Update
I added the flag -E to the compilation rules and things seem improved... but not completely solved. Now, I have trouble with libspecial4artemis.so.
Here are the configuration files I used: compared with my previous message, I put back the following dependencies:
- OpenMPI (from Synaptic),
- AED (from sources, shared object could be built),
- MED (from Synaptic),
- METIS (from Synaptic),
- MUMPS (from Synaptic)
--- pysource.template.sh ---
# This file is a template for a Linux environment file
# running "source pysource.template.sh" will position all
# the necessary environment variables for telemac
# To adapt to your installation replace word <word> by their local value
###
### TELEMAC settings -----------------------------------------------------------
###
# Path to telemac root dir
export HOMETEL=/home/mouton/ext/telemac-mascaret
# Adding python scripts to PATH
export PATH=$HOMETEL/scripts/python3:.:$PATH
# Configuration file
export SYSTELCFG=$HOMETEL/configs/systel.myconfig.cfg
# Name of the configuration to use
export USETELCFG=C9.gfortran.dyn
# Path to this file
export SOURCEFILE=$HOMETEL/configs/pysource.template.sh
### Python
# To force python to flush its output
export PYTHONUNBUFFERED='true'
### API
export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH
export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH
###
### COMPILERS -----------------------------------------------------------
###
# Here are a few examples for external libraries
#export SYSTEL=/data/projets/projets.002/systel.002
### MPI -----------------------------------------------------------
#export MPIHOME=/usr/lib/x86_64-linux-gnu
#export PATH=$MPIHOME/bin:$PATH
#export LD_LIBRARY_PATH=$MPIHOME/lib:$LD_LIBRARY_PATH
###
### EXTERNAL LIBRARIES -----------------------------------------------------------
###
### HDF5 -----------------------------------------------------------
#export HDF5HOME=$SYSTEL/LIBRARY/hdf5-1.8.14/arch/C9
#export LD_LIBRARY_PATH=$HDF5HOME/lib:$LD_LIBRARY_PATH
#export LD_RUN_PATH=$HDF5HOME/lib:$MEDHOME/lib:$LD_RUN_PATH
### MED -----------------------------------------------------------
#export MEDHOME=$SYSTEL/LIBRARY/med-3.2.0/arch/C9
#export LD_LIBRARY_PATH=$MEDHOME/lib:$LD_LIBRARY_PATH
#export PATH=$MEDHOME/bin:$PATH
### MUMPS -------------------------------------------------------------
#export MUMPSHOME=$SYSTEL/LIBRARY/mumps/gnu
#export SCALAPACKHOME=$SYSTEL/LIBRARY/scalapack/gnu
#export BLACSHOME=$SYSTEL/LIBRARY/blacs/gnu
### METIS -------------------------------------------------------------
#export METISHOME=$SYSTEL/LIBRARY/metis-5.1.0/arch/C9
#export LD_LIBRARY_PATH=$METISHOME/lib:$LD_LIBRARY_PATH
--- systel.myconfig.cfg ---
###
### See http://wiki.opentelemac.org/doku.php?id=installation_notes_2_beta
### On how to install telemac
###
# _____ _______________________________
# ____/ TELEMAC Project Definitions /______________________________/
#
[Configurations]
configs: C9.gfortran.dyn C9.gfortran.debug
S9.gfortran.dyn S9.gfortran S9.gfortran.debug
# _____ ____________________________________
# ____/ General /___________________________________/
# Global declaration that are true for all the C9.* configurations
[general]
language: 2
modules: clean system -api
version: v8p2
#
sfx_zip: gztar
sfx_lib: .a
sfx_obj: .o
sfx_mod: .mod
sfx_exe:
#
#
val_root: <root>/examples
#
val_rank: all
#
mods_all: -I <config>
ar: ar
lib_flags: cru
#
# MPI info
#
fc: mpif90.openmpi
#fc: gfortran
flags_mpi: -DHAVE_MPI
# Those are for nag.ad
incs_mpi: -I/usr/lib/x86_64-linux-gnu/openmpi/include
libs_mpi: -L/usr/lib/x86_64-linux-gnu/openmpi/lib/ -lmpi_mpif -lmpi -L/usr/lib/x86_64-linux-gnu -lopa -lmpl -lrt -lpthread
#cmd_doxygen:doxygen
#
# METIS info
#
libs_metis: -lmetis
#
# MED info
#
incs_med: -I/usr/include
flags_med: -DHAVE_MED
libs_med: -lm -lmed -lhdf5 -ldl -lstdc++ -lz
#
# MUMPS info
#
incs_mumps: -I/usr/include
flags_mumps: -DHAVE_MUMPS
libs_mumps: /usr/lib/x86_64-linux-gnu/libdmumps.a
/usr/lib/x86_64-linux-gnu/libmumps_common.a
/usr/lib/x86_64-linux-gnu/libpord.a
/usr/local/ff-petsc/real/lib/libscalapack.a
-L/usr/lib/x86_64-linux-gnu -lblas
libs_so_mumps: -ldmumps -lmumps_common -lpord -lscalapack-openmpi -lblas
#
# AED info
#
incs_aed: -I /home/mouton/ext/aed2_1.2/include
flags_aed: -DHAVE_AED2
libs_aed: -L/home/mouton/ext/aed2_1.2/libaed2.a
#
# GOTM info
#
#incs_gotm: ##-I $GOTMHOME/include
#flags_gotm: ##-DHAVE_GOTM
#libs_gotm: ##-L$GOTMHOME/lib -lturbulence -lutil
#
# Gfortran info
#
fflags_gfo: -E -cpp -fconvert=big-endian -frecord-marker=4 -DHAVE_I16 -lgfortran
fflags_debug_gfo: -E -g -Wall -fcheck=all -fbacktrace -fbounds-check -finit-integer=-1 -finit-real=nan -ffpe-trap=invalid,zero,overflow -lgfortran
#
# Generic info
#
mpi_cmdexec: mpirun -np <ncsize> <exename>
cmd_obj: [fc] -c [obj_flags] <mods> <incs> <f95name>
cmd_lib: [ar] [lib_flags] <libname> <objs>
cmd_exe: [fc] [exe_flags] -o <exename> <objs> <libs>
#incs_all: [incs_med] [incs_mumps] [incs_aed] [incs_gotm]
#libs_all: [libs_mumps] [libs_med] [libs_metis] [libs_aed] [libs_gotm]
incs_all: [incs_mpi] [incs_med] [incs_mumps] [incs_aed]
libs_all: [libs_mumps] [libs_med] [libs_metis] [libs_aed] -lgfortran
# Link with shared libraries
#libs_so: [libs_so_mumps] [libs_med] [libs_metis] [libs_aed] [libs_gotm]
libs_so: [libs_so_mumps] [libs_metis] [libs_med] [libs_aed]
#
cmd_obj_c: gcc -c [cflags] <srcName> -o <objName>
cflags: -cpp
#
# _____ __________________________________
# ____/ Calibre9 _________________________________/
#
# Gfortran
#
[C9.gfortran.dyn]
brief: Gfortran compiler 4.9.2 with open_mpi for a debian 8 all libraries are compiled in dynamic
options: api utils
#
f2py_name: f2py3
pyd_fcompiler: gnu95
sfx_lib: .so
#
#obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed] [flags_gotm]
obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed]
lib_flags: -fPIC -shared [fflags_gfo]
#
exe_flags: -fPIC [fflags_gfo]
#
cmd_lib: [fc] [lib_flags] -o <libname> <objs>
libs_all: [libs_so] -lgfortran
cflags: -fPIC -cpp
#
[C9.gfortran.debug]
brief: Debug mode Gfortran compiler 4.9.2 with open_mpi for a debian 8
options: api utils
#
f2py_name: f2py3
pyd_fcompiler: gnu95
sfx_lib: .so
#
#obj_flags: -c -O0 -fPIC [fflags_gfo] [fflags_debug_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed] [flags_gotm]
obj_flags: -c -O0 -fPIC [fflags_gfo] [fflags_debug_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed]
lib_flags: -fPIC -shared [fflags_gfo] [fflags_debug_gfo]
#
exe_flags: -fPIC [fflags_gfo]
libs_all: [libs_so] -lgfortran
#
cflags: -fPIC -cpp
#
cmd_lib: [fc] [lib_flags] -o <libname> <objs>
#
# _____ __________________________________
# ____/ Scibian9 _________________________________/
#
# Gfortran
#
[S9.gfortran]
brief: Gfortran compiler 6.3.2 with open_mpi for a debian 9
options: api utils
#
f2py_name: f2py3
pyd_fcompiler: gnu95
sfx_lib: .so
#
#obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed] [flags_gotm]
obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed]
lib_flags: -fPIC -shared [fflags_gfo]
#
exe_flags: -fPIC [fflags_gfo]
#
cmd_lib: [fc] [lib_flags] -o <libname> <objs>
libs_all: [libs_so] -lgfortran
cflags: -fPIC -cpp
#
[S9.gfortran.dyn]
brief: Gfortran compiler 6.3.2 with open_mpi for a debian 9 with real dynamic compilation You need to add $HOMETEL/builds/$USETELCFG/lib to LD_LIBRARY_PATH to make it work
options: api dyn utils
#
f2py_name: f2py3
pyd_fcompiler: gnu95
sfx_lib: .so
#
#obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed] [flags_gotm]
obj_flags: -O2 -fPIC [fflags_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed]
lib_flags: -fPIC -shared [fflags_gfo]
#
exe_flags: -fPIC [fflags_gfo]
#
cmd_lib: [fc] [lib_flags] -o <libname> <objs> <libs>
libs_all: [libs_so] -lgfortran
cflags: -fPIC -cpp
#
[S9.gfortran.debug]
brief: Debug mode Gfortran compiler 6.3.2 with open_mpi for a debian 9
options: api utils
#
f2py_name: f2py3
pyd_fcompiler: gnu95
sfx_lib: .so
#
#obj_flags: -c -O0 -fPIC [fflags_gfo] [fflags_debug_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed] [flags_gotm]
obj_flags: -c -O0 -fPIC [fflags_gfo] [fflags_debug_gfo] [flags_mpi] [flags_mumps] [flags_med] [flags_aed]
lib_flags: -fPIC -shared [fflags_gfo] [fflags_debug_gfo]
#
exe_flags: -fPIC [fflags_gfo]
libs_all: [libs_so] -lgfortran
#
cflags: -fPIC -cpp
#
cmd_lib: [fc] [lib_flags] -o <libname> <objs>
#
... and the end of the compilation log:
- completed: .../telemac-mascaret/sources/artemis/homere_artemis.f
- completed: .../telemac-mascaret/sources/artemis/point_artemis.f
- completed: .../telemac-mascaret/sources/artemis/get_tomspec_dimensions.f
- completed: .../telemac-mascaret/sources/artemis/allspec.f
gfortran: error: ./declarations_special.o: Aucun fichier ou dossier de ce type
gfortran: error: ./gracestop.o: Aucun fichier ou dossier de ce type
gfortran: error: ./plante.o: Aucun fichier ou dossier de ce type
gfortran: error: ./check_allocate.o: Aucun fichier ou dossier de ce type
gfortran: error: ./write_error.o: Aucun fichier ou dossier de ce type
gfortran: error: ./check_call.o: Aucun fichier ou dossier de ce type
gfortran: error: ./get_free_id.o: Aucun fichier ou dossier de ce type
gfortran: error: ./get_nodes_per_element.o: Aucun fichier ou dossier de ce type
gfortran: error: ./sumtwo.o: Aucun fichier ou dossier de ce type
gfortran: error: ./blanc2uscore.o: Aucun fichier ou dossier de ce type
gfortran: error: ./extens.o: Aucun fichier ou dossier de ce type
gfortran: error: ./print_header.o: Aucun fichier ou dossier de ce type
Traceback (most recent call last):
File "compile_telemac.py", line 143, in <module>
main()
File "compile_telemac.py", line 129, in main
compile_cmdf(options.ncsize, modules, options.verbose)
File "/home/mouton/ext/telemac-mascaret/scripts/python3/compilation/compil_tools.py", line 1312, in compile_cmdf
'\n +> failed: ' + file_name + '\n')
utils.exceptions.TelemacException:
+> failed: .../telemac-mascaret/builds/C9.gfortran.dyn/lib/libspecial4artemis.so
(see attachments)
