Ubuntu:Intel+fftw+openmpi+openmx (sequent)

2023年12月29日发(作者：)

Ubuntu：Intel+fftw+openmpi+openmx (sequent)2016年5月4日21:39Step 1. Intel1.更新编译器sudo apt-get update

sudo apt-get install gccsudo apt-get install g++sudo apt-get install python

gcc --versiong++ --versionpython --version2.进入目录cd parallel_studio_xe_2013_update2_intel643.启动./4.欢迎界面，根据提示，基本都是默认选项直接按‘Enter’;5.选择Root选项：passwd；如果是首次使用root，可能会出现密码错误，需要先重设root passwd： passwd root6.进入设置界面Step no: 1 of 7 | Welcome--------------------------------------------------------------------------------Welcome to the Intel(R) Parallel Studio XE 2013 Update 2 for Linux* installationprogram.--------------------------------------------------------------------------------You will complete the steps below during this installation:Step 1 : WelcomeStep 2 : LicenseStep 3 : ActivationStep 4 : Intel(R) Software Improvement ProgramStep 5 : OptionsStep 6 : InstallationStep 7 : Complete--------------------------------------------------------------------------------Press "Enter" key to continue or "q" to quit: ‘Enter'操作系统会提示不支持，跳过。Step no: 1 of 7 | Options > Missing Optional Pre-requisite(s)--------------------------------------------------------------------------------There are one or more optional unresolved issues. It is highly recommended toresolve them all before you continue the installation. You can fix them withoutexiting from the installation and re-check. Or you can quit from theinstallation, fix them and run the installation again.--------------------------------------------------------------------------------Missing optional pre-requisites--Intel(R) Composer XE 2013 Update 2 for Linux*: unsupported OS--------------------------------------------------------------------------------1. Skip missing optional pre-requisites [default]2. Show the detailed info about issue(s)3. Re-check the pre-requisitesh. Helpb. Back to the previous menuq. Quit--------------------------------------------------------------------------------Please type a selection or press "Enter" to accept default choice [1]: 'Enter'8.提示证书协议，选择接受license，输入: accept'9.选择激活方式，使用文件激活，选择3

Step no: 3 of 7 | Activation--------------------------------------------------------------------------------If you have purchased this product and have the serial number and a connectionto the internet you can choose to activate the product at this time. Activationis a secure and anonymous one-time process that verifies your software licensingrights to use the product. Alternatively, you can choose to evaluate theproduct or defer activation by choosing the evaluate option. Evaluation software 分区OpenMx 的第1 页/configure --prefix=/usr/local/fftw3 --enable-shared

指定安装路径 make install4.安装完成，设置环境变量。在/etc/profile , ~/.bashrc文件的末尾添加，重启sudo gedit /etc/profileexport LD_LIBRARY_PATH=/usr/local/fftw3/lib:$LD_LIBRARY_PATH

sudo gedit ~/.bashrcexport LD_LIBRARY_PATH=/usr/local/fftw3/lib:$LD_LIBRARY_PATHsu

gedit ~/.bashrcexport LD_LIBRARY_PATH=/usr/local/fftw3/lib:$LD_LIBRARY_PATHrestart5.实例调试：#include "fftw3.h"#include #include #include #define N4#define REAL0#define IMAG1#define PI3.98int main (void){ fftw_complex *in, *out; fftw_plan p; double constants[N] = {10, 2.1, 4.7, 1.3}; double f; int i, j; /* Allocate memory for the arrays */ in = fftw_malloc(sizeof(fftw_complex) * N); out = fftw_malloc(sizeof(fftw_complex) * N); if ((in == NULL) || (out == NULL)) {printf ("Error: insufficient available memoryn"); } else {/* Create the FFTW execution plan */p = fftw_plan_dft_1d(N, in, out, FFTW_FORWARD, FFTW_ESTIMATE);/* Initialize the input data */for (i = 0; i < N; i++) { /* All sampling points */ in[i][REAL] = constants[0]; in[i][IMAG] = 0; for (j = 1; j < N; j++) { /* All frequencies */ in[i][REAL] += constants[j] * cos(j * i * 2 * PI / (double)N); in[i][IMAG] += constants[j] * sin(j * i * 2 * PI / (double)N); }}/* Execute plan */fftw_execute(p);/* Destroy plan */fftw_destroy_plan(p);/* Display results */printf ("Constants[] = {");for (i = 0; i < N; i++) printf("%lf%s", constants[i], (i == N-1) ? "}n" : ", ");printf ("Input[][REAL] = {");for (i = 0; i < N; i++) printf("%lf%s", in[i][REAL], (i == N-1) ? "}n" : ", ");printf ("Output[][REAL] = {");for (i = 0; i < N; i++) printf("%lf%s", out[i][REAL], (i == N-1) ? "}n" : ", ");/* Scale output */f = 1.0/sqrt((double)N);for (i = 0; i < N; i++) out[i][REAL] *= f;/* Display final results */printf ("Scaled[][REAL] = {");for (i = 0; i < N; i++) printf("%lf%s", out[i][REAL], (i == N-1) ? "}n" : ", "); } /* Free allocated memory */ if (in != NULL) fftw_free(in); if (out != NULL) fftw_free(out); return 0;}6.编译测试：[root@sonky examples]# gcc fftw1.c -o fftw -lfftw3 -lm[root@sonky examples]# ./fftw运行结果：Constants[] = {10.000000, 2.100000, 4.700000, 1.300000}Input[][REAL] = {18.100000, 5.300000, 11.300000, 5.300000}Output[][REAL] = {40.000000, 8.400000, 18.800000, 5.200000}Scaled[][REAL] = {20.000000, 4.200000, 9.400000, 2.600000}

will time out in about one month. Also you can use license file, licensemanager, or remote activation if the system you are installing on does nothave internet access activation options.--------------------------------------------------------------------------------1. I want to activate my product using a serial number [default]2. I want to evaluate my product or activate later3. I want to activate either remotely, or by using a license file, or by using alicense managerh. Helpb. Back to the previous menuq. Quit--------------------------------------------------------------------------------Please type a selection or press "Enter" to accept default choice [1]:3 ‘Enter’10.指定license文件Step i1.解压缩，进入安装目录tar xvf openmpi-1.1.02.切换到root环境，否则下一步configure会报错，如果仍然报错，打开 ~/.bashrc

and /etc/profile 检查intel的 ‘source LD_~~’ 是否已经添加：supasswd3.指定安装目录：prefix；指定intel编译器：CC=icc CXX=icpc FC=ifort F77=ifort./configure --prefix=/opt/openmpi-165 CC=icc CXX=icpc FC=ifort F77=ifortStep no: 3 of 7 | Activation > Advanced activation--------------------------------------------------------------------------------You can use license file, license manager, or the system you are installing ondoes not have internet access activation options.--------------------------------------------------------------------------------1. Use a different computer with internet access [default]2. Use a license file3. Use a license serverh. Helpb. Back to the previous menuq. Quit--------------------------------------------------------------------------------Please type a selection or press "Enter" to accept default choice [1]: 2Note: Press "Enter" key to back to the previous type the full path to your license file(s):

../../intel_parallel_studio_xe_2013_update_3'Enter'--------------------------------------------------------------------------------Activation completed successfully.--------------------------------------------------------------------------------Press "Enter" key to continue: 'Enter'11.是否加入改进计划，任意：Step no: 4 of 7 | Intel(R) Software Improvement Program--------------------------------------------------------------------------------Help improve your experience with Intel(R) softwareParticipate in the design of future Intel software. Select 'Yes' to give uspermission to learn about how you use your Intel software and we will do therest.-No Personal contact information is collected-There are no surveys or additional follow-up emails by opting in-You can stop participating at any timeLearn more about Intel(R) Software Improvement Program/en-us/articles/software-improvement-programWith your permission, Intel may automatically receive anonymous informationabout how you use your current and future Intel software.--------------------------------------------------------------------------------1. Yes, I am willing to participate and improve Intel software. (Recommended)2. No, I don't want to participate in the Intel(R) Software Improvement Programat

this time.b. Back to the previous menuq. Quit--------------------------------------------------------------------------------Please type a selection: 2 ‘Enter’12.此处可以修改安装目录和要安装的组件，默认安装到/opt/intel目录下：Step no: 5 of 7 | Options--------------------------------------------------------------------------------You are now ready to begin installation. You can use all default installationsettings by simply choosing the "Start installation Now" option or you cancustomize these settings by selecting any of the change options given belowfirst. You can view a summary of the settings by selecting"Show pre-install summary".--------------------------------------------------------------------------------1. Start installation Now2. Change install directory [ /opt/intel ]3. Change components to install [ All ]4. Change advanced options5. Show pre-install summary 分区OpenMx 的第2 页4.开始编译（可以使用-j后面跟数字进行多核编译，能减少编译时间）：make –j45.开始安装：make install6.安装完成，设置环境变量。在/etc/profile , ~/.bashrc文件的末尾添加，重启sudo gedit /etc/profilesudo gedit ~/.bashrcsu

gedit ~/.bashrcrestart7.确认安装成功[root@hpc ~]# which mpicc/opt/openmpi-165/bin/mpicc[root@hpc ~]# mpicc -vicc version 15.1.0 (gcc version 4.4.6 compatibility)Step 1.解压缩，进入安装目录tar xvf openmx3.8cd source2.修改makefile，配置调用库路径：CC = mpicc -openmp -O3 -I/usr/local/fftw3/include -I/opt/intel/mkl/includeFC = mpifort -openmp -O3 -I/opt/intel/mkl/includeLIB = -L/usr/local/fftw3/lib -lfftw3 -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lifcore -L/opt/openmpi/lib -lmpi -lmpi_mpifh -lmpi_usempif083.安装sudo make install4.安装完毕，测试：cd ../work../source/openmx 5.查看mpirun路径

export MPI_HOME=/opt/openmpi-165 export PATH=$MPI_HOME/bin:$PATH export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH export MPI_HOME=/opt/openmpi-165 export PATH=$MPI_HOME/bin:$PATH export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH export MPI_HOME=/opt/openmpi-165 export PATH=$MPI_HOME/bin:$PATH export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH

1. Start installation Now2. Change install directory [ /opt/intel ]3. Change components to install [ All ]4. Change advanced options5. Show pre-install summaryh. Helpb. Back to the previous menuq. Quit--------------------------------------------------------------------------------Please type a selection or press "Enter" to accept default choice [1]:WARNING: Destination directory already you like to overwrite this directory? ( Yes/No ) [ Yes ] : ‘Enter’13.提示我的虚拟机不支持此功能，跳过即可：Step no: 5 of 7 | Options > Missing Optional Pre-requisite(s)--------------------------------------------------------------------------------There are one or more optional unresolved issues. It is highly recommended toresolve them all before you continue the installation. You can fix them withoutexiting from the installation and re-check. Or you can quit from theinstallation, fix them and run the installation again.--------------------------------------------------------------------------------Missing optional pre-requisites--Intel(R) VTune(TM) Amplifier XE 2013 Update 4: Power analysis is not

enabled--------------------------------------------------------------------------------1. Skip missing optional pre-requisites [default]2. Show the detailed info about issue(s)3. Re-check the pre-requisitesh. Helpb. Back to the previous menuq. Quit--------------------------------------------------------------------------------Please type a selection or press "Enter" to accept default choice [1]: ‘Enter’14.开始安装，不断的Enter & Space：Step no: 6 of 7 | Installation--------------------------------------------------------------------------------Each component will be installed individually. If you cancel the installation,components that have been completely installed will remain on your system. Thisinstallation may take several minutes, depending on your system and the optionsyou selected.--------------------------------------------------------------------------------Installing Amplifier XE Command line done--------------------------------------------------------------------------------Installing Amplifier XE Sampling driver WARNING: NMI watchdog timer is tion: turn off the nmi_watchdog timer before running sampling.--------------------------------------------------------------------------------Installing Amplifier XE Power driver done--------------------------------------------------------------------------------Installing Amplifier XE Graphical user done--------------------------------------------------------------------------------Installing Inspector XE Command line done--------------------------------------------------------------------------------Installing Inspector XE Graphical user done--------------------------------------------------------------------------------Installing Advisor XE Command line done--------------------------------------------------------------------------------Installing Advisor XE Graphical user done--------------------------------------------------------------------------------Installing Intel Fortran Compiler XE 13.1 on Intel(R) done--------------------------------------------------------------------------------Installing Intel C++ Compiler XE 13.1 on Intel(R) done--------------------------------------------------------------------------------Installing Intel Debugger 13.0 on Intel(R) done--------------------------------------------------------------------------------Installing Intel Math Kernel Library 11.0 Update 2 on Intel(R) done--------------------------------------------------------------------------------Installing Intel Integrated Performance Primitives 7.1 Update 1 on Intel(R) done--------------------------------------------------------------------------------Installing Intel Threading Building Blocks 4.1 Update 2 core files done-------------------------------------------------------------------------------- doneStep no: 7 of 7 | Complete--------------------------------------------------------------------------------Thank you for installing and using theIntel(R) Parallel Studio XE 2013 Update 2 for Linux*Reminder: Intel(R) VTune(TM) Amplifier XE users must be members of the "vtune"permissions group in order to use Event-based register your product purchase, visit/RegCenter/?media=5G9To get started using Intel(R) VTune(TM) Amplifier XE 2013 Update 4:-To set your environment variables:# source/opt/intel/vtune_amplifier_xe_2013/-To start the graphical user interface: amplxe-gui-To use the command-line interface: amplxe-cl-For more getting started resources: /opt/intel/vtune_amplifier_xe_2013/documentation/en/welcomepage/get_ get started using Intel(R) Inspector XE 2013 Update 4:-To set your environment variables:# source/opt/intel/inspector_xe_2013/-To start the graphical user interface: inspxe-gui-To use the command-line interface: inspxe-cl-For more getting started resources: /opt/intel/inspector_xe_2013/documentation/en/welcomepage/get_ get started using Intel(R) Advisor XE 2013 Update 2:-To set your environment variables:# source/opt/intel/advisor_xe_2013/ 分区OpenMx 的第3 页cd ../work../source/openmx 5.查看mpirun路径which mpirun/opt/openmpi/bin/mpirun

6.并行计算/opt/openmmpi/bin/mpirun -np 4 /home/openmx3.8/source/openmx

> nt 2Attention（可能会用上的指令）:echo $LD_LIBRARY_PATH

echoLD_LIBRARY_PATH=>d+清空路径：LD_LIBRARY_PATH=echo LD_LIBRARY_PATH= > d +x

/opt/intel/advisor_xe_2013/-To start the graphical user interface: advixe-gui-To use the command-line interface: advixe-cl-For more getting started resources: /opt/intel/advisor_xe_2013/documentation/en/welcomepage/get_ get started using Intel(R) Composer XE 2013 Update 2 for Linux*:-Set the environment variables for a terminal window using one of thefollowing (replace "intel64" with "ia32" if you are using a 32-bitplatform).For csh/tcsh:$ source /opt/intel/bin/ intel64For bash:$ source /opt/intel/bin/ intel64$ source /opt/intel/bin/ intel64*****将这两条命令写入到bashrc,再注销重新登入就好了******************************************************To invoke the installed compilers:For C++: icpcFor C: iccFor Fortran: ifortTo get help, append the -help option or precede with the man command.-For more getting started resources:/opt/intel/composer_xe_2013/Documentation/en_US/get_started_./opt/intel/composer_xe_2013/Documentation/en_US/get_started_ view movies and additional training, visit/software/products.--------------------------------------------------------------------------------q. Quit [default]--------------------------------------------------------------------------------Please type a selection or press "Enter" to accept default choice [q]: q[root@hpc parallel_studio_xe_2013_update2_intel64]#15.安装完成，设置环境变量，最好把root环境下的环境变量也仪器设置。在/etc/profile , ~/.bashrc文件的末尾加入如下命令，重新登录后生效:sudo gedit /etc/profilepasswodsource /opt/intel/bin/ intel64source /opt/intel/bin/ intel64source /opt/intel/bin/ intel64sudo gedit ~/.bashrcsource /opt/intel/bin/ intel64source /opt/intel/bin/ intel64source /opt/intel/bin/ intel64su

passwdgedit ~/.bashrcsource /opt/intel/bin/ intel64source /opt/intel/bin/ intel64source /opt/intel/bin/ intel64restart16.确认安装成功[root@~]# icc -vicc version 15.1.0 (gcc version 4.4.6 compatibility) 分区OpenMx 的第4 页