open TELEMAC-MASCARET The mathematically superior suite of solvers

hi, I am installing OpenTelemac in a Fedora based linux, i have this compilation error:

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
[root@software v7p2r0]# compileTELEMAC.py


Loading Options and Configurations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

_ _ _
| | (_) (_)
_ _ _ __ | | __ _ __ ___ __ __ _ __ _ __ ___ __ __ _ ___ _ ___ _ __
| | | || '_ \ | |/ /| '_ \ / _ \ \ \ /\ / /| '_ \ | '__| / _ \\ \ / /| |/ __|| | / _ \ | '_ \
| |_| || | | || < | | | || (_) | \ V V / | | | | | | | __/ \ V / | |\__ \| || (_) || | | |
\__,_||_| |_||_|\_\|_| |_| \___/ \_/\_/ |_| |_| |_| \___| \_/ |_||___/|_| \___/ |_| |_|


... parsing configuration file: /root/Downloads/v7p2r0/configs/systel.cis-fedora.cfg


__ _ __ _
/ _| | | / _| (_)
| |_ ___ __| | __ _ | |_ ___ _ __ ___ _ __ _ __ ___ _ __ _
| _| / _ \ / _` | / _` || _| / _ \ | '_ \ / _ \| '_ \ | '_ ` _ \ | '_ \ | |
| | | __/| (_| || (_| || | | (_) || |_) || __/| | | || | | | | || |_) || |
|_| \___| \__,_| \__, ||_| \___/ | .__/ \___||_| |_||_| |_| |_|| .__/ |_|
__/ | | | | |
|___/ |_| |_|
Scanning the source code for:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

+> configuration: fedgfopenmpi
+> parallel mode, using mpiexec directly (of the openMPI package).
| The only difference with the scalar versions (optimised) is the presence
| of the key mpi_cmdexec and the -DHAVE_MPI compilation directive.
| Of course, you also need the key par_cmdexec.
| Finally, note that this configuration also works whether
| processor is 0 or 1.
+> root: /root/Downloads/v7p2r0
+> modules: system

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



Compiling the program SPLITSEL and dependents
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

+> There is no need to compile any object
+> There is no need to package any library
Driving: /usr/bin/gfortran -fconvert=big-endian -frecord-marker=4 -lpthread -v -lgfortranbegin -lgfortran -lm -lz -o /root/Downloads/v7p2r0/builds/fedgfopenmpi/bin/splitsel pair.o splitsel.o -I/opt/apps/openmpi-2.0.2/include -pthread -I/opt/apps/openmpi-2.0.2/lib -Wl,-rpath -Wl,/opt/apps/openmpi-2.0.2/lib -Wl,--enable-new-dtags -L/opt/apps/openmpi-2.0.2/lib -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -shared-libgcc
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/
LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-fconvert=big-endian' '-frecord-marker=4' '-v' '-o' '/root/Downloads/v7p2r0/builds/fedgfopenmpi/bin/splitsel' '-I/opt/apps/openmpi-2.0.2/include' '-pthread' '-I/opt/apps/openmpi-2.0.2/lib' '-L/opt/apps/openmpi-2.0.2/lib' '-shared-libgcc' '-mtune=generic'
/usr/libexec/gcc/x86_64-redhat-linux/4.4.7/collect2 --eh-frame-hdr --build-id -m elf_x86_64 --hash-style=gnu -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o /root/Downloads/v7p2r0/builds/fedgfopenmpi/bin/splitsel /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbegin.o -L/opt/apps/openmpi-2.0.2/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lpthread -lgfortranbegin -lgfortran -lm -lz pair.o splitsel.o -rpath /opt/apps/openmpi-2.0.2/lib --enable-new-dtags -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lgcc_s -lgcc -lpthread -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o
splitsel.o: In function `MAIN__':
splitsel.f:(.text+0x4e): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0xa7): undefined reference to `__declarations_special_MOD_li'
splitsel.f:(.text+0xfe): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x157): undefined reference to `__declarations_special_MOD_li'
splitsel.f:(.text+0x1ae): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x207): undefined reference to `__declarations_special_MOD_li'
splitsel.f:(.text+0x263): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x2bc): undefined reference to `__declarations_special_MOD_li'
splitsel.f:(.text+0x318): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x371): undefined reference to `__declarations_special_MOD_li'
splitsel.f:(.text+0x5c5): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x63e): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x6a7): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x715): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x783): undefined reference to `__declarations_special_MOD_lu'
splitsel.o:splitsel.f:(.text+0x7f1): more undefined references to `__declarations_special_MOD_lu' follow
splitsel.o: In function `MAIN__':
splitsel.f:(.text+0x878): undefined reference to `__bief_def_MOD_ncsize'
splitsel.f:(.text+0x887): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x8e5): undefined reference to `__bief_def_MOD_ncsize'
splitsel.f:(.text+0x8ee): undefined reference to `get_free_id_'
splitsel.f:(.text+0x919): undefined reference to `open_mesh_'
splitsel.f:(.text+0x92d): undefined reference to `check_call_'
splitsel.f:(.text+0x9be): undefined reference to `__bief_def_MOD_nptir'
splitsel.f:(.text+0x9c7): undefined reference to `read_mesh_info_'
splitsel.f:(.text+0xa25): undefined reference to `check_allocate_'
splitsel.f:(.text+0xa76): undefined reference to `check_allocate_'
splitsel.f:(.text+0xaca): undefined reference to `read_mesh_conn_'
splitsel.f:(.text+0xad0): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0xbc1): undefined reference to `check_allocate_'
splitsel.f:(.text+0xc17): undefined reference to `check_allocate_'
splitsel.f:(.text+0xc68): undefined reference to `check_allocate_'
splitsel.f:(.text+0xcdb): undefined reference to `read_mesh_coord_'
splitsel.f:(.text+0xd3f): undefined reference to `find_variable_'
splitsel.f:(.text+0xd73): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0xdd2): undefined reference to `plante_'
splitsel.f:(.text+0xe51): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0xeaa): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0xf54): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0xff8): undefined reference to `check_allocate_'
splitsel.f:(.text+0x1051): undefined reference to `check_allocate_'
splitsel.f:(.text+0x10aa): undefined reference to `check_allocate_'
splitsel.f:(.text+0x1103): undefined reference to `check_allocate_'
splitsel.f:(.text+0x115c): undefined reference to `check_allocate_'
splitsel.o:splitsel.f:(.text+0x11b5): more undefined references to `check_allocate_' follow
splitsel.o: In function `MAIN__':
splitsel.f:(.text+0x13f4): undefined reference to `open_bnd_'
splitsel.f:(.text+0x1421): undefined reference to `get_bnd_numbering_'
splitsel.f:(.text+0x1435): undefined reference to `check_call_'
splitsel.f:(.text+0x1504): undefined reference to `get_bnd_value_'
splitsel.f:(.text+0x1518): undefined reference to `check_call_'
splitsel.f:(.text+0x152b): undefined reference to `close_bnd_'
splitsel.f:(.text+0x153f): undefined reference to `check_call_'
splitsel.f:(.text+0x155a): undefined reference to `close_mesh_'
splitsel.f:(.text+0x156e): undefined reference to `check_call_'
splitsel.f:(.text+0x1583): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x15dc): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x1686): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x172f): undefined reference to `check_allocate_'
splitsel.f:(.text+0x178d): undefined reference to `check_allocate_'
splitsel.f:(.text+0x17f0): undefined reference to `check_allocate_'
splitsel.f:(.text+0x1853): undefined reference to `check_allocate_'
splitsel.f:(.text+0x18ac): undefined reference to `check_allocate_'
splitsel.o:splitsel.f:(.text+0x1905): more undefined references to `check_allocate_' follow
splitsel.o: In function `MAIN__':
splitsel.f:(.text+0x1b5c): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x24e4): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x26e5): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x2944): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x2a12): undefined reference to `check_allocate_'
splitsel.f:(.text+0x2a66): undefined reference to `check_allocate_'
splitsel.f:(.text+0x2ac2): undefined reference to `check_allocate_'
splitsel.f:(.text+0x2d85): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x2dde): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x2e88): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x2f37): undefined reference to `check_allocate_'
splitsel.f:(.text+0x30a1): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x30fa): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x31a4): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x3240): undefined reference to `check_allocate_'
splitsel.f:(.text+0x3299): undefined reference to `check_allocate_'
splitsel.f:(.text+0x331f): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x33c4): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x3427): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x37e3): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x3897): undefined reference to `__declarations_special_MOD_lu'
splitsel.o:splitsel.f:(.text+0x38fd): more undefined references to `__declarations_special_MOD_lu' follow
splitsel.o: In function `MAIN__':
splitsel.f:(.text+0x4481): undefined reference to `check_allocate_'
splitsel.f:(.text+0x44d5): undefined reference to `check_allocate_'
splitsel.f:(.text+0x4529): undefined reference to `check_allocate_'
splitsel.f:(.text+0x4582): undefined reference to `check_allocate_'
splitsel.f:(.text+0x45db): undefined reference to `check_allocate_'
splitsel.o:splitsel.f:(.text+0x4634): more undefined references to `check_allocate_' follow
splitsel.o: In function `MAIN__':
splitsel.f:(.text+0x4858): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x48b2): undefined reference to `get_free_id_'
splitsel.f:(.text+0x4b18): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x4c41): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x4cf0): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x4f7f): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x5025): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x507a): undefined reference to `get_free_id_'
splitsel.f:(.text+0x50af): undefined reference to `open_mesh_'
splitsel.f:(.text+0x50c3): undefined reference to `check_call_'
splitsel.f:(.text+0x5116): undefined reference to `check_allocate_'
splitsel.f:(.text+0x5195): undefined reference to `set_header_'
splitsel.f:(.text+0x51a9): undefined reference to `check_call_'
splitsel.f:(.text+0x5243): undefined reference to `check_allocate_'
splitsel.f:(.text+0x5388): undefined reference to `set_mesh_'
splitsel.f:(.text+0x539c): undefined reference to `check_call_'
splitsel.f:(.text+0x53ff): undefined reference to `add_data_'
splitsel.f:(.text+0x5413): undefined reference to `check_call_'
splitsel.f:(.text+0x542b): undefined reference to `close_mesh_'
splitsel.f:(.text+0x543f): undefined reference to `check_call_'
splitsel.f:(.text+0x546d): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x54c6): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x561b): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x5684): undefined reference to `__declarations_special_MOD_lu'
splitsel.f:(.text+0x56ed): undefined reference to `__declarations_special_MOD_lu'
splitsel.o:splitsel.f:(.text+0x5756): more undefined references to `__declarations_special_MOD_lu' follow
collect2: ld returned 1 exit status

compileTELEMAC::main:
+> creating executable: splitsel:
|createExeFiles: something went wrong, I am not sure why (runcode=1).
|
|... The following command failed for the reason above (or below)
|/opt/apps/openmpi-2.0.2/bin/mpif90 -fconvert=big-endian -frecord-marker=4 -lpthread -v -lm -lz -o /root/Downloads/v7p2r0/builds/fedgfopenmpi/bin/splitsel pair.o splitsel.o



this is my systel file.


# _____ _______________________________
# ____/ TELEMAC Project Definitions /______________________________/
#
# space delimited list of active configurations
#
[Configurations]
configs: fedgfopenmpi
#
# _____ ___________________________________________________
# ____/ GENERAL /__________________________________________________/
[general]
version: v7p2r0
modules: system
#
cmd_lib: ar cru <libname> <objs>
#
mods_all: -I <config>
#
sfx_zip: .gztar
sfx_lib: .a
sfx_obj: .o
sfx_mod: .mod
sfx_exe:
#
val_root: /root/Downloads/v7p2r0
val_rank: all
# also possible val_rank: <3 >7 6
cmd_obj_c: gcc -c <srcName> -o <objName>
#
# _____ ___________________________________
# ____/ Fedora gfortran openMPI /__________________________________/
[fedgfopenmpi]
#
brief: parallel mode, using mpiexec directly (of the openMPI package).
The only difference with the scalar versions (optimised) is the presence
of the key mpi_cmdexec and the -DHAVE_MPI compilation directive.
Of course, you also need the key par_cmdexec.
Finally, note that this configuration also works whether
processor is 0 or 1.
#
mpi_cmdexec: /opt/apps/openmpi-2.0.2/bin/mpiexec -wdir <wdir> -n <ncsize> <exename>
#
cmd_obj: gfortran -c -O3 -DHAVE_MPI -DHAVE_MUMPS -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_exe: /opt/apps/openmpi-2.0.2/bin/mpif90 -fconvert=big-endian -frecord-marker=4 -lpthread -v -lm -lz -o <exename> <objs>
#
incs_parallel: -I /opt/apps/openmpi-2.0.2/include/
incs_special: -I /opt/apps/openmpi-2.0.2/include/
libs_partel: /root/Downloads/v7p2r0/optionals/metis-5.1.0/build/Linux-x86_64/libmetis/libmetis.a
libs_all: /opt/apps/openmpi-2.0.2/lib/libmpi.so
#incs_all: -I /opt/apps/openmpi-2.0.2/include/openmpi -I /root/Downloads/v7p2r0/mumps/MUMPS_5.0.0/include/ -I /opt/apps/openmpi-2.0.2/include/
#libs_all: /opt/apps/openmpi-2.0.2/lib/libmpi.so -L /root/Downloads/v7p2r0/mumps/MUMPS_5.0.0/lib -ldmumps -lmumps_common -lpord /root/Downloads/v7p2r0/mumps/SCALAPACK/libscalapack.a -L /root/Downloads/v7p2r0/mumps/BLAS-3.5.0 /root/Downloads/v7p2r0/mumps/BLAS-3.5.0/blas_LINUX.a /root/Downloads/v7p2r0/mumps/BLACS/LIB/blacs_MPI-LINUX-0.a /root/Downloads/v7p2r0/mumps/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /root/Downloads/v7p2r0/mumps/BLACS/LIB/blacs_MPI-LINUX-0.a /root/Downloads/v7p2r0/optionals/metis-5.1.0/build/Linux-x86_64/libmetis/libmetis.a

I commented out the original systel file whit what worked for my ubuntu system.
I also tried it whit the original systel file adding 2 paths.

Thank you in advanced for your time.

Greetings,
Chelo.


|

Can you try compileTELEMAC.py --clean ?

Also, before that, you need to replace

incs_parallel: -I /opt/apps/openmpi-2.0.2/include/
and
incs_special: -I /opt/apps/openmpi-2.0.2/include/
by
incs_all: -I /opt/apps/openmpi-2.0.2/include/

and remove
libs_partel: /root/Downloads/v7p2r0/optionals/metis-5.1.0/build/Linux-x86_64/libmetis/libmetis.a

and change
libs_all: /opt/apps/openmpi-2.0.2/lib/libmpi.so
into
libs_all: /root/Downloads/v7p2r0/optionals/metis-5.1.0/build/Linux-x86_64/libmetis/libmetis.a
/opt/apps/openmpi-2.0.2/lib/libmpi.so

Hope this helps,

Sébastien.

Thank you it is already solved.

Greetings,
Chelo.