PTEROSOR/QuantumPackage
10
0
Fork 0
mirror of https://github.com/QuantumPackage/qp2.git synced 2024-11-19 04:22:32 +01:00
Code Releases Activity

Merge pull request #17 from kgasperich/dev-pbc-config

Browse Source 
Dev pbc config
This commit is contained in:
Kevin Gasperich 2022-06-27 14:27:56 -05:00 committed by GitHub
commit 469df719e7
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
50 changed files with 1188 additions and 433 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
.gitmodules vendored Normal file
View File

@ -0,0 +1,9 @@
[submodule "external/ezfio"]
path = external/ezfio
url = https://gitlab.com/scemama/ezfio.git
[submodule "external/irpf90"]
path = external/irpf90
url = https://gitlab.com/scemama/irpf90.git
[submodule "external/qp2-dependencies"]
path = external/qp2-dependencies
url = https://github.com/QuantumPackage/qp2-dependencies.git

44
bin/qp_convert_h5_to_ezfio
View File

@ -18,6 +18,7 @@ import sys
import numpy as np
import os
from docopt import docopt
import gzip
#fname = sys.argv[1]
#qph5name = sys.argv[2]
@ -27,6 +28,40 @@ def get_full_path(file_path):
# file_path = os.path.abspath(file_path)
return file_path
def flatten(l):
res = []
for i in l:
if hasattr(i, "__iter__") and not isinstance(i, str):
res.extend(flatten(i))
else:
res.append(i)
return res
def save_array_do(ezfioname,subdir,data,chunksize=16384):
dims = list(reversed(data.shape))
rank = len(dims)
flatdata = data.reshape(-1)
dim_max = 1
for i in dims:
dim_max *= i
with gzip.open(os.path.join(ezfioname,subdir)+'.gz','wb') as f:
f.write(f'{rank:3d}\n'.encode())
for d in dims:
f.write(f'{d:20d} '.encode())
f.write("\n".encode())
fmtstring = chunksize*'{:24.15E}\n'
for i in range(dim_max//chunksize):
#f.write((chunksize*'{:24.15E}\n').format(*flatdata[i*chunksize:(i+1)*chunksize]).encode())
#f.write(fmtstring.format(*flatdata[i*chunksize:(i+1)*chunksize]).encode())
f.write((''.join("%24.15E\n" % xi for xi in flatdata[i*chunksize:(i+1)*chunksize])).encode())
print(f'{100.*i/(dim_max//chunksize):7.3f}% complete')
rem = dim_max%chunksize
if rem:
f.write((rem*'{:24.15E}\n').format(*flatdata[-rem:]).encode())
return
def convert_mol(filename,qph5path):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(False)
@ -582,8 +617,13 @@ def convert_kpts(filename,qph5path,qmcpack=True):
# dfao_im0=qph5['ao_two_e_ints/df_ao_integrals_imag'][()].transpose((3,2,1,0))
# dfao_cmplx0 = np.stack((dfao_re0,dfao_im0),axis=-1).tolist()
# ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0)
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
#dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()]
save_array_do(filename,'ao_two_e_ints/df_ao_integrals_complex',dfao_reim)
#ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
#dfao_dims = list(reversed(dfao_reim.shape))
#test_write_df_ao(,5,dfao_dims,dfao_reim.size,dfao_reim.ravel())
ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
if 'mo_two_e_ints' in qph5.keys():

79
bin/qp_convert_output_to_ezfio
View File

@ -121,6 +121,7 @@ def write_ezfio(res, filename):
exponent = []
res.convert_to_cartesian()
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
@ -178,6 +179,72 @@ def write_ezfio(res, filename):
print("OK")
# _
# |_) _. _ o _
# |_) (_| _> | _>
#
print("Basis\t\t...\t", end=' ')
# ~#~#~#~ #
# I n i t #
# ~#~#~#~ #
coefficient = []
exponent = []
# ~#~#~#~#~#~#~ #
# P a r s i n g #
# ~#~#~#~#~#~#~ #
inucl = {}
for i, a in enumerate(res.geometry):
inucl[a.coord] = i
nbasis = 0
nucl_index = []
curr_center = -1
nucl_shell_num = []
ang_mom = []
nshell = 0
nshell_tot = 0
shell_index = []
shell_prim_num = []
for b in res.basis:
s = b.sym
if str.count(s, "y") + str.count(s, "x") == 0:
c = inucl[b.center]
nshell += 1
nshell_tot += 1
if c != curr_center:
curr_center = c
nucl_shell_num.append(nshell)
nshell = 0
nbasis += 1
nucl_index.append(c+1)
coefficient += b.coef[:len(b.prim)]
exponent += [p.expo for p in b.prim]
ang_mom.append(str.count(s, "z"))
shell_prim_num.append(len(b.prim))
shell_index += [nshell_tot+1] * len(b.prim)
# ~#~#~#~#~ #
# W r i t e #
# ~#~#~#~#~ #
ezfio.set_basis_basis("Read from ResultsFile")
ezfio.set_basis_shell_num(len(ang_mom))
ezfio.set_basis_basis_nucleus_index(nucl_index)
ezfio.set_basis_prim_num(len(coefficient))
ezfio.set_basis_nucleus_shell_num(nucl_shell_num)
ezfio.set_basis_prim_coef(coefficient)
ezfio.set_basis_prim_expo(exponent)
ezfio.set_basis_shell_ang_mom(ang_mom)
ezfio.set_basis_shell_prim_num(shell_prim_num)
ezfio.set_basis_shell_index(shell_index)
print("OK")
# _
# |\/| _ _ |_) _. _ o _
# | | (_) _> |_) (_| _> | _>
@ -227,10 +294,15 @@ def write_ezfio(res, filename):
for i in range(mo_num):
energies.append(MOs[i].eigenvalue)
if res.occ_num is not None:
OccNum = []
if res.occ_num is not None:
for i in MOindices:
OccNum.append(res.occ_num[MO_type][i])
else:
for i in range(res.num_beta):
OccNum.append(2.)
for i in range(res.num_beta,res.num_alpha):
OccNum.append(1.)
while len(OccNum) < mo_num:
OccNum.append(0.)
@ -255,8 +327,9 @@ def write_ezfio(res, filename):
# ~#~#~#~#~ #
ezfio.set_mo_basis_mo_num(mo_num)
ezfio.set_mo_basis_mo_occ(OccNum)
ezfio.set_mo_basis_mo_coef(MoMatrix)
ezfio.set_mo_basis_mo_occ(OccNum)
print("OK")
@ -317,8 +390,6 @@ def write_ezfio(res, filename):
n_beta = res.num_beta
for i in range(nucl_num):
charge[i] -= nucl_charge_remove[i]
n_alpha -= nucl_charge_remove[i]/2
n_beta -= nucl_charge_remove[i]/2
ezfio.set_nuclei_nucl_charge(charge)
ezfio.set_electrons_elec_alpha_num(n_alpha)
ezfio.set_electrons_elec_beta_num(n_beta)

6
bin/qp_export_as_tgz
View File

@ -99,7 +99,9 @@ function find_libs () {
}
function find_exec () {
find ${QP_ROOT}/$1 -perm /u+x -type f
for i in $@ ; do
find ${QP_ROOT}/$i -perm /u+x -type f
done
}
@ -119,7 +121,7 @@ fi
echo "Copying binary files"
# --------------------
FORTRAN_EXEC=$(find_exec src)
FORTRAN_EXEC=$(find_exec src/*/)
if [[ -z $FORTRAN_EXEC ]] ; then
error 'No Fortran binaries found.'
exit 1

2
bin/qp_name
View File

@ -30,7 +30,7 @@ try:
from docopt import docopt
from qp_path import QP_SRC, QP_ROOT
except ImportError:
print("source .quantum_package.rc")
print("source quantum_package.rc")
raise

5
bin/qp_plugins
View File

@ -6,6 +6,7 @@ Usage:
qp_plugins download <url> [-n <name>]
qp_plugins install <name>...
qp_plugins uninstall <name>
qp_plugins remove <name>
qp_plugins update [-r <repo>]
qp_plugins create -n <name> [-r <repo>] [<needed_modules>...]
@ -24,6 +25,8 @@ Options:
uninstall Uninstall a plugin
remove Uninstall a plugin
update Update the repository
create
@ -274,7 +277,7 @@ def main(arguments):
subprocess.check_call(["qp_create_ninja", "update"])
print("[ OK ]")
elif arguments["uninstall"]:
elif arguments["uninstall"] or arguments["remove"]:
m_instance = ModuleHandler([QP_SRC])
d_descendant = m_instance.dict_descendant

7
bin/qp_set_frozen_core
View File

@ -7,12 +7,13 @@ setting all MOs as Active, except the n/2 first ones which are set as Core.
If pseudo-potentials are used, all the MOs are set as Active.
Usage:
qp_set_frozen_core [-q|--query] [(-l|-s|--large|--small)] EZFIO_DIR
qp_set_frozen_core [-q|--query] [(-l|-s|-u|--large|--small|--unset)] EZFIO_DIR
Options:
-q --query Prints in the standard output the number of frozen MOs
-l --large Use a small core
-s --small Use a large core
-u --unset Unset frozen core
Default numbers of frozen electrons:
@ -49,7 +50,7 @@ import os.path
try:
import qp_path
except ImportError:
print("source .quantum_package.rc")
print("source quantum_package.rc")
raise
from docopt import docopt
@ -88,7 +89,9 @@ def main(arguments):
elif charge <= 54: n_frozen += 9
elif charge <= 86: n_frozen += 18
elif charge <= 118: n_frozen += 27
elif arguments["--unset"]:
n_frozen = 0
else: # default
for charge in ezfio.nuclei_nucl_charge:
if charge <= 4: pass

2
bin/qp_set_frozen_large_core
View File

@ -23,7 +23,7 @@ import os.path
try:
import qp_path
except ImportError:
print("source .quantum_package.rc")
print("source quantum_package.rc")
raise
from docopt import docopt

10
config/gfortran.cfg
View File

@ -10,10 +10,10 @@
#
#
[COMMON]
FC : gfortran -ffree-line-length-none -I . -fPIC
FC : gfortran -g -ffree-line-length-none -I . -fPIC
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
# Global options
################
@ -22,7 +22,7 @@ IRPF90_FLAGS : --ninja --align=32
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
MODE : DEBUG ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
@ -35,7 +35,7 @@ OPENMP : 1 ; Append OpenMP flags
# -ffast-math and the Fortran-specific
# -fno-protect-parens and -fstack-arrays.
[OPT]
FCFLAGS : -Ofast -msse4.2
FCFLAGS : -Ofast
# Profiling flags
#################
@ -51,7 +51,7 @@ FCFLAGS : -Ofast
# -g : Extra debugging information
#
[DEBUG]
FCFLAGS : -fcheck=all -g
FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
# OpenMP flags
#################

2
config/gfortran_avx.cfg
View File

@ -13,7 +13,7 @@
FC : gfortran -ffree-line-length-none -I . -mavx -g -fPIC
LAPACK_LIB : -llapack -lblas
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED
# Global options
################

5
config/gfortran_debug.cfg
View File

@ -13,7 +13,7 @@
FC : gfortran -g -ffree-line-length-none -I . -fPIC
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert
IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED
# Global options
################
@ -51,7 +51,8 @@ FCFLAGS : -Ofast
# -g : Extra debugging information
#
[DEBUG]
FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
#FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
FCFLAGS : -g -msse4.2 -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow -finit-real=nan
# OpenMP flags
#################

2
config/gfortran_mpi.cfg
View File

@ -13,7 +13,7 @@
FC : mpif90 -ffree-line-length-none -I . -g -fPIC
LAPACK_LIB : -lblas -llapack
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI
IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED
# Global options
################

63
config/ifort_2019_avx.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -xAVX -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

64
config/ifort_2019_avx_mpi.cfg Normal file
View File

@ -0,0 +1,64 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FCFLAGS : -mavx -axAVX -O2 -ip -ftz -g -traceback
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -march=corei7 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

63
config/ifort_2019_mpi_rome.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback -shared-intel
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

63
config/ifort_2019_rome.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback -shared-intel
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

6
config/ifort_rome.cfg → config/ifort_2019_sse4.cfg
View File

@ -7,9 +7,9 @@
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
IRPF90_FLAGS : --ninja --align=32 -DINTEL -DSET_NESTED
# Global options
################
@ -32,7 +32,7 @@ OPENMP : 1 ; Append OpenMP flags
#
[OPT]
FC : -traceback
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
FCFLAGS : -xSSE4.2 -O2 -ip -ftz -g
# Profiling flags
#################

64
config/ifort_2019_sse4_mpi.cfg Normal file
View File

@ -0,0 +1,64 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FCFLAGS : -msse4.2 -O2 -ip -ftz -g -traceback
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -msse4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

63
config/ifort_2019_xHost.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=64 -DINTEL -DSET_NESTED
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -xHost -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

6
config/ifort_avx.cfg → config/ifort_2021_avx.cfg
View File

@ -7,9 +7,9 @@
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
IRPF90_FLAGS : --ninja --align=32 -DINTEL
# Global options
################
@ -32,7 +32,7 @@ OPENMP : 1 ; Append OpenMP flags
#
[OPT]
FC : -traceback
FCFLAGS : -mavx -O2 -ip -ftz -g
FCFLAGS : -xAVX -O2 -ip -ftz -g
# Profiling flags
#################

4
config/ifort_avx_mpi.cfg → config/ifort_2021_avx_mpi.cfg
View File

@ -7,9 +7,9 @@
#
[COMMON]
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL
# Global options
################

63
config/ifort_2021_mpi_rome.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DINTEL
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback -shared-intel
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

63
config/ifort_2021_rome.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DINTEL
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback -shared-intel
FCFLAGS : -O2 -ip -g -march=core-avx2 -align array64byte -fma -ftz -fomit-frame-pointer
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

4
config/ifort.cfg → config/ifort_2021_sse4.cfg
View File

@ -7,9 +7,9 @@
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32
IRPF90_FLAGS : --ninja --align=32 -DINTEL
# Global options
################

4
config/ifort_mpi.cfg → config/ifort_2021_sse4_mpi.cfg
View File

@ -7,9 +7,9 @@
#
[COMMON]
FC : mpiifort -fpic
LAPACK_LIB : -mkl=parallel
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 -DMPI
IRPF90_FLAGS : --ninja --align=32 -DMPI -DINTEL
# Global options
################

63
config/ifort_2021_xHost.cfg Normal file
View File

@ -0,0 +1,63 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel -lirc -lsvml -limf -lipps
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=64 -DINTEL
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : OPT ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -xHost -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -xSSE4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -xSSE2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -xSSE2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

66
config/ifort_debug.cfg
View File

@ -1,66 +0,0 @@
# Common flags
##############
#
# -mkl=[parallel|sequential] : Use the MKL library
# --ninja : Allow the utilisation of ninja. It is mandatory !
# --align=32 : Align all provided arrays on a 32-byte boundary
#
[COMMON]
FC : ifort -fpic
LAPACK_LIB : -mkl=parallel
IRPF90 : irpf90
IRPF90_FLAGS : --ninja --align=32 --assert
# Global options
################
#
# 1 : Activate
# 0 : Deactivate
#
[OPTION]
MODE : DEBUG ; [ OPT | PROFILE | DEBUG ] : Chooses the section below
CACHE : 0 ; Enable cache_compile.py
OPENMP : 1 ; Append OpenMP flags
# Optimization flags
####################
#
# -xHost : Compile a binary optimized for the current architecture
# -O2 : O3 not better than O2.
# -ip : Inter-procedural optimizations
# -ftz : Flushes denormal results to zero
#
[OPT]
FC : -traceback
FCFLAGS : -msse4.2 -O2 -ip -ftz -g
# Profiling flags
#################
#
[PROFILE]
FC : -p -g
FCFLAGS : -msse4.2 -O2 -ip -ftz
# Debugging flags
#################
#
# -traceback : Activate backtrace on runtime
# -fpe0 : All floating point exaceptions
# -C : Checks uninitialized variables, array subscripts, etc...
# -g : Extra debugging information
# -msse4.2 : Valgrind needs a very simple x86 executable
#
[DEBUG]
FC : -g -traceback
FCFLAGS : -msse4.2 -C -fpe0 -implicitnone
# OpenMP flags
#################
#
[OPENMP]
FC : -qopenmp
IRPF90_FLAGS : --openmp

269
configure vendored
View File

@ -3,8 +3,6 @@
# Quantum Package configuration script
#
TEMP=$(getopt -o c:i:h -l config:,install:,help -n $0 -- "$@") || exit 1
eval set -- "$TEMP"
export QP_ROOT="$( cd "$(dirname "$0")" ; pwd -P )"
echo "QP_ROOT="$QP_ROOT
@ -14,24 +12,9 @@ unset CCXX
# Force GCC instead of ICC for dependencies
export CC=gcc
# /!\ When updating version, update also etc files
EZFIO_TGZ="EZFIO-v2.0.3.tar.gz"
BATS_URL="https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz"
BUBBLE_URL="https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz"
DOCOPT_URL="https://github.com/docopt/docopt/archive/0.6.2.tar.gz"
BSE_URL="https://github.com/MolSSI-BSE/basis_set_exchange/archive/v0.8.11.tar.gz"
F77ZMQ_URL="https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz"
GMP_URL="ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2"
IRPF90_URL="https://gitlab.com/scemama/irpf90/-/archive/v2.0.0/irpf90-v2.0.0.tar.gz"
LIBCAP_URL="https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz"
NINJA_URL="https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip"
OCAML_URL="https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh"
RESULTS_URL="https://gitlab.com/scemama/resultsFile/-/archive/v2.0/resultsFile-v2.0.tar.gz"
ZEROMQ_URL="https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz"
ZLIB_URL="https://www.zlib.net/zlib-1.2.11.tar.gz"
# Download submodules
git submodule init
git submodule update
function help()
{
@ -39,15 +22,15 @@ function help()
Quantum Package configuration script.
Usage:
$(basename $0) -c <file> | --config=<file>
$(basename $0) -h | --help
$(basename $0) -i <package> | --install=<package>
$(basename $0) -c <file>
$(basename $0) -h
$(basename $0) -i <package>
Options:
-c, --config=<file> Define a COMPILATION configuration file,
-c <file> Define a COMPILATION configuration file,
in "${QP_ROOT}/config/".
-h, --help Print the HELP message
-i, --install=<package> INSTALL <package>. Use at your OWN RISK:
-h Print the HELP message
-i <package> INSTALL <package>. Use at your OWN RISK:
no support will be provided for the installation of
dependencies.
@ -83,33 +66,30 @@ function execute () {
}
PACKAGES=""
OCAML_PACKAGES="ocamlbuild cryptokit zmq sexplib ppx_sexp_conv ppx_deriving getopt"
while true ; do
case "$1" in
-c|--config)
case "$2" in
while getopts "d:c:i:h" c ; do
case "$c" in
c)
case "$OPTARG" in
"") help ; break;;
*) if [[ -f $2 ]] ; then
CONFIG="$2"
*) if [[ -f $OPTARG ]] ; then
CONFIG="$OPTARG"
else
error "error: configuration file $2 not found."
error "error: configuration file $OPTARG not found."
exit 1
fi
esac
shift 2;;
-i|--install)
case "$2" in
esac;;
i)
case "$OPTARG" in
"") help ; break;;
*) PACKAGES="${PACKAGE} $2"
esac
shift 2;;
-h|-help|--help)
*) PACKAGES="${PACKAGE} $OPTARG"
esac;;
h)
help
exit 0;;
--) shift ; break ;;
*)
error $(basename $0)": unknown option $1, try --help"
error $(basename $0)": unknown option $c, try -h for help"
exit 2;;
esac
done
@ -126,23 +106,13 @@ source quantum_package.rc
function fail() {
echo "You can try to install it using the -i option."
echo "Please refer to INSTALL.rst to install the missing dependencies."
exit 1
exit -1
}
function success() {
echo ""
echo "Configuration successful."
exit 1
}
function download() {
echo "Downloading $1"
echo ""
printf "\e[0;34m"
wget --no-check-certificate $1 --output-document=$2 || error "Unable to download $1"
printf "\e[m"
echo "Saved dowloaded file as $2"
echo ""
exit 0
}
function not_found() {
@ -177,16 +147,15 @@ function find_dir() {
fi
}
# Make program believe stdin is a tty
function faketty() {
script -qfc "$(printf "%q " "$@")" /dev/null
}
# Extract EZFIO if needed
EZFIO=$(find_dir "${QP_ROOT}"/external/ezfio)
if [[ ${EZFIO} = $(not_found) ]] ; then
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file ${EZFIO_TGZ}
rm -rf ezfio
mv EZFIO ezfio || mv EZFIO-v*/ ezfio
EOF
# Install IRPF90 if needed
IRPF90=$(find_exe irpf90)
if [[ ${IRPF90} = $(not_found) ]] ; then
make -C ${QP_ROOT}/external/irpf90
fi
@ -211,7 +180,7 @@ if [[ "${PACKAGES}.x" != ".x" ]] ; then
fi
if [[ ${PACKAGES} = all ]] ; then
PACKAGES="zlib ninja irpf90 zeromq f77zmq gmp libcap bwrap ocaml ezfio docopt resultsFile bats"
PACKAGES="zlib ninja zeromq f77zmq gmp ocaml docopt resultsFile bats"
fi
@ -219,159 +188,72 @@ for PACKAGE in ${PACKAGES} ; do
if [[ ${PACKAGE} = ninja ]] ; then
download ${NINJA_URL} "${QP_ROOT}"/external/ninja.zip
execute << EOF
rm -f "\${QP_ROOT}"/bin/ninja
unzip "\${QP_ROOT}"/external/ninja.zip -d "\${QP_ROOT}"/bin
unzip "\${QP_ROOT}"/external/qp2-dependencies/ninja-linux.zip -d "\${QP_ROOT}"/bin
EOF
elif [[ ${PACKAGE} = gmp ]] ; then
download ${GMP_URL} "${QP_ROOT}"/external/gmp.tar.bz2
execute << EOF
cd "\${QP_ROOT}"/external
tar --bzip2 --extract --file gmp.tar.bz2
rm gmp.tar.bz2
cd gmp*
tar --bzip2 --extract --file qp2-dependencies/gmp-6.1.2.tar.bz2
cd gmp-6.1.2
./configure --prefix=$QP_ROOT && make -j 8
make install
make -j 8 install
EOF
elif [[ ${PACKAGE} = libcap ]] ; then
download ${LIBCAP_URL} "${QP_ROOT}"/external/libcap.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file libcap.tar.gz
rm libcap.tar.gz
cd libcap-*/libcap
prefix=$QP_ROOT make install
EOF
elif [[ ${PACKAGE} = bwrap ]] ; then
download ${BUBBLE_URL} "${QP_ROOT}"/external/bwrap.tar.xz
execute << EOF
cd "\${QP_ROOT}"/external
tar --xz --extract --file bwrap.tar.xz
rm bwrap.tar.xz
cd bubblewrap*
./configure --prefix=$QP_ROOT && make -j 8
make install-exec-am
EOF
elif [[ ${PACKAGE} = irpf90 ]] ; then
# When changing version of irpf90, don't forget to update etc/irpf90.rc
download ${IRPF90_URL} "${QP_ROOT}"/external/irpf90.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file irpf90.tar.gz
rm irpf90.tar.gz
cd irpf90-*
make
EOF
elif [[ ${PACKAGE} = zeromq ]] ; then
download ${ZEROMQ_URL} "${QP_ROOT}"/external/zeromq.tar.gz
execute << EOF
export CC=gcc
export CXX=g++
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file zeromq.tar.gz
rm zeromq.tar.gz
tar --gunzip --extract --file qp2-dependencies/zeromq-4.2.5.tar.gz
cd zeromq-*
./configure --prefix="\$QP_ROOT" --without-libsodium --enable-libunwind=no
make
make -j 8
make install
EOF
elif [[ ${PACKAGE} = f77zmq ]] ; then
download ${F77ZMQ_URL} "${QP_ROOT}"/external/f77_zmq.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file f77_zmq.tar.gz
rm f77_zmq.tar.gz
cd f77_zmq-*
tar --gunzip --extract --file qp2-dependencies/f77-zmq-4.3.2.tar.gz
cd f77-zmq-*
./configure --prefix=\$QP_ROOT
export ZMQ_H="\$QP_ROOT"/include/zmq.h
make
cp libf77zmq.a "\${QP_ROOT}"/lib
cp libf77zmq.so "\${QP_ROOT}"/lib
cp f77_zmq_free.h "\${QP_ROOT}"/include
make && make check && make install
EOF
elif [[ ${PACKAGE} = ocaml ]] ; then
download ${OCAML_URL} "${QP_ROOT}"/external/opam_installer.sh
if [[ -n ${TRAVIS} ]] ; then
# Special commands for Travis CI
chmod +x "${QP_ROOT}"/external/opam_installer.sh
rm --force ${QP_ROOT}/bin/opam
if [[ -n ${NO_CACHE} ]] ; then
rm -rf ${HOME}/.opam
fi
export OPAMROOT=${HOME}/.opam
cat << EOF | bash ${QP_ROOT}/external/opam_installer.sh --no-backup
${QP_ROOT}/bin
execute <<EOF
source "${QP_ROOT}"/quantum_package.rc
cd "${QP_ROOT}"/external/
tar --gunzip --extract --file qp2-dependencies/ocaml-bundle_x86.tar.gz
echo "" | ./ocaml-bundle/bootstrap.sh "${QP_ROOT}"
./ocaml-bundle/configure.sh "${QP_ROOT}"
echo "" | ./ocaml-bundle/compile.sh "${QP_ROOT}"
EOF
rm ${QP_ROOT}/external/opam_installer.sh
# source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
#
# opam switch create ocaml-base-compiler.4.10.0
opam init --verbose --yes --compiler=4.10.0 --disable-sandboxing
eval $(opam env)
opam install -y ${OCAML_PACKAGES} || exit 1
else
# Conventional commands
execute << EOF
chmod +x "${QP_ROOT}"/external/opam_installer.sh
"${QP_ROOT}"/external/opam_installer.sh --no-backup
EOF
execute << EOF
rm --force ${QP_ROOT}/bin/opam
export OPAMROOT=${OPAMROOT:-${QP_ROOT}/external/opam}
echo ${QP_ROOT}/bin \
| sh ${QP_ROOT}/external/opam_installer.sh
EOF
rm ${QP_ROOT}/external/opam_installer.sh
# source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true
# opam switch create ocaml-base-compiler.4.10.0 || exit 1
opam init --verbose --yes --compiler=4.10.0 --disable-sandboxing
eval $(opam env)
execute << EOF
opam install -y \${OCAML_PACKAGES} || exit 1
EOF
fi
elif [[ ${PACKAGE} = bse ]] ; then
download ${BSE_URL} "${QP_ROOT}"/external/bse.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file bse.tar.gz
tar --gunzip --extract --file qp2-dependencies/bse-v0.8.11.tar.gz
pip install -e basis_set_exchange-*
EOF
elif [[ ${PACKAGE} = zlib ]] ; then
download ${ZLIB_URL} "${QP_ROOT}"/external/zlib.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file zlib.tar.gz
rm zlib.tar.gz && \
tar --gunzip --extract --file qp2-dependencies/zlib-1.2.11.tar.gz
cd zlib-*/
./configure --prefix=${QP_ROOT} && \
make && make install
@ -380,35 +262,32 @@ EOF
elif [[ ${PACKAGE} = docopt ]] ; then
download ${DOCOPT_URL} "${QP_ROOT}"/external/docopt.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file docopt.tar.gz
tar --gunzip --extract --file qp2-dependencies/docopt-0.6.2.tar.gz
mv docopt-*/docopt.py "\${QP_ROOT}/external/Python"
rm --recursive --force -- docopt-*/ docopt.tar.gz
EOF
elif [[ ${PACKAGE} = resultsFile ]] ; then
download ${RESULTS_URL} "${QP_ROOT}"/external/resultsFile.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar --gunzip --extract --file resultsFile.tar.gz
tar --gunzip --extract --file qp2-dependencies/resultsFile-v2.3.tar.gz
mv resultsFile-*/resultsFile "\${QP_ROOT}/external/Python/"
rm --recursive --force resultsFile-* resultsFile.tar.gz
EOF
elif [[ ${PACKAGE} = bats ]] ; then
download ${BATS_URL} "${QP_ROOT}"/external/bats.tar.gz
execute << EOF
cd "\${QP_ROOT}"/external
tar -zxf bats.tar.gz
tar -zxf qp2-dependencies/bats-v1.1.0.tar.gz
( cd bats-core-1.1.0/ ; ./install.sh \${QP_ROOT})
rm --recursive --force -- bats-core-1.1.0 \ "\${QP_ROOT}"/external/bats.tar.gz
EOF
else
error "${PACKAGE} unknown."
fail
fi
@ -422,12 +301,6 @@ if [[ ${NINJA} = $(not_found) ]] ; then
fail
fi
IRPF90=$(find_exe irpf90)
if [[ ${IRPF90} = $(not_found) ]] ; then
error "IRPf90 (irpf90) is not installed."
fail
fi
ZEROMQ=$(find_lib -lzmq)
if [[ ${ZEROMQ} = $(not_found) ]] ; then
error "ZeroMQ (zeromq) is not installed."
@ -446,24 +319,6 @@ if [[ ${ZLIB} = $(not_found) ]] ; then
fail
fi
LIBCAP=$(find_lib -lcap)
if [[ ${LIBCAP} = $(not_found) ]] ; then
error "Libcap (libcap) is not installed."
fail
fi
BWRAP=$(find_exe bwrap)
if [[ ${BWRAP} = $(not_found) ]] ; then
error "Bubblewrap (bwrap) is not installed."
fail
fi
OPAM=$(find_exe opam)
if [[ ${OPAM} = $(not_found) ]] ; then
error "OPAM (ocaml) package manager is not installed."
fail
fi
OCAML=$(find_exe ocaml)
if [[ ${OCAML} = $(not_found) ]] ; then
error "OCaml (ocaml) compiler is not installed."

1
etc/cflags.rc Normal file
View File

@ -0,0 +1 @@
export CFLAGS="$CFLAGS --std=gnu99"

2
etc/irpf90.rc
View File

@ -1,7 +1,7 @@
# Configuration of IRPF90 package
# Set the path of IRPF90 here:
export IRPF90_PATH=${QP_ROOT}/external/irpf90-v2.0.0
export IRPF90_PATH=${QP_ROOT}/external/irpf90
export PATH=${PATH}:${IRPF90_PATH}/bin
export IRPF90=${IRPF90_PATH}/bin/irpf90

1
etc/local.rc
View File

@ -19,4 +19,3 @@
# export QP_NIC=lo
# export QP_NIC=ib0

13
etc/ninja.rc
View File

@ -1,13 +0,0 @@
# Configuration for the Ninja package
export NINJA=${QP_ROOT}/bin/ninja
function ninja () {
if [[ -f ${QP_ROOT}/build.ninja ]] ; then
${QP_ROOT}/bin/ninja "$@"
else
>&2 echo "Error: build.ninja does not exists.
You need to run ./configure first."
fi
}

6
etc/ocaml.rc
View File

@ -4,8 +4,10 @@ if [[ -z $OPAMROOT ]]
then
# Comment these lines if you have a system-wide OCaml installation
export OPAMROOT=${QP_ROOT}/external/opam
export PATH="${QP_ROOT}/external/ocaml-bundle/bootstrap/bin:$PATH"
if [[ -f "${QP_ROOT}/external/ocaml-bundle/bootstrap/bin/opam" ]] ; then
eval $(opam env --root "${QP_ROOT}/external/ocaml-bundle/opam" --set-root)
fi
fi
source ${OPAMROOT}/opam-init/init.sh > /dev/null 2> /dev/null || true

1
etc/openmp.rc Normal file
View File

@ -0,0 +1 @@
export OMP_NESTED=True

4
etc/paths.rc
View File

@ -3,7 +3,7 @@
QP_PYTHON=
# Load dependencies
for i in ezfio.rc irpf90.rc ninja.rc ocaml.rc
for i in ezfio.rc irpf90.rc ocaml.rc
do
source $i
done
@ -34,9 +34,9 @@ export PATH=$(qp_prepend_export "PATH" "${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROO
export LD_LIBRARY_PATH=$(qp_prepend_export "LD_LIBRARY_PATH" "${QP_ROOT}"/lib)
export LIBRARY_PATH=$(qp_prepend_export "LIBRARY_PATH" "${QP_ROOT}"/lib:"${QP_ROOT}"/lib64)
export PKG_CONFIG_PATH=$(qp_prepend_export "PKG_CONFIG_PATH" "${QP_ROOT}"/lib/pkgconfig)
export C_INCLUDE_PATH=$(qp_prepend_export "C_INCLUDE_PATH" "${QP_ROOT}"/include)
export CPATH=$(qp_prepend_export "CPATH" "${QP_ROOT}"/include)

5
etc/qp.rc
View File

@ -93,7 +93,7 @@ function qp()
"prompt")
shift
python2 $QP_ROOT/scripts/hello.py
python3 $QP_ROOT/scripts/hello.py
function _check_ezfio() {
if [[ -d ${EZFIO_FILE} ]] ; then
printf "\e[0;32m|${EZFIO_FILE}>\e[m"
@ -204,6 +204,9 @@ _qp_Complete()
uninstall)
COMPREPLY=( $(compgen -W "$(qp_plugins list -i)" -- $cur ) )
return 0;;
remove)
COMPREPLY=( $(compgen -W "$(qp_plugins list -i)" -- $cur ) )
return 0;;
create)
COMPREPLY=( $(compgen -W "-n " -- $cur ) )
return 0;;

2
external/.gitignore vendored
View File

@ -1,2 +1,2 @@
*
#*

BIN
external/EZFIO-v2.0.3.tar.gz vendored
View File

Binary file not shown.

46
external/Python/.gitignore vendored
View File

@ -1,46 +0,0 @@
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml
# Translations
*.mo
*.pot
# Django stuff:
*.log
# Sphinx documentation
docs/_build/
# PyBuilder
target/

1
external/ezfio vendored Submodule

@ -0,0 +1 @@
Subproject commit d5805497fa0ef30e70e055cde1ecec2963303e93

1
external/irpf90 vendored Submodule

@ -0,0 +1 @@
Subproject commit ab88cc01a6598a34e47989fa13b8fcadab703419

1
external/qp2-dependencies vendored Submodule

@ -0,0 +1 @@
Subproject commit 242151e03d1d6bf042387226431d82d35845686a

73
scripts/compilation/qp_create_ninja
View File

@ -43,6 +43,7 @@ EZFIO_LIB = join("$QP_ROOT", "lib", "libezfio_irp.a")
ZMQ_LIB = join("$QP_ROOT", "lib", "libf77zmq.a") + " " + join("$QP_ROOT", "lib", "libzmq.a") + " -lstdc++ -lrt -ldl"
ROOT_BUILD_NINJA = join("$QP_ROOT", "config", "build.ninja")
ROOT_BUILD_NINJA_EXP = join(QP_ROOT, "config", "build.ninja")
ROOT_BUILD_NINJA_EXP_tmp = join(QP_ROOT, "config", "build.ninja.tmp")
header = r"""#
# _______ _____
# __ __ \___ _______ _________ /____ ________ ___
@ -57,7 +58,7 @@ header = r"""#
# /_/ \__,_/ \___/ /_/|_| \__,_/ _\__, / \___/
# /____/
#
# https://github.com/LCPQ/quantum_package,
# https://github.com/QuantumPackage/qp2,
#
# Generated automatically by {0}
#
@ -107,6 +108,17 @@ def ninja_create_env_variable(pwd_config_file):
lib_usr = get_compilation_option(pwd_config_file, "LIB")
str_lib = " ".join([lib_lapack, EZFIO_LIB, ZMQ_LIB, LIB, lib_usr])
# Read all LIB files in modules
libfile = "LIB"
try:
content = ""
with open(libfile,'r') as f:
content = f.read()
str_lib += " "+content
except IOError:
pass
l_string.append("LIB = {0} ".format(str_lib))
l_string.append("")
@ -149,7 +161,7 @@ def get_l_module_with_ezfio_cfg():
from os import listdir
from os.path import isfile
return [real_join(QP_SRC, m) for m in listdir(QP_SRC)
return [real_join(QP_SRC, m) for m in sorted(listdir(QP_SRC))
if isfile(real_join(QP_SRC, m, "EZFIO.cfg"))]
@ -328,13 +340,13 @@ def ninja_symlink_build(path_module, l_symlink):
if not l_symlink:
return []
l_folder = [s.destination for s in l_symlink]
l_folder = [s.destination for s in sorted(l_symlink,key=lambda x:x.destination)]
l_string = ["build l_symlink_{0} : phony {1}".format(path_module.rel,
" ".join(map(comp_path,l_folder))),
""]
for symlink in l_symlink:
for symlink in sorted(l_symlink, key=lambda x: x.source+x.destination):
l_string += ["build {0}: build_symlink {1}".format(*list(map(comp_path,(symlink.destination, symlink.source)))), ""]
return l_string
@ -360,7 +372,7 @@ def ninja_gitignore_build(path_module, d_binaries, l_symlink):
path_gitignore = comp_path(join(path_module.abs, ".gitignore"))
l_b = list(map(comp_path,[i.abs for i in d_binaries[path_module]]))
l_b = sorted(list(map(comp_path,[i.abs for i in d_binaries[path_module]])))
root = "build {0}: build_gitignore {1}".format(path_gitignore,
" ".join(l_b))
@ -389,7 +401,7 @@ def get_l_file_for_module(path_module):
l_template = []
for f in os.listdir(path_module.abs):
for f in sorted(os.listdir(path_module.abs)):
if f.lower().endswith(tuple([".template.f", ".include.f"])):
l_template.append(join(path_module.abs, f))
elif f.endswith(".irp.f"):
@ -495,10 +507,10 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
# D e p e n d a n c y #
# ~#~#~#~#~#~#~#~#~#~ #
l_depend = list(map(comp_path,d_irp[path_module]["l_depend"]))
l_src = list(map(comp_path,d_irp[path_module]["l_src"]))
l_obj = list(map(comp_path,d_irp[path_module]["l_obj"]))
l_template = list(map(comp_path,d_irp[path_module]["l_template"]))
l_depend = sorted(list(map(comp_path,d_irp[path_module]["l_depend"])))
l_src = sorted(list(map(comp_path,d_irp[path_module]["l_src"])))
l_obj = sorted(list(map(comp_path,d_irp[path_module]["l_obj"])))
l_template = sorted(list(map(comp_path,d_irp[path_module]["l_template"])))
if l_needed_molule:
l_symlink = ["l_symlink_{0}".format(path_module.rel)]
@ -511,7 +523,7 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
# N i n j a _ b u i l d #
# ~#~#~#~#~#~#~#~#~#~#~ #
l_include_dir = ["-I {0}".format(m.rel) for m in l_needed_molule]
l_include_dir = ["-I {0}".format(m.rel) for m in sorted(l_needed_molule, key=lambda x:x.rel+x.abs) ]
l_string = [
"build {0}: build_irpf90.ninja {1}".format(str_creation, str_depend),
@ -642,7 +654,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
# ~#~#~ #
ninja_module_path = join(comp_path(path_module.abs), "IRPF90_temp/build.ninja")
l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]]))
l_abs_bin = sorted(list(map(comp_path,[binary.abs for binary in d_binaries[path_module]])))
# ~#~#~#~#~#~ #
# s t r i n g #
@ -659,8 +671,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
def ninja_module_build(path_module, d_binaries):
l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]]))
l_abs_bin = sorted(list(map(comp_path,[binary.abs for binary in d_binaries[path_module]])))
path_readme = os.path.join(comp_path(path_module.abs), "README.rst")
l_string = ["build module_{0}: phony {1}".format(path_module.rel,
@ -698,6 +709,11 @@ def save_subninja_file(path_module):
" description = Cleaning module {0}".format(path_module.rel),
""]
l_string += ["rule make_tidy",
" command = module_handler.py tidy {0}".format(path_module.rel),
" description = Cleaning module {0}".format(path_module.rel),
""]
l_string += ["rule executables",
" command = make -C {0} executables .gitignore qp_edit.native qp_run.native".format(join("$QP_ROOT","ocaml")),
" description = Updating OCaml executables",
@ -708,6 +724,7 @@ def save_subninja_file(path_module):
"build local: make_local_binaries dummy_target", "",
"build executables: executables local dummy_target", "",
"default executables", "", "build clean: make_clean dummy_target",
"", "build tidy: make_tidy dummy_target",
""]
path_ninja_cur = join(path_module.abs, "build.ninja")
@ -734,6 +751,10 @@ def create_build_ninja_global():
" command = module_handler.py clean --all",
" description = Cleaning all modules", ""]
l_string += ["rule make_tidy",
" command = module_handler.py tidy --all",
" description = Cleaning all modules", ""]
l_string += ["rule make_ocaml",
" command = make -C {0}/ocaml".format("$QP_ROOT"),
" pool = console",
@ -748,6 +769,8 @@ def create_build_ninja_global():
"default ocaml_target",
"",
"build clean: make_clean dummy_target",
"",
"build tidy: make_tidy dummy_target",
"", ]
path_ninja_cur = join(QP_ROOT, "build.ninja")
@ -830,14 +853,14 @@ if __name__ == "__main__":
dict_root = module_instance.dict_root
dict_root_path = dict_module_genelogy_path(dict_root)
l_all_module = list(d_genealogy_path.keys())
l_all_module = sorted(list(d_genealogy_path.keys()))
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# M o d u l e _ t o _ i r p #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
d_binaries = get_dict_binaries(l_all_module, mode="development")
l_module = list(d_binaries.keys())
l_module = sorted(list(d_binaries.keys()), key=lambda x: x.rel+x.abs)
# ~#~#~#~#~#~#~#~#~#~#~#~ #
@ -851,7 +874,6 @@ if __name__ == "__main__":
# ~#~#~#~#~#~#~#~#~#~#~#~ #
for module_to_compile in l_module:
if module_to_compile.rel == "dummy":
continue
@ -884,6 +906,21 @@ if __name__ == "__main__":
# S a v e s #
# ~#~#~#~#~ #
with open(ROOT_BUILD_NINJA_EXP, "w+") as f:
with open(ROOT_BUILD_NINJA_EXP_tmp, "w+") as f:
f.write(header)
f.write("\n".join(l_string))
with open(ROOT_BUILD_NINJA_EXP_tmp, "r") as f:
a = f.read()
try:
with open(ROOT_BUILD_NINJA_EXP, "r") as f:
b = f.read()
except:
b = None
if a != b:
os.rename(ROOT_BUILD_NINJA_EXP_tmp, ROOT_BUILD_NINJA_EXP)
else:
os.remove(ROOT_BUILD_NINJA_EXP_tmp)

2
scripts/ezfio_interface/ezfio_generate_provider.py
View File

@ -82,6 +82,8 @@ END_PROVIDER
mpi_correspondance = {"integer": "MPI_INTEGER",
"integer*8": "MPI_INTEGER8",
"character*(32)": "MPI_CHARACTER",
"character*(64)": "MPI_CHARACTER",
"character*(256)": "MPI_CHARACTER",
"logical": "MPI_LOGICAL",
"double precision": "MPI_DOUBLE_PRECISION"}

17
scripts/module/module_handler.py
View File

@ -6,12 +6,18 @@ Module utilitary
Usage:
module_handler.py print_descendant [<module_name>...]
module_handler.py clean [ --all | <module_name>...]
module_handler.py create_git_ignore [<module_name>...]
module_handler.py tidy [ --all | <module_name>...]
module_handler.py create_git_ignore [ --all | <module_name>...]
Options:
print_descendant Print the genealogy of the needed modules
clean Used for ninja clean
tidy A light version of clean, where only the intermediate
files are removed
create_git_ignore deprecated
NEED The path of NEED file.
by default try to open the file in the current path
"""
import os
import sys
@ -25,7 +31,7 @@ try:
from docopt import docopt
from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO
except ImportError:
print("source .quantum_package.rc")
print("source quantum_package.rc")
raise
@ -110,6 +116,7 @@ def get_l_module_descendant(d_child, l_module):
print("Error: ", file=sys.stderr)
print("`{0}` is not a submodule".format(module), file=sys.stderr)
print("Check the typo (spelling, case, '/', etc.) ", file=sys.stderr)
# pass
sys.exit(1)
return list(set(l))
@ -230,7 +237,7 @@ if __name__ == '__main__':
for module in l_module:
print(" ".join(sorted(m.l_descendant_unique([module]))))
if arguments["clean"]:
if arguments["clean"] or arguments["tidy"]:
l_dir = ['IRPF90_temp', 'IRPF90_man']
l_file = ["irpf90_entities", "tags", "irpf90.make", "Makefile",
@ -242,7 +249,6 @@ if __name__ == '__main__':
l_symlink = m.l_descendant_unique([module])
l_exe = get_binaries(module_abs)
if arguments["clean"]:
for f in l_dir:
try:
shutil.rmtree(os.path.join(module_abs, f))
@ -261,6 +267,7 @@ if __name__ == '__main__':
except:
pass
if arguments["clean"]:
for f in l_exe:
try:
@ -268,6 +275,4 @@ if __name__ == '__main__':
except:
pass
if arguments["create_git_ignore"]:
pass

175
scripts/verif_omp/check_omp.f90 Normal file
View File

@ -0,0 +1,175 @@
program check_omp_v2
use omp_lib
implicit none
integer :: accu, accu2
integer :: s, n_setting
logical :: verbose, test_versions
logical, allocatable :: is_working(:)
verbose = .False.
test_versions = .True.
n_setting = 4
allocate(is_working(n_setting))
is_working = .False.
! set the number of threads
call omp_set_num_threads(2)
do s = 1, n_setting
accu = 0
accu2 = 0
call omp_set_max_active_levels(1)
call omp_set_nested(.False.)
if (s==1) then
!call set_multiple_levels_omp()
cycle
elseif (s==2) then
call omp_set_max_active_levels(5)
elseif (s==3) then
call omp_set_nested(.True.)
else
call omp_set_nested(.True.)
call omp_set_max_active_levels(5)
endif
! Level 1
!$OMP PARALLEL
if (verbose) then
print*,'Num threads level 1:',omp_get_num_threads()
endif
! Level 2
!$OMP PARALLEL
if (verbose) then
print*,'Num threads level 2:',omp_get_num_threads()
endif
! Level 3
!$OMP PARALLEL
if (verbose) then
print*,'Num threads level 3:',omp_get_num_threads()
endif
call check_omp_in_subroutine(accu2)
! Level 4
!$OMP PARALLEL
if (verbose) then
print*,'Num threads level 4:',omp_get_num_threads()
endif
!$OMP ATOMIC
accu = accu + 1
!$OMP END ATOMIC
!$OMP END PARALLEL
!$OMP END PARALLEL
!$OMP END PARALLEL
!$OMP END PARALLEL
if (verbose) then
print*,'Setting:',s,'accu=',accu
print*,'Setting:',s,'accu2=',accu2
endif
if (accu == 16 .and. accu2 == 16) then
is_working(s) = .True.
endif
enddo
if (verbose) then
if (is_working(2)) then
print*,'The parallelization works on 4 levels with:'
print*,'call omp_set_max_active_levels(5)'
print*,''
print*,'Please use the irpf90 flags -DSET_MAX_ACT in qp2/config/${compiler_name}.cfg'
elseif (is_working(3)) then
print*,'The parallelization works on 4 levels with:'
print*,'call omp_set_nested(.True.)'
print*,''
print*,'Please use the irpf90 flag -DSET_NESTED in qp2/config/${compiler_name}.cfg'
elseif (is_working(4)) then
print*,'The parallelization works on 4 levels with:'
print*,'call omp_set_nested(.True.)'
print*,'+'
print*,'call omp_set_max_active_levels(5)'
print*,''
print*,'Please use the irpf90 flags -DSET_NESTED -DSET_MAX_ACT in qp2/config/${compiler_name}.cfg'
else
print*,'The parallelization on multiple levels does not work with:'
print*,'call omp_set_max_active_levels(5)'
print*,'or'
print*,'call omp_set_nested(.True.)'
print*,'or'
print*,'call omp_set_nested(.True.)'
print*,'+'
print*,'call omp_set_max_active_levels(5)'
print*,''
print*,'Try an other compiler and good luck...'
endif
! if (is_working(1)) then
! print*,''
! print*,'=========================================================='
! print*,'Your actual set up works for parallelization with 4 levels'
! print*,'=========================================================='
! print*,''
! else
! print*,''
! print*,'==================================================================='
! print*,'Your actual set up does not work for parallelization with 4 levels'
! print*,'Please look at the previous messages to understand the requirements'
! print*,'==================================================================='
! print*,''
! endif
endif
! List of working flags
if (test_versions) then
print*,'Tests:',is_working(2:4)
endif
! IRPF90_FLAGS
if (is_working(2)) then
print*,'-DSET_MAX_ACT'
elseif (is_working(3)) then
print*,'-DSET_NESTED'
elseif (is_working(4)) then
print*,'-DSET_MAX_ACT -DSET_NESTED'
else
print*,'ERROR'
endif
end
subroutine check_omp_in_subroutine(accu2)
implicit none
integer, intent(inout) :: accu2
!$OMP PARALLEL
!$OMP ATOMIC
accu2 = accu2 + 1
!$OMP END ATOMIC
!$OMP END PARALLEL
end

19
scripts/verif_omp/check_required_setup.sh Executable file
View File

@ -0,0 +1,19 @@
#!/bin/sh
# take one argument which is the compiler used
# return the required IRPF90_FLAGS for the $1 compiler
if [ -z "$1" ]
then
echo "Give the compiler in argument"
else
$1 --version > /dev/null \
&& $1 -O0 -fopenmp check_omp.f90 \
&& ./a.out | tail -n 1
# if there is an error or if the compiler is not found
$1 --version > /dev/null || echo 'compiler not found'
fi

30
scripts/verif_omp/study_omp.sh Executable file
View File

@ -0,0 +1,30 @@
#!/bin/sh
# list of compilers
list_comp="ifort gfortran-7 gfortran-8 gfortran-9"
# file to store the results
FILE=results.dat
touch $FILE
rm $FILE
# Comments
echo "1: omp_set_max_active_levels(5)" >> $FILE
echo "2: omp_set_nested(.True.)" >> $FILE
echo "3: 1 + 2" >> $FILE
echo "" >> $FILE
echo "1 2 3" >> $FILE
# loop on the comp
for comp in $list_comp
do
$comp --version > /dev/null \
&& $comp -O0 -fopenmp check_omp.f90 \
&& echo $(./a.out | grep "Tests:" | cut -d ":" -f2- ) $(echo " : ") $($comp --version | head -n 1) >> $FILE
done
# Display
cat $FILE

49
scripts/verif_omp/update_comp.sh Executable file
View File

@ -0,0 +1,49 @@
#!/bin/bash
# Compiler
COMP=$1
# Path to file.cfg
config_PATH="../../config/"
END="*.cfg"
CONFIG="/config/"
#LIST=${config_PATH}${COMP}${END} # without ${QP_ROOT}
LIST=${QP_ROOT}${CONFIG}${COMP}${END}
if [ -z "$1" ]
then
echo "Give the compiler in argument"
else
# List of the config files for the compiler
#list_files=$(ls ../../config/$comp*.cfg) #does not give the right list
list_files=${LIST}
echo "Files that will be modified:"
echo $list_files
# Flags that must be added
FLAGS=$(./check_required_setup.sh $COMP)
# Add the flags
for file in $list_files
do
echo $file
BASE="IRPF90_FLAGS : --ninja"
ACTUAL=$(grep "$BASE" $file)
# To have only one time each flag
grep " -DSET_MAX_ACT" $file && ${ACTUAL/" -DSET_MAX"/""}
grep " -DSET_NESTED" $file && ${ACTUAL/" -DSET_NESTED"/""}
SPACE=" "
NEW=${ACTUAL}${SPACE}${FLAGS}
# Debug
#echo ${NEW}
sed "s/${ACTUAL}/${NEW}/" $file
# -i # to change the files
done
fi

1
src/utils_complex/MolPyscfToQPkpts.py
View File

@ -855,6 +855,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
with h5py.File(qph5path,'a') as qph5:
kcon_f_phys = np.array(kconserv.transpose((1,2,0)),order='c')
qph5.create_dataset('nuclei/kconserv',data=kcon_f_phys+1)
qph5.create_dataset('nuclei/kpts',data=kpts)
if print_debug:
print_kcon_chem_to_phys(kconserv,'K.qp')