《斤竹精舍·游艺集》 2020 Crystal

Crystal安装及测试 UNIX/Linux

Posted by XiLock on July 16, 2020

前言

Crystal主要包括两个模块：crystal和properties

  1. crystal:compute the energy, analytical gradient and wave function for a given geometry, which can also be fully optimized, compute frequencies at Gamma.
  2. properties:compute one electron properties (electrostatic potential, charge density, …); analyse the wave function in direct and reciprocal space transform the Bloch functions (BF) into Wannier functions (localization of BF)
crystal的运行模式
  1. crystal sequential execution
  2. Pcrystal replicated data parallel execution
  3. MPPcrystal distributed data parallel execution (需要额外的库)

本文以sequential为例介绍安装，Pcrystal和MPPcrystal的安装参见http://www.crystal.unito.it => documentation

软件计算过程

The two programs, crystal and properties, interact via files stored on disk.

  1. crystal: Unformatted wave function information is written by crystal in file fort.9; formatted wave function (wf) information is written by crystal in file fort.98.
  2. properties: properties can read wf information computed by crystal unformatted (file fort.9) or formatted (file fort.98). Formatted data written in file fort.98 can be moved from one platform to another (e.g.: from Opteron to Itanium).
部分术语
  1. “ARCH” string to identify the operating system and/or the compiler (e.g. Linux-pgf, Linux-ifort, MacOsx)
  2. “VERSION” string to identify the crystal version (e.g. v1.0.3)
  3. d12 extension of file meant to be input to crystal
  4. d3 extension of file meant to be input to properties

注：sequential版本不需要安装ifort，并行版的话需要，具体参见Pcrystal和MPPcrystal的安装教程。

安装过程

bin包
  1. log in as a generic user, and cd to your home directory
  2. make the crystal root directory - it is called $CRY2K14_ROOT in the following
  3. change directory to $CRY2K14_ROOT
  4. 下载与自己系统适配的代码包至$CRY2K14_ROOT，如crystal14_v1_0_3_Linux-ifort_XE_openmpi-1.6_amd64.exe.tar.gz
  5. decompress the files: gunzip crystal14_v1_0_3_Linux-ifort_XE_openmpi-1.6_amd64.exe.tar.gz， 得到crystal14_v1_0_3_Linux-ifort_XE_openmpi-1.6_amd64.exe.tar
  6. untar the files: tar -xvf crystal14_v1_0_3_Linux_XE_openmpi-1.6_amd64.exe.tar， 得到解压后的文件夹（The directory bin contains a sub-directory foreach type of executable, identified by a string (ARCH), and for each release (the first one being v1.0.0).）
    utils(Scripts to run CRYSTAL)

    为了更方便的运行CRYSTAL

  7. 下载utils（如utils14.zip）至$CRY2K14_ROOT
  8. decompress and untar the file: gunzip utils14.tar.gz 和 tar -xvf utils14.tar，得到一堆文件：runcry14、runmpi14、runprop14、cry2k14.cshrc、cry2k14.bashrc、runcry14mp2、runcryscor09
  9. 进入utils14文件夹后提升其中执行文件的权限: chmod +x run*
  10. 备份cry2k14.bashrc文件（cry2k14_copy.bashrc）后对cry2k14.bashrc中的3个变量进行修改：CRY2K14_ROOT:CRYSTAL14 root directory(e.g. CRYSTAL14), CRY2K14_ARCH:ARCH string to identify the executable(e.g. Linux-pgf), CRY2K14_SCRDIR:temporary directory for scratch files(e.g. $HOME)
  11. 将cry2k14.bashrc文件复制到home文件夹中，在~/.bashrc中添加 source cry2k14.bashrc 并在terminal中执行一下该命令
    测试case
  12. 下载case文件：http://www.crystal.unito.it/test_cases/inputs_wf.tar.gz
  13. 或者For tests on geometry optimization and vibrational frequencies calculation see the CRYSTAL tutorials home page: http://www.crystal.unito.it/tutorials/index.html， 或者move to http://www.crystal.unito.it ==> documentation ==> test cases and download input files.
  14. 解压算例文件: gunzip *.gz 和 tar -xvf inputs.......tar，之后得到一堆文件：crystal (.d12) and properties (.d3)
  15. 新建文件夹test_case并将test11 (bulk MgO) 复制进去，运行算例: runcry14 test11，开始计算，完成后得到文件: test11.out: standard output (crystal+properties); test11.f9: unformatted wf data (written by crystal); test11.f98: formatted wf data (written by crystal)
  16. 查看单点能: grep "GY(HF" test11.out, 结果应为:TOTAL ENERGY(HF)(AU)( 7) -2.7466419188884E+02 DE 3.7E-08 tst 3.2E-09 PX 4.1E-04
    可视化软件Crgra2006安装（非必要）
  17. The package for visualization of bands, doss, maps, from the data written in file fort.25 by the program properties. 下载链接: http://www.crystal.unito.it/crgra2006/crgra2006.html ；
  18. 确认电脑上有A standard postscript visualizer, called by the command gv，可以用whereis gv查看；
  19. 解压缩 gunzip Crgra2006.tar.gz tar -xvf Crgra2006.tar，得到一堆band, doss, maps之类的文件和文件夹；
  20. 将Crgra2006添加到环境变量里（在cry2k14.bashrc里修改默认路径即可）

Pcrystal式并行版安装

法1 - 重新编译 (参见:howtoinstall_from_objects.txt)
准备工作

准备文件pr14e-compiled objects modules ：如crystal14_v1_0_1_Linux-ifort_emt64_Pdistrib.tar.gz

mkdir CRYSTAL14
cp crystal14_v1_0_1_Linux-ifort_emt64_Pdistrib.tar.gz CRYSTAL14/.
cd CRYSTAL14
tar -zxvf crystal14_v1_0_1_Linux-ifort_emt64_Pdistrib.tar.gz
cd build
cd Xmakes
编译
  1. 修改Linux-ifort_XE_emt64.inc文件中的变量MPIBIN，将其指向MPI的位置，假如使用mpif90的话就要指向mpif90的位置以实现对其调用.
  2. 返回上级文件夹进行编译，瞬间完成，得到bin文件夹及其下子文件，例如/bin/Linux-ifort_XE_emt64/v1_0_1.
cd ..
make parallel
配置环境变量

参见:https://www.crystal.unito.it/Manuals/crystal17_P.pdf

  1. 像非并行版那样解压utils并赋予权限；
  2. 在runmpi14里指定mpirun的bin位置
  3. 在utils文件夹里添加两个文件 machines.LINUX 和 nodes.par并赋予其权限，两个文件中的内容相同，均为每行一个节点名，如第一行node5，第二行node1，第三行node6等，第一行的被默认设为master host.
  4. 测试： runmpi14 nprocs inputfilename，如 runmpi14 4 test11， nproc指要调用的cpu个数，现阶段只能实现将nprocs平均分配到每个node上，之后考虑如何实现指定每个node分别调用几个cpu.
法2 - 利用已编译好的mpi版本（未必可行）

该法不兼容1.6以下的mpi，低版本mpi请参考法1

准备工作
  1. 准备文件：crystal14_v1_0_4_Linux-ifort_openmpi-1.6_emt64_exe.tar
  2. 像非并行版那样安装
    配置环境变量

    参见:https://www.crystal.unito.it/Manuals/crystal17_P.pdf

  3. 在runmpi14里指定mpirun的bin位置
  4. 在utils文件夹里添加两个文件 machines.LINUX 和 nodes.par并赋予其权限，两个文件中的内容相同，均为每行一个节点名，如第一行node5，第二行node1，第三行node6等，第一行的被默认设为master host（若要指定每个节点可用的processes，在machinefile.LINUX中的节点名之后用slots指定）.
  5. 测试： runmpi14 nprocs inputfilename，如 runmpi14 4 test11， nproc指要调用的cpu个数，mpirun会根据machinefile.LINUX来进行分配.

machinefile.LINUX (用于mpirun命令，调用node5和node6且分别指定可调用7和3个processes)

node5 slots=7
node6 slots=3

nodes.par （用于runmpi14脚本）

node5
node6

PBS脚本示例

#!/bin/sh
#
#This is an example script CRYSTAL14 JOB SCRIPT
#
#These commands set up the Grid Environment for your job:
#PBS -N CRYSTAL14-JOB
#PBS -l nodes=1:ppn=8
#PBS -l walltime=2400:00:00
#PBS -l mem=7500MB
#PBS -V
#PBS -M email
#PBS -m abe
##### 
NPROCS=`wc -l < $PBS_NODEFILE`
#####changing path
cd `eval echo $(echo $PBS_O_WORKDIR | sed 's/export/share/g')`
cat ${PBS_NODEFILE} | sort -u > $PWD/nodes.par
cat ${PBS_NODEFILE} | sort -u > $PWD/machines.LINUX
########### Running commands############################
###########runmpi14
runmpi14 $NPROCS $INPUT
###########runprop14
#runprop14 test11 test11
###########runmpi_prop14
#runmpi_prop14 $NPROCS test11 test11
###########runcryscor09
#runcryscor09 test11
###########runcry14mp2
#runcry14mp2 test11
###########runcry14
#runcry14 test11

参考资料:

  1. howtorun
  2. howtoinstall
  3. Tutorials
  4. A quick tour of CRYSTAL: Wave function calculation input and output
  5. Specifying Number of Processes

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