -ln -s $1/lib64 $1/lib \ No newline at end of file + +cd .. +make -j $(nproc) + +cp lib*.a $1/lib64 +cp -r $1/lib64 $1/lib \ No newline at end of file diff --git a/package/lapack/3.8.0/bisheng/install.sh b/package/lapack/3.8.0/bisheng/install.sh index 4af2ad401b8a56327a8fec0c1ed96637ae381bda..c486c816093d37a64c41b1065a7367ab1a406d96 100755 --- a/package/lapack/3.8.0/bisheng/install.sh +++ b/package/lapack/3.8.0/bisheng/install.sh @@ -3,6 +3,7 @@ set -x set -e . $DOWNLOAD_TOOL -u https://www.cp2k.org/static/downloads/lapack-3.8.0.tgz cd ${JARVIS_TMP} +rm -rf lapack-3.8.0 tar -xvf ${JARVIS_DOWNLOAD}/lapack-3.8.0.tgz cd lapack-3.8.0 cp make.inc.example make.inc @@ -15,6 +16,7 @@ sed -i '30s/gfortran/flang/g' ./make.inc sed -i '50s/^/# /g' ./make.inc sed -i '54s/^#//g' ./make.inc make -j +rm -rf $1/lib/ mkdir $1/lib/ cp *.a $1/lib/ cp -r LAPACKE/include $1/ diff --git a/package/lapack/3.8.0/install.sh b/package/lapack/3.8.0/install.sh index 2dde522ee434d37c2060c7707d0bd8ce97a623fb..edb68a6542de599d1e44158d693a951c6c41f2c7 100755 --- a/package/lapack/3.8.0/install.sh +++ b/package/lapack/3.8.0/install.sh @@ -8,5 +8,6 @@ tar -xvf ${JARVIS_DOWNLOAD}/lapack-3.8.0.tgz cd lapack-3.8.0 cp make.inc.example make.inc make -j +rm -rf $1/lib/ mkdir $1/lib/ cp *.a $1/lib/ diff --git a/package/libvdwxc/0.4.1/install.sh b/package/libvdwxc/0.4.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..daabd9bda0e8af31143892382ec575743d3d0e2e --- /dev/null +++ b/package/libvdwxc/0.4.1/install.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://launchpad.net/libvdwxc/stable/0.4.0/+download/libvdwxc-0.4.0.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/libvdwxc-0.4.0.tar.gz +cd libvdwxc-0.4.0 +./configure --prefix=$1 --enable-shared=yes --enable-static=yes +make -j +make install diff --git a/package/libxc/4.0.1/install.sh b/package/libxc/4.0.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..a8d76c58c8a0d8d5a1640b0f1b47603e8cf371e4 --- /dev/null +++ b/package/libxc/4.0.1/install.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u http://forge.abinit.org/fallbacks/libxc-4.0.1.tar.gz +cd ${JARVIS_TMP} +rm -rf libxc-4.0.1 +tar -xvf ${JARVIS_DOWNLOAD}/libxc-4.0.1.tar.gz +cd libxc-4.0.1 +./configure --prefix=$1 -enable-shared=yes --enable-static=yes +make -j +make install + diff --git a/package/netcdf/4.7.0/clang/install.sh b/package/netcdf/4.7.0/clang/install.sh index 5696ac436db48af74b47d90aefc0cade5ea1ac4a..3ce87f05478daa42e634d639b1127231e63e8957 100755 --- a/package/netcdf/4.7.0/clang/install.sh +++ b/package/netcdf/4.7.0/clang/install.sh @@ -4,6 +4,10 @@ set -x set -e netcdf_c_version='4.7.0' netcdf_f_version='4.4.5' +pnetcdf_ver='1.11.2' + + + . ${DOWNLOAD_TOOL} -u https://codeload.github.com/Unidata/netcdf-fortran/tar.gz/refs/tags/v${netcdf_f_version} -f netcdf-fortran-${netcdf_f_version}.tar.gz . ${DOWNLOAD_TOOL} -u https://codeload.github.com/Unidata/netcdf-c/tar.gz/refs/tags/v${netcdf_c_version} -f netcdf-c-${netcdf_c_version}.tar.gz cd ${JARVIS_TMP} @@ -22,11 +26,22 @@ PNETCDF_DIR=${PNETCDF_PATH} cd include/ rm -rf ncconfigure.h + +cd $JARVIS_TMP_DOWNLOAD +exist_path=`md5sum ncconfigure.zip|awk '{print $1}'` +if [ -z "$exist_path" ]; then +wget http://github.com/Unidata/netcdf-c/files/3234181/ncconfigure.zip --no-ch +elif [ $exist_path != bf6777c8001d006bd5a6707ff74a2a1d ];then wget $JARVIS_PROXY/Unidata/netcdf-c/files/3234181/ncconfigure.zip --no-ch +fi +cd - +cp $JARVIS_TMP_DOWNLOAD/ncconfigure.zip . + unzip ncconfigure.zip cd .. -./configure --prefix=$1 ${build_type} --enable-shared --enable-netcdf-4 --disable-dap --with-pic --disable-doxygen --enable-static --enable-pnetcdf --enable-largefile CPPFLAGS="-O3 -I${HDF5_DIR}/include -I${PNETCDF_DIR}/include" LDFLAGS="-L${HDF5_DIR}/lib -L${PNETCDF_DIR}/lib -Wl,-rpath=${HDF5_DIR}/lib -Wl,-rpath=${PNETCDF_DIR}/lib" CFLAGS="-O3 -L${HDF5_DIR}/lib -L${PNETCDF_DIR}/lib -I${HDF5_DIR}/include -I${PNETCDF_DIR}/include" + +./configure --prefix=$1 ${build_type} --enable-shared --enable-netcdf-4 --disable-dap --with-pic --disable-doxygen --enable-static --enable-pnetcdf --enable-largefile CPPFLAGS="-O3 -I${HDF5_DIR}/include -I${PNETCDF_DIR}/include" LDFLAGS="-L${HDF5_DIR}/lib -L${PNETCDF_DIR}/lib" CFLAGS="-O3 -L${HDF5_DIR}/lib -L${PNETCDF_DIR}/lib -I${HDF5_DIR}/include -I${PNETCDF_DIR}/include" make -j16 make install @@ -36,7 +51,7 @@ export LD_LIBRARY_PATH=$1/lib:$LD_LIBRARY_PATH export NETCDF=${1} cd ../netcdf-fortran-${netcdf_f_version} -./configure --prefix=$1 ${build_type} --enable-shared --with-pic --disable-doxygen --enable-largefile --enable-static CPPFLAGS="-O3 -I${HDF5_DIR}/include -I${1}/include" LDFLAGS="-L${HDF5_DIR}/lib -L${1}/lib -Wl,-rpath=${HDF5_DIR}/lib -Wl,-rpath=${1}/lib" CFLAGS="-O3 -L${HDF5_DIR}/HDF5/lib -L${1}/lib -I${HDF5_DIR}/include -I${1}/include" CXXFLAGS="-O3 -L${HDF5_DIR}/lib -L${1}/lib -I${HDF5_DIR}/include -I${1}/include" FCFLAGS="-O3 -L${HDF5_DIR}/lib -L${1}/lib -I${HDF5_DIR}/include -I${1}/include" +./configure --prefix=$1 ${build_type} --enable-shared --with-pic --disable-doxygen --enable-largefile --enable-static CPPFLAGS="-O3 -I${HDF5_DIR}/include -I${1}/include" LDFLAGS="-L${HDF5_DIR}/lib -L${1}/lib -Wl" CFLAGS="-O3 -L${HDF5_DIR}/HDF5/lib -L${1}/lib -I${HDF5_DIR}/include -I${1}/include" CXXFLAGS="-O3 -L${HDF5_DIR}/lib -L${1}/lib -I${HDF5_DIR}/include -I${1}/include" FCFLAGS="-O3 -L${HDF5_DIR}/lib -L${1}/lib -I${HDF5_DIR}/include -I${1}/include" sed -i '11686c wl="-Wl,"' libtool sed -i '11838c wl="-Wl,"' libtool make -j16 diff --git a/templates/CP2K/7.1/bisheng/Linux-arm-clang.psmp b/templates/CP2K/7.1/bisheng/Linux-arm-clang.psmp index c3ed6b8f6ecd8377953fbe9733f2cbc83e893d5c..2569943d167bb1a5f8785bc9b77d12cf01b262b7 100644 --- a/templates/CP2K/7.1/bisheng/Linux-arm-clang.psmp +++ b/templates/CP2K/7.1/bisheng/Linux-arm-clang.psmp @@ -57,7 +57,7 @@ LIBS += $(FFTW_LIB)/libfftw3_threads.a LIBS += #LIBS += $(LIBXSMM_LIB)/libxsmmf.a #LIBS += $(LIBXSMM_LIB)/libxsmm.a -LIBS += $(MPI_PATH)/scalapack-lapack-bisheng/2.1.0/lib/libscalapack.a +LIBS += $(MPI_PATH)/scalapack-clang/2.1.0/lib/libscalapack.a LIBS += $(GNU_PATH)/lapack-bisheng/3.8.0/lib/liblapack.a LIBS += $(GNU_PATH)/lapack-bisheng/3.8.0/lib/librefblas.a LIBS += -ldl -lpthread -lstdc++ diff --git a/templates/CP2K/7.1/bisheng/data.CP2K.arm.cpu.config b/templates/CP2K/7.1/bisheng/data.CP2K.arm.cpu.config index e5bd41a0256860e28c205528436f7ce71a493b58..44652ab5a925664a5a09625922109c84f000f2c5 100644 --- a/templates/CP2K/7.1/bisheng/data.CP2K.arm.cpu.config +++ b/templates/CP2K/7.1/bisheng/data.CP2K.arm.cpu.config @@ -31,13 +31,15 @@ module load gsl/2.6 module load hmpi/1.1.1 module load gmp/6.2.0 module load boost/1.72.0 +module load lapack-bisheng/3.8.0 export CC=mpicc CXX=mpicxx FC=mpifort ./jarvis -install libint/2.6.0 clang+mpi ./jarvis -install fftw/3.3.8 clang+mpi -./jarvis -install scalapack/2.1.0/lapack-bisheng clang+mpi +#./jarvis -install scalapack/2.1.0/lapack-bisheng clang+mpi +./jarvis -install scalapack/2.1.0/clang bisheng+mpi ./jarvis -install plumed/2.6.2 clang+mpi -module load scalapack-lapack-bisheng/2.1.0 openblas/0.3.18 +module load scalapack-clang/2.1.0 openblas/0.3.18 ./jarvis -install elpa/2019.05.001 clang+mpi tar -zxvf $JARVIS_DOWNLOAD/cp2k-7.1.tar.gz @@ -52,15 +54,19 @@ module load gsl/2.6 [APP] app_name = CP2K -build_dir = ${JARVIS_ROOT}/cp2k-7.1.0 +build_dir = ${JARVIS_ROOT} binary_dir = ${JARVIS_ROOT}/cp2k-7.1.0/exe/Linux-arm-clang/ case_dir = ${JARVIS_ROOT}/cp2k-7.1.0/benchmarks/QS/ [BUILD] +rm -rf cp2k-7.1.0 +tar -zxvf $JARVIS_DOWNLOAD/cp2k-7.1.tar.gz +tar -zxvf $JARVIS_DOWNLOAD/dbcsr-2.0.1.tar.gz -C ${JARVIS_ROOT}/cp2k-7.1.0/exts/dbcsr --strip-components=1 +cd cp2k-7.1.0 cd ./arch cp ${JARVIS_ROOT}/templates/CP2K/7.1/bisheng/Linux-arm-clang.psmp ./ -sed -i "10s%path1%${JARVIS_ROOT}/software/libs/bisheng2.1.0/hmpi1.1.11%g" Linux-arm-clang.psmp -sed -i "11s%path2%${JARVIS_ROOT}/software/libs/bisheng2%g" Linux-arm-clang.psmp +sed -i "10s%path1%${JARVIS_ROOT}/software/libs/bisheng2.1.0/hmpi1.1.1%g" Linux-arm-clang.psmp +sed -i "11s%path2%${JARVIS_ROOT}/software/libs/bisheng2.1.0/%g" Linux-arm-clang.psmp cd .. make -j 128 ARCH=Linux-arm-clang VERSION=psmp diff --git a/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config b/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config index 13494baae9e405896fdb91a6ab3ad294bdfbd8d6..cf29696698d9f502f0965c62c4590e5a6dca18f2 100644 --- a/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config +++ b/templates/abinit/8.10.3/bisheng/data.abinit.arm.gpu.config @@ -10,6 +10,7 @@ wannier90/2.0.1.1 http://forge.abinit.org/fallbacks/wannier90-2.0.1.1.tar.gz abinit_package $JARVIS_PROXY/abinit/abinit/files/3586400/0001-Patching-m_polynomial_coeff.F90-for-ability-to-compi.patch.txt abinit_patch-8.10.3.patch [DEPENDENCY] +os=`cat /etc/os-release|grep VERSION_ID|awk -F \" '{print $2}'` module use ./software/modulefiles module purge ./jarvis -install bisheng/2.1.0 com @@ -19,22 +20,49 @@ export CC=clang CXX=clang++ FC=flang ./jarvis -install hmpi/1.1.1 clang module load hmpi/1.1.1 export CC=mpicc CXX=mpicxx FC=mpifort + + + + +if [ "$os" == "22.03" ] || [ "$os" == "V10" ] ;then ./jarvis -install package/hdf5/1.10.1/clang clang+mpi -./jarvis -install package/pnetcdf/1.11.2 clang+mpi module load hdf5-clang/1.10.1 -module load pnetcdf/1.11.2 +./jarvis -install package/pnetcdf/1.11.2 clang+mpi +module load pnetcdf/1.11.2 +./jarvis -install package/netcdf/4.7.4/clang clang+mpi + + +else +./jarvis -install package/hdf5/1.10.1 clang+mpi +module load hdf5/1.10.1 +./jarvis -install package/pnetcdf/1.11.2 clang+mpi +module load pnetcdf/1.11.2 ./jarvis -install package/netcdf/4.7.0/clang clang+mpi +fi + + [ENV] +os=`cat /etc/os-release|grep VERSION_ID|awk -F \" '{print $2}'` module use ./software/modulefiles module purge #module load kgcc/9.3.1 module load bisheng/2.1.0 module load hmpi/1.1.1 +if [ "$os" == "22.03" ] || [ "$os" == "V10" ] ;then module load hdf5-clang/1.10.1 module load pnetcdf/1.11.2 -module load netcdf-clang/4.7.0 +module load netcdf-clang/4.7.4 + + +else +module load hdf5/1.10.1 +module load pnetcdf/1.11.2 +module load netcdf/4.7.0 +fi + + module load openblas/0.3.18 export CC=mpicc CXX=mpicxx FC=mpifort diff --git a/templates/abinit/8.10.3/data.abinit.arm.gpu.config b/templates/abinit/8.10.3/data.abinit.arm.gpu.config index 4a82d86eae2af4090ace376eb8223e992bf80a36..e2da81c2c192a111b42bf75826369772a7941b50 100644 --- a/templates/abinit/8.10.3/data.abinit.arm.gpu.config +++ b/templates/abinit/8.10.3/data.abinit.arm.gpu.config @@ -18,11 +18,20 @@ export CC=gcc CXX=g++ FC=gfortran ./jarvis -install hmpi/1.1.1 gcc module load hmpi/1.1.1 export CC=mpicc CXX=mpicxx FC=mpifort + ./jarvis -install package/hdf5/1.10.1 gcc+mpi +module load hdf5/1.10.1 ./jarvis -install package/pnetcdf/1.11.2 gcc+mpi +module load pnetcdf/1.11.2 + +./jarvis -install package/curl/7.82.0 gcc +module load curl/7.82.0 + ./jarvis -install package/netcdf/4.7.0 gcc+mpi -./jarvis -install package/openblas/0.3.18 gcc +module load netcdf/4.7.0 +./jarvis -install package/openblas/0.3.18 gcc +module load openblas/0.3.18 [ENV] module use ./software/modulefiles diff --git a/templates/gromacs/2019.3/bisheng/.data.gromacs.arm.gpu.config.swp b/templates/gromacs/2019.3/bisheng/.data.gromacs.arm.gpu.config.swp deleted file mode 100644 index 3a5508f4c5eca968907fdca512d72adb3e626c02..0000000000000000000000000000000000000000 Binary files a/templates/gromacs/2019.3/bisheng/.data.gromacs.arm.gpu.config.swp and /dev/null differ diff --git a/templates/nwchem/6.8.1/data.nwchem.arm.cpu.config b/templates/nwchem/6.8.1/data.nwchem.arm.cpu.config index 9f0c058016c40a24f6d9e9b9a201e6bb02c75299..b1882df678a4bbafaed328894a2734ad66bd0b7d 100644 --- a/templates/nwchem/6.8.1/data.nwchem.arm.cpu.config +++ b/templates/nwchem/6.8.1/data.nwchem.arm.cpu.config @@ -40,7 +40,13 @@ export NWCHEM_MODULES=all export USE_MPI=y export USE_INTERNALBLAS=y export NWCHEM_LONG_PATHS=Y + + + +cd ${JARVIS_TMP}/nwchem-6.8.1-release +mv $JARVIS_DOWNLOAD/ga-5.6.5.tar.gz src/tools cd ${JARVIS_TMP}/nwchem-6.8.1-release/src + make nwchem_config make FC=flang diff --git a/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config b/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config index 30c925e37e1223ef5759c922ba46ed48bd8b0440..9e9da4f653c32c98078bac3dd1813ceaabe5bfed 100644 --- a/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config +++ b/templates/octopus/10.3/data.octopus.arm.kpgcc.cpu.config @@ -2,7 +2,7 @@ 11.11.11.11 [DOWNLOAD] -octopus/10.3 https://octopus-code.org/down.php?file=10.3/octopus-10.3.tar.gz octopus-10.3.tar.gz +octopus/10.3 https://octopus-code.org/download/10.3/octopus-10.3.tar.gz octopus-10.3.tar.gz [DEPENDENCY] module purge diff --git a/templates/octopus/11.4/data.octopus.arm.kpgcc.cpu.config b/templates/octopus/11.4/data.octopus.arm.kpgcc.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..16fa3699cd4ac0fc30923f35e8f5648544833030 --- /dev/null +++ b/templates/octopus/11.4/data.octopus.arm.kpgcc.cpu.config @@ -0,0 +1,100 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +octopus/11.4 https://octopus-code.org/download/11.4/octopus-11.4.tar.gz octopus-11.4.tar.gz + +[DEPENDENCY] +module purge + +./jarvis -install bisheng/2.4.0 com +module use ./software/modulefiles +module load bisheng/2.1.0 + +module purge +./jarvis -install kgcc/9.3.1 com +module use ./software/modulefiles + +module load kgcc/9.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` +./jarvis -install hmpi/1.1.1 gcc +./jarvis -install gsl/2.5 gcc +./jarvis -install lapack/3.10.1 gcc +./jarvis -install libxc/4.0.1 gcc + + + + + +module load hmpi/1.1.1 +export CC=`which mpicc` +export CXX=`which mpicxx` +export FC=`which mpifort` +export OPAL_PREFIX=$JARVIS_MPI/hmpi1.1.1-kgcc9.3.1/1.1.1 +./jarvis -install fftw/3.3.8 gcc+mpi +./jarvis -install libvdwxc/0.4.0 gcc+mpi +tar -xvf ${JARVIS_DOWNLOAD}/octopus-11.4.tar.gz + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles + +module load kgcc/9.3.1 + + +export OPAL_PREFIX=$JARVIS_MPI/hmpi1.1.1-bisheng2.4.0/1.1.1 +module load lapack/3.10.1 +module load gsl/2.5 +module load libxc/4.0.1 + +module add bisheng/2.4.0 +module load hmpi/1.1.1 + + + + + +[APP] +app_name = octopus +build_dir = ${JARVIS_ROOT}/octopus-11.4 +binary_dir = ./software/apps/bisheng/octopus/11.4 +case_dir = + +[BUILD] + + +./configure CC=mpicc CXX=mpicxx FC=mpifort \ +--prefix=${JARVIS_ROOT}/software/apps/bisheng/octopus/11.4 \ +CFLAGS='-lgfortran' \ +FCFLAGS=' -lgfortran' \ +--with-gsl-prefix==${JARVIS_LIBS}/kgcc9.3.1/gsl/2.5 \ +--with-libxc-prefix=${JARVIS_LIBS}/kgcc9.3.1/libxc/4.0.1 \ +--with-fftw-prefix=${JARVIS_LIBS}/kgcc9.3.1/hmpi1.1.1/fftw/3.3.8 \ +--with-libvdwxc-prefix=${JARVIS_LIBS}/kgcc9.3.1/hmpi1.1.1/libvdwxc/4.0.0 \ +--with-blas=${JARVIS_LIBS}/kgcc9.3.1/lapack/3.10.1/lib/librefblas.a \ +--with-lapack=${JARVIS_LIBS}/kgcc9.3.1/lapack/3.10.1/lib/liblapack.a \ +--enable-mpi \ +--disable-zdotc-test + + + + +sed -i -e '0,/FINISHED/{s/FINISHED/FINISHED1/}' -e 's/(FINISHED/(FINISHED1/g' src/multisystem/propagator.F90 +sed -i 's/type(\*)/type(c_ptr)/g' src/basic/cuda.F90 +sed -i '0,/private/{s/private/\!private/}' src/basic/clock.F90 +sed -i 's/FINISHED/FINISHED1/g' src/multisystem/system.F90 +sed -i -e 's/test_clock_a .lt. test_clock_b/clock_is_earlier(test_clock_a,test_clock_b)/g' -e 's/test_clock_a .le. test_clock_b/clock_is_equal_or_earlier(test_clock_a,test_clock_b)/g' -e 's/test_clock_a .gt. test_clock_b/clock_is_later(test_clock_a,test_clock_b)/g' -e 's/test_clock_a .ge. test_clock_b/clock_is_equal_or_later(test_clock_a,test_clock_b)/g' -e 's/test_clock_a .eq. test_clock_b/clock_is_equal(test_clock_a,test_clock_b)/g' src/main/test.F90 +sed -i '/SAFE_DEALLOCATE_P(systems)/s+^+!+g' src/main/run.F90 +sed -i -e 's/cuda_memcpy_htod(this%mem, data(1)/cuda_memcpy_htod(this%mem, c_loc(data(1))/g' -e 's/cuda_memcpy_htod(this%mem, data(1, 1)/cuda_memcpy_htod(this%mem, c_loc(data(1, 1))/g' -e 's/cuda_memcpy_htod(this%mem, data(1, 1, 1)/cuda_memcpy_htod(this%mem, c_loc(data(1, 1, 1))/g' -e 's/cuda_memcpy_dtoh(this%mem, data(1)/cuda_memcpy_dtoh(this%mem, c_loc(data(1))/g' -e 's/cuda_memcpy_dtoh(this%mem, data(1, 1)/cuda_memcpy_dtoh(this%mem, c_loc(data(1, 1))/g' -e 's/cuda_memcpy_dtoh(this%mem, data(1, 1, 1)/cuda_memcpy_dtoh(this%mem, c_loc(data(1, 1, 1))/g' src/basic/accel_inc.F90 + +make -j +make install + + +[RUN] +run = +binary = +nodes = 1 +