[visit-users] SILO problem

Mark Miller miller86 at llnl.gov
Mon Apr 20 19:52:41 EDT 2009


I don't see 'silo_f.o' in your ar output. That is what implements the
fortran interface. I think you *need* --enable-fortran on your
configuration line in order for it to compile silo_f.o and include it in
your library.

Mark

On Mon, 2009-04-20 at 19:41 -0400, Mark F. Adams wrote:
> Mark,
> 
> The 'they' are the silo methods such as dbcreate.
> 
> So the code links without the -enable-fortran but the code exits when  
> the first silo method is called (ie, dbcreate_) with the message  
> "dbcreate: Not implemented:"  And there is no .silo file create at all.
> 
> I've appended the ar command that you asked for,
> 
> Thanks,
> Mark
> 
> adams>  ar t libsiloh5.a
> siloh5_version.o
> memmove.o
> scctla.o
> scctl.o
> schash.o
> scstr.o
> pdb.o
> pdbdir.o
> pdbio.o
> pdbmm.o
> pdbx.o
> pdconv.o
> pdlow.o
> pdmemb.o
> pdpath.o
> pdrdwr.o
> alloc.o
> extface.o
> silo.o
> silo_debug.o
> api.o
> ent.o
> netcdf.o
> obj.o
> silo_netcdf.o
> table.o
> pjgroup.o
> pjjacket.o
> pjobj.o
> silo_pdb.o
> silo_hdf5.o
> silo_taurus.o
> taurus.o
> hzmdecoder.o
> hzmencoder.o
> hzmio.o
> hzmpredictor.o
> hzmread.o
> hzmwrite.o
> hznio.o
> hznpredictor.o
> hznread.o
> hznwrite.o
> hzutil.o
> rcdecoder.o
> rcencoder.o
> rcqsmodel.o
> read.o
> write.o
> silo_unknown.o
> f_ale3d.o
> f_sample.o
> 
> 
> 
> On Apr 20, 2009, at 7:30 PM, Mark Miller wrote:
> 
> > What does the command...
> >
> > ar t libsiloh5.a
> >
> > produce?
> >
> > What is the 'they' in the statement 'Now it seems they are empty.'.  
> > The
> > files you produce? The symbol references in the library file? I am
> > confused by what you mean.
> >
> >
> > On Mon, 2009-04-20 at 19:14 -0400, Mark F. Adams wrote:
> >> I'm getting this run time message:
> >>
> >> dbcreate: Not implemented: output.0000001.silo
> >>
> >> This is a fortran code.  I found that I had to remove the -enable-
> >> fortran entry from configure to get a library libsiloh5.a that
> >> contains a dbcreate_, etc. But now it seems that they are empty.  Any
> >> ideas?
> >>
> >> Mark
> >>
> >> On Apr 20, 2009, at 3:25 PM, Mark Miller wrote:
> >>
> >>> I think in addition to adding '--enable-fortran', try also  
> >>> specifying
> >>> explicitly the fortran compiler like so...
> >>>
> >>> ./configure FC=g77 F77=g77 --enable-fortran
> >>>
> >>> Note, set BOTH FC/F77 symbols to same thing. Don't ask why ;)
> >>>
> >>> Mark
> >>>
> >>> On Mon, 2009-04-20 at 14:37 -0400, Mark F. Adams wrote:
> >>>> Thanks Mark,
> >>>>
> >>>> That was the problem, I had IDL in my path and configure was  
> >>>> picking
> >>>> up its install ... now I run:
> >>>>
> >>>> mpif90 reconSilo.F -I/u/adams/silo-4.6.2/src/silo -o reconsilo -L/ 
> >>>> u/
> >>>> adams/silo-4.6.2/lib -lsiloh5
> >>>>
> >>>> and I do not find any SILO methods like dbcreate_
> >>>>
> >>>> They do not seem to be in the libsiloh5.a library:
> >>>>
> >>>> nm /u/adams/silo-4.6.2/lib/libsiloh5.a | grep -i create
> >>>> 0000000000001678 T lite_PD_create
> >>>> 00000000000000c8 C _lite_PD_create_err
> >>>> 0000000000000060 D DBCreateCB
> >>>> 000000000000a6c6 T DBCreateReal
> >>>>                 U db_debug_create
> >>>>                 U db_hdf5_Create
> >>>>                 U db_pdb_Create
> >>>> 0000000000000057 T db_debug_create
> >>>> 00000000000007d9 T db_pdb_Create
> >>>> 000000000000002e T db_hdf5_Create
> >>>> 0000000000000324 T hzip_mesh_create_file
> >>>> 0000000000000388 T hzip_mesh_create_mem
> >>>> 0000000000000526 T hzip_node_create_file
> >>>> 000000000000059c T hzip_node_create_mem
> >>>>
> >>>> I build a non-hdf5 version and it creates a libsilo.a which does  
> >>>> have
> >>>> these methods ... Any ideas?
> >>>>
> >>>> Mark
> >>>>
> >>>>
> >>>> On Apr 20, 2009, at 2:13 PM, Mark Miller wrote:
> >>>>
> >>>>> Hi Mark,
> >>>>>
> >>>>> I think you might need to explicitly tell Silo which 'install'
> >>>>> binary to
> >>>>> use. It looks like it found /usr/pppl/itt/idl70/bin/install during
> >>>>> configure, maybe because that is all that is in your path. So,
> >>>>> that is
> >>>>> what it codes into the Makefile files from the Makefile.in files.
> >>>>> That
> >>>>> isn't a path that we have hard-coded into Silo, anywhere.
> >>>>>
> >>>>> Mark
> >>>>>
> >>>>> PS: on my system...
> >>>>>
> >>>>> alderaan [~/itaps/MOAB_trunk/trunk] 1447% which install
> >>>>> /usr/bin/install
> >>>>> alderaan [~/itaps/MOAB_trunk/trunk] 1448% install --version
> >>>>> install (coreutils) 4.5.3
> >>>>> Written by David MacKenzie.
> >>>>>
> >>>>> Copyright (C) 2002 Free Software Foundation, Inc.
> >>>>> This is free software; see the source for copying conditions.   
> >>>>> There
> >>>>> is NO
> >>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> >>>>> PURPOSE.
> >>>>>
> >>>>> On Mon, 2009-04-20 at 14:07 -0400, Mark F. Adams wrote:
> >>>>>> Thanks Mark,
> >>>>>>
> >>>>>> I found this thread also ... I see that SILO is using IDL in the
> >>>>>> Makefile:
> >>>>>>
> >>>>>> INSTALL = /usr/pppl/itt/idl70/bin/install -c
> >>>>>>
> >>>>>> Does this look correct?  Perhaps I could specify another
> >>>>>> "install".  I
> >>>>>> do not need IDL.
> >>>>>>
> >>>>>> BTW, I've messed with lots of configure options but these are my
> >>>>>> most
> >>>>>> recent:
> >>>>>>
> >>>>>> ./configure --with-hdf5 X_LIBS=-L/usr/X11R6/lib64 CC=mpicc
> >>>>>> CXX=mpiCC
> >>>>>> F77=mpif90 --with-readline=no --without-exodus -enable-fortran --
> >>>>>> enable-static --disable-shared
> >>>>>>
> >>>>>> I need HDF5 and I have an F90 code,
> >>>>>>
> >>>>>> Mark
> >>>>>>
> >>>>>> On Apr 20, 2009, at 1:49 PM, Mark Miller wrote:
> >>>>>>
> >>>>>>> Hello Mark,
> >>>>>>>
> >>>>>>> That message is NOT familiar to me from anything in Silo. It has
> >>>>>>> got
> >>>>>>> to
> >>>>>>> be coming from some script(s) on your system. I google'd the  
> >>>>>>> error
> >>>>>>> message and got this...
> >>>>>>>
> >>>>>>> http://    ubuntuforums.org/archive/index.php/t-943932.html
> >>>>>>>
> >>>>>>> Don't know if its helpful. Unfortunately, I have never seen this
> >>>>>>> kind of
> >>>>>>> thing before. Let me know what you discover. Thanks.
> >>>>>>>
> >>>>>>> Mark
> >>>>>>>
> >>>>>>> On Mon, 2009-04-20 at 13:37 -0400, Mark F. Adams wrote:
> >>>>>>>> Note sure if this this the correct forum for this question but,
> >>>>>>>>
> >>>>>>>> I'm trying to build silo on a linux cluster and am getting this
> >>>>>>>> error
> >>>>>>>> when I try to install it.  Do you have any ideas?
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>> mark
> >>>>>>>>
> >>>>>>>> make[5]: Nothing to be done for `install-exec-am'.
> >>>>>>>> test -z "/u/adams/silo-4.6.2/include" || /bin/mkdir -p "/u/ 
> >>>>>>>> adams/
> >>>>>>>> silo-4.6.2/include"
> >>>>>>>> /usr/pppl/itt/idl70/bin/install -c -m 644 'silo.h' '/u/adams/
> >>>>>>>> silo-4.6.2/include/silo.h'
> >>>>>>>>
> >>>>>>>> The current directory must be set to the ITT directory.
> >>>>>>>> Change the default to the ITT directory and re-run
> >>>>>>>> this script.
> >>>>>>>>
> >>>>>>>> /usr/pppl/itt/idl70/bin/install -c -m 644 'silo.inc' '/u/adams/
> >>>>>>>> silo-4.6.2/include/silo.inc'
> >>>>>>>>
> >>>>>>>> The current directory must be set to the ITT directory.
> >>>>>>>> Change the default to the ITT directory and re-run
> >>>>>>>> this script.
> >>>>>>>>
> >>>>>>>> /usr/pppl/itt/idl70/bin/install -c -m 644 'pmpio.h' '/u/adams/
> >>>>>>>> silo-4.6.2/include/pmpio.h'
> >>>>>>>>
> >>>>>>>> The current directory must be set to the ITT directory.
> >>>>>>>> Change the default to the ITT directory and re-run
> >>>>>>>> this script.
> >>>>>>>>
> >>>>>>>> --
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> >>>>>>>>
> >>>>>>> -- 
> >>>>>>> Mark C. Miller, Lawrence Livermore National Laboratory
> >>>>>>> email: mailto:miller86 at llnl.gov
> >>>>>>> (M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
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> >>>>> -- 
> >>>>> Mark C. Miller, Lawrence Livermore National Laboratory
> >>>>> email: mailto:miller86 at llnl.gov
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> >>> -- 
> >>> Mark C. Miller, Lawrence Livermore National Laboratory
> >>> email: mailto:miller86 at llnl.gov
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> > -- 
> > Mark C. Miller, Lawrence Livermore National Laboratory
> > email: mailto:miller86 at llnl.gov
> > (M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
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> 
-- 
Mark C. Miller, Lawrence Livermore National Laboratory
email: mailto:miller86 at llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F)  (530)-753-8511 (!!LLNL BUSINESS ONLY!!)



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