Merge branch 'macos' into dev-stable

bin/python

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+exec python3 $@
+

bin/qpsh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
-export QP_ROOT=$(dirname "$(readlink -f "$0")")/..
+REALPATH=$( cd "$(dirname "$0")" ; pwd -P )
+export QP_ROOT=${REALPATH}/..
 
 bash --init-file <(cat << EOF
     [[ -f /etc/bashrc ]] && source /etc/bashrc 

bin/zcat

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# On Darwin: try gzcat if available, otherwise use Python
+
+if [[ $(uname -s) = Darwin ]] ; then
+   which gzcat &> /dev/null
+   if [[ $? -eq 0 ]] ; then 
+      exec gzcat $@
+   else
+
+      exec python3 << EOF
+import sys
+import gzip
+with gzip.open("$1", "rt") as f:
+    print(f.read())
+EOF
+   fi
+else
+   command=$(which -a zcat | grep -v 'qp2/bin/' | head -1)
+   exec $command $@
+fi
+

config/gfortran.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
 LAPACK_LIB   : -lblas -llapack
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

config/gfortran_armpl.cfg

@@ -13,7 +13,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
 LAPACK_LIB   : -larmpl_lp64_mp
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

config/gfortran_avx.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -ffree-line-length-none -I . -mavx -g -fPIC
+FC           : gfortran -ffree-line-length-none -I . -mavx -g -fPIC -std=legacy
 LAPACK_LIB   : -llapack -lblas
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED

config/gfortran_debug.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -std=legacy
 LAPACK_LIB   : -lblas -llapack
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

config/gfortran_macos.cfg

@@ -0,0 +1,62 @@
+# Common flags
+##############
+#
+# -ffree-line-length-none : Needed for IRPF90 which produces long lines
+# -lblas -llapack         : Link with libblas and liblapack libraries provided by the system
+# -I .                    : Include the curent directory (Mandatory)
+#
+# --ninja                 : Allow the utilisation of ninja. (Mandatory)
+# --align=32              : Align all provided arrays on a 32-byte boundary
+#
+#
+[COMMON]
+FC           : gfortran -ffree-line-length-none -I . -g -fPIC -std=legacy
+LAPACK_LIB   : -llapack -lblas
+IRPF90       : irpf90
+IRPF90_FLAGS : --ninja --align=32 -DSET_NESTED -DMACOS
+
+# 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
+####################
+#
+# -Ofast                  : Disregard strict standards compliance. Enables all -O3 optimizations.
+#                           It also enables optimizations that are not valid
+#                           for all standard-compliant programs.  It turns on
+#                           -ffast-math and the Fortran-specific
+#                           -fno-protect-parens and -fstack-arrays.
+[OPT]
+FCFLAGS : -Ofast -march=native
+
+# Profiling flags
+#################
+#
+[PROFILE]
+FC      : -p -g
+FCFLAGS : -Ofast
+
+# Debugging flags
+#################
+#
+# -fcheck=all  : Checks uninitialized variables,  array subscripts, etc...
+# -g           : Extra debugging information
+#
+[DEBUG]
+FCFLAGS : -fcheck=all -g
+
+# OpenMP flags
+#################
+#
+[OPENMP]
+FC           : -fopenmp
+IRPF90_FLAGS : --openmp
+

config/gfortran_mpi.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : mpif90 -ffree-line-length-none -I . -g -fPIC
+FC           : mpif90 -ffree-line-length-none -I . -g -fPIC -std=legacy
 LAPACK_LIB   :  -lblas -llapack
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 -DMPI -DSET_NESTED

config/gfortran_openblas.cfg

@@ -10,7 +10,7 @@
 #
 #
 [COMMON]
-FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native
+FC           : gfortran -g -ffree-line-length-none -I . -fPIC -march=native -std=legacy
 LAPACK_LIB   : -lopenblas
 IRPF90       : irpf90
 IRPF90_FLAGS : --ninja --align=32 --assert -DSET_NESTED

configure

@@ -19,7 +19,11 @@ git submodule init
 git submodule update
 
 # Update ARM or x86 dependencies
-ARCHITECTURE=$(uname -m)
+SYSTEM=$(uname -s)
+if [[ $SYSTEM = "Linux" ]] ; then
+  SYSTEM=""
+fi
+ARCHITECTURE=$(uname -m)$SYSTEM
 cd ${QP_ROOT}/external/qp2-dependencies
 git checkout master
 git pull
@@ -275,6 +279,7 @@ EOF
               cd "\${QP_ROOT}"/external
               tar --gunzip --extract --file qp2-dependencies/zeromq-4.2.5.tar.gz
               cd zeromq-*
+              [[ "${SYSTEM}" = "Darwin" ]] && ./autogen.sh
               ./configure --prefix="\$QP_ROOT" --without-libsodium --enable-libunwind=no
               make -j 8
               make install

scripts/module/create_executables_list.sh

@@ -11,7 +11,11 @@ fi
 
 cd ${QP_ROOT}/data
 rm -f executables
+if [[ "$(uname -s)" = "Darwin" ]] ; then
+EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -perm +111 -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort ) 
+else
 EXES=$(find -L ${QP_ROOT}/src -maxdepth 2 -depth -executable -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort ) 
+fi
 
 for EXE in $EXES
 do

src/ezfio_files/00.create.bats

@@ -53,7 +53,6 @@ function run {
 
 
 @test "B-B" {
-  qp set_file b2_stretched.ezfio
   run b2_stretched.zmt 1 0 6-31g
 }
 

src/ezfio_files/ezfio.irp.f

@@ -33,6 +33,8 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
 
   call ezfio_set_file(ezfio_filename)
 
+IRP_IF MACOS
+IRP_ELSE
   ! Adjust out-of-memory killer flag such that the current process will be
   ! killed first by the OOM killer, allowing compute nodes to survive
   integer :: getpid
@@ -40,6 +42,7 @@ BEGIN_PROVIDER [ character*(1024), ezfio_filename ]
   write(pidc,*) getpid()
   write(command,*) 'echo 15 > /proc//'//trim(adjustl(pidc))//'/oom_adj'
   call system(command)
+IRP_ENDIF
 
   PROVIDE file_lock
 

src/hartree_fock/10.hf.bats

@@ -39,7 +39,7 @@ rm -rf $EZFIO
 qp create_ezfio -b def2-svp hcn.xyz -o $EZFIO
 qp run scf
 mv hcn_charges.xyz ${EZFIO}_point_charges.xyz
-python write_pt_charges.py ${EZFIO}
+python3 write_pt_charges.py ${EZFIO}
 qp set nuclei point_charges True
 qp run scf | tee ${EZFIO}.pt_charges.out
   energy="$(ezfio get hartree_fock energy)"

src/nuclei/write_pt_charges.py

@@ -52,7 +52,7 @@ fncharges.write(" "+str(n_charges)+'\n')
 fncharges.close()
 mv_in_ezfio(EZFIO,tmp)
 
-# Write the file containing the charges and set in EZFIO folder 
+# Write the file containing the charges and set in EZFIO folder
 tmp="pts_charge_z"
 fcharges = open(tmp,'w')
 fcharges.write(" 1\n")

src/utils/memory.irp.f

@@ -33,6 +33,8 @@ subroutine resident_memory(value)
   call usleep(10)
 
   value = 0.d0
+IRP_IF MACOS
+IRP_ELSE
   iunit = getUnitAndOpen('/proc/self/status','r')
   do
     read(iunit,*,err=10,end=20) key, value
@@ -43,6 +45,7 @@ subroutine resident_memory(value)
   end do
   20 continue
   close(iunit)
+IRP_ENDIF
   value = value / (1024.d0*1024.d0)
   call unlock_io()
 end function
@@ -58,6 +61,9 @@ subroutine total_memory(value)
   double precision, intent(out) :: value
 
   call lock_io()
+  value = 0.d0
+IRP_IF MACOS
+IRP_ELSE
   iunit = getUnitAndOpen('/proc/self/status','r')
   do
     read(iunit,*,err=10,end=20) key, value
@@ -68,6 +74,7 @@ subroutine total_memory(value)
   end do
   20 continue
   close(iunit)
+IRP_ENDIF
   value = value / (1024.d0*1024.d0)
   call unlock_io()
 end function