[petsc-users] Error configuring with Ctetgen

[Satish Balay]

Looks like this gdb is from homebrew - and has issues. Try using

Perhaps you need to use lldb

lldb ./ex1

http://stackoverflow.com/questions/18423124/please-check-gdb-is-codesigned-see-taskgated8-how-to-get-gdb-installed-w

Satish

On Mon, 20 Oct 2014, Justin Chang wrote:

> Barry, I am not sure if this is what you're asking for (I am not too
> familiar with gdb) but here's what happened after following your
> instructions:
> 
> GNU gdb (GDB) 7.8
> Copyright (C) 2014 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html
> >
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-apple-darwin13.4.0".
> Type "show configuration" for configuration details.
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>.
> Find the GDB manual and other documentation resources online at:
> <http://www.gnu.org/software/gdb/documentation/>.
> For help, type "help".
> Type "apropos word" to search for commands related to "word"...
> Reading symbols from ./ex1...
> warning: `/Users/jychang48/petsc-dev/src/vec/vec/examples/tutorials/ex1.o':
> can't open to read symbols: No such file or directory.
> (no debugging symbols found)...done.
> (gdb) run
> Starting program:
> /Users/jychang48/petsc-dev/src/vec/vec/examples/tutorials/ex1
> Unable to find Mach task port for process-id 57136: (os/kern) failure (0x5).
>  (please check gdb is codesigned - see taskgated(8))
> (gdb) bt carriage
> No stack.
> (gdb)
> 
> 
> On Mon, Oct 20, 2014 at 10:50 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> 
> >
> >
> >    cd src/vec/vec/examples/tutorials
> >    make ex1
> >    gdb ./ex1
> >    run
> >
> >     if it stops type bt carriage return and send all the output
> >
> >
> > > On Oct 20, 2014, at 10:37 PM, Justin Chang <jychang48 at gmail.com> wrote:
> > >
> > > I did rm-rf arch-darwin-c-debug and ran config with the following
> > options:
> > >
> > > ./configure --download-exodusii --download-hdf5 --download-metis
> > --download-mpich --download-mumps --download-netcdf --download-parmetis
> > --download-scalapack --download-triangle --with-cc=gcc --with-cxx=g++
> > --with-debugging=1 --with-fc=gfortran --with-valgrind=1 -with-cmake=cmake
> > --download-ctetgen
> > >
> > > And it compiles. However, once I run make all test I get the error
> > "Attempting to use an MPI routine before initializing MPICH" when it
> > attempts to run the test examples. Now I can't run any PETSc code
> > whatsoever. Attached are the new make and configure log files.
> > >
> > > Thanks,
> > > Justin
> > >
> > > On Mon, Oct 20, 2014 at 9:57 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> > > Try:
> > >
> > > rm -rf arch-darwin-c-debug
> > > and rerun onfigure
> > >
> > > [basically you have old version of ctetgen - and configure does not
> > > have smarts to detect this or update to the appropriate version
> > > automatically.  And its likely you have old versions of other packages
> > > aswell - so its best to do a clean build]
> > >
> > > BTW - you shouldn't need --download-fblaslapack on OSX [as it provides
> > > -llapack -lblas via vecLib]
> > >
> > > Satish
> > >
> > > On Mon, 20 Oct 2014, Justin Chang wrote:
> > >
> > > > Hi all,
> > > >
> > > > On my MacOSx I am trying to install the developer's version of petsc
> > with
> > > > the following options:
> > > >
> > > > ./configure --download-exodusii --download-fblaslapack --download-hdf5
> > > > --download-metis --download-mpich --download-mumps --download-netcdf
> > > > --download-parmetis --download-scalapack --download-triangle
> > --with-cc=gcc
> > > > --with-cxx=g++ --with-debugging=1 --with-fc=gfortran --with-valgrind=1
> > > > -with-cmake=cmake --download-ctetgen
> > > >
> > > > The error I get is with the --download-ctetgen option
> > > >
> > > >
> > *******************************************************************************
> > > >          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log
> > for
> > > > details):
> > > >
> > -------------------------------------------------------------------------------
> > > > Error running make on Ctetgen: Could not execute "cd
> > > >
> > /Users/jychang48/petsc-dev/arch-darwin-c-debug/externalpackages/ctetgen &&
> > > > /usr/bin/make PETSC_DIR=/Users/jychang48/petsc-dev install-ctetgen":
> > > > make: *** No rule to make target `install-ctetgen'.  Stop.
> > > >
> > *******************************************************************************
> > > >
> > > > Do you guys know what is wrong? Attached are the make and log files.
> > > >
> > > > Thanks,
> > > > Justin
> > > >
> > >
> > >
> > > <configure.log><make.log>
> >
> >
>