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mirror of https://github.com/QuantumPackage/qp2.git synced 2024-12-30 15:15:38 +01:00

Merge branch 'dev' of github.com:QuantumPackage/qp2 into dev

This commit is contained in:
Anthony Scemama 2021-11-29 10:06:43 +01:00
commit 3d3751fc78
23 changed files with 634 additions and 63 deletions

83
bin/qp_gaussian Executable file
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@ -0,0 +1,83 @@
#!/usr/bin/env python3
#
"""
Runs a Quantum Package calculation using a Gaussian input file.
Usage:
qp_gaussian INPUT
"""
# Requires pymatgen (https://pymatgen.org/)
# pip install pymatgen
import os
import sys
import os.path
try:
import qp_path
except ImportError:
print("source quantum_package.rc")
from docopt import docopt
import pymatgen
from pymatgen.io.gaussian import GaussianInput
def main(arguments):
filename = arguments["INPUT"]
with open(filename,'r') as f:
text = f.read()
in_file = GaussianInput.from_string(text)
d = in_file.as_dict()
charge = ("%d"%(d["charge"])).replace('-','m')
basis = d["basis_set"]
mult = d["spin_multiplicity"]
natoms = len(d["molecule"]["sites"])
with open("g09.xyz","w") as f:
f.write("%d\n"%natoms)
f.write("%s\n"%d["title"])
f.write("%s\n"%in_file.get_cart_coords())
if basis is None:
print("Basis set not found. Use '/' before basis set")
sys.exit(1)
command = f"rm -rf g09.ezfio"
os.system(command)
command = f"qp_create_ezfio -c {charge} -m {mult} g09.xyz -b {basis} -o g09.ezfio"
os.system(command)
command = f"rm -rf g09.xyz"
os.system(command)
command = f"qp_run scf g09.ezfio"
os.system(command)
command = f"qp_set_frozen_core g09.ezfio"
os.system(command)
if d["functional"] == "FCI":
command = f"qp_run fci g09.ezfio"
elif d["functional"] == "CIS":
command = f"qp_run cis g09.ezfio"
elif d["functional"] == "CISD":
command = f"qp_run cisd g09.ezfio"
os.system(command)
if __name__ == '__main__':
ARGUMENTS = docopt(__doc__)
main(ARGUMENTS)

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@ -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 -DGNU_CHECK_OMP
# Global options
################

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

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

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

53
configure vendored
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@ -3,8 +3,6 @@
# Quantum Package configuration script
#
TEMP=$(getopt -o d:c:i:h -l download:,config:,install:,help -n $0 -- "$@") || exit 1
eval set -- "$TEMP"
export QP_ROOT="$( cd "$(dirname "$0")" ; pwd -P )"
echo "QP_ROOT="$QP_ROOT
@ -24,17 +22,17 @@ 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 $0) -i <package>
Options:
-c, --config=<file> Define a COMPILATION configuration file,
in "${QP_ROOT}/config/".
-h, --help Print the HELP message
-i, --install=<package> INSTALL <package>. Use at your OWN RISK:
no support will be provided for the installation of
dependencies.
-c <file> Define a COMPILATION configuration file,
in "${QP_ROOT}/config/".
-h Print the HELP message
-i <package> INSTALL <package>. Use at your OWN RISK:
no support will be provided for the installation of
dependencies.
Example:
./$(basename $0) -c config/gfortran.cfg
@ -68,32 +66,31 @@ function execute () {
}
PACKAGES=""
echo $@
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 --help"
exit 2;;
esac
done

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@ -0,0 +1,12 @@
#!/bin/sh
# go in qp2/src/fci to run check_omp_actual_setup
# to see if we can run in parallel an omp section in another one
echo ""
echo "Please wait..."
echo ""
cd ../../src/fci
ninja || echo "Please recompile from the root"
echo ""
./check_omp_actual_setup
cd ../../scripts/verif_omp

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@ -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

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@ -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_v2.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
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@ -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_v2.f90 \
&& echo $(./a.out | grep "Tests:" | cut -d ":" -f2- ) $(echo " : ") $($comp --version | head -n 1) >> $FILE
done
# Display
cat $FILE

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@ -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

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@ -28,6 +28,7 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integrals, (ao_num,ao_num)]
END_PROVIDER
BEGIN_PROVIDER [ double precision, ao_pseudo_integrals_local, (ao_num,ao_num)]
use omp_lib
implicit none
BEGIN_DOC
! Local pseudo-potential
@ -42,7 +43,6 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integrals_local, (ao_num,ao_num)]
double precision :: wall_1, wall_2, wall_0
integer :: thread_num
integer :: omp_get_thread_num
double precision :: c
double precision :: Z
@ -158,6 +158,7 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integrals_local, (ao_num,ao_num)]
BEGIN_PROVIDER [ double precision, ao_pseudo_integrals_non_local, (ao_num,ao_num)]
use omp_lib
implicit none
BEGIN_DOC
! Non-local pseudo-potential
@ -169,7 +170,6 @@ BEGIN_PROVIDER [ double precision, ao_pseudo_integrals_local, (ao_num,ao_num)]
integer :: power_A(3),power_B(3)
integer :: i,j,k,l,m
double precision :: Vloc, Vpseudo
integer :: omp_get_thread_num
double precision :: wall_1, wall_2, wall_0
integer :: thread_num

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@ -5,4 +5,3 @@ interface: ezfio
size: (determinants.n_states)

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@ -79,6 +79,6 @@ subroutine run
call ezfio_set_cis_energy(CI_energy)
psi_coef = ci_eigenvectors
SOFT_TOUCH psi_coef
call save_wavefunction_truncated(1.d-12)
call save_wavefunction_truncated(save_threshold)
end

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@ -63,7 +63,7 @@ subroutine run
endif
psi_coef = ci_eigenvectors
SOFT_TOUCH psi_coef
call save_wavefunction
call save_wavefunction_truncated(save_threshold)
call ezfio_set_cisd_energy(CI_energy)
do i = 1,N_states

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@ -59,24 +59,30 @@
endif
endif
ncfg = ncfgpersomo - ncfgprev
if(iand(MS,1) .EQ. 0) then
!dimcsfpercfg = max(1,nint((binom(i,i/2)-binom(i,i/2+1))))
binom1 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*((i/2)+1)) &
- logabsgamma(1.0d0*(i-((i/2))+1)));
binom2 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*(((i/2)+1)+1)) &
- logabsgamma(1.0d0*(i-((i/2)+1)+1)));
dimcsfpercfg = max(1,nint(binom1 - binom2))
if(i .EQ. 0 .OR. i .EQ. 1) then
dimcsfpercfg = 1
elseif( i .EQ. 3) then
dimcsfpercfg = 2
else
!dimcsfpercfg = max(1,nint((binom(i,(i+1)/2)-binom(i,(i+3)/2))))
binom1 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*(((i+1)/2)+1)) &
- logabsgamma(1.0d0*(i-(((i+1)/2))+1)));
binom2 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*((((i+3)/2)+1)+1)) &
- logabsgamma(1.0d0*(i-(((i+3)/2)+1)+1)));
dimcsfpercfg = max(1,nint(binom1 - binom2))
if(iand(MS,1) .EQ. 0) then
!dimcsfpercfg = max(1,nint((binom(i,i/2)-binom(i,i/2+1))))
binom1 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*((i/2)+1)) &
- logabsgamma(1.0d0*(i-((i/2))+1)));
binom2 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*(((i/2)+1)+1)) &
- logabsgamma(1.0d0*(i-((i/2)+1)+1)));
dimcsfpercfg = max(1,nint(binom1 - binom2))
else
!dimcsfpercfg = max(1,nint((binom(i,(i+1)/2)-binom(i,(i+3)/2))))
binom1 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*(((i+1)/2)+1)) &
- logabsgamma(1.0d0*(i-(((i+1)/2))+1)));
binom2 = dexp(logabsgamma(1.0d0*(i+1)) &
- logabsgamma(1.0d0*((((i+3)/2)+1)+1)) &
- logabsgamma(1.0d0*(i-(((i+3)/2)+1)+1)));
dimcsfpercfg = max(1,nint(binom1 - binom2))
endif
endif
n_CSF += ncfg * dimcsfpercfg
if(cfg_seniority_index(i+2) > ncfgprev) then

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@ -508,7 +508,8 @@ subroutine H_S2_u_0_nstates_zmq(v_0,s_0,u_0,N_st,sze)
endif
call omp_set_max_active_levels(5)
!call omp_set_max_active_levels(5)
call set_multiple_levels_omp()
!$OMP PARALLEL DEFAULT(shared) NUM_THREADS(2) PRIVATE(ithread)
ithread = omp_get_thread_num()

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@ -464,7 +464,9 @@ subroutine H_u_0_nstates_zmq(v_0,u_0,N_st,sze)
print *, irp_here, ': Failed in zmq_set_running'
endif
call omp_set_max_active_levels(4)
!call omp_set_max_active_levels(4)
call set_multiple_levels_omp()
!$OMP PARALLEL DEFAULT(shared) NUM_THREADS(2) PRIVATE(ithread)
ithread = omp_get_thread_num()
if (ithread == 0 ) then

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@ -464,7 +464,9 @@ subroutine H_u_0_nstates_zmq(v_0,u_0,N_st,sze)
print *, irp_here, ': Failed in zmq_set_running'
endif
call omp_set_max_active_levels(4)
!call omp_set_max_active_levels(4)
call set_multiple_levels_omp()
!$OMP PARALLEL DEFAULT(shared) NUM_THREADS(2) PRIVATE(ithread)
ithread = omp_get_thread_num()
if (ithread == 0 ) then

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@ -136,3 +136,9 @@ doc: If |true|, discard any Slater determinants with an interaction smaller than
interface: ezfio,provider,ocaml
default: False
[save_threshold]
type: Threshold
doc: Cut-off to apply to the CI coefficients when the wave function is stored
interface: ezfio,provider,ocaml
default: 0.

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@ -0,0 +1,174 @@
program check_omp_actual_setup
use omp_lib
implicit none
integer :: accu, accu2
integer :: s, n_setting
logical :: verbose, test_versions
logical, allocatable :: is_working(:)
verbose = .True.
test_versions = .False.
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()
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/${compiler_name}.cfg'
else
print*,'The parallelization on multiple levels does not work with:'
print*,'call omp_set_max_active_levels(5)'
print*,'or'
print*,'call omp_set_nested(.True.)'
print*,'or'
print*,'call omp_set_nested(.True.)'
print*,'+'
print*,'call omp_set_max_active_levels(5)'
print*,''
print*,'Try an other compiler and good luck...'
endif
if (is_working(1)) then
print*,''
print*,'=========================================================='
print*,'Your actual set up works for parallelization with 4 levels'
print*,'=========================================================='
print*,''
else
print*,''
print*,'==================================================================='
print*,'Your actual set up does not work for parallelization with 4 levels'
print*,'Please look at the previous messages to understand the requirements'
print*,'==================================================================='
print*,''
endif
endif
! List of working flags
if (test_versions) then
print*,is_working(2:4)
endif
! IRPF90_FLAGS
if (is_working(2)) then
print*,'-DSET_MAX_ACT'
elseif (is_working(3)) then
print*,'-DSET_NESTED'
elseif (is_working(4)) then
print*,'-DSET_MAX_ACT -DSET_NESTED'
else
print*,'ERROR'
endif
end
subroutine check_omp_in_subroutine(accu2)
implicit none
integer, intent(inout) :: accu2
!$OMP PARALLEL
!$OMP ATOMIC
accu2 = accu2 + 1
!$OMP END ATOMIC
!$OMP END PARALLEL
end

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@ -0,0 +1,16 @@
subroutine set_multiple_levels_omp()
! Doc : idk
implicit none
IRP_IF SET_MAX_ACT
!print*,'SET_MAX_ACT: True, call omp_set_max_active_levels(5)'
call omp_set_max_active_levels(5)
IRP_ENDIF
IRP_IF SET_NESTED
!print*,'SET_NESTED: True, call omp_set_nested(.True.)'
call omp_set_nested(.True.)
IRP_ENDIF
end

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@ -300,12 +300,12 @@ subroutine wall_time(t)
end
BEGIN_PROVIDER [ integer, nproc ]
use omp_lib
implicit none
BEGIN_DOC
! Number of current OpenMP threads
END_DOC
integer :: omp_get_num_threads
nproc = 1
!$OMP PARALLEL
!$OMP MASTER