saturne stopped working - pls help

Hi again - to make a (very) long story short: openmpi is not working.

When I recently compiled Code_Saturne-1.3.2, I used the installed openmpi (1.2.5) on my ubuntu I got this return from configuring 'fvm':

Configuration options:
use debugging code: false
MPI (Message Passing Interface) support: yes
MPI I/O support: no
MPI2 one-sided communication support: yes
HDF (Hierarchical Data Format) support: yes
CGNS (CFD General Notation System) support: yes
MED (Model for Exchange of Data) support: yes

awright, I was able to finish the visualization for my project (thx!) using ONE core, since sat-1.3.2 segfaulted when enabling 2 cores

Today I tried to recompile 'fvm' using --prefix=..../opt/openmpi-1.2.6 etc. but the make-process errors out (see below)

So I tried compiling and using openmpi-1.2.5 but I get the same error as with 1.2.6 - what could be wrong?

Heres the 'configure' command and errormessage from 'make -j 2':

Hope I have provided the necessary information - thx

[code:1]
./configure --prefix=/optsaturne-1.3.2/opt/fvm-0.10.0/arch/Linux --with-bft=/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux --with-hdf5=/usr/ --with-cgns=/opt/saturne-1.3.2/opt/cgnslib_2.5/arch/Linux/ --with-mpi=/opt/saturne-1.3.2/opt/openmpi-1.2.*/arch/Linux/ && make -j 2
[/code:1]

[code:1]
--snip--
mkdir .libs
cc -std=c99 -funsigned-char -pedantic -W -Wall -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wunused -Wfloat-equal -Wpadded -funroll-loops -O2 -Wuninitialized -march=i686 -O -o .libs/fvm_file_test fvm_file_test.o -L/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux/lib -L/usr//lib -L/opt/saturne-1.3.2/opt/cgnslib_2.5/arch/Linux//lib -L/opt/saturne-1.3.2/opt/openmpi-1.2.5/arch/Linux//lib ../src/.libs/libfvm.so //opt/saturne-1.3.2//opt/bft-1.0.6/arch/Linux/lib/libbft.so /usr/lib/libmedC.so -L/usr/lib -lcgns /usr/lib/libhdf5.so -L/usr/lib/mpich/lib/ -lpthread -lz -lmpi -lm -Wl,--rpath -Wl,/optsaturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib -Wl,--rpath -Wl,//opt/saturne-1.3.2//opt/bft-1.0.6/arch/Linux/lib
fvm_file_test.o: In function `main':
fvm_file_test.c:«»(.text+0x64): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x74): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x8a): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x2c2): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x2d6): undefined reference to `ompi_mpi_int'
fvm_file_test.c:«»(.text+0x5be): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x5d2): undefined reference to `ompi_mpi_int'
fvm_file_test.c:«»(.text+0x867): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x8b7): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0x8cb): undefined reference to `ompi_mpi_int'
fvm_file_test.c:«»(.text+0xbed): undefined reference to `ompi_mpi_comm_world'
fvm_file_test.c:«»(.text+0xc01): undefined reference to `ompi_mpi_int'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_info_null'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_short'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_op_min'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned_short'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_comm_null'
../src/.libs/libfvm.so: undefined reference to `MPI_File_read_ordered'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_long_long_int'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_op_max'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_file_null'
../src/.libs/libfvm.so: undefined reference to `MPI_File_read_shared'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_datatype_null'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned_long_long'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_double'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_long_int'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned_long'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_op_sum'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_float'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_byte'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_long'
collect2: ld returned 1 exit status
make[2]: *** [fvm_file_test] Error 1
make[2]: *** Waiting for unfinished jobs....
cc -std=c99 -funsigned-char -pedantic -W -Wall -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wunused -Wfloat-equal -Wpadded -funroll-loops -O2 -Wuninitialized -march=i686 -O -o .libs/fvm_interface_test fvm_interface_test.o -L/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux/lib -L/usr//lib -L/opt/saturne-1.3.2/opt/cgnslib_2.5/arch/Linux//lib -L/opt/saturne-1.3.2/opt/openmpi-1.2.5/arch/Linux//lib ../src/.libs/libfvm.so //opt/saturne-1.3.2//opt/bft-1.0.6/arch/Linux/lib/libbft.so /usr/lib/libmedC.so -L/usr/lib -lcgns /usr/lib/libhdf5.so -L/usr/lib/mpich/lib/ -lpthread -lz -lmpi -lm -Wl,--rpath -Wl,/optsaturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib -Wl,--rpath -Wl,//opt/saturne-1.3.2//opt/bft-1.0.6/arch/Linux/lib
fvm_interface_test.o: In function `main':
fvm_interface_test.c:«»(.text+0x55): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x68): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x7b): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x245): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x259): undefined reference to `ompi_mpi_int'
fvm_interface_test.c:«»(.text+0x712): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x726): undefined reference to `ompi_mpi_int'
fvm_interface_test.c:«»(.text+0x92b): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x93f): undefined reference to `ompi_mpi_int'
fvm_interface_test.c:«»(.text+0x962): undefined reference to `ompi_mpi_comm_world'
fvm_interface_test.c:«»(.text+0x976): undefined reference to `ompi_mpi_int'
fvm_interface_test.o: In function `_bft_printf_proxy':
fvm_interface_test.c:«»(.text+0xc24): undefined reference to `ompi_mpi_comm_world'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_info_null'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_short'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_op_min'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned_short'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_comm_null'
../src/.libs/libfvm.so: undefined reference to `MPI_File_read_ordered'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_long_long_int'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_op_max'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_file_null'
../src/.libs/libfvm.so: undefined reference to `MPI_File_read_shared'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_datatype_null'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned_long_long'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_double'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_long_int'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_unsigned_long'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_op_sum'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_float'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_byte'
../src/.libs/libfvm.so: undefined reference to `ompi_mpi_long'
collect2: ld returned 1 exit status
make[2]: *** [fvm_interface_test] Error 1
make[2]: Leaving directory `/opt/saturne-1.3.2/src/fvm-0.10.0/tests'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/opt/saturne-1.3.2/src/fvm-0.10.0'
make: *** [all] Error 2
claus@kafka:/opt/saturne-1.3.2/src/fvm-0.10.0$ ./configure --prefix=/optsaturne-1.3.2/opt/fvm-0.10.0/arch/Linux --with-bft=/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux --with-hdf5=/usr/ --with-cgns=/opt/saturne-1.3.2/opt/cgnslib_2.5/arch/Linux/ && make -j 2
[/code:1]

well - you were right, fvm compiles now, but launching a two-core calculation results in this error (see below)

Maybe I need to recompile a local HDF5 for saturne instead of using the one on ubuntu.

your thoughts?

/usr/bin/gfortran -o "cs13.exe" -O \
-L/opt/saturne-1.3.2/Noyau/ncs-1.3.2/arch/Linux/lib -lsaturneBASE -lsaturneCFBL -lsaturneCOGZ -lsaturneCPLV -lsaturneELEC -lsaturneFUEL -lsaturneLAGR -lsaturneMATI -lsaturneRAYT -lsaturneBASE -lsaturneCFBL -lsaturneCOGZ -lsaturneCPLV -lsaturneELEC -lsaturneFUEL -lsaturneLAGR -lsaturneMATI -lsaturneRAYT -L/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib -lfvm -L/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux/lib -lbft -L/opt/saturne-1.3.2/opt/cgnslib_2.5/arch/Linux//lib -lcgns -lhdf5 -lmedC -lhdf5 -rdynamic -Wl,-rpath -Wl,/usr/lib:/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib:/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux/lib:/usr/lib:/usr/lib:/opt/saturne-1.3.2/opt/openmpi-1.2.6/arch/Linux/lib:/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux/lib:/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib -L/usr/lib -lxml2 -L/usr/lib -lcblas -latlas -pthread -L/opt/saturne-1.3.2/opt/openmpi-1.2.6/arch/Linux/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl -L/opt/saturne-1.3.2/opt/bft-1.0.6/arch/Linux/lib -lbft -L/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib -lfvm -lm -lpthread
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_info_null'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_short'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_int'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_op_min'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_unsigned_short'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_comm_null'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_read_ordered'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_long_long_int'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_op_max'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_file_null'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_read_shared'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_unsigned'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_datatype_null'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_unsigned_long_long'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_double'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_long_int'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_unsigned_long'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_op_sum'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_float'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_byte'
/opt/saturne-1.3.2/opt/fvm-0.10.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_long'
collect2: ld returned 1 exit status
make[4]: *** [privcmdlink] Error 1
make[4]: Leaving directory `/home/claus/tmp_Saturne/PIPE.CAS1.05201955/fort_saturne'
make[3]: *** [privmodlink] Error 2
make[3]: Leaving directory `/home/claus/tmp_Saturne/PIPE.CAS1.05201955/fort_saturne'
make[2]: *** [privlink] Error 2
make[2]: Leaving directory `/home/claus/tmp_Saturne/PIPE.CAS1.05201955/fort_saturne'
make[1]: *** [link] Error 2
make[1]: Leaving directory `/home/claus/tmp_Saturne/PIPE.CAS1.05201955/fort_saturne'
make: *** [saturne] Error 2

Awright - so far so good. I corrected the macros.Linux.mk to this

[code:1]
# Macro pour XML
#

---

# Option XML
XML =1

XML_HOME =

XML_INC =-i/usr/include/libxml2/
XML_LIB =-lxml2
[/code:1]

and the compile of ran - next the preprocessor complained about not finding 'med' although it is placed in the correct folder. Installed 'med' via synaptic. Now the preprocessor also runs. Alas I thought the solution would run, but this error occurs (see below), I'll also include the 'listing' file, but it seems mpi (which IS 1.2.6 since I installed it system-wide) still doesn't want to play nice. Single-core works fine though.

[code:1] ********************************************
Execution
********************************************

Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_SPLIT and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_SIZE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_SIZE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_FREE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_SPLIT and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_SIZE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_RANK and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_SIZE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_COMM_FREE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_BARRIER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_BARRIER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_BARRIER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLREDUCE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_BARRIER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLREDUCE and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
Fatal error; unknown error handler
May be MPI call before MPI_INIT. Error message is MPI_ALLGATHER and code is 197
[/code:1]

end of 'listing'

[code:1]

---

Renumerotation du maillage:

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** VECTORISATION (1 : POSSIBLE, 0 : IMPOSSIBLE)

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Faces internes Faces de bord
IVECTI 0 IVECTB 0

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