[FLASH-USERS] Problem with Compiling Flash3.0
Seyit Hocuk
seyit at astro.rug.nl
Tue Jun 3 13:20:06 EDT 2008
ulimit -s
8192
Brock Palen wrote:
> What is the output of
>
> ulimit -s
>
> on your system?
>
> Brock Palen
> www.umich.edu/~brockp
> Center for Advanced Computing
> brockp at umich.edu
> (734)936-1985
>
>
>
> On Jun 3, 2008, at 10:56 AM, Seyit Hocuk wrote:
>> 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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