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Merge pull request #17918 from ItIsI-Orient/20230516152355_new_pr_Yam…
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{phys}[intel/2021b] Yambo v5.1.2
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@boegel
boegel authored Aug 17, 2023
2 parents e80846b + 18582cb commit e7f94d3
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92 changes: 92 additions & 0 deletions easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb
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easyblock = 'MakeCp'

name = 'Yambo'
# see https://github.com/yambo-code/yambo/wiki/Releases-%28tar.gz-format%29
version = '5.1.2'
local_yambo_libs_ver = '1.0'

homepage = 'http://www.yambo-code.org'
description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics.
Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf."""

toolchain = {'name': 'intel', 'version': '2021b'}
toolchainopts = {'usempi': True}

local_yambo_ext_cmd = 'mkdir yambo-%(version)s && '
local_yambo_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s'
local_yambo_lib_ext_cmd = 'mkdir -p yambo-%(version)s/lib/yambo/ && '
local_yambo_lib_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/'

source_urls = ['https://github.com/yambo-code/yambo/archive/']
sources = [
{
'download_filename': '%(version)s.tar.gz',
'filename': 'yambo-%(version)s.tar.gz',
'extract_cmd': local_yambo_ext_cmd,
},
{
'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'],
'download_filename': '%s.tar.gz' % local_yambo_libs_ver,
'filename': 'yambo-libraries-%s.tar.gz' % local_yambo_libs_ver,
'extract_cmd': local_yambo_lib_ext_cmd,
},
{
# see https://github.com/yambo-code/yambo/wiki/Libraries#external-libraries
'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'],
'filename': 'iotk-y1.2.2.tar.gz',
'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/',
},
]
patches = ['Yambo-5.1.2_fix-SLEPc.patch']
checksums = [
{'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'},
{'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'},
{'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'},
{'Yambo-5.1.2_fix-SLEPc.patch': 'e44a0f85ec5eb55da7c7d42937b4c452bde2ed2c6d2f98fffca15696c82b7df6'},
]

dependencies = [
('HDF5', '1.12.1'),
('netCDF', '4.8.1'),
('netCDF-Fortran', '4.5.3'),
('PETSc', '3.18.4'),
('SLEPc', '3.18.2'),
('libxc', '5.1.6'),
]

with_configure = True

configopts = 'FC=mpiifort CC=mpiicc --enable-msgs-comps '
configopts += '--prefix=%(builddir)s/%(namelower)s-%(version)s/ '
configopts += '--enable-open-mp --enable-hdf5-par-io '
configopts += '--with-blas-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread '
configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" '
configopts += '--with-lapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread '
configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-blacs-libs=mkl '
configopts += '--with-scalapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread '
configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" '
configopts += '--with-fft-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread '
configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-fft-includedir="${MKLROOT}/include" '
configopts += '--with-netcdf-path=$EBROOTNETCDF '
configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" '
configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" '
configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" '
configopts += '--enable-par-linalg --enable-slepc-linalg '

prebuildopts = "export SHELL='sh -x' && "
buildopts = 'all'

files_to_copy = [
(['bin/*'], 'bin'),
(['%(builddir)s/%(namelower)s-%(version)s/lib/external/intel/mpiifort/bin/*'], 'bin')
]

sanity_check_paths = {
'files': ['bin/' + x for x in ['a2y', 'p2y', 'yambo', 'yambo_ph', 'ypp', 'ypp_ph',
'iotk', 'iotk.x']],
'dirs': []
}

sanity_check_commands = ["yambo -h"]

moduleclass = 'phys'
172 changes: 172 additions & 0 deletions easybuild/easyconfigs/y/Yambo/Yambo-5.1.2_fix-SLEPc.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,172 @@
Fixes a bug with some parts of Yambo that use SLEPc
Applies most of this commit to this version
https://github.com/yambo-code/yambo/commit/1846c85fdd08ec80ecf90082821cf957a0c93747
diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F
--- yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:31:48.203323300 +0200
+++ yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:35:13.933323300 +0200
@@ -1,5 +1,5 @@
!
-! Copyright (C) 2000-2023 the YAMBO team
+! Copyright (C) 2000-2022 the YAMBO team
! http://www.yambo-code.org
!
! Authors (see AUTHORS file for details): HM DS IMA
@@ -26,7 +26,7 @@
! Interface with the K_multiply_by_V from the Haydock method
! This function has to take the same arguments as MatMult from PETSC
!
- use pars, ONLY : SP
+ use pars, ONLY : SP,cI
use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp
use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim
use parallel_m, ONLY : PAR_IND_T_Haydock
@@ -45,7 +45,7 @@
!
implicit none
!
- PetscScalar :: tmp_value(1)
+ PetscScalar :: tmp_value(1),tmp_value_star(1)
PetscInt :: H_pos(1), pet_one
PetscErrorCode :: ierr
!
@@ -108,12 +108,13 @@
do i_c=1,BS_T_grp(i_g)%size
H_pos=start_index+i_c
tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1))
+ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1))
!SLEPC funcitons expect C indexes both in Fortran and C
call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr )
if(BSS_slepc_double_grp) then
! Expand vo to anti-resonant block
H_pos=start_index_dg+i_c
- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr )
+ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr )
endif
enddo
enddo
diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_transpose_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_transpose_slepc.F
--- yambo-5.1.2.orig/src/bse/K_multiply_by_V_transpose_slepc.F 2023-07-24 14:31:48.203323300 +0200
+++ yambo-5.1.2/src/bse/K_multiply_by_V_transpose_slepc.F 2023-07-24 14:34:40.413323300 +0200
@@ -1,5 +1,5 @@
!
-! Copyright (C) 2000-2023 the YAMBO team
+! Copyright (C) 2000-2022 the YAMBO team
! http://www.yambo-code.org
!
! Authors (see AUTHORS file for details): HM DS IMA
@@ -26,7 +26,7 @@
! Interface with the K_multiply_by_V from the Haydock method
! This function has to take the same arguments as MatMult from PETSC
!
- use pars, ONLY : SP
+ use pars, ONLY : SP,cI
use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp
use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim
use parallel_m, ONLY : PAR_IND_T_Haydock
@@ -45,7 +45,7 @@
!
implicit none
!
- PetscScalar :: tmp_value(1)
+ PetscScalar :: tmp_value(1),tmp_value_star(1)
PetscInt :: H_pos(1), pet_one
PetscErrorCode :: ierr
!
@@ -109,12 +109,13 @@
do i_c=1,BS_T_grp(i_g)%size
H_pos=start_index+i_c
tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1))
+ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1))
!SLEPC funcitons expect C indexes both in Fortran and C
call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr )
if(BSS_slepc_double_grp) then
! Expand vo to anti-resonant block
H_pos=start_index_dg+i_c
- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr )
+ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr )
endif
enddo
enddo
diff -ruN yambo-5.1.2.orig/src/bse/K_stored_in_a_slepc_matrix.F yambo-5.1.2/src/bse/K_stored_in_a_slepc_matrix.F
--- yambo-5.1.2.orig/src/bse/K_stored_in_a_slepc_matrix.F 2023-07-24 14:31:48.203323300 +0200
+++ yambo-5.1.2/src/bse/K_stored_in_a_slepc_matrix.F 2023-07-24 14:35:46.923323300 +0200
@@ -1,5 +1,5 @@
!
-! Copyright (C) 2000-2023 the YAMBO team
+! Copyright (C) 2000-2022 the YAMBO team
! http://www.yambo-code.org
!
! Authors (see AUTHORS file for details): HM DS
@@ -53,7 +53,7 @@
Mat, intent(out) :: slepc_mat
!
integer :: i_c,i_r,i_Tk,i_Tp,i_B,H_shift(2)
- PetscScalar :: Mij
+ PetscScalar :: Mij,Mij_star
PetscInt :: H_pos(2),SL_K_dim(2),SL_H_dim
PetscErrorCode :: ierr
!
@@ -95,14 +95,17 @@
if (H_pos(1)+H_shift(1)>H_pos(2)+H_shift(2)) cycle
if (l_BS_ares_from_res.and.H_pos(1)>H_pos(2)) cycle
!
- Mij=BS_blk(i_B)%mat(i_r,i_c)
+ Mij = BS_blk(i_B)%mat(i_r,i_c)
+ Mij_star= real(BS_blk(i_B)%mat(i_r,i_c))-cI*aimag(BS_blk(i_B)%mat(i_r,i_c))
!
! Add energies to the diagonal
!
if(H_pos(1)+H_shift(1)==H_pos(2)+H_shift(2)) then
- Mij=real(Mij)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE
+ Mij =real(Mij) +BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE
+ Mij_star=real(Mij_star)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE
if (allocated(BSS_eh_W).and..not.BSS_perturbative_width) then
- Mij=Mij+cI*BSS_eh_W(H_pos(1)+H_shift(1)+1)
+ Mij =Mij +cI*BSS_eh_W(H_pos(1)+H_shift(1)+1)
+ Mij_star=Mij_star -cI*BSS_eh_W(H_pos(1)+H_shift(1)+1)
endif
endif
!
@@ -110,35 +113,35 @@
case("R")
call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr )
! The resonant block is hermitial
- call MatSetValue( slepc_mat, H_pos(2), H_pos(1), conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star, INSERT_VALUES, ierr )
if (l_BS_ares_from_res.and.BS_K_coupling) then
! The anti-resonant block is A=-R*
- call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1),-conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), -Mij_star, INSERT_VALUES, ierr )
! The anti-resonant block is hermitian
call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), -Mij, INSERT_VALUES, ierr )
endif
case("C")
call MatSetValue( slepc_mat, H_pos(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr )
! Anti-coupling from coupling: the whole BSE matrix is Pseudo-HErmitian
- call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1),-conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1), -Mij_star , INSERT_VALUES, ierr )
if (l_BS_ares_from_res) then
! The coupling block and the anti-coupling block are symmetric
call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), Mij , INSERT_VALUES, ierr )
- call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2),-conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), -Mij_star , INSERT_VALUES, ierr )
endif
case("A")
! The anti-resonant block is hermitial
if(BS_res_ares_n_mat==1) then
call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr )
- call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), Mij_star , INSERT_VALUES, ierr )
else
call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr )
- call MatSetValue( slepc_mat, H_pos(2), H_pos(1), conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star , INSERT_VALUES, ierr )
endif
case("Q")
call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), Mij , INSERT_VALUES, ierr )
! Coupling from anti-coupling: the whole BSE matrix is Pseudo-HErmitian
- call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1),-conjg(Mij), INSERT_VALUES, ierr )
+ call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), -Mij_star , INSERT_VALUES, ierr )
end select
!
enddo

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