编译yambo
下载源代码
yambo
本次使用yambo-5.1.1[2022/07/25]
备注
- 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
$(compdir)/log/compile_$@.log,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.
编译环境
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]$ls bin/
a2y c2y p2y yambo ypp
但是建议分步编译
make iotk
make qe_pseudo
#上面两个能正常结束后,再
make core
报错解决
Error in opening the compiled module file. Check INCLUDE paths.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
make[1]: *** [atom.o] 错误 1
atom.f90(14): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [RADIAL_GRIDS]
通过log/compile_qe_pseudo.log发现,是编译依赖关系没弄好
atom.f90(14): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [RADIAL_GRIDS]
USE radial_grids, ONLY : radial_grid_type
------^
atom.f90(19): error #6406: Conflicting attributes or multiple declaration of name. [RADIAL_GRID_TYPE]
通过rm log/compile_qe_pseudo.log; make qe_pseudo; cat log/compile_qe_pseudo.log一套组合拳,找到所有的依赖关系,把下面的内容添加到config/mk/local/makefile,再make就解决了
atom.o:radial_grids.o
radial_grids.o:kind.o
radial_grids.o:constants.o
becmod.o:qe_auxdata.o recvec.o
qe_auxdata.o:parameters.o
s_psi.o:spin_orb.o uspp.o
uspp.o:invmat.o
init_us_1.o:us_module.o
#upf.o需要iotk，先make iotk
upf.o:read_upf_v1.o read_upf_v2.o
read_pseudo.o:read_uspp.o
备注
Makefile 引用的
config/mk/global/actions/compile_internal_libraries.mk包含了qe_pseudo等库的的编译方式,如qe_pseudo: @+LIBS="qe_pseudo"; BASE="lib" ; ADF="$(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/$$lib lib || { grep Error $(compdir)/log/compile_$@.log ; \ touch $(compdir)/config/stamps_and_lists/compilation_stop_$@.stamp; exit "$$?"; } ; 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
$(compdir)/log/compile_$@.log
(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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