[FLASH-USERS] Problem with Compiling Flash3.0
Seyit Hocuk
seyit at astro.rug.nl
Tue Jun 3 10:56:42 EDT 2008
Hi,
Putting the correct HDF5 path solved only part of the problem. I still
have a lot of warnings and the simulation does not start, giving the
error below, even though making ends with success. Both for FLASH2.5 and
for FLASH3.0.
Regards,
Seyit.
amr_prolong_cc_fun_init.F90(115): (col. 7) remark: LOOP WAS VECTORIZED.
amr_prolong_cc_fun_init.F90(134): (col. 7) remark: LOOP WAS VECTORIZED.
amr_prolong_cc_fun_init.F90(136): (col. 7) remark: LOOP WAS VECTORIZED.
amr_prolong_cc_fun_init.F90(156): (col. 7) remark: LOOP WAS VECTORIZED.
amr_prolong_cc_fun_init.F90(158): (col. 7) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(39): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(40): (col. 9) remark: FUSED LOOP WAS VECTORIZED.
amr_initialize.F90(44): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(45): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(46): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(47): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(48): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(49): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(52): (col. 9) remark: LOOP WAS VECTORIZED.
amr_initialize.F90(53): (col. 2) remark: FUSED LOOP WAS VECTORIZED.
amr_initialize.F90(56): (col. 9) remark: FUSED LOOP WAS VECTORIZED.
multifluid.F90(327): (col. 11) remark: FUSED LOOP WAS VECTORIZED.
init_block.F90(220): (col. 7) remark: FUSED LOOP WAS VECTORIZED.
init_block.F90(341): (col. 11) remark: FUSED LOOP WAS VECTORIZED.
init_block.F90(347): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(347): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(347): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(348): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(348): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(348): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(349): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(349): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(349): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(350): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(350): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(350): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(351): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(351): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(351): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(353): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(353): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(353): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(354): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(354): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(354): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(356): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(356): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(356): (col. 16) remark: LOOP WAS VECTORIZED.
init_block.F90(360): (col. 19) remark: LOOP WAS VECTORIZED.
init_block.F90(360): (col. 19) remark: LOOP WAS VECTORIZED.
init_block.F90(360): (col. 19) remark: LOOP WAS VECTORIZED.
perfmon.F90(266): (col. 19) remark: LOOP WAS VECTORIZED.
perfmon.F90(315): (col. 10) remark: LOOP WAS VECTORIZED.
perfmon.F90(319): (col. 8) remark: PARTIAL LOOP WAS VECTORIZED.
perfmon.F90(319): (col. 8) remark: PARTIAL LOOP WAS VECTORIZED.
init_global_parms_checkpoint.F90(118): (col. 12) remark: LOOP WAS
VECTORIZED.
init_from_checkpoint.F90(139): (col. 18) remark: LOOP WAS VECTORIZED.
init_from_checkpoint.F90(139): (col. 18) remark: LOOP WAS VECTORIZED.
init_from_checkpoint.F90(141): (col. 18) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(196): (col. 11) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(196): (col. 11) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(197): (col. 6) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(198): (col. 11) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(233): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(233): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(234): (col. 12) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(235): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(239): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(239): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(241): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(247): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(247): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(249): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(266): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(266): (col. 17) remark: LOOP WAS VECTORIZED.
init_from_scratch.F90(268): (col. 17) remark: LOOP WAS VECTORIZED.
init_flash.F90(343): (col. 15) remark: PARTIAL LOOP WAS VECTORIZED.
init_flash.F90(343): (col. 15) remark: PARTIAL LOOP WAS VECTORIZED.
echo SUCCESS
SUCCESS
make[1]: Leaving directory `/home/users/seyit/FLASH2.5/object'
seyit at si01:~/FLASH2.5/object$ ./flash2
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line
Source
libhdf5-1.6.5.so. 00002B76BF056F08 Unknown Unknown Unknown
libhdf5-1.6.5.so. 00002B76BF05931F Unknown Unknown Unknown
flash2 00000000004FFE9B Unknown Unknown Unknown
flash2 00000000004EA435 Unknown Unknown Unknown
flash2 00000000004F365B Unknown Unknown Unknown
flash2 00000000004060E8 Unknown Unknown Unknown
flash2 00000000004060A2 Unknown Unknown Unknown
libc.so.6 00002B76BFBFEB44 Unknown Unknown Unknown
flash2 0000000000405FE9 Unknown Unknown Unknown
Anshu Dubey wrote:
> It appears that in your Makefile.h you haven't specified the correct
> path for hdf5 library.
> Anshu
>
> On Mon, Jun 2, 2008 at 11:20 AM, Seyit Hocuk <seyit at astro.rug.nl
> <mailto:seyit at astro.rug.nl>> wrote:
>
> Hi,
>
> I am in the middle of switching to FLASH3.0 after a lot of
> suggestions to do that. However, whenever I compile a standard
> problem, while making I get the error message shown below. It
> might be related to my compiler or to HDF5.
>
> The compiler is this:
> /opt/intel/fce/10.1.012/bin/ifort
>
> HDF5 version:
> I tried both 1.6.6 and 1.6.7
>
> The flags for the compiler I use are this:
> FFLAGS_OPT = -c -r8 -i4 -fast -ipo -I $(MPI_PATH)/include
> FFLAGS_DEBUG = -c -r8 -i4 -I $(MPI_PATH)/include
> FFLAGS_TEST = -c -r8 -i4 -I $(MPI_PATH)/include
>
> CFLAGS_HDF5 = -I $(HDF5_PATH)/include
>
> CFLAGS_OPT = -c -I$(MPI_PATH)/include
> CFLAGS_DEBUG = -c -g
> CFLAGS_TEST = -c -02
>
>
> UNAME -a :
> Linux si01 2.6.22-14 #6 SMP Tue Mar 11 15:43:58 CET 2008 x86_64
> GNU/Linux
>
>
>
> Does anyone have any experience on this problem.
>
> Thanks,
> Seyit
>
>
>
>
>
> workspace.o -L/home/users/seyit/Libraries/Hdf5-166/lib -lhdf5 -lz
> -L /home/users/seyit/mpi/mpich2/lib -lmpich
> ipo: warning #11043: unresolved H5Fclose
> Referenced in io_h5file_interface.o
> ipo: warning #11043: unresolved H5check_version
> Referenced in io_h5file_interface.o
> ipo: warning #11043: unresolved H5Fopen
> Referenced in io_h5file_interface.o
> ipo: warning #11043: unresolved H5Fcreate
> Referenced in io_h5file_interface.o
> ipo: warning #11043: unresolved H5Dopen
> Referenced in io_h5read_bflags.o
> Referenced in io_h5read_blk_particle_info.o
> Referenced in io_h5read_blksize.o
> Referenced in io_h5read_bndbox.o
> Referenced in io_h5read_coords.o
> Referenced in io_h5read_generic_int_arr.o
> Referenced in io_h5read_generic_real_arr.o
> Referenced in io_h5read_gid.o
> Referenced in io_h5read_lists.o
> Referenced in io_h5read_localnp.o
> Referenced in io_h5read_lrefine.o
> Referenced in io_h5read_nodetype.o
> Referenced in io_h5read_particles.o
> Referenced in io_h5read_unknowns.o
> Referenced in io_h5read_which_child.o
> Referenced in io_h5write_bflags.o
> Referenced in io_h5write_blk_particle_info.o
> Referenced in io_h5write_blksize.o
> ...
> ...
> ... etc.
> ... etc.
> ...
> ...
> amr_initialize.F90(734): (col. 9) remark: LOOP WAS VECTORIZED.
> amr_initialize.F90(735): (col. 9) remark: FUSED LOOP WAS VECTORIZED.
> amr_initialize.F90(737): (col. 9) remark: FUSED LOOP WAS VECTORIZED.
> amr_initialize.F90(741): (col. 9) remark: LOOP WAS VECTORIZED.
> amr_initialize.F90(742): (col. 9) remark: LOOP WAS VECTORIZED.
> amr_initialize.F90(838): (col. 7) remark: LOOP WAS VECTORIZED.
> amr_initialize.F90(839): (col. 7) remark: LOOP WAS VECTORIZED.
> gr_initParameshArrays.F90(78): (col. 12) remark: LOOP WAS VECTORIZED.
> gr_initParameshArrays.F90(78): (col. 12) remark: LOOP WAS VECTORIZED.
> Grid_dump.F90(156): (col. 11) remark: LOOP WAS VECTORIZED.
> PhysicalConstants_init.F90(127): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(130): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(133): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(136): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(139): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(142): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(145): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(148): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(151): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(154): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(157): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(160): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(165): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(167): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> PhysicalConstants_init.F90(169): (col. 8) remark: BLOCK WAS
> VECTORIZED.
> Grid_init.F90(280): (col. 3) remark: LOOP WAS VECTORIZED.
> Grid_init.F90(375): (col. 3) remark: LOOP WAS VECTORIZED.
> Grid_init.F90(385): (col. 6) remark: LOOP WAS VECTORIZED.
> Particles_init.F90(108): (col. 3) remark: LOOP WAS VECTORIZED.
> Particles_init.F90(135): (col. 3) remark: LOOP WAS VECTORIZED.
> Particles_init.F90(182): (col. 6) remark: LOOP WAS VECTORIZED.
> Grid_initDomain.F90(96): (col. 11) remark: LOOP WAS VECTORIZED.
> Grid_initDomain.F90(114): (col. 20) remark: LOOP WAS VECTORIZED.
> Grid_initDomain.F90(117): (col. 12) remark: FUSED LOOP WAS VECTORIZED.
> Grid_initDomain.F90(124): (col. 17) remark: LOOP WAS VECTORIZED.
> Grid_initDomain.F90(133): (col. 17) remark: LOOP WAS VECTORIZED.
> Grid_initDomain.F90(136): (col. 14) remark: LOOP WAS VECTORIZED.
> Grid_initDomain.F90(171): (col. 12) remark: FUSED LOOP WAS VECTORIZED.
> Grid_initDomain.F90(189): (col. 14) remark: LOOP WAS VECTORIZED.
> Driver_verifyInitDt.F90(98): (col. 14) remark: LOOP WAS VECTORIZED.
> CosmologicalFunctions.F90(611): (col. 6) remark: LOOP WAS VECTORIZED.
> CosmologicalFunctions.F90(618): (col. 6) remark: LOOP WAS VECTORIZED.
> ld: skipping incompatible
> /home/users/seyit/Libraries/Hdf5-166/lib/libhdf5.so when searching
> for -lhdf5
> ld: skipping incompatible
> /home/users/seyit/Libraries/Hdf5-166/lib/libhdf5.a when searching
> for -lhdf5
> ld: cannot find -lhdf5
> make: *** [flash3] Error 1
>
>
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