saturne stopped working - pls help

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15 years 10 months ago #1983 by Claus
saturne stopped working - pls help was created by Claus
Hi - after I was messing around with getting saturne-1.3.2 to work and failed, I've broken saturne-1.3.1 in the process, apparently.

When I try to run a study i get this error (look last in this msg.)

I can simply not understand what Im doing wrong.

it's completely 'vanilla' binary pack from this site, openmpi is present in /opt/saturne/opt/openmpi-1.2.3 - $CS_MPI_PATH is set to /opt.../arch/Linux/bin

what is the matter?? pls see if you can help out - my project is due soon and i'd like to include a 'proof-of-concept' simulation.

Thanks!


*** Linking
make[3]: Entering directory `/home/claus/tmp_Saturne/SIMPLE_JUNCTION.4.05111458/fort_saturne'
libpath=-rdynamic -Wl,-rpath -Wl,/home/saturne/opt/gcc-4.2.2/arch/Linux/lib:/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib:/opt/saturne/opt/bft-1.0.5/arch/Linux/lib:/opt/saturne/opt/med-2.3.1/arch/Linux/lib:/opt/saturne/opt/hdf5-1.6.5/arch/Linux/lib:/usr/lib:/opt/saturne/opt/openmpi-1.2.3/arch/Linux/lib:/opt/saturne/opt/bft-1.0.5/arch/Linux/lib:/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib
make[4]: Entering directory `/home/claus/tmp_Saturne/SIMPLE_JUNCTION.4.05111458/fort_saturne'
g77-3.3.6 -o "cs13.exe" -O \
-L/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib -lsaturneBASE -lsaturneCFBL -lsaturneCOGZ -lsaturneCPLV -lsaturneELEC -lsaturneFUEL -lsaturneLAGR -lsaturneMATI -lsaturneRAYT -lsaturneBASE -lsaturneCFBL -lsaturneCOGZ -lsaturneCPLV -lsaturneELEC -lsaturneFUEL -lsaturneLAGR -lsaturneMATI -lsaturneRAYT -L/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib -lfvm -L/opt/saturne/opt/bft-1.0.5/arch/Linux/lib -lbft -L/opt/saturne/opt/cgnslib_2.4/arch/Linux/lib -lcgns -lhdf5 -L/opt/saturne/opt/med-2.3.1/arch/Linux/lib -lmedC -L/opt/saturne/opt/hdf5-1.6.5/arch/Linux/lib -lhdf5 -rdynamic -Wl,-rpath -Wl,/home/saturne/opt/gcc-4.2.2/arch/Linux/lib:/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib:/opt/saturne/opt/bft-1.0.5/arch/Linux/lib:/opt/saturne/opt/med-2.3.1/arch/Linux/lib:/opt/saturne/opt/hdf5-1.6.5/arch/Linux/lib:/usr/lib:/opt/saturne/opt/openmpi-1.2.3/arch/Linux/lib:/opt/saturne/opt/bft-1.0.5/arch/Linux/lib:/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib -L/usr/lib -lxml2 -L/opt/saturne/src/atlas-3.8.0/build/lib -lcblas -latlas -pthread -L/opt/saturne/opt/openmpi-1.2.3/arch/Linux/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl -L/opt/saturne/opt/bft-1.0.5/arch/Linux/lib -lbft -L/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib -lfvm -lm -lpthread
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh.o): In function `_sync_cell_fam':
cs_mesh.c:(.text+0xbd): undefined reference to `ompi_mpi_int'
cs_mesh.c:(.text+0x175): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh.o): In function `_print_halo_info':
cs_mesh.c:(.text+0x4f9): undefined reference to `ompi_mpi_int'
cs_mesh.c:(.text+0x501): undefined reference to `ompi_mpi_int'
cs_mesh.c:(.text+0x563): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh.o):cs_mesh.c:(.text+0x56d): more undefined references to `ompi_mpi_int' follow
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh.o): In function `cs_mesh_info':
cs_mesh.c:(.text+0x11cb): undefined reference to `ompi_mpi_op_min'
cs_mesh.c:(.text+0x11d0): undefined reference to `ompi_mpi_double'
cs_mesh.c:(.text+0x11ec): undefined reference to `ompi_mpi_op_max'
cs_mesh.c:(.text+0x11f1): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh.o): In function `cs_mesh_init_parall':
cs_mesh.c:(.text+0x12ad): undefined reference to `ompi_mpi_op_sum'
cs_mesh.c:(.text+0x12b2): undefined reference to `ompi_mpi_unsigned'
cs_mesh.c:(.text+0x1341): undefined reference to `ompi_mpi_op_max'
cs_mesh.c:(.text+0x1346): undefined reference to `ompi_mpi_unsigned'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh_quality.o): In function `_display_histograms':
cs_mesh_quality.c:(.text+0xed): undefined reference to `ompi_mpi_op_sum'
cs_mesh_quality.c:(.text+0xf2): undefined reference to `ompi_mpi_unsigned'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh_quality.o): In function `_histogram':
cs_mesh_quality.c:(.text+0x298): undefined reference to `ompi_mpi_op_min'
cs_mesh_quality.c:(.text+0x29d): undefined reference to `ompi_mpi_double'
cs_mesh_quality.c:(.text+0x2ba): undefined reference to `ompi_mpi_op_max'
cs_mesh_quality.c:(.text+0x2bf): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh_quality.o): In function `_int_face_histogram':
cs_mesh_quality.c:(.text+0x3f1): undefined reference to `ompi_mpi_op_min'
cs_mesh_quality.c:(.text+0x3f6): undefined reference to `ompi_mpi_double'
cs_mesh_quality.c:(.text+0x413): undefined reference to `ompi_mpi_op_max'
cs_mesh_quality.c:(.text+0x418): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh_warping.o): In function `_define_periodic_index':
cs_mesh_warping.c:(.text+0x268): undefined reference to `ompi_mpi_int'
cs_mesh_warping.c:(.text+0x2e2): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh_warping.o): In function `_fill_perio_buffers':
cs_mesh_warping.c:(.text+0x5d5): undefined reference to `ompi_mpi_int'
cs_mesh_warping.c:(.text+0x69a): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_mesh_warping.o): In function `cs_mesh_warping_cut_faces':
cs_mesh_warping.c:(.text+0x156a): undefined reference to `ompi_mpi_op_sum'
cs_mesh_warping.c:(.text+0x156f): undefined reference to `ompi_mpi_int'
cs_mesh_warping.c:(.text+0x158c): undefined reference to `ompi_mpi_op_sum'
cs_mesh_warping.c:(.text+0x1591): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `_sync_cells':
cs_parall.c:(.text+0xbf): undefined reference to `ompi_mpi_double'
cs_parall.c:(.text+0x19e): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parcmx_':
cs_parall.c:(.text+0x2f4): undefined reference to `ompi_mpi_op_max'
cs_parall.c:(.text+0x2f9): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parcpt_':
cs_parall.c:(.text+0x324): undefined reference to `ompi_mpi_op_sum'
cs_parall.c:(.text+0x329): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parsom_':
cs_parall.c:(.text+0x354): undefined reference to `ompi_mpi_op_sum'
cs_parall.c:(.text+0x359): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parmax_':
cs_parall.c:(.text+0x38a): undefined reference to `ompi_mpi_op_max'
cs_parall.c:(.text+0x38f): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parmin_':
cs_parall.c:(.text+0x3c0): undefined reference to `ompi_mpi_op_min'
cs_parall.c:(.text+0x3c5): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parmxl_':
cs_parall.c:(.text+0x409): undefined reference to `ompi_mpi_op_maxloc'
cs_parall.c:(.text+0x40e): undefined reference to `ompi_mpi_double_int'
cs_parall.c:(.text+0x439): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parmnl_':
cs_parall.c:(.text+0x473): undefined reference to `ompi_mpi_op_minloc'
cs_parall.c:(.text+0x478): undefined reference to `ompi_mpi_double_int'
cs_parall.c:(.text+0x4a3): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parism_':
cs_parall.c:(.text+0x4fa): undefined reference to `ompi_mpi_op_sum'
cs_parall.c:(.text+0x4ff): undefined reference to `ompi_mpi_int'
cs_parall.c:(.text+0x547): undefined reference to `ompi_mpi_op_sum'
cs_parall.c:(.text+0x54c): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parimx_':
cs_parall.c:(.text+0x5c3): undefined reference to `ompi_mpi_op_max'
cs_parall.c:(.text+0x5c8): undefined reference to `ompi_mpi_int'
cs_parall.c:(.text+0x610): undefined reference to `ompi_mpi_op_max'
cs_parall.c:(.text+0x615): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parimn_':
cs_parall.c:(.text+0x68c): undefined reference to `ompi_mpi_op_min'
cs_parall.c:(.text+0x691): undefined reference to `ompi_mpi_int'
cs_parall.c:(.text+0x6d9): undefined reference to `ompi_mpi_op_min'
cs_parall.c:(.text+0x6de): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parrsm_':
cs_parall.c:(.text+0x755): undefined reference to `ompi_mpi_op_sum'
cs_parall.c:(.text+0x75a): undefined reference to `ompi_mpi_double'
cs_parall.c:(.text+0x7aa): undefined reference to `ompi_mpi_op_sum'
cs_parall.c:(.text+0x7af): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parrmx_':
cs_parall.c:(.text+0x831): undefined reference to `ompi_mpi_op_max'
cs_parall.c:(.text+0x836): undefined reference to `ompi_mpi_double'
cs_parall.c:(.text+0x886): undefined reference to `ompi_mpi_op_max'
cs_parall.c:(.text+0x88b): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parrmn_':
cs_parall.c:(.text+0x90d): undefined reference to `ompi_mpi_op_min'
cs_parall.c:(.text+0x912): undefined reference to `ompi_mpi_double'
cs_parall.c:(.text+0x962): undefined reference to `ompi_mpi_op_min'
cs_parall.c:(.text+0x967): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parbci_':
cs_parall.c:(.text+0x9ba): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parbcr_':
cs_parall.c:(.text+0x9df): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `paragv_':
cs_parall.c:(.text+0xa42): undefined reference to `ompi_mpi_int'
cs_parall.c:(.text+0xa4a): undefined reference to `ompi_mpi_int'
cs_parall.c:(.text+0xa81): undefined reference to `ompi_mpi_double'
cs_parall.c:(.text+0xa8b): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parfpt_':
cs_parall.c:(.text+0xaf8): undefined reference to `ompi_mpi_op_minloc'
cs_parall.c:(.text+0xafd): undefined reference to `ompi_mpi_double_int'
cs_parall.c:(.text+0xb24): undefined reference to `ompi_mpi_int'
cs_parall.c:(.text+0xb3f): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parhis_':
cs_parall.c:(.text+0xb98): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parcel_':
cs_parall.c:(.text+0xbe7): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `parmem_':
cs_parall.c:(.text+0xcd3): undefined reference to `ompi_mpi_op_maxloc'
cs_parall.c:(.text+0xcd8): undefined reference to `ompi_mpi_long_int'
cs_parall.c:(.text+0xcfa): undefined reference to `ompi_mpi_char'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_parall.o): In function `cs_parall_interface_sr':
cs_parall.c:(.text+0xe6b): undefined reference to `ompi_mpi_double'
cs_parall.c:(.text+0xf57): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_perio.o): In function `cs_perio_define_couples':
cs_perio.c:(.text+0x4542): undefined reference to `ompi_mpi_unsigned'
cs_perio.c:(.text+0x455f): undefined reference to `ompi_mpi_unsigned'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_post.o): In function `cs_post_ajoute_maillage_existant':
cs_post.c:(.text+0x125d): undefined reference to `ompi_mpi_op_min'
cs_post.c:(.text+0x1262): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_post.o): In function `_cs_post_definit_maillage':
cs_post.c:(.text+0x25df): undefined reference to `ompi_mpi_op_min'
cs_post.c:(.text+0x25e4): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_sles.o): In function `_sles_info_dump':
cs_sles.c:(.text+0x189): undefined reference to `ompi_mpi_op_min'
cs_sles.c:(.text+0x18e): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1ac): undefined reference to `ompi_mpi_op_max'
cs_sles.c:(.text+0x1b1): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1cc): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1d1): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_sles.o): In function `_conjugate_gradient_sp':
cs_sles.c:(.text+0xc43): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0xc48): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0xc96): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0xc9b): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0xcda): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0xcdf): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0xd31): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0xd36): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0xd66): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0xd6b): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0xda8): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0xdad): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_sles.o): In function `_conjugate_gradient_mp':
cs_sles.c:(.text+0x13d7): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x13dc): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x142d): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1432): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1483): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1488): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x14c1): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x14c6): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1503): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1508): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_sles.o): In function `_jacobi':
cs_sles.c:(.text+0x1710): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1715): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_sles.o): In function `_bi_cgstab':
cs_sles.c:(.text+0x1d28): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1d2d): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1d93): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1d98): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1dd5): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1dda): undefined reference to `ompi_mpi_double'
cs_sles.c:(.text+0x1e2b): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x1e30): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_sles.o): In function `reslin_':
cs_sles.c:(.text+0x20cc): undefined reference to `ompi_mpi_op_sum'
cs_sles.c:(.text+0x20d1): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_suite.o): In function `cs_loc_suite_cree_listes_ent':
cs_suite.c:(.text+0x1e28): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x1e35): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x1e9f): undefined reference to `ompi_mpi_op_max'
cs_suite.c:(.text+0x1ea4): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_suite.o): In function `cs_loc_suite_lit_val_ent':
cs_suite.c:(.text+0x1f30): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x1f45): undefined reference to `ompi_mpi_double'
cs_suite.c:(.text+0x20fe): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x22e7): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_suite.o): In function `cs_loc_suite_ecr_val_ent':
cs_suite.c:(.text+0x2515): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x2527): undefined reference to `ompi_mpi_double'
cs_suite.c:(.text+0x267a): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x26b1): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x290b): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x293d): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_suite.o): In function `cs_loc_suite_distr_val':
cs_suite.c:(.text+0x2a92): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x2a99): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_suite.o): In function `cs_loc_suite_prepare_index':
cs_suite.c:(.text+0x38f6): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x39dd): undefined reference to `ompi_mpi_int'
cs_suite.c:(.text+0x3a75): undefined reference to `ompi_mpi_char'
cs_suite.c:(.text+0x3bd0): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o): In function `cs_base_mpi_init':
cs_base.c:(.text+0x59): undefined reference to `ompi_mpi_comm_world'
cs_base.c:(.text+0x70): undefined reference to `ompi_mpi_comm_world'
cs_base.c:(.text+0xbd): undefined reference to `ompi_mpi_comm_world'
cs_base.c:(.text+0xe5): undefined reference to `ompi_mpi_comm_null'
cs_base.c:(.text+0x109): undefined reference to `ompi_mpi_comm_world'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o): In function `cs_exit':
cs_base.c:(.text+0x16b): undefined reference to `ompi_mpi_comm_world'
cs_base.c:(.text+0x17f): undefined reference to `ompi_mpi_comm_world'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o): In function `cs_base_mem_fin':
cs_base.c:(.text+0x457): undefined reference to `ompi_mpi_op_min'
cs_base.c:(.text+0x45c): undefined reference to `ompi_mpi_int'
cs_base.c:(.text+0x481): undefined reference to `ompi_mpi_op_sum'
cs_base.c:(.text+0x486): undefined reference to `ompi_mpi_double'
cs_base.c:(.text+0x4d4): undefined reference to `ompi_mpi_op_minloc'
cs_base.c:(.text+0x4d9): undefined reference to `ompi_mpi_double_int'
cs_base.c:(.text+0x4fb): undefined reference to `ompi_mpi_op_maxloc'
cs_base.c:(.text+0x500): undefined reference to `ompi_mpi_double_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o): In function `cs_base_bilan_temps':
cs_base.c:(.text+0x88c): undefined reference to `ompi_mpi_op_sum'
cs_base.c:(.text+0x891): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o): In function `_cs_base_sig_fatal':
cs_base.c:(.text+0x1155): undefined reference to `ompi_mpi_comm_world'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o): In function `_cs_base_mpi_fin':
cs_base.c:(.text+0x1172): undefined reference to `ompi_mpi_comm_null'
cs_base.c:(.text+0x1192): undefined reference to `ompi_mpi_comm_null'
cs_base.c:(.text+0x119e): undefined reference to `ompi_mpi_comm_world'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_base.o):(.data+0x8): undefined reference to `ompi_mpi_comm_null'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_benchmark.o): In function `_print_overhead':
cs_benchmark.c:(.text+0x9b): undefined reference to `ompi_mpi_op_min'
cs_benchmark.c:(.text+0xa0): undefined reference to `ompi_mpi_double'
cs_benchmark.c:(.text+0xc0): undefined reference to `ompi_mpi_op_max'
cs_benchmark.c:(.text+0xc5): undefined reference to `ompi_mpi_double'
cs_benchmark.c:(.text+0xe0): undefined reference to `ompi_mpi_op_sum'
cs_benchmark.c:(.text+0xe5): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_benchmark.o): In function `_print_stats':
cs_benchmark.c:(.text+0x1a2): undefined reference to `ompi_mpi_op_min'
cs_benchmark.c:(.text+0x1a7): undefined reference to `ompi_mpi_long'
cs_benchmark.c:(.text+0x1d0): undefined reference to `ompi_mpi_op_max'
cs_benchmark.c:(.text+0x1d5): undefined reference to `ompi_mpi_long'
cs_benchmark.c:(.text+0x1f2): undefined reference to `ompi_mpi_op_sum'
cs_benchmark.c:(.text+0x1f7): undefined reference to `ompi_mpi_long'
cs_benchmark.c:(.text+0x214): undefined reference to `ompi_mpi_op_min'
cs_benchmark.c:(.text+0x219): undefined reference to `ompi_mpi_double'
cs_benchmark.c:(.text+0x233): undefined reference to `ompi_mpi_op_max'
cs_benchmark.c:(.text+0x238): undefined reference to `ompi_mpi_double'
cs_benchmark.c:(.text+0x252): undefined reference to `ompi_mpi_op_sum'
cs_benchmark.c:(.text+0x257): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_benchmark.o): In function `_dot_product_1':
cs_benchmark.c:(.text+0x462): undefined reference to `ompi_mpi_op_sum'
cs_benchmark.c:(.text+0x467): undefined reference to `ompi_mpi_double'
cs_benchmark.c:(.text+0x54f): undefined reference to `ompi_mpi_op_sum'
cs_benchmark.c:(.text+0x554): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_comm.o): In function `cs_loc_comm_mpi_ouvre':
cs_comm.c:(.text+0xc3d): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xca3): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xcad): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0xd1e): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xd28): undefined reference to `ompi_mpi_char'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_comm.o): In function `cs_loc_comm_mpi_entete':
cs_comm.c:(.text+0xd94): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xd9e): undefined reference to `ompi_mpi_packed'
cs_comm.c:(.text+0xdcc): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xdd1): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0xdf3): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xdf8): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0xe14): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xe19): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0xe3f): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xe44): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0xe76): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xe85): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0xe9d): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xeac): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0xec1): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xed0): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0xee8): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xef4): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0xf09): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xf13): undefined reference to `ompi_mpi_packed'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_comm.o): In function `cs_loc_comm_mpi_corps':
cs_comm.c:(.text+0xf75): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xf7f): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0xf8d): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xf97): undefined reference to `ompi_mpi_double'
cs_comm.c:(.text+0xfac): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xfb6): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0xfd7): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xfe1): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0xfeb): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0xff5): undefined reference to `ompi_mpi_double'
cs_comm.c:(.text+0xfff): undefined reference to `ompi_mpi_comm_world'
cs_comm.c:(.text+0x1009): undefined reference to `ompi_mpi_char'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_comm.o): In function `cs_loc_comm_sock_connect':
cs_comm.c:(.text+0x1132): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0x113b): undefined reference to `ompi_mpi_char'
cs_comm.c:(.text+0x1173): undefined reference to `ompi_mpi_int'
cs_comm.c:(.text+0x117b): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_couplage.o): In function `defcpl_':
cs_couplage.c:(.text+0x118): undefined reference to `ompi_mpi_op_max'
cs_couplage.c:(.text+0x11d): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_couplage.o): In function `tbicpl_':
cs_couplage.c:(.text+0x95b): undefined reference to `ompi_mpi_comm_null'
cs_couplage.c:(.text+0x97e): undefined reference to `ompi_mpi_int'
cs_couplage.c:(.text+0x98b): undefined reference to `ompi_mpi_int'
cs_couplage.c:(.text+0x9b4): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_couplage.o): In function `tbrcpl_':
cs_couplage.c:(.text+0xa62): undefined reference to `ompi_mpi_comm_null'
cs_couplage.c:(.text+0xa85): undefined reference to `ompi_mpi_double'
cs_couplage.c:(.text+0xa92): undefined reference to `ompi_mpi_double'
cs_couplage.c:(.text+0xabb): undefined reference to `ompi_mpi_double'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_couplage.o): In function `cs_loc_couplage_cree':
cs_couplage.c:(.text+0xc41): undefined reference to `ompi_mpi_comm_null'
cs_couplage.c:(.text+0xc52): undefined reference to `ompi_mpi_comm_world'
cs_couplage.c:(.text+0xc65): undefined reference to `ompi_mpi_op_min'
cs_couplage.c:(.text+0xc6a): undefined reference to `ompi_mpi_int'
cs_couplage.c:(.text+0xc87): undefined reference to `ompi_mpi_op_max'
cs_couplage.c:(.text+0xc8c): undefined reference to `ompi_mpi_int'
cs_couplage.c:(.text+0xca7): undefined reference to `ompi_mpi_comm_world'
cs_couplage.c:(.text+0xd20): undefined reference to `ompi_mpi_comm_null'
cs_couplage.c:(.text+0xd54): undefined reference to `ompi_mpi_comm_world'
cs_couplage.c:(.text+0xdb1): undefined reference to `ompi_mpi_op_min'
cs_couplage.c:(.text+0xdb6): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_couplage.o): In function `cs_loc_couplage_detruit':
cs_couplage.c:(.text+0xebd): undefined reference to `ompi_mpi_comm_world'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_ext_neighborhood.o): In function `redvse_':
cs_ext_neighborhood.c:(.text+0x126a): undefined reference to `ompi_mpi_op_sum'
cs_ext_neighborhood.c:(.text+0x126f): undefined reference to `ompi_mpi_unsigned_long'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_gradient.o): In function `clmgrd_':
cs_gradient.c:(.text+0xf05): undefined reference to `ompi_mpi_op_max'
cs_gradient.c:(.text+0xf0a): undefined reference to `ompi_mpi_double'
cs_gradient.c:(.text+0xf33): undefined reference to `ompi_mpi_op_min'
cs_gradient.c:(.text+0xf38): undefined reference to `ompi_mpi_double'
cs_gradient.c:(.text+0xf61): undefined reference to `ompi_mpi_op_sum'
cs_gradient.c:(.text+0xf66): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_halo.o): In function `_fill_out_halo':
cs_halo.c:(.text+0x1521): undefined reference to `ompi_mpi_int'
cs_halo.c:(.text+0x15f0): undefined reference to `ompi_mpi_int'
cs_halo.c:(.text+0x171f): undefined reference to `ompi_mpi_int'
cs_halo.c:(.text+0x17b7): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_halo.o):cs_halo.c:(.text+0x18e8): more undefined references to `ompi_mpi_int' follow
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_halo.o): In function `cs_halo_get_n_g_ghost_cells':
cs_halo.c:(.text+0x3dfa): undefined reference to `ompi_mpi_op_sum'
cs_halo.c:(.text+0x3dff): undefined reference to `ompi_mpi_int'
/opt/saturne/Noyau/ncs-1.3.1/arch/Linux/lib/libsaturneBASE.a(cs_tpar1d.o): In function `lect1d_':
cs_tpar1d.c:(.text+0x77c): undefined reference to `ompi_mpi_op_sum'
cs_tpar1d.c:(.text+0x781): undefined reference to `ompi_mpi_int'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_info_null'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_short'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_unsigned_short'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_open'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_read_all'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_read_ordered'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_long_long_int'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_file_null'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_read_shared'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_read_at_all'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_close'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_datatype_null'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `MPI_File_set_view'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_unsigned_long_long'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_float'
/opt/saturne/opt/fvm-0.9.0/arch/Linux/lib/libfvm.so: undefined reference to `ompi_mpi_byte'
collect2: ld returned 1 exit status
make[4]: *** [privcmdlink] Error 1
make[4]: Leaving directory `/home/claus/tmp_Saturne/SIMPLE_JUNCTION.4.05111458/fort_saturne'
make[3]: *** [privmodlink] Error 2
make[3]: Leaving directory `/home/claus/tmp_Saturne/SIMPLE_JUNCTION.4.05111458/fort_saturne'
make[2]: *** [privlink] Error 2
make[2]: Leaving directory `/home/claus/tmp_Saturne/SIMPLE_JUNCTION.4.05111458/fort_saturne'
make[1]: *** [link] Error 2
make[1]: Leaving directory `/home/claus/tmp_Saturne/SIMPLE_JUNCTION.4.05111458/fort_saturne'
make: *** [saturne] Error 2
claus@kafka:~/saturne/Noyau/ncs-1.3.1/doc/TUTORIAL/TEST_CASES/SIMPLE_JUNCTION/4/DATA$

Code_Aster release : STA11.4 on OpenSUSE 12.3 64 bits - EDF/Intel version

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15 years 10 months ago #1990 by David Monfort
Replied by David Monfort on topic Re:saturne stopped working - pls help
Hi,

This indeed is a weird error I also ran into a few weeks ago on my Ubuntu laptop... Unfortunately, I have not been able to solve the issue :( The new version of Ubuntu works better, but if anyone has as a clue, I am interested too !

I think it is an issue with OpenMPI (I "solved" the problem by using MPICH2) but have no idea why it sometimes works and sometimes don't.

David

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15 years 10 months ago #1991 by David Monfort
Replied by David Monfort on topic Re:saturne stopped working - pls help
After talking with a colleague of mine, I have a couple of questions.

Are you using the CAELinux 2008 or 2007 ?
Also, did you reinstall OpenMPI while trying to install Code_Saturne 1.3.2 ?
This might indeed be a conflict between several version of OpenMPI.

You could also check the OpenMPI library.
The library libmpi.so or libmpi.a must exist:
[code:1]ls /opt/saturne/opt/openmpi-1.2.3/arch/Linux/lib[/code:1]
The symbol ompi_mpi_int (or another one) must exist (it appears with the symbol D at the beginnin of the line):
[code:1]nm /opt/saturne/opt/openmpi-1.2.3/arch/Linux/lib/libmpi.so| grep ompi_mpi_int[/code:1]

Sorry if it sounds a bit complex, but I cannot see another way of finding why you get this issue :(

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15 years 10 months ago #1992 by David Monfort
Replied by David Monfort on topic Re:saturne stopped working - pls help
At last I found the bug !

In the file /opt/saturne/Noyau/ncs-1.3.1/bin/macros_Linux.mk (or the one corresponding to your system) you have to change these lines
[code:1]XML_HOME = /usr
XML_INC =-I$(XML_HOME)/include/libxml2
XML_LIB =-L$(XML_HOME)/lib -lxml2[/code:1]
into
[code:1]XML_HOME =
XML_INC =-I/usr/include/libxml2
XML_LIB =-lxml2[/code:1]

The fact is that the MPI library was looked for in the /usr/lib directory instead of the /opt/saturne/openmpi-1.2.3/arch/Linux/lib directory, resulting in finding a non-OpenMPI library.
:(

Tell me if you still have a problem after this patch, but I think it should work now!

David

edit: I don't know why there is a &quot;&lt;?php&quot; symbol in the code boxes, but it shouldn't appear...<br /><br />Post edited by: David Monfort, at: 2008/05/15 19:49

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15 years 10 months ago #1995 by Claus
Replied by Claus on topic Re:saturne stopped working - pls help
In frustration I did something I haven't done in years to fix a bug in a program in Linux - I reinstalled Linux - I know, I'm not proud :)

Interesting though - I successfully compiled Saturne-1.3.2 and can run it, but now 1.3.1 is broken with the same error - even after 'sourcing' the different cs_profiles correctly - I'll investigate later.

Btw. Im using uBuntu 8.04

Thx for clearing it up - hopefully it can help others as well :)

Code_Aster release : STA11.4 on OpenSUSE 12.3 64 bits - EDF/Intel version

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15 years 10 months ago #1999 by David Monfort
Replied by David Monfort on topic Re:saturne stopped working - pls help
Impressive ;)

I would advise you not to use the 1.3.1 which can be considered as a development version (1.3.2 has the same &quot;trunk&quot;, plus several corrections).

As for Ubuntu, Code_Saturne runs fine on it (I installed it on the same distro, same version). You can even install OpenMPI, Libxml2, HDF5, MED, Tcl/Tk/Tix via Synaptic! I did so, and can provide the &quot;apt-get&quot; command if needed.
The only problem you will run into is due to Tk and Tix (directories doesn't show up when browsing for in some boxes), but it will be fixed in a next version of Code_Saturne.

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