本帖最后由 Tosykie 于 2024-12-24 06:49 编辑
听闻VASP有重大更新，课题组恰好购买了版权。作为课题组服务器的（免费）维护员，特来尝试编译一下新版。6.5.0 (December 17, 2024)主要新特性：电声耦合
服务器软硬件概要： # 登录节点CPU的型号/主频等和计算节点不同，计算节点采用了核心更多，主频稍高的Gold 6336Y CPU @ 2.40GHz
$ lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 46 bits physical, 57 bits virtual
Byte Order: Little Endian
CPU(s): 80
On-line CPU(s) list: 0-79
Vendor ID: GenuineIntel
Model name: Intel(R) Xeon(R) Silver 4316 CPU @ 2.30GHz
CPU family: 6
Model: 106
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
...... $ cat /etc/os-release
PRETTY_NAME="Ubuntu 22.04.4 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.4 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
......
0. 编译环境准备Intel OneAPI 套件 $ module avail -t intel
/mnt/data/apps/modules/programming/compilers:
intel-oneapi/2023.2
intel-oneapi/2024.0
intel-oneapi/2024.1笔者的服务器上安装了三个OneAPI套件版本。这里选择intel-oneapi/2023.2。 关于OneAPI版本： intel-oneapi/2023.2是这一系列套件中最后一个支持经典C/C++/Fortran编译器的版本， 也就是icc/icpc/ifort。 “Intel® C++ Compiler Classic (icc) is deprecated and was discontinued in the oneAPI 2024.0 release.”
对于只支持经典C/C++/Fortran的VASP版本，比如VASP5.4.4，需要使用OneAPI <=2023.2，在>=2024的OneAPI的套件里，已经弃用了icc/icpx/ifort这三个编译器，而是换成了icx/icpx/ifx这几个基于LLVM的编译器。 可选择使用GCC+OpenMPI替代，并加配FFTW3+SCALAPACK等数学库替代MKL。
VASP开发组强烈建议添加HDF5支持来增强I/O，笔者之前也编译了多个HDF5。 $ module avail -t hdf5
/mnt/data/apps/modules/libraries/io:
hdf5/1.12.3-gcc8
hdf5/1.12.3-gcc8-mpi
hdf5/1.12.3-gcc11
hdf5/1.12.3-intel-oneapi2023.2
hdf5/1.12.3-intel-oneapi2023.2-mpi读者可根据上述兼容工具链的网址里挑选兼容的HDF5版本。这里选择hdf5/1.12.3-intel-oneapi2023.2-mpi。
1. 编译1.1 加载环境带有[color=var(--main-6)]module的系统 $ module load intel-oneapi/2023.2
$ module load compiler mpi mkl
$ module load hdf5/1.12.3-intel-oneapi2023.2-mpi不带module的系统 使用类似 $ source /opt/intel/oneapi/setvars.sh
$ source /opt/intel/oneapi/compiler/latest/env/vars.sh intel64/opt/intel/具体换为读者所安装OneAPI的路径 注意事项：如果读者是自己手动安装OneAPI，例如是2023.2.4版本，intel mpi相关的编译器和LIB可能不能直接加载到PATH和LD_LIBRARY_PATH里，导致mpiifort not found读者需要自己手动定位mpi的路径进行修复。 1.2 解压VASP6.5.0源码 $ tar -xzf vasp.6.5.0.tgz
$ cd vasp.6.5.0
$ ls
arch/ src/ build/ makefile README_ELPHON.md
......
1.3 C/C++/Fortran Classic先尝试用C/C++ Classic $ cp arch/makefile.include.intel ./makefile.include
$ vim makefile.include修改 makefile.include，一个参考： # Default precompiler options
CPP_OPTIONS = -DHOST=\"Khompute\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Dtbdyn \
-Dfock_dblbuf
CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)
FC = mpiifort
FCL = mpiifort
FREE = -free -names lowercase
FFLAGS = -assume byterecl -w
OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0
# For what used to be vasp.5.lib
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icc -diag-disable=10441
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)
OBJECTS_LIB = linpack_double.o
# For the parser library
CXX_PARS = icpc -diag-disable=10441
LLIBS = -lstdc++
##
## Customize as of this point! Of course you may change the preceding
## part of this file as well if you like, but it should rarely be
## necessary ...
##
# When compiling on the target machine itself, change this to the
# relevant target when cross-compiling for another architecture
VASP_TARGET_CPU ?= -xHOST
FFLAGS += $(VASP_TARGET_CPU)
# Intel MKL (FFTW, BLAS, LAPACK, and scaLAPACK)
# (Note: for Intel Parallel Studio's MKL use -mkl instead of -qmkl)
FCL += -qmkl=sequential
MKLROOT ?= /path/to/your/mkl/installation
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
INCS =-I$(MKLROOT)/include/fftw
# HDF5-support (optional but strongly recommended, and mandatory for some features)
CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /path/to/your/hdf5/installation
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
INCS += -I$(HDF5_ROOT)/include
# For the VASP-2-Wannier90 interface (optional)
#CPP_OPTIONS += -DVASP2WANNIER90
#WANNIER90_ROOT ?= /path/to/your/wannier90/installation
#LLIBS += -L$(WANNIER90_ROOT)/lib -lwannier
# For machine learning library vaspml (experimental)
#CPP_OPTIONS += -Dlibvaspml
#CPP_OPTIONS += -DVASPML_USE_CBLAS
#CPP_OPTIONS += -DVASPML_USE_MKL
#CPP_OPTIONS += -DVASPML_DEBUG_LEVEL=3
#CXX_ML = mpiicpc -cxx=icpx
#CXXFLAGS_ML = -O3 -std=c++17 -Wall
#INCLUDE_ML =说明： 第2行，HOST笔者改为课题组服务器的名字；（可选） 第27和35行，笔者添加了-diag-disable=10441是为了不让icc和icpc编译器在编译代码时每调用一次就跳出很烦人的弃用警告。 第52和58行，笔者在用module load mkl hdf5时会分别自动设置了MKLROOT和HDF5_ROOT这两个变量。对于后者，如果echo $HDF5_ROOT没有输出，则读者需要手动设置。
当然也可以不去掉第57-60行的注释，不打开HDF5支持。 总体来讲，不怎么需要修改makefile.include
编译 $ make DEPS=1 -j40 all40改成读者服务器合适的CPU核心数量。注意-jN并行编译的特性只有VASP6才支持，VASP5不支持。 编译成功后在bin/目录下生成vasp_gam vasp_std和vasp_ncl三个可执行文件。 1.4 添加到module中 $ cp -rp bin/ oneapi2023.2-hdf5
$ cd oneapi2023.2-hdf5/
$ ls
vasp_gam vasp_ncl vasp_std
$ pwd
/mnt/data/apps/vasp/vasp.6.5.0/oneapi2023.2编写如下module file，名为6.5.0-oneapi2023.2-hdf5 #%Module1.0#####################################################################
set rootdir /mnt/data/apps/vasp/vasp.6.5.0/oneapi2023.2
module-whatis "Name: VASP"
module-whatis "Version: 6.5.0"
module-whatis "Category: Computational Materials Science"
module-whatis "Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. "
module-whatis "URL: http://vasp.at"
proc ModulesHelp { } {
global rootdir
puts stderr "Name: VASP"
puts stderr "Version: 6.5.0"
puts stderr "Category: Computational Materials Science"
puts stderr "URL: http://vasp.at"
puts stderr ""
puts stderr "Package specification:"
puts stderr "Manually compiled"
puts stderr ""
puts stderr "Directory Location:"
puts stderr "$rootdir"
puts stderr ""
puts stderr "Description:"
puts stderr "The Vienna Ab initio Simulation Package (VASP) is a computer program"
puts stderr "for atomic scale materials modelling, e.g. electronic structure"
puts stderr "calculations and quantum-mechanical molecular dynamics, from first"
puts stderr "principles."
puts stderr ""
puts stderr "Additional Notes:"
puts stderr ""
puts stderr "1. VASP is a licensed software"
}
conflict vasp
if { [ module-info mode load ] } {
module load intel-oneapi/2023.2
module load compiler mpi mkl
module load hdf5/1.12.3-intel-oneapi2023.2-mpi
}
prepend-path PATH $rootdir
setenv OMP_NUM_THREADS 1放到MODULEPATH变量包含的目录下，即可。 注意： setenv OMP_NUM_THREADS 1会把OMP_NUM_THREADS强制设为1，读者要注意这是否是预期的，一般来说VASP其值为1，但是读者应该小心测试，否则应该要删除这一行。 测试： $ module avail -t vasp
/mnt/data/apps/modules/compmatsci/dft:
vasp/5.4.4-oneapi2023.2
vasp/6.3.2-oneapi2023.2-hdf5
vasp/6.5.0-oneapi2023.2-hdf5
$ module help vasp/6.5.0-oneapi2023.2-hdf5
-------------------------------------------------------------------
Module Specific Help for /mnt/data/apps/modules/compmatsci/dft/vasp/6.5.0-oneapi2023.2-hdf5:
Name: VASP
Version: 6.5.0
Category: Computational Materials Science
URL: http://vasp.at
Package specification:
Manually compiled
Directory Location:
/mnt/data/apps/vasp/vasp.6.5.0/oneapi2023.2
Description:
The Vienna Ab initio Simulation Package (VASP) is a computer program
for atomic scale materials modelling, e.g. electronic structure
calculations and quantum-mechanical molecular dynamics, from first
principles.
Additional Notes:
1. VASP is a licensed software
-------------------------------------------------------------------最后一个即刚刚添加的VASP6.5.0。
1.5 C/C++/Fortran LLVM如法炮制，仅仅某些行不同。 复制使用于OneAPI (LLVM)套件的makefile.include $ cp arch/makefile.include.oneapi ./makefile.include
$ make veryclean
$ rm bin/vasp_*
$ make DEPS=1 -j40 all编译结束发现vasp_gam没有生成，另外两个是正常的，如果直接make gam会报编译器错误。 即便先清除-j40编译生成的文件，然后用单核单线程编译，仍然报错。错误来源于使用mpiifort -fc=ifx编译greens_real_space.f90。 $ make veryclean
$ make gam
mpiifort -fc=ifx -free -names lowercase -assume byterecl -w -xHOST -O2 -I/mnt/data/apps/intel/oneapi/2023.2/mkl/2023.2.0/include/fftw -I/mnt/data/apps/hdf5/1.12.3/intel-oneapi2023.2-mpi/include -c greens_real_space.f90
#0 0x0000000002203192
#1 0x0000000002266e47
#2 0x0000000002266f70
#3 0x00007f01ad517520
#4 0x0000000001fa52da
#5 0x0000000001fe414c
#6 0x000000000200350e
#7 0x0000000001fe45a2
#8 0x000000000200f2fa
#9 0x00000000020073e7
#10 0x0000000001fe42fb
#11 0x0000000001fe0db1
#12 0x0000000001fe00aa
#13 0x000000000206039d
#14 0x000000000224c731
#15 0x000000000214f026
#16 0x000000000231f37e
#17 0x00007f01ad4fed90
#18 0x00007f01ad4fee40 __libc_start_main + 128
#19 0x0000000001f8fa69
greens_real_space.f90: error #5633: **Internal compiler error: segmentation violation signal raised** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for greens_real_space.f90 (code 3)
make[2]: *** [makefile:195: greens_real_space.o] Error 3
make[2]: Leaving directory '/mnt/data/apps/vasp/vasp.6.5.0/build/gam'
cp: cannot stat 'vasp': No such file or directory
make[1]: *** [makefile:150: all] Error 1
make[1]: Leaving directory '/mnt/data/apps/vasp/vasp.6.5.0/build/gam'
make: *** [makefile:17: gam] Error 2猜测可能是编译器的问题，随即加载了更新的OneAPI套件（这里是2024.1），并顺利编译通过。 $ module purge
$ module load intel-oneapi/2024.1
$ module load compiler mpi mkl
$ make veryclean
$ rm bin/vasp_*
$ make DEPS=1 -j40 all
2. 结束本文到此，后面有空更新VASP6.5.0+GPU (nvhpc)和AMD CPU的编译经验。 转载请注明出处。 欢迎交流。
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发表于 Post on 2024-12-24 06:49:46
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