Re: [FLASH-USERS] setup problems

I think all of FLASH's c routines use mangle_names.h, so to fix the
linker problem it should look something like:

#ifndef MANGLE_NAMES_H
#define MANGLE_NAMES_H

#ifdef IBM
#define FTOC(x) x

#else
#ifdef G95
#define FTOC(x) x##__

#else /* default * /
#define FTOC(x) x##_
#endif /* G95 */

#endif /* IBM */

#endif /* MANGLE_NAMES_H */

Alvaro
Tomasz Plewa wrote:
> Thanks, Georgi. I reckon the same may work for hdf5.
>
> Still the permanent solution is to fix the FLASH source code. It is
> certainly doable.
>
> Tomek
> --
> On Tue, Oct 04, 2005 at 05:32:56PM +0100, Georgi Pavlovski wrote:
>
>>hi,
>>
>>I'm not sure if this is the cure, but it worth a try. While compiling
>>mpich set the environment variable,
>>
>>setenv pac_cv_prog_f77_name_mangle 'lower underscore'
>>
>>I remember having similar problems it the past, but I used intel fortran
>>compiler.
>>
>>- Georgi
>>
>>On Tue, 2005-10-04 at 10:06 -0500, Tomasz Plewa wrote:
>>
>>>Steve -
>>>
>>>You can disregard warnings. However, compilation process fails during
>>>linking. Apparently, gcc/g95 combination produces object symbols with
>>>inconsistent number of underscores. There are some folks who are
>>>working on the workaround for this problem. (If someone has a working
>>>solution, please let us know!)
>>>
>>>Tomek
>>>--
>>>On Tue, Oct 04, 2005 at 03:48:54PM +0100, Steve Spreckley wrote:
>>>
>>>>Hi,
>>>>
>>>>I am new to flash, but I have been trying to install and run the software
>>>>for some time with little success. I have used g95 compilers to compile
>>>>and install mpich 1.2.7 and hdf5 1.6.4, and the example code for these
>>>>compiled and ran fine. However, when trying to compile flash 2.3 I get a
>>>>number of warnings as follows:
>>>>
>>>>In file logfile.F90:625
>>>>
>>>>write (log_lun, "(X, A30, ' : ', A20)") trim(adjustl(str_array(i,
>>>> 1
>>>>Warning (100): X descriptor requires leading space count in format string
>>>>at (1)
>>>>In file logfile.F90:628
>>>>
>>>> write (log_lun, "(X, A15, 22X, A8, 2X, A9, 4X, A8, 2X, A8)") trim
>>>> 1
>>>>Warning (100): X descriptor requires leading space count in format string
>>>>at (1)
>>>>
>>>>
>>>>and then a number of lines like this for several functions:
>>>>
>>>>
>>>>dBaseAPI.c: In function write_logfile:
>>>>dBaseAPI.c:11: warning: incompatible implicit declaration of built-in
>>>>function strlen
>>>>dBaseAPI.c: In function stamp_logfile:
>>>>dBaseAPI.c:16: warning: incompatible implicit declaration of built-in
>>>>function strlen.
>>>>
>>>>
>>>>The code gets past these though and kicks out more F90 warnings:
>>>>
>>>>
>>>>In file checkpoint_re.F90:542
>>>>
>>>> write (num_to_str, '(I)') tot_blocks
>>>> 1
>>>>Warning (100): Nonnegative width required in format string at (1)
>>>>
>>>>In file checkpoint_re.F90:547
>>>>
>>>> write (num_to_str, '(I)') ReNumParts
>>>> 1
>>>>Warning (100): Nonnegative width required in format string at (1)
>>>>
>>>>mpif90 -c -r8 -i4 -I/home/sas/mpich-1.2.7/include -DN_DIM=2
>>>>-DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1 checkpoint_wr.F90
>>>>In file checkpoint_wr.F90:221
>>>>
>>>> write (num_to_str, '(I)') MAX_BLK_MSGS
>>>> 1
>>>>Warning (100): Nonnegative width required in format string at (1).
>>>>
>>>>
>>>>I then get a number of warnings associated with hdf5:
>>>>
>>>>
>>>>h5_write.c: In function h5_write_tree_info_:
>>>>h5_write.c:943: warning: pointer targets in passing argument 3 of
>>>>H5Sselect_hyperslab differ in signedness
>>>>h5_write.c:1030: warning: pointer targets in passing argument 3 of
>>>>H5Sselect_hyperslab differ in signedness
>>>>h5_write.c:1117: warning: pointer targets in passing argument 3 of
>>>>H5Sselect_hyperslab differ in signedness
>>>>h5_write.c:1204: warning: pointer targets in passing argument 3 of
>>>>H5Sselect_hyperslab differ in signedness
>>>>h5_write.c:1230: warning: pointer targets in passing argument 3 of
>>>>H5Sselect_hyperslab differ in signednes
>>>>
>>>>
>>>>and these continue for more h5_ funtions.
>>>>
>>>>The code finally crashes though when linking:
>>>>
>>>>
>>>>aseAPI.o(.text+0x1c): In function `write_logfile':
>>>>dBaseAPI.c: undefined reference to `xwrite_logfile_'
>>>>dBaseAPI.o(.text+0x44): In function `stamp_logfile':
>>>>dBaseAPI.c: undefined reference to `xstamp_logfile_'
>>>>dBaseAPI.o(.text+0x6f): In function `get_real_parm_from_glob_context':
>>>>dBaseAPI.c: undefined reference to `xget_real_parm_from_glob_contex_'
>>>>dBaseAPI.o(.text+0x9b): In function `get_int_parm_from_glob_context':
>>>>dBaseAPI.c: undefined reference to `xget_int_parm_from_glob_context_'
>>>>dBaseAPI.o(.text+0xd6): In function `get_str_parm_from_glob_context':
>>>>dBaseAPI.c: undefined reference to `xget_str_parm_from_glob_context_'
>>>>init_flash.o(.text+0x11): In function `init_flash__':
>>>>init_flash.F90: undefined reference to `init_signal_handler__'
>>>>driverAPI.o(.text+0x1c): In function `abort_flash':
>>>>driverAPI.c: undefined reference to `xabort_flash_'
>>>>checkpoint_re.o(.text+0x8fa): In function `checkpoint_filename_re__':
>>>>checkpoint_re.F90: undefined reference to `h5_open_file_for_read__'
>>>>checkpoint_re.o(.text+0x97e):checkpoint_re.F90: undefined reference to
>>>>`h5_read_timers__'
>>>>checkpoint_re.o(.text+0x9d3):checkpoint_re.F90: undefined reference to
>>>>`h5_read_header_info__'
>>>>checkpoint_re.o(.text+0x19e3):checkpoint_re.F90: undefined reference to
>>>>`get_numparticles__'
>>>>checkpoint_re.o(.text+0x1cf5):checkpoint_re.F90: undefined reference to
>>>>`h5_read_particles__'
>>>>checkpoint_re.o(.text+0x22a9):checkpoint_re.F90: undefined reference to
>>>>`h5_read_tree_info__'
>>>>checkpoint_re.o(.text+0x24bc):checkpoint_re.F90: undefined reference to
>>>>`h5_read_grid_info__'
>>>>checkpoint_re.o(.text+0x25fd):checkpoint_re.F90: undefined reference to
>>>>`h5_read_unknowns__'
>>>>checkpoint_re.o(.text+0x3ab3):checkpoint_re.F90: undefined reference to
>>>>`h5_close_file__'
>>>>checkpoint_wr.o(.text+0xd77): In function `checkpoint_wr__':
>>>>checkpoint_wr.F90: undefined reference to `h5_initialize_file__'
>>>>checkpoint_wr.o(.text+0x14f1):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_header_info__'
>>>>checkpoint_wr.o(.text+0x1730):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_runtime_parameters__'
>>>>checkpoint_wr.o(.text+0x299e):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_particles__'
>>>>checkpoint_wr.o(.text+0x2a16):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_tree_info__'
>>>>checkpoint_wr.o(.text+0x2a60):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_grid_info__'
>>>>checkpoint_wr.o(.text+0x2b97):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_unknowns__'
>>>>checkpoint_wr.o(.text+0x3e38):checkpoint_wr.F90: undefined reference to
>>>>`h5_write_timers__'
>>>>checkpoint_wr.o(.text+0x4022):checkpoint_wr.F90: undefined reference to
>>>>`h5_close_file__'
>>>>plotfile.o(.text+0xc6a): In function `plotfile_':
>>>>plotfile.F90: undefined reference to `h5_initialize_file__'
>>>>plotfile.o(.text+0x12ce):plotfile.F90: undefined reference to
>>>>`h5_write_header_info_sp__'
>>>>plotfile.o(.text+0x1504):plotfile.F90: undefined reference to
>>>>`h5_write_runtime_parameters__'
>>>>plotfile.o(.text+0x1e8f):plotfile.F90: undefined reference to
>>>>`h5_write_tree_info_sp__'
>>>>plotfile.o(.text+0x220c):plotfile.F90: undefined reference to
>>>>`h5_write_grid_info_sp__'
>>>>plotfile.o(.text+0x2be4):plotfile.F90: undefined reference to
>>>>`h5_write_unknowns_sp__'
>>>>plotfile.o(.text+0x2cca):plotfile.F90: undefined reference to
>>>>`h5_write_unknowns_sp__'
>>>>plotfile.o(.text+0x2da3):plotfile.F90: undefined reference to
>>>>`h5_write_unknowns_sp__'
>>>>plotfile.o(.text+0x3a78):plotfile.F90: undefined reference to
>>>>`h5_close_file__'
>>>>init_global_parms_checkpoint.o(.text+0x2cd): In function
>>>>`init_global_parms_checkpoint__':
>>>>init_global_parms_checkpoint.F90: undefined reference to
>>>>`h5_open_file_for_read__'
>>>>init_global_parms_checkpoint.o(.text+0x3ac):init_global_parms_checkpoint.F90:
>>>>undefined reference to `h5_read_runtime_parameters__'
>>>>init_global_parms_checkpoint.o(.text+0x3b8):init_global_parms_checkpoint.F90:
>>>>undefined reference to `h5_close_file__'
>>>>multifluidAPI.o(.text+0x1f): In function `find_fluid_index':
>>>>multifluidAPI.c: undefined reference to `xfind_fluid_index_'
>>>>memory_report.o(.text+0x61): In function `memory_report__':
>>>>memory_report.F90: undefined reference to `memory_usage__'
>>>>gmake[1]: *** [flash2] Error 1
>>>>gmake[1]: Leaving directory
>>>>`/home/sas/work/exoplanets/MHD/FLASH2.5/object'
>>>>gmake: *** [default] Error 2
>>>>
>>>>As can be seen the majority of the problms are with the c code, and there
>>>>is a correlation between the functions that cause warnings early on and
>>>>the undefined reference problems later. I thought that maybe the problem
>>>>could be to do with name mangling but I am not sure, and if it is I am not
>>>>entirely sure how to fix the problem.
>>>>
>>>>Any help is greatly appreciated.
>>>>
>>>>Steve Spreckley
>>>>
>>>>
>>>>
>>>>
>>>>-----------------------------------------------------------------------
>>>>Steve Spreckley
>>>>Astrophysics and Space Research Group
>>>>School of Physics and Astronomy
>>>>The University of Birmingham
>>>>Edgbaston, Birmingham, UK Tel: +44 (0)1214158410
>>>>B15 2TT E-mail: sas@star.sr.bham.ac.uk
>>>>-----------------------------------------------------------------------
>>>
>>--
>>===================================================================
>> Dr Georgi B. Pavlovski School of Physics and Astronomy
>> Tel: +44-(0)-23-8059-2446 University of Southampton
>> Fax: +44-(0)-23-8059-3910 Southampton SO17 1BJ, U.K.
>> Email: gbp@phys.soton.ac.uk Web: www.astro.soton.ac.uk/~gbp
>>===================================================================
>>
>
>
Received on Tue Oct 4 12:27:28 2005