【DFT】Centos7下安装vasp5.4.4
VASP是维也纳大学Hafner小组开发的进行电子结构计算和量子力学-分子动力学模拟软件包。它是目前材料模拟和计算物质科学研究中最流行的商用软件之一。
一、环境介绍：
系统：Centos7.6
所需软件包：vasp5.4.4、parallel_studio_xe_2017_update5
二、上传、解压、软件包：
1、为了方便，新建一个目录，把intel和vasp软件包拷贝或直接上传到新建目录中。
[zh@zh ~]$ mkdir vasp ###新建名为vasp的目录###
[zh@zh ~]$ cd vasp ###进入vasp目录###
[zh@zh vasp]$ ls ###查看当前目录下文件###
parallel_studio_xe_2017_update5.tgz vasp.5.4.4.tar license
[zh@zh vasp]$ tar xf vasp.5.4.4.tar ###解压vasp源码包###
[zh@zh vasp]$ tar xf parallel_studio_xe_2017_update5.tgz ###解压intel安装包###
三、安装intel编译器：
第一步、进入intel安装包目录，并执行安装程序，由于是普通用户，所以输入3。
[zh@zh vasp]$ cd parallel_studio_xe_2017_update5/ ###进入解压后的intel文件夹###
[zh@zh parallel_studio_xe_2017_update5]$ ./install.sh ###执行安装程序###
Please make your selection by entering an option.
Root access is recommended for evaluation.
1. Run as a root for system wide access for all users [default]
2. Run using sudo privileges and password for system wide access for all users
3. Run as current user to limit access to user level
Please make your selection by entering an option.
h. Help
q. Quit
Please type a selection [1]: 3
第二步、协议条款，一直按回车。直到最后输入accept同意。
Step 1 of 7 | Welcome
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Welcome to the Intel(R) Parallel Studio XE 2017 Update 5 for Linux* setup program.
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You will complete the steps below during setup process:
Step 1 : Welcome
Step 2 : License agreement
Step 3 : License activation
Step 4 : Intel® Software Improvement Program Data Collection
Step 5 : Options
Step 6 : Installation
Step 7 : Complete
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Press "Enter" key to continue or "q" to quit:
Type "accept" to continue or "decline" to go back to the previous menu: accept
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Checking the prerequisites. It can take several minutes. Please wait...
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第三步：选择激活方式，我采用License文件激活，所以选择2。
Step 3 of 7 | License activation
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If you have purchased this product and have the serial number and a connection
to the internet you can choose to activate the product at this time.
Alternatively, you can choose to evaluate the product or defer activation by
choosing the evaluate option. Evaluation software will time out in about one
month. You can also use license file or Intel(R) Software License Manager.
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1. I want to activate my product using a serial number [default]
2. I want to activate by using a license file, or by using Intel(R) Software
License Manager
h. Help
b. Back to the previous menu
q. Quit
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Please type a selection or press "Enter" to accept default choice [1]:
第四步、选择1，离线激活，并输入License文件路径。
Step 3 of 7 | License activation > Alternative activation
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Your license file is available for download from
https://registrationcenter.intel.com. Further instructions are available at
http://software.intel.com/en-us/articles/offline-activation-of-intel-software-de
velopment-products.
The Intel(R) Software License Manager User's Guide explains how to download,
install, configure and troubleshoot the Intel(R) Software License Manager. The
guide is available at:
http://software.intel.com/en-us/articles/license-manager-for-flexlm-users-guide.
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1. Activate offline [default]
2. Use Intel(R) Software License Manager
h. Help
b. Back to the previous menu
q. Quit
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Please type a selection or press "Enter" to accept default choice [1]: 1
Please type the full path to your license file(s):
/home/test/vasp/license
Activation completed successfully.
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Press "Enter" key to continue:
第五步、intel改进计划，可拒绝，输入2。
Step 4 of 7 | Intel® Software Improvement Program Data Collection
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Intel® Software automatically collects technical information about the program
runtime status (such as counters, flags, and timestamps) and development
environment (such as operating system, CPU architecture, and other Intel
products installed) ("Information").
- No personally identifiable information is collected. The Information
collected will be used to better understand how customers use Intel® Software
and how to improve our software in the future.
- If you choose to opt in, the data will be sent to Intel and be retained
indefinitely. If you choose to opt out, the Information will NOT be sent to
Intel and will be automatically deleted.
- You will not receive additional emails from Intel if you choose to opt in
to the program.
- You can stop participating at any time by choosing "Improvement Program
Options" in "Settings" Tab of the Intel® Software Manager and selecting "OPT
OUT" option.
Learn more about the Intel® Software Improvement Program
http://software.intel.com/en-us/articles/software-improvement-program
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1. I would like to OPT IN and participate to improve Intel® Software
2. I would like to OPT OUT and not participate
b. Back to the previous menu
q. Quit
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Please type a selection: 2
第六步、配置集群安装选择，看情况选择，为方便大家操作，直接选择1，如有需要可以选择2定制安装（定制安装中可以选择安装路径和安装组件）。
Step 5 of 7 | Options > Configure Cluster Installation
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This product can be installed on cluster nodes.
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1. Finish configuring installation target [default]
2. Installation target [ Current system only ]
h. Help
b. Back to the previous menu
q. Quit
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Please type a selection or press "Enter" to accept default choice [1]: 1
第七步、开始安装，选择1。
Install location:
/home/test/intel ###安装路径，要记一下###
Intel(R) Data Analytics Acceleration Library 2017 Update 4 3.4GB
Intel(R) Data Analytics Acceleration Library 2017 Update 4
Intel(R) MPI Library 2017 Update 4 1.0GB
Intel MPI Benchmarks 2017 Update 3
Intel MPI Library for applications running on Intel(R) 64 Architecture
Intel MPI Library for applications running on Intel(R) Many Integrated
Core Architecture
Intel(R) Debugger for Heterogeneous Compute 2017 621MB
GNU* GDB 7.6 and ELFDWARF library
GNU* GDB 7.10 95MB
GNU* GDB 7.10 on Intel(R) 64
Intel(R) Debugger for Intel(R) MIC Architecture 2017 Update 5 135MB
GNU* GDB 7.8
GDB Eclipse* Integration
Install space required: 14.5GB
Driver parameters:
Sampling driver install type: Only driver kit files will be installed
Installation target:
Install on the current system only
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1. Start installation Now [default]
2. Customize installation
h. Help
b. Back to the previous menu
q. Quit
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Please type a selection or press "Enter" to accept default choice [1]: 1
正式安装前intel会检查系统中的各个组件是否齐全，只要不是关键组件都可以选择1，直接跳过。没有遇到的，略过这一步。
Step 5 of 7 | Prerequisites > Missing Optional Prerequisite(s)
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There are one or more optional unresolved issues. It is highly recommended to
resolve them all before you continue. You can fix them without exiting the setup
program and re-check. Or you can exit the setup program, fix them and run the
setup program again.
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Missing optional prerequisites
-- 32-bit libraries not found
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1. Skip missing optional prerequisites [default]
2. Show the detailed info about issue(s)
3. Re-check the prerequisites
h. Help
b. Back to the previous menu
q. Quit
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Please type a selection or press "Enter" to accept default choice [1]: 1
第八步、安装完成，配置环境变量。
Step 7 of 7 | Complete
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Thank you for installing Intel(R) Parallel Studio XE 2017 Update 5
Cluster Edition for Linux*.
If you have not done so already, please register your product with Intel
Registration Center to create your support account and take full advantage of
your product purchase.
Your support account gives you access to free product updates and upgrades
as well as Priority Customer support at the Online Service Center
https://supporttickets.intel.com.
Click here https://software.intel.com/en-us/python-distribution
to download Intel(R) Distribution for Python*
This download will initiate separately. You can proceed with the installation
screen instructions.
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Press "Enter" key to quit:
[zh@zh bin~]$ cd /home/test/intel/bin ###进入intel安装目录的bin目录下###
[zh@zh bin~]$ pwd ###查看当前路径###
/home/test/intel/bin
[zh@zh bin~]$ ls compilervars.sh ###查看intel环境变量文件是否生成###
compilervars.sh
[zh@zh bin~]$ vim ~/.bashrc ###通过vim编辑用户环境变量文件###
把下面这句写入~/.bashrc文件中，注意替换成自己的安装路径！！！
source /home/test/intel/bin/compilervars.sh intel64
[zh@zh bin~]$ source ~/.bashrc ###让刚刚写入的环境变量生效###
[zh@zh bin~]$ icc -v ###查看intel版本，出现如下字样则说明intel安装成功###
icc version 17.0.5 (gcc version 4.8.5 compatibility)
四、编译vasp：
1、进入vasp源码包目录，拷贝一份makefile.include文件。
[zh@zh ~]$ cd vasp.5.4.4 ###进入vasp源码包目录###
[zh@zh vasp.5.4.4~]$ cp arch/makefile.include.linux_intel ./makefile.include ###由于我们用的是intel所以从arch中拷贝makefile.include.linux_intel到当前目录下，并重命名为makefile.include
[zh@zh vasp.5.4.4~]$ ls ###查看当前目录下的文件###
arch bin build makefile makefile.include README src
[zh@zh vasp.5.4.4~]$ make all ###开始编译####
2、编译过程中如没有报错，则会出现如下字样。
mpiifort -free -names lowercase -assume byterecl -w -O2 -I/home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/include/fftw -c elphon.f90
fpp -f_com=no -free -w0 fftmpiw.F fftmpiw.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Duse_bse_te -Dtbdyn -Duse_shmem
mpiifort -free -names lowercase -assume byterecl -w -O1 -I/home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/include/fftw -c fftmpiw.f90
fpp -f_com=no -free -w0 fftmpi_map.F fftmpi_map.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Duse_bse_te -Dtbdyn -Duse_shmem
mpiifort -free -names lowercase -assume byterecl -w -O2 -I/home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/include/fftw -c fftmpi_map.f90
fpp -f_com=no -free -w0 fft3dlib.F fft3dlib.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Duse_bse_te -Dtbdyn -Duse_shmem
mpiifort -free -names lowercase -assume byterecl -w -O2 -I/home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/include/fftw -c fft3dlib.f90
fpp -f_com=no -free -w0 fftw3d.F fftw3d.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Duse_bse_te -Dtbdyn -Duse_shmem
mpiifort -free -names lowercase -assume byterecl -w -O1 -I/home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/include/fftw -c fftw3d.f90
fpp -f_com=no -free -w0 main.F main.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Duse_bse_te -Dtbdyn -Duse_shmem
mpiifort -free -names lowercase -assume byterecl -w -O0 -I/home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/include/fftw -c main.f90
mpiifort -mkl=sequential -lstdc++ -o vasp c2f_interface.o base.o profiling.o openmp.o mpi.o mpi_shmem.o smart_allocate.o xml.o constant.o jacobi.o main_mpi.o scala.o asa.o lattice.o poscar.o ini.o mgrid.o xclib.o vdw_nl.o xclib_grad.o radial.o pseudo.o gridq.o ebs.o mkpoints.o wave.o wave_mpi.o wave_high.o bext.o spinsym.o symlib.o symmetry.o lattlib.o random.o nonl.o nonlr.o nonl_high.o dfast.o choleski2.o mix.o hamil.o xcgrad.o xcspin.o potex1.o potex2.o constrmag.o cl_shift.o relativistic.o LDApU.o paw_base.o metagga.o egrad.o pawsym.o pawfock.o pawlhf.o rhfatm.o hyperfine.o paw.o mkpoints_full.o charge.o Lebedev-Laikov.o stockholder.o dipol.o solvation.o pot.o dos.o elf.o tet.o tetweight.o hamil_rot.o chain.o dyna.o k-proj.o sphpro.o us.o core_rel.o aedens.o wavpre.o wavpre_noio.o broyden.o dynbr.o reader.o writer.o tutor.o xml_writer.o brent.o stufak.o fileio.o opergrid.o stepver.o chgloc.o fast_aug.o fock_multipole.o fock.o fock_dbl.o mkpoints_change.o subrot_cluster.o sym_grad.o mymath.o npt_dynamics.o subdftd3.o internals.o dynconstr.o dimer_heyden.o dvvtrajectory.o vdwforcefield.o hamil_high.o nmr.o pead.o subrot.o subrot_scf.o paircorrection.o rpa_force.o force.o pwlhf.o gw_model.o optreal.o steep.o rmm-diis.o davidson.o david_inner.o lcao_bare.o locproj.o electron.o rot.o electron_all.o shm.o pardens.o optics.o constr_cell_relax.o stm.o finite_diff.o elpol.o hamil_lr.o rmm-diis_lr.o subrot_lr.o lr_helper.o hamil_lrf.o elinear_response.o ilinear_response.o linear_optics.o setlocalpp.o wannier.o electron_OEP.o electron_lhf.o twoelectron4o.o gauss_quad.o m_unirnk.o varpro.o minimax.o mlwf.o wnpr.o ratpol.o pade_fit.o screened_2e.o wave_cacher.o crpa.o chi_base.o wpot.o local_field.o ump2.o ump2kpar.o fcidump.o ump2no.o bse_te.o bse.o acfdt.o chi.o sydmat.o rmm-diis_mlr.o linear_response_NMR.o wannier_interpol.o linear_response.o dmft.o auger.o dmatrix.o elphon.o fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o main.o -Llib -ldmy /home/test/intel/compilers_and_libraries_2017.5.239/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -lmkl_blacs_intelmpi_lp64 -Lparser -lparser -lstdc++
make[2]: Leaving directory `/home/test/vasp/vasp.5.4.4/build/ncl'
make[1]: Leaving directory `/home/test/vasp/vasp.5.4.4/build/ncl'
3、查看生成的可执行程序。
(1) vasp_std: 标准的版本;
(2) vasp_gam: 如果只用一个Gamma点的话，用这个版本较快;
(3) vasp_ncl: 适用于需要non-collinear自旋的计算;
[zh@zh vasp.5.4.4~]$ ls bin/ ###查看是否生成可执行程序###
vasp_gam vasp_ncl vasp_std
4、测试，上传一个示例。
[zh@zh test]$ ls ###准备如下四个文件###
INCAR KPOINTS POSCAR POTCAR
[zh@zh test]$ mpirun -np 64 /home/test/vasp/vasp.5.4.4/bin/vasp_std ###mpirun是并行计算命令，-np 指的是核数，由于vasp没有写入环境变量，所以直接使用绝对路径。
running on 64 total cores
distrk: each k-point on 64 cores, 1 groups
distr: one band on 16 cores, 4 groups
using from now: INCAR
vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Nov 12 2019 12:51:09) complex
POSCAR found type information on POSCAR Ir Ba O
POSCAR found : 3 types and 28 ions
scaLAPACK will be used
-----------------------------------------------------------------------------
| |
| ADVICE TO THIS USER RUNNING 'VASP/VAMP' (HEAR YOUR MASTER'S VOICE ...): |
| |
| You have a (more or less) 'large supercell' and for larger cells |
| it might be more efficient to use real space projection opertators |
| So try LREAL= Auto in the INCAR file. |
| Mind: For very accurate calculation you might also keep the |
| reciprocal projection scheme (i.e. LREAL=.FALSE.) |
| |
-----------------------------------------------------------------------------
LDA part: xc-table for Pade appr. of Perdew
generate k-points for: 12 12 5
POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ...
WAVECAR not read
entering main loop
N E dE d eps ncg rms rms(c)
DAV: 1 0.181165210671E+04 0.18117E+04 -0.10359E+05403272 0.145E+03
DAV: 2 0.169452485252E+02 -0.17947E+04 -0.16775E+04424720 0.341E+02
DAV: 3 -0.204560200396E+03 -0.22151E+03 -0.21442E+03481048 0.133E+02
DAV: 4 -0.219097880192E+03 -0.14538E+02 -0.14332E+02618392 0.335E+01
DAV: 5 -0.219556625237E+03 -0.45875E+00 -0.45724E+00609432 0.567E+00 0.808E+01
DAV: 6 -0.188251800443E+03 0.31305E+02 -0.23965E+02590152 0.500E+01 0.588E+01
DAV: 7 -0.185788153496E+03 0.24636E+01 -0.46488E+01586600 0.294E+01 0.294E+01
DAV: 8 -0.185846696654E+03 -0.58543E-01 -0.48652E+00503848 0.656E+00 0.151E+01
DAV: 9 -0.186670861042E+03 -0.82416E+00 -0.70837E+00594664 0.567E+00 0.152E+01
DAV: 10 -0.185725485792E+03 0.94538E+00 -0.63152E+00572344 0.452E+00 0.396E+00
DAV: 11 -0.185734038896E+03 -0.85531E-02 -0.23003E-01546648 0.157E+00 0.125E+00
DAV: 12 -0.185748972292E+03 -0.14933E-01 -0.89443E-02563008 0.857E-01 0.124E+00
DAV: 13 -0.185747314551E+03 0.16577E-02 -0.74086E-02608352 0.806E-01 0.828E-01
DAV: 14 -0.185745508468E+03 0.18061E-02 -0.21428E-02561752 0.425E-01 0.366E-01
DAV: 15 -0.185746186807E+03 -0.67834E-03 -0.69378E-03542616 0.185E-01 0.337E-01
DAV: 16 -0.185746339096E+03 -0.15229E-03 -0.38476E-03561104 0.164E-01 0.166E-01
DAV: 17 -0.185746598612E+03 -0.25952E-03 -0.23108E-03530344 0.109E-01 0.263E-01
DAV: 18 -0.185746595818E+03 0.27936E-05 -0.19902E-03543008 0.655E-02 0.854E-02
DAV: 19 -0.185746638193E+03 -0.42375E-04 -0.16070E-04482376 0.280E-02 0.230E-02
DAV: 20 -0.185746652286E+03 -0.14093E-04 -0.24656E-05529168 0.130E-02 0.249E-02
DAV: 21 -0.185746654590E+03 -0.23036E-05 -0.79027E-06451104 0.624E-03 0.245E-02
DAV: 22 -0.185746654511E+03 0.78813E-07 -0.25888E-07298344 0.217E-03
1 F= -.19067686E+03 E0= -.19067686E+03 d E =0.000000E+00 mag= -0.0016 -0.0018 0.0012
5、查看任务耗时
[zh@zh test]$ vim OUTCAR ###打开OUTCAR，在文件最后查看耗时###
General timing and accounting informations for this job:
========================================================
Total CPU time used (sec): 10588.441
User time (sec): 10367.378
System time (sec): 221.063
Elapsed time (sec): 10644.442
Maximum memory used (kb): 3158164.
Average memory used (kb): 0.
Minor page faults: 1133860
Major page faults: 0
Voluntary context switches: 41728