bombing out writing large scratch files

[Randall Mackie]

I can't seem to get the debugger to pop up on my screen.

When I'm logged into the cluster I'm working on, I can
type xterm &, and an xterm pops up on my display. So I know
I can get something from the remote cluster.

Now, when I try this using PETSc, I'm getting the following error
message, for example:

------------------------------------------------------------------------
[17]PETSC ERROR: PETSC: Attaching gdb to /home/randy/d3inv/PETSC_V3.3/d3inv_3_3_petsc of pid 3628 on display 24.5.142.138:0.0 on 
machine compute-0-23.local
------------------------------------------------------------------------

I'm using this in my command file:

source ~/.bashrc
time /opt/mpich/intel/bin/mpirun -np 20 -nolocal -machinefile machines \
          /home/randy/d3inv/PETSC_V3.3/d3inv_3_3_petsc \
          -start_in_debugger \
          -debugger_node 1 \
          -display 24.5.142.138:0.0 \
          -em_ksp_type bcgs \
          -em_sub_pc_type ilu \
          -em_sub_pc_factor_levels 8 \
          -em_sub_pc_factor_fill 4 \
          -em_sub_pc_factor_reuse_ordering \
          -em_sub_pc_factor_reuse_fill \
          -em_sub_pc_factor_mat_ordering_type rcm \
          -divh_ksp_type cr \
          -divh_sub_pc_type icc \
          -ppc_sub_pc_type ilu \
<< EOF
...


Randy


Matthew Knepley wrote:
> 1) Make sure ssh is forwarding X (-Y I think)
> 
> 2) -start_in_debugger
> 
> 3) -display <your machine>:0.0
> 
> should do it.
> 
>    Matt
> 
> On 5/27/06, *Randall Mackie* <randy at geosystem.us 
> <mailto:randy at geosystem.us>> wrote:
> 
>     This is a stupid question, but how do I start in the debugger if I'm
>     running
>     on a cluster half-way around the world and I'm working on that cluster
>     via ssh?
> 
>     Randy
> 
> 
>     Matthew Knepley wrote:
>      > The best thing to do here is get a stack trace from the debugger.
>     From the
>      > description, it is hard to tell what statement is trying to
>     access which
>      > illegal
>      > memory.
>      >
>      >    Matt
>      >
>      > On 5/27/06, *Randall Mackie* < randy at geosystem.us
>     <mailto:randy at geosystem.us>
>      > <mailto:randy at geosystem.us <mailto:randy at geosystem.us>>> wrote:
>      >
>      >     In my PETSc based modeling code, I write out intermediate
>     results to
>      >     a scratch
>      >     file, and then read them back later. This has worked fine up
>     until
>      >     today,
>      >     when for a large model, this seems to be causing my program
>     to crash
>      >     with
>      >     errors like:
>      >
>      >    
>     ------------------------------------------------------------------------
>      >     [9]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>      >     Violation, probably memory access out of range
>      >
>      >
>      >     I've tracked down the offending code to:
>      >
>      >                IF (rank == 0) THEN
>      >                  irec=(iper-1)*2+ipol
>      >                  write(7,rec=irec) (xvec(i),i=1,np)
>      >                END IF
>      >
>      >     It writes out xvec for the first record, but then on the second
>      >     record my program is crashing.
>      >
>      >     The record length (from an inquire statement) is  recl    
>     22626552
>      >
>      >     The size of the scratch file when my program crashes is 98M.
>      >
>      >     PETSc is compiled using the intel compilers ( v9.0 for fortran),
>      >     and the users manual says that you can have record lengths of
>      >     up to 2 billion bytes.
>      >
>      >     I'm kind of stuck as to what might be the cause. Any ideas
>     from anyone
>      >     would be greatly appreciated.
>      >
>      >     Randy Mackie
>      >
>      >     ps. I've tried both the optimized and debugging versions of
>     the PETSc
>      >     libraries, with the same result.
>      >
>      >
>      >     --
>      >     Randall Mackie
>      >     GSY-USA, Inc.
>      >     PMB# 643
>      >     2261 Market St.,
>      >     San Francisco, CA 94114-1600
>      >     Tel (415) 469-8649
>      >     Fax (415) 469-5044
>      >
>      >     California Registered Geophysicist
>      >     License No. GP 1034
>      >
>      >
>      >
>      >
>      > --
>      > "Failure has a thousand explanations. Success doesn't need one"
>     -- Sir
>      > Alec Guiness
> 
>     --
>     Randall Mackie
>     GSY-USA, Inc.
>     PMB# 643
>     2261 Market St.,
>     San Francisco, CA 94114-1600
>     Tel (415) 469-8649
>     Fax (415) 469-5044
> 
>     California Registered Geophysicist
>     License No. GP 1034
> 
> 
> 
> 
> -- 
> "Failure has a thousand explanations. Success doesn't need one" -- Sir 
> Alec Guiness

-- 
Randall Mackie
GSY-USA, Inc.
PMB# 643
2261 Market St.,
San Francisco, CA 94114-1600
Tel (415) 469-8649
Fax (415) 469-5044

California Registered Geophysicist
License No. GP 1034