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pierrehirel / atomsk

Atomsk: A Tool For Manipulating And Converting Atomic Data Files -
https://atomsk.univ-lille.fr
GNU General Public License v3.0
198 stars 75 forks source link

Parallel compilation of atomsk requires multiple runs of make. #54

Closed hongyi-zhao closed 5 months ago

hongyi-zhao commented 5 months ago

See below:

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.3 LTS
Release:    22.04
Codename:   jammy

werner@X10DAi:~/Public/repo/github.com/pierrehirel/atomsk.git/src$ make all -j 44
mkdir -p OBJ
       o---o     ___________
      o---o|     A T O M S K
make -j44 --jobserver-auth=3,9 -j1 -C include
      |   |o
      o---o      Version master
make[1]: warning: -j1 forced in submake: resetting jobserver mode.
make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/include'
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/globalvar.o  -c globalvar.f90 

gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/constants.o  -c constants.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/math.o  -c math.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/random.o  -c random.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/functions.o  -c functions.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/atoms.o  -c atoms.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/subroutines.o  -c subroutines.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/crystallography.o  -c crystallography.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/elasticity.o  -c elasticity.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/sort.o  -c sort.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/display_messages.o  -c display_messages.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/messages_EN.o  -c messages_EN.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/messages_FR.o  -c messages_FR.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/messages_DE.o  -c messages_DE.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/messages.o  -c messages.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/expreval.o  -c expreval.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/resize.o  -c resize.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/spacegroups.o  -c spacegroups.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/neighbors.o  -c neighbors.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/files.o  -c files.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/symops.o  -c symops.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/guess_format.o  -c guess_format.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/read_cla.o  -c read_cla.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/determine_H.o  -c determine_H.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/readconf.o  -c readconf.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/qepw_ibrav.o  -c qepw_ibrav.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/in_stl.o  -c in_stl.f90 
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -fno-tree-pre -cpp -o ../OBJ/average_env.o  -c average_env.f90 
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/include'
make -j44 --jobserver-auth=3,9 -C compute
..> Compiling input, options and output modules...
make -j44 --jobserver-auth=3,9 caux
make[1]: warning: -j44 forced in submake: resetting jobserver mode.
make[1]: warning: -j44 forced in submake: resetting jobserver mode.
make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/compute'
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/compute_G.o  -c compute_G.f90
make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make -w -j44 --jobserver-auth=4,11 -C input
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/compute_rdf.o  -c compute_rdf.f90
make -w -j44 --jobserver-auth=4,11 -C options
make -w -j44 --jobserver-auth=4,11 -C output
make[2]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make[2]: warning: -j44 forced in submake: resetting jobserver mode.
make[2]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make[2]: warning: -j44 forced in submake: resetting jobserver mode.
make[2]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make[2]: warning: -j44 forced in submake: resetting jobserver mode.
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_abinit.o  -c in_abinit.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/disloc_iso.o  -c disloc_iso.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_abinit.o  -c out_abinit.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_atsk.o  -c in_atsk.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/disloc_aniso.o  -c disloc_aniso.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_atsk.o  -c out_atsk.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_bop.o  -c in_bop.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_bop.o  -c out_bop.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/disloc_loop.o  -c disloc_loop.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_bopfox.o  -c out_bopfox.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_bopfox.o  -c in_bopfox.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_addatom.o  -c opt_addatom.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_cel.o  -c out_cel.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_cel.o  -c in_cel.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_addshells.o  -c opt_addshells.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_cfg.o  -c out_cfg.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_alignx.o  -c opt_alignx.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_cfg.o  -c in_cfg.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_cif.o  -c out_cif.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_bindshells.o  -c opt_bindshells.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_cif.o  -c in_cif.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_crystal.o  -c out_crystal.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_cart2frac.o  -c opt_cart2frac.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_crystal.o  -c in_crystal.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_csv.o  -c out_csv.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_csv.o  -c in_csv.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_cell.o  -c opt_cell.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_dat.o  -c out_dat.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_center.o  -c opt_center.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_dlpoly_config.o  -c in_dlpoly_config.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_dd.o  -c out_dd.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_gulp_gin.o  -c in_gulp_gin.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_crack.o  -c opt_crack.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_dlpoly_config.o  -c out_dlpoly_config.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_gulp_gin.o  -c out_gulp_gin.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_imd.o  -c in_imd.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_cut_cell.o  -c opt_cut_cell.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_jems.o  -c in_jems.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_imd.o  -c out_imd.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_deform.o  -c opt_deform.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_jems.o  -c out_jems.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_lammps_custom.o  -c in_lammps_custom.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_disloc.o  -c opt_disloc.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_lammps_data.o  -c out_lammps_data.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_lammps_data.o  -c in_lammps_data.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_disturb.o  -c opt_disturb.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_mbpp_coorat.o  -c out_mbpp_coorat.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_mbpp_coorat.o  -c in_mbpp_coorat.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_duplicate.o  -c opt_duplicate.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_moldy_system.o  -c out_moldy_system.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_moldy_system.o  -c in_moldy_system.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_fix.o  -c opt_fix.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_pdb.o  -c out_pdb.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_pdb.o  -c in_pdb.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_qe_pw.o  -c out_qe_pw.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_mirror.o  -c opt_mirror.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_qe_pw.o  -c in_qe_pw.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_siesta_fdf.o  -c out_siesta_fdf.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_orient.o  -c opt_orient.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_siesta_xv.o  -c out_siesta_xv.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_orthocell.o  -c opt_orthocell.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_siesta_fdf.o  -c in_siesta_fdf.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_str.o  -c out_str.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_properties.o  -c opt_properties.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_siesta_xv.o  -c in_siesta_xv.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_vasp_poscar.o  -c out_vasp_poscar.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_reduce_cell.o  -c opt_reduce_cell.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_str.o  -c in_str.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_vesta.o  -c out_vesta.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_remdoubles.o  -c opt_remdoubles.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_xmd.o  -c out_xmd.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_vasp_poscar.o  -c in_vasp_poscar.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_xsf.o  -c out_xsf.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_rmatom.o  -c opt_rmatom.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_vesta.o  -c in_vesta.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/out_xyz.o  -c out_xyz.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_rmprop.o  -c opt_rmprop.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_xmd.o  -c in_xmd.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_rmshells.o  -c opt_rmshells.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_xsf.o  -c in_xsf.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_roll.o  -c opt_roll.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/in_xyz.o  -c in_xyz.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_rotate.o  -c opt_rotate.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_roundoff.o  -c opt_roundoff.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_select.o  -c opt_select.f90
opt_disloc.f90:49:5:

   49 | USE dislocation_iso
      |     1
Fatal Error: Cannot open module file ‘dislocation_iso.mod’ for reading at (1): No such file or directory
compilation terminated.
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_separate.o  -c opt_separate.f90
make[2]: *** [Makefile:12: opt_disloc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/writeout.o -c writeout.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/readin.o  -c readin.f90
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/compute'
make[2]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/output'
make[2]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/input'
make[2]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/options'
make[1]: *** [Makefile:199: options] Error 2
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make: *** [Makefile:188: aux] Error 2
werner@X10DAi:~/Public/repo/github.com/pierrehirel/atomsk.git/src$ make all -j 44
mkdir -p OBJ
       o---o     ___________
      o---o|     A T O M S K
make -j44 --jobserver-auth=3,9 -j1 -C include
      |   |o
      o---o      Version master
make[1]: warning: -j1 forced in submake: resetting jobserver mode.

make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/include'
make[1]: Nothing to be done for 'general'.
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/include'
make -j44 --jobserver-auth=3,9 -C compute
..> Compiling input, options and output modules...
make -j44 --jobserver-auth=3,9 caux
make[1]: warning: -j44 forced in submake: resetting jobserver mode.
make[1]: warning: -j44 forced in submake: resetting jobserver mode.
make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/compute'
make[1]: Nothing to be done for 'compute'.
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/compute'
make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make -w -j44 --jobserver-auth=4,11 -C input
make -w -j44 --jobserver-auth=4,11 -C options
make -w -j44 --jobserver-auth=4,11 -C output
make[2]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make[2]: warning: -j44 forced in submake: resetting jobserver mode.
make[2]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make[2]: warning: -j44 forced in submake: resetting jobserver mode.
make[2]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make[2]: warning: -j44 forced in submake: resetting jobserver mode.
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_disloc.o  -c opt_disloc.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/readin.o  -c readin.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/writeout.o -c writeout.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_shift.o  -c opt_shift.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_sort.o  -c opt_sort.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_spacegroup.o  -c opt_spacegroup.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_stress.o  -c opt_stress.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_substitute.o  -c opt_substitute.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_swap.o  -c opt_swap.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_torsion.o  -c opt_torsion.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_unit.o  -c opt_unit.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_unskew.o  -c opt_unskew.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_velocity.o  -c opt_velocity.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/opt_wrap.o  -c opt_wrap.f90
make[2]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/input'
make[2]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/output'
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/options.o  -c options.f90
make[2]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/options'
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src'
make -j44 --jobserver-auth=3,9 -C modes
make[1]: warning: -j44 forced in submake: resetting jobserver mode.
make[1]: Entering directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/modes'
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_difference.o  -c mode_difference.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_normal.o  -c mode_normal.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_cpprop.o  -c mode_cpprop.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_matchid.o  -c mode_matchid.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_create.o  -c mode_create.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_merge.o  -c mode_merge.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/1ia_dlpoly_history.o  -c 1ia_dlpoly_history.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/1ia_qe_out.o  -c 1ia_qe_out.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/1ia_vasp_outcar.o  -c 1ia_vasp_outcar.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/1ia_lmc.o  -c 1ia_lmc.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/1ia_xsf.o  -c 1ia_xsf.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/1ia_xyz.o  -c 1ia_xyz.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_unwrap.o  -c mode_unwrap.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_allinone.o  -c mode_allinone.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_epola.o  -c mode_epola.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_electricdipoles.o  -c mode_electricdipoles.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_rdf.o  -c mode_rdf.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_polycrystal.o  -c mode_polycrystal.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_interpolate.o  -c mode_interpolate.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_nye.o  -c mode_nye.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_average.o  -c mode_average.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_density.o  -c mode_density.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_localsym.o  -c mode_localsym.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/mode_list.o -c mode_list.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -o ../OBJ/modes.o -c modes.f90
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o ../OBJ/mode_interactive.o -c mode_interactive.f90
make[1]: Leaving directory '/home/werner/Public/repo/github.com/pierrehirel/atomsk.git/src/modes'
gfortran -O2 -DOPENMP -fopenmp -fno-backslash -I../OBJ -J../OBJ -cpp -o atomsk OBJ/*.o atomsk.f90 -I OBJ -llapack
f951: Warning: Nonexistent include directory ‘../OBJ’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘../OBJ’ [-Wmissing-include-dirs]

    \o/ Compilation was successful!

    <i> To install Atomsk system-wide, you may now run:
          sudo make install

So, it seems that atomsk did not specifically design and optimize the corresponding makefile for parallel compilation.

Regards, Zhao

pierrehirel commented 5 months ago

Hello,

The Makefile does support multi-thread compilation, but maybe not with that many threads (you used 44 threads, which is not really a typical value).

Try with 8 threads and it should work just fine.

Regards

hongyi-zhao commented 5 months ago

Yes, the following doesn't trigger the problem discussed here:

werner@X10DAi:~/Public/repo/github.com/pierrehirel/atomsk.git/src$ make all -j 8