Cannot build STELLOPT develop branch anymore on Ubuntu

[eguiraud]

Hello,

I just noticed that current develop branch does not build correctly anymore with the following make.inc, that used to work until recently on Ubuntu 22.04.

git-bisecting I found the last working commit was 9b630f938ebb49f94e53bd38a291ba0fb9a6ab42, although I do not understand at all how the next commit broke compilation.

make.inc

#######################################################################
#            System-specific path and binary definitions
#######################################################################
FC = gfortran
BLASHOME = /usr
BLACS_HOME = /usr
SCALAPACK_HOME = /usr
MPIHOME = /usr
NETCDF_HOME = /usr
HDF5_HOME = /usr
PGPLOT_DIR = /usr
SILOHOME = /usr
COILOPT_PATH =
GSLHOME = /usr
GCC49_HOME=/usr/lib/gcc/x86_64-linux-gnu/4.9

#######################################################################
#            Define Basic Utilities
#######################################################################
  SHELL = /bin/sh
  PWD1 = `pwd`
  MYHOME = $(HOME)/bin
  PRECOMP:= /usr/bin/cpp -traditional -DLINUX
  COMPILE = $(FC)
  COMPILE_FREE = $(FC) -ffree-form -ffree-line-length-none -ffixed-line-length-none
  LINK    = ld $(FLAGS) -o
  LINK_AR = ar -ruv
  LINK_C  = $(CC) -shared -Wl,-z-defs

#######################################################################
#            Define Compiler Flags
#######################################################################
#  FLAGS_R = -O2 -g -fexternal-blas -fbacktrace -fcheck=all
  FLAGS_R = -g -O2 -fexternal-blas -fbacktrace -fallow-argument-mismatch
  FLAGS_D = -g -O0 -fexternal-blas -fcheck=all
  LIBS    = -L$(SCALAPACK_HOME)/lib -llapack -lscalapack-openmpi \
            -L$(BLASHOME)/lib/libblas -lblas

#######################################################################
#            MPI Options
#######################################################################
  LMPI    = T
  MPI_COMPILE = $(MPIHOME)/bin/mpif90
  MPI_COMPILE_FREE = $(MPIHOME)/bin/mpif90 -ffree-form \
                     -ffree-line-length-none -ffixed-line-length-none
  MPI_COMPILE_C = $(MPIHOME)/bin/mpicc
  MPI_LINK = $(MPIHOME)/bin/mpif90

  # For GCC6
  #MPI_COMPILE = mpif90
  #MPI_COMPILE_FREE = mpif90 -ffree-form \
  #                   -ffree-line-length-none -ffixed-line-length-none
  #MPI_COMPILE_C = mpicc
  #MPI_LINK = mpif90

#######################################################################
#            NAG Options
#######################################################################
  LNAG = F
  NAG_LIB = -L$(NAG_ROOT)/lib -lnag_nag

#######################################################################
#            NETCDF Options
#######################################################################
  LNETCDF = T
  NETCDF_INC = -I$(NETCDF_HOME)/include
  NETCDF_LIB = -L$(NETCDF_HOME)/lib/x86_64-linux-gnu -lnetcdf -lnetcdff

  # FOR GCC6
  #NETCDF_LIB = -L$(NETCDF_HOME)/lib -lnetcdff

#######################################################################
#            NTCC Options
#######################################################################
  LNTCC = F
  NTCC_INC = -I$(NTCCHOME)/mod
  NTCC_LIB = -L$(NTCCHOME)/lib -laladdinsub -lr8slatec -ladpak\
             -lcppsub -lcomput -lpspline -lportlib -lezcdf -lmds_sub \
             -lmdstransp -lvaxonly

#######################################################################
#            HDF5 Options
#######################################################################
  LHDF5 = F
  HDF5_INC = -I$(HDF5_HOME)/include/hdf5/serial
  HDF5_LIB = -L$(HDF5_HOME)/lib/x86_64-linux-gnu -L$(HDF5_HOME)/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_hl -lhdf5_fortran -lhdf5 \
             -lhdf5hl_fortran -lpthread -lz -lm

#######################################################################
#             PGPLOT Options
#######################################################################
  LPGPLOT = F
  PGPLOT_INC = -I$(PGPLOT_DIR)
  PGPLOT_LIB = -L$(PGPLOT_DIR) -lpgplot -L/usr/lib/x86_64-linux-gnu -lX11

#######################################################################
#             SILO Options
#######################################################################
  LSILO = F
  SILO_INC = -I$(SILOHOME)/include
  SILO_LIB = -L$(SILOHOME)/lib/x86_64-linux-gnu -lsiloh5

#######################################################################
#            GENE Options
#######################################################################
  LGENE = F
  GENE_INC = -I$(GENE_PATH)
  GENE_DIR = $(GENE_PATH)
  LIB_GENE = libgene.a
  GENE_LIB = $(GENE_DIR)/$(LIB_GENE) \
             -L/u/slazerso/src/GENE17_2016/external/pppl_cluster/futils/src -lfutils \
             -L$(FFTWHOME)/lib -lfftw3 \
             -L$(SLEPC_DIR)/$(PETSC_ARCH)/lib -lslepc \
             -L$(PETSC_DIR)/$(PETSC_ARCH)/lib -lpetsc -lX11

#######################################################################
#            COILOPT++ Options
#######################################################################
  LCOILOPT = F
  COILOPT_INC = -I$(COILOPT_PATH)
  COILOPTPP_DIR = $(COILOPT_PATH)
  LIB_COILOPTPP = libcoilopt++.a
  COILOPT_LIB = $(COILOPT_PATH)/$(LIB_COILOPTPP) \
                -L$(GSLHOME)/lib/x86_64-linux-gnu -lgsl -lgslcblas -lstdc++ -lmpi_cxx

#######################################################################
#            TERPSICHORE Options
#######################################################################
  LTERPSICHORE= F
  TERPSICHORE_INC = -I$(TERPSICHORE_PATH)
  TERPSICHORE_DIR = $(TERPSICHORE_PATH)
  LIB_TERPSICHORE = libterpsichore.a
  TERPSICHORE_LIB = $(TERPSICHORE_DIR)/$(LIB_TERPSICHORE)

#######################################################################
#            TRAVIS Options
#######################################################################
  LTRAVIS= F
  TRAVIS_DIR = $(TRAVIS_PATH)
  LIB_TRAVIS = libtravis64_sopt.a
  LIB_MCONF  = libmconf64.a
  TRAVIS_LIB = $(TRAVIS_DIR)/lib/$(LIB_TRAVIS) \
               $(TRAVIS_DIR)/mag_conf/lib/$(LIB_MCONF) -lstdc++

#######################################################################
#            LIBSTELL Shared Options
#######################################################################
#LIB_SHARE = $(BLASHOME)/lib/libblas.so \
          $(SCALAPACK_HOME)/lib/libscalapack-openmpi.so \
          $(BLACS_HOME)/lib/libblacs-openmpi.so  $(BLACS_HOME)/lib/libblacsCinit-openmpi.so $(BLACS_HOME)/lib/libblacsF77init-openmpi.so \
          $(HDF5_HOME)/lib/x86_64-linux-gnu/libhdf5_hl.so $(HDF5_HOME)/lib/x86_64-linux-gnu/libhdf5_fortran.so $(HDF5_HOME)/lib/x86_64-linux-gnu/libhdf5hl_fortran.so $(HDF5_HOME)/lib/x86_64-linux-gnu/libhdf5.so \
          $(HDF5_HOME)/lib/x86_64-linux-gnu/libmpi_usempif08.so $(HDF5_HOME)/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.so \
          $(NETCDF_HOME)/lib/x86_64-linux-gnu/libnetcdf.so $(NETCDF_HOME)/lib/x86_64-linux-gnu/libnetcdff.so $(NETCDF_HOME)/lib/x86_64-linux-gnu/libnetcdf_c++.so \
          $(SILOHOME)/lib/x86_64-linux-gnu/libsiloh5.so \
          $(GSLHOME)/lib/x86_64-linux-gnu/libgsl.so \
          $(GCC6_HOME)/libgfortran.so $(GCC6_HOME)/libstdc++.so \
          $(MPIHOME)/lib/x86_64-linux-gnu/libmpi.so $(MPIHOME)/lib/x86_64-linux-gnu/libmpi_mpifh.so \
          /usr/lib/x86_64-linux-gnu/libm.so /usr/lib/liblapack.so /usr/lib/x86_64-linux-gnu/libdl.so
LIB_SHARE = $(BLASHOME)/lib/libblas.so \
          $(SCALAPACK_HOME)/lib/libscalapack-openmpi.so.1 \
          $(BLACS_HOME)/lib/libblacs-openmpi.so.1 \
          $(BLACS_HOME)/lib/libblacsCinit-openmpi.so.1 \
          $(BLACS_HOME)/lib/libblacsF77init-openmpi.so.1 \
          $(HDF5_HOME)/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.so \
          $(NETCDF_HOME)/lib/libnetcdf.so \
          $(NETCDF_HOME)/lib/libnetcdff.so \
          $(NETCDF_HOME)/lib/libnetcdf_c++.so \
          $(SILOHOME)/lib/x86_64-linux-gnu/libsiloh5.so \
          $(GSLHOME)/lib/x86_64-linux-gnu/libgsl.so \
          $(GCC49_HOME)/libgfortran.so \
          $(GCC49_HOME)/libstdc++.so \
          $(MPIHOME)/lib/libmpi.so \
          $(MPIHOME)/lib/libmpif77.so \
          /usr/lib/x86_64-linux-gnu/libm.so \
          /usr/lib/liblapack.so \
          /usr/lib/x86_64-linux-gnu/libdl.so


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#######################################################################
#######################################################################
#   DO NOT EDIT BELOW HERE DO NOT EDIT BELOW HERE

#######################################################################
#######################################################################
#######################################################################
#######################################################################
#######################################################################
#######################################################################
#######################################################################
#######################################################################

# Some Initial stuff
# HOME_BIN = $(MYHOME)
HOME_BIN = ../../
MOD1_PATH = -I$(MYHOME)/libstell_dir
MOD_PATH =
CLEAN_ARCH =
LIB_DIR = ../../LIBSTELL
LIB = libstell.a

# Handle Which Code is being CALLED
ifeq ($(MAKECMDGOALS),xstelloptv2)
  PRECOMP += -DBNORM -DDKES_OPT -DBEAMS3D_OPT -DJINV_OPT -DNEO_OPT -DTXPORT_OPT -DDIAGNO_OPT  -DDKES_OPT  -DNEO_OPT  -DSKS  -DSKS2
  VMEC_DIR ?= ../../VMEC2000
  LIB_VMEC= libvmec.a
  MOD_PATH+= -I$(VMEC_DIR)/$(LOCTYPE)
  BEAMS3D_DIR = ../../BEAMS3D
  LIB_BEAMS3D = libbeams3d.a
  MOD_PATH+= -I$(BEAMS3D_DIR)/$(LOCTYPE)
  BOOTSJ_DIR = ../../BOOTSJ
  LIB_BOOTSJ = libbootsj.a
  MOD_PATH+= -I$(BOOTSJ_DIR)/$(LOCTYPE)
  BNORM_DIR = ../../BNORM
  LIB_BNORM = libbnorm.a
  MOD_PATH+= -I$(BNORM_DIR)/$(LOCTYPE)
  BOOZ_DIR = ../../BOOZ_XFORM
  LIB_BOOZ= libbooz.a
  MOD_PATH+= -I$(BOOZ_DIR)/$(LOCTYPE)
  COBRA_DIR = ../../COBRAVMEC
  LIB_COBRA = libcobra.a
  MOD_PATH+= -I$(COBRA_DIR)/$(LOCTYPE)
  DIAGNO_DIR = ../../DIAGNO
  LIB_DIAGNO= libdiagno.a
  MOD_PATH+= -I$(DIAGNO_DIR)/$(LOCTYPE)
  DKES_DIR= ../../DKES
  LIB_DKES= libdkes.a
  MOD_PATH+= -I$(DKES_DIR)/$(LOCTYPE)
  JINV_DIR = ../../J_INVARIANT
  LIB_JINV = libjinv.a
  MOD_PATH+= -I$(JINV_DIR)/$(LOCTYPE)
  MGRID_DIR= ../../MAKEGRID
  LIB_MGRID= libmakegrid.a
  MOD_PATH+= -I$(MGRID_DIR)/$(LOCTYPE)
  NEO_DIR = ../../NEO
  LIB_NEO = libneo.a
  MOD_PATH+= -I$(NEO_DIR)/$(LOCTYPE)
  LIB_LINK=  $(VMEC_DIR)/$(LOCTYPE)/$(LIB_VMEC)  \
	$(BEAMS3D_DIR)/$(LOCTYPE)/$(LIB_BEAMS3D) \
	$(BOOTSJ_DIR)/$(LOCTYPE)/$(LIB_BOOTSJ) \
	$(BNORM_DIR)/$(LOCTYPE)/$(LIB_BNORM) \
	$(BOOZ_DIR)/$(LOCTYPE)/$(LIB_BOOZ) \
	$(COBRA_DIR)/$(LOCTYPE)/$(LIB_COBRA) \
	$(DIAGNO_DIR)/$(LOCTYPE)/$(LIB_DIAGNO) \
	$(DKES_DIR)/$(LOCTYPE)/$(LIB_DKES) \
	$(JINV_DIR)/$(LOCTYPE)/$(LIB_JINV) \
	$(MGRID_DIR)/$(LOCTYPE)/$(LIB_MGRID) \
	$(NEO_DIR)/$(LOCTYPE)/$(LIB_NEO)
else
  LGENE = F
  LCOILOPT = F
  LTERPSICHORE = F
  LTRAVIS = F
endif
ifeq ($(MAKECMDGOALS),xanimec)
  PRECOMP += -D_ANIMEC
endif
ifeq ($(MAKECMDGOALS),xparvmec)
  PRECOMP += -DSKS  -DSKS2
endif
ifeq ($(MAKECMDGOALS),xsiesta)
  PRECOMP += -DSKS  -DSKS2
endif
ifeq ($(MAKECMDGOALS),xgtovmi)
  ifeq ($(LPGPLOT),T)
    MOD1_PATH += $(PGPLOT_INC)
    LIB_LINK += $(PGPLOT_LIB)
  endif
endif
ifeq ($(MAKECMDGOALS),xdes_plot)
  ifeq ($(LPGPLOT),T)
    MOD1_PATH += $(PGPLOT_INC)
    LIB_LINK += $(PGPLOT_LIB)
  endif
endif

# Other Codes
ifeq ($(LGENE),T)
  MOD1_PATH += $(GENE_INC)
  PRECOMP += -DGENE
  MOD_PATH += -I$(GENE_DIR)
else
  GENE_LIB =
  GENE_DIR =
  LIB_GENE =
endif
ifeq ($(LCOILOPT),T)
  MOD1_PATH += $(COILOPT_INC)
  PRECOMP += -DCOILOPTPP
  MOD_PATH += -I$(COILOPTPP_DIR)
else
  COILOPT_LIB =
  COILOPTPP_DIR =
  LIB_COILOPTPP =
endif
ifeq ($(LTERPSICHORE),T)
  MOD1_PATH += $(TERPSICHORE_INC)
  PRECOMP += -DTERPSICHORE
  MOD_PATH += -I$(TERPSICHORE_DIR)
else
  TERPSICHORE_LIB =
  TERPSICHORE_DIR =
  LIB_TERPSICHORE =
endif
ifeq ($(LTRAVIS),T)
  PRECOMP += -DTRAVIS
else
  TRAVIS_LIB =
  TRAVIS_DIR =
  LIB_TRAVIS =
endif

# Handle other codes
LIB_LINK += $(GENE_LIB) $(COILOPT_LIB) $(TERPSICHORE_LIB) $(TRAVIS_LIB)

# Add libraries to LIB_LINK
# LIB_LINK+= $(MYHOME)/libstell.a $(LIBS)
# This version avoids referencing the bin directory for the symbolic link to lib.
# Which we can't reference since we now have the awk file in the main directory.
LIB_LINK+= $(LIB_DIR)/$(LOCTYPE)/$(LIB) $(LIBS)

# 3rd Party Libs
ifeq ($(LMPI),T)
  PRECOMP += -DMPI_OPT
  VMEC_DIR = ../../PARVMEC
  COMPILE = $(MPI_COMPILE)
  COMPILE_FREE = $(MPI_COMPILE_FREE)
  LINK    = $(MPI_COMPILE) $(FLAGS) -o
  LINK_C  = $(MPI_COMPILE_C) -shared -Wl,-z,defs
endif
ifeq ($(LNETCDF),T)
  MOD1_PATH += $(NETCDF_INC)
  PRECOMP += -DNETCDF
  LIB_LINK += $(NETCDF_LIB)
  MOD_PATH += $(NETCDF_INC)
endif
ifeq ($(LHDF5),T)
  MOD1_PATH += $(HDF5_INC)
  PRECOMP += -DLHDF5 -DH5_USE_16_API
  LIB_LINK += $(HDF5_LIB)
  MOD_PATH += $(HDF5_INC)
endif
ifeq ($(LNAG),T)
  PRECOMP += -DNAG
  LIB_LINK += $(NAG_LIB)
endif
ifeq ($(LNTCC),T)
  MOD1_PATH += $(NTCC_INC)
  PRECOMP += -DLADAS -DNTCC
  LIB_LINK += $(NTCC_LIB)
  MOD_PATH += $(NTCC_INC)
endif
ifeq ($(LSILO),T)
  MOD1_PATH += $(SILO_INC)
  PRECOMP += -DSILO_AVAI
  LIB_LINK += $(SILO_LIB)
endif

# This is hear because of MPI above resetting LINK
ifeq ($(MAKECMDGOALS),libstell.a)
  LINK = $(LINK_AR)
  COMPILE += -fPIC
  COMPILE_FREE += -fPIC
  INC_PATH =
endif
ifeq ($(MAKECMDGOALS),libstell.so)
  LIB_LINK = $(LIB_SHARE)
  COMPILE += -fPIC
  COMPILE_FREE += -fPIC
  INC_PATH =
endif

#This must come here
MOD_PATH+= -I

build error with current develop branch (although unfortunately build_all returns with exit code 0 anyways):

make: *** [makefile:36: clean_release] Error 2
Beginning release compilation and archiving of shared libstell
make[1]: Entering directory '/home/devuser/STELLOPT/LIBSTELL/Release'
make[1]: *** No rule to make target 'libstell'.  Stop.
make[1]: Leaving directory '/home/devuser/STELLOPT/LIBSTELL/Release'
make: *** [makefile:59: shared_release] Error 2

[lazersos]

@eguiraud Can you pleas upload the log file produced by the following command?

./build_all > log.txt

You probably need to set MACHINE=debian but the log file will help us to confirm what is going wrong. The make.inc you've posted is VERY old and should no longer be used. Currently the code uses the MACHINE variable to determin which SHARE/make_machine.inc file to use to build the code.

[lazersos]

@eguiraud Has there been an update to this issue?

[eguiraud-pf]

Hi, no progress sorry, I have been out of office for the past few weeks and still am. I'll try what's suggested above and report here when I have a moment.