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{phys}[intel/2021b] Yambo v5.1.2 #17918

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merged 10 commits into from
Aug 17, 2023
Merged

{phys}[intel/2021b] Yambo v5.1.2 #17918

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b37c3d8
adding easyconfigs: Yambo-5.2-intel-2021b.eb
May 16, 2023
77e292b
Fixed typo - used backslash instead of slash + added checksums
May 16, 2023
bbdf095
Added requested changes
May 16, 2023
9fd424e
Added correct checksums
May 16, 2023
a3f9162
Added the rest of requested changes + edited the format of checksums
May 17, 2023
2555a34
Fixed checksums
ItIsI-Orient May 18, 2023
90153d6
Moved version to 5.1.2 + added a patchfix for Yambo pre-5.2 SLEPc bug
Jul 24, 2023
5ec33fc
Added patch description
Jul 24, 2023
c8d8eb7
Removed unused prebuildopts
Jul 24, 2023
18582cb
rename patch for Yambo 5.1.2 to fix compilation with SLEPc
boegel Aug 17, 2023
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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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Original file line number Diff line number Diff line change
@@ -0,0 +1,92 @@
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