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Intel MPI编译yambo

 1 year ago
source link: https://cndaqiang.github.io/2022/10/23/intel-yambo/
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编译yambo

下载源代码

yambo
本次使用yambo-5.1.1[2022/07/25]

  • 从todo和mk中都看到了./sbin/compilation/helper.sh是用于生成Makefile的,我们如果因为各种原因需要修改Makefile可以改这里
  • 编译的日志在$(compdir)/log/[email protected],yambo编译过程不显示日志,找不到报错原因,看这个文件，例如log/compile_qe_pseudo.log可以看到编译失败的原因
  • 编译次数多了后,建议重新解压,make clean_all没用.

以怀柔服务器为例

module unload openmpi3/3.1.4
module load parallel_studio/2020.2.254
module load intelmpi/2020.2.254
module load gnu8/8.3.0

配置编译参数

configure和编译

[HUAIROU cndaqiang@login01 yambo-5.1.1]$./configure  FC=ifort CC=icc MPIFC=mpiifort MPICC=mpiicc
....
# - COMPILERS -
#
# FC kind = intel ifort version 19.1.2.254
# MPI kind= Intel(R) MPI Library 2019 Update 8 for Linux* OS
#
# [ CPP ] icc -E -ansi -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW -D_FFTW_OMP       -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] fpp -free -P -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW -D_FFTW_OMP       -D_TIMING
# [ CC  ] mpiicc -O2 -std=gnu99 -no-multibyte-chars -D_C_US -D_FORTRAN_US
# [ FC  ] mpiifort -assume bscc -O3 -g -ip
# [ FCUF] -assume bscc -O0 -g
# [ F77 ] mpiifort -assume bscc -O3 -g -ip
# [ F77U] -assume bscc -O0 -g
# [Cmain] -nofor_main
#
# You can modify compilers and flags by editing the file "config/setup"
#

编译全部

[HUAIROU cndaqiang@login01 yambo-5.1.1]$make core -j 60

如果没有问题就编译通过了

[HUAIROU cndaqiang@login01 yambo-5.1.1]$ls bin/
a2y  c2y  p2y  yambo  ypp

但是建议分步编译

make iotk
make qe_pseudo
#上面两个能正常结束后,再
make core

Error in opening the compiled module file. Check INCLUDE paths.

	[lib/qe_pseudo] qe_pseudo (checking work to be done)
make[1]: *** [atom.o] 错误 1
atom.f90(14): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [RADIAL_GRIDS]

通过log/compile_qe_pseudo.log发现,是编译依赖关系没弄好

atom.f90(14): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [RADIAL_GRIDS]
  USE radial_grids, ONLY : radial_grid_type
------^
atom.f90(19): error #6406: Conflicting attributes or multiple declaration of name.   [RADIAL_GRID_TYPE]

通过rm log/compile_qe_pseudo.log; make qe_pseudo; cat log/compile_qe_pseudo.log一套组合拳,找到所有的依赖关系,把下面的内容添加到config/mk/local/makefile,再make就解决了

atom.o:radial_grids.o
radial_grids.o:kind.o
radial_grids.o:constants.o
becmod.o:qe_auxdata.o recvec.o
qe_auxdata.o:parameters.o
s_psi.o:spin_orb.o uspp.o
uspp.o:invmat.o
init_us_1.o:us_module.o
#upf.o需要iotk，先make iotk
upf.o:read_upf_v1.o read_upf_v2.o
read_pseudo.o:read_uspp.o

Makefile 引用的

  • config/mk/global/actions/compile_internal_libraries.mk 包含了qe_pseudo等库的的编译方式,如 
    qe_pseudo:
      @+LIBS="qe_pseudo"; BASE="lib" ; ADF="$(STAMP_DBLE)"; LAB=""; $(todo_lib); $(mk_lib)
  • 上面的$(todo_lib) 在config/mk/global/functions/todo.mk中定义 
    define todo_lib
 for lib in $$LIBS; do \
$(ECHO) "\t[$$BASE/$$lib] $$lib (checking work to be done)"; \
./sbin/compilation/helper.sh -n -t lib$$LAB$$lib -d $$BASE/$$lib -N $(MAKEFLAGS) -m $(fast) -g $@  -- $(xcpp) $$ADF;\
 done
endef
  • 上面的$(mk_lib) 在config/mk/global/functions/mk_lib.mk中定义 
    define mk_lib
 for lib in $$LIBS; do \
if test ! -f $(compdir)/config/stamps_and_lists/lib$$LAB$$lib.a.stamp; then \
 if test ! -d "$$BASE/$$lib" ; then mkdir -p "$$BASE/$$lib" ; fi ; \
 ./sbin/compilation/helper.sh -d $$BASE/$$lib -t lib$$LAB$$lib.a -o .objects -m l -g $@ -- "$(xcpp) $$ADF" ; \
 cd $$BASE/$$lib ; $(MAKE) $(MAKEFLAGS) VPATH=$(srcdir)/$$BASE/$$lib lib || { grep Error $(compdir)/log/[email protected] ; \
 touch $(compdir)/config/stamps_and_lists/[email protected];  exit "$$?"; } ; cd $(compdir); \
fi;\
 done
endef
  • 从todo和mk中都看到了./sbin/compilation/helper.sh是用于生成Makefile的
  • 编译的日志在$(compdir)/log/[email protected]
(python37) [HUAIROU chendq@login01 yambo-5.1.1]$grep include Makefile
 include config/mk/global/defs.mk
 include config/mk/defs.mk
 include config/mk/global/no_configure_help.mk
include config/mk/global/targets.mk
include config/mk/global/libraries.mk
include config/mk/global/actions/download_external_libraries.mk
include config/mk/global/actions/compile_external_libraries.mk
include config/mk/global/actions/compile_internal_libraries.mk
include config/mk/global/actions/compile_yambo_libraries.mk
include config/mk/global/actions/compile_yambo.mk
include config/mk/global/actions/compile_interfaces.mk
include config/mk/global/actions/compile_ypp.mk
include config/mk/global/actions/clean.mk
include config/mk/global/functions/global_check.mk
include config/mk/global/functions/get_libraries.mk
include config/mk/global/actions/dependencies.mk
include config/mk/global/functions/todo.mk
include config/mk/global/functions/help.mk
include config/mk/global/functions/mk_lib.mk
include config/mk/global/functions/mk_external_lib.mk
include config/mk/global/functions/mk_exe.mk
include config/mk/global/functions/cleaning.mk

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