[petsc-users] gnu debugger

[Barry Smith]

> On Jul 24, 2015, at 3:43 PM, Anthony Haas <aph at email.arizona.edu> wrote:
> 
> Hi,
> 
> I am trying to run my code through the gnu debugger with:
> 
> ${PETSC_DIR}/${PETSC_ARCH}/bin/mpirun -n 2 ./BiGlobal_Spectral_Petsc.x -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package superlu_dist -eps_view -st_ksp_type preonly -st_pc_type lu -st_pc_factor_mat_solver_package superlu_dist -start_in_debugger
> 
> Following that command, I can see on my main screen:
> 
> 3D POISEUILLE BASEFLOW COMPUTED ON GRID WITH NX = 15 NY = 15  ==> this is a comment in my program
> 
> [0]PETSC ERROR: PETSC: Attaching gdb to ./BiGlobal_Spectral_Petsc.x of pid 30562 on display :0 on machine veltins.cfd.ame.arizona.edu
> [1]PETSC ERROR: PETSC: Attaching gdb to ./BiGlobal_Spectral_Petsc.x of pid 30563 on display :0 on machine veltins.cfd.ame.arizona.edu
> 
> 
> And at the same time, I have 2 xterms that open. I have attached (see below) the content of 1 of the xterms since their content is very similar. Upon opening, the xterms seem to load some debugging info and then, I get:
> 
> (gdb)
> 
> At that point I type continue in both xterms which then show something like: [Inferior 1 (process 30563) exited normally] (see below). And at the same time, 2 other xterms open (I have then 4 xterms open).

   This is not expected.  Are you calling PetscInitialize() multiple times? 

> If I type continue in these 2 new xterms, I get: The program is not being run.

   Strange.

   
> 
> 
> Is the command continue that I have used suitable here?

  Yes that is what I do.

> Does the [Inferior 1 (process 30563) exited normally] means that no bug was detected?

  Usually yes.

> Or does [0]PETSC ERROR: PETSC: Attaching gdb to ... means that something is going wrong?

  Our printing the string PETSC ERROR here is kind of silly cause there is not really an error, I'll see if I can eliminate this.

  What happens if you use just one MPI process?
     1) do you still get the "extra" xterm and gdb?
     2) if you use start_in_debugger with one MPI process does it again offer an "extra" gdb after the first one?

  Barry

> 
> 
> Thanks
> 
> Anthony
> 
> 
> 
> 
> 
> 
> 
> 
> GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-64.el7
> Copyright (C) 2013 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-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /home/anthony/Desktop/BiGlobal-Fortran-New/PETSc/Build-BiGlobal-Matrices/BiGlobal_Spectral_Petsc.x...done.
> Attaching to program: /home/anthony/Desktop/BiGlobal-Fortran-New/PETSc/Build-BiGlobal-Matrices/./BiGlobal_Spectral_Petsc.x, process 30563
> Reading symbols from /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libpetsc.so.3.6...done.
> Loaded symbols for /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libpetsc.so.3.6
> Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done.
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib64/libthread_db.so.1".
> Loaded symbols for /lib64/libpthread.so.0
> Reading symbols from /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libparmetis.so...done.
> Loaded symbols for /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libparmetis.so
> Reading symbols from /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmetis.so...done.
> Loaded symbols for /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmetis.so
> Reading symbols from /lib64/libX11.so.6...Reading symbols from /lib64/libX11.so.6...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libX11.so.6
> Reading symbols from /lib64/libssl.so.10...Reading symbols from /lib64/libssl.so.10...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libssl.so.10
> Reading symbols from /lib64/libcrypto.so.10...Reading symbols from /lib64/libcrypto.so.10...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libcrypto.so.10
> Reading symbols from /lib64/libgfortran.so.3...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libgfortran.so.3
> Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libm.so.6
> Reading symbols from /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmpifort.so.12...done.
> Loaded symbols for /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmpifort.so.12
> Reading symbols from /lib64/libquadmath.so.0...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libquadmath.so.0
> Reading symbols from /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmpicxx.so.12...done.
> Loaded symbols for /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmpicxx.so.12
> Reading symbols from /lib64/libstdc++.so.6...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libstdc++.so.6
> Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libdl.so.2
> Reading symbols from /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superlu
> dist-complex/lib/libmpi.so.12...done.
> Loaded symbols for /home/anthony/LIB/petsc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libmpi.so.12
> Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libgcc_s.so.1
> Reading symbols from /home/anthony/LIB/slepc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libslepc.so.3.6...done.
> Loaded symbols for /home/anthony/LIB/slepc-3.6.0/linux-gnu-debug-mumps-superludist-complex/lib/libslepc.so.3.6
> Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libc.so.6
> Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
> Loaded symbols for /lib64/ld-linux-x86-64.so.2
> Reading symbols from /lib64/libxcb.so.1...Reading symbols from /lib64/libxcb.so.1...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libxcb.so.1
> Reading symbols from /lib64/libgssapi_krb5.so.2...Reading symbols from /lib64/libgssapi_krb5.so.2...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libgssapi_krb5.so.2
> Reading symbols from /lib64/libkrb5.so.3...Reading symbols from /lib64/libkrb5.so.3...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libkrb5.so.3
> Reading symbols from /lib64/libcom_err.so.2...Reading symbols from /lib64/libcom_err.so.2...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libcom_err.so.2
> Reading symbols from /lib64/libk5crypto.so.3...Reading symbols from /lib64/libk5crypto.so.3...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libk5crypto.so.3
> Reading symbols from /lib64/libz.so.1...Reading symbols from /lib64/libz.so.1...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libz.so.1
> Reading symbols from /lib64/librt.so.1...(no debugging symbols found)...done.
> Loaded symbols for /lib64/librt.so.1
> Reading symbols from /lib64/libXau.so.6...Reading symbols from /lib64/libXau.so.6...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libXau.so.6
> Reading symbols from /lib64/libkrb5support.so.0...Reading symbols from /lib64/libkrb5support.so.0...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libkrb5support.so.0
> Reading symbols from /lib64/libkeyutils.so.1...Reading symbols from /lib64/libkeyutils.so.1...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libkeyutils.so.1
> Reading symbols from /lib64/libresolv.so.2...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libresolv.so.2
> Reading symbols from /lib64/libselinux.so.1...Reading symbols from /lib64/libselinux.so.1...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libselinux.so.1
> Reading symbols from /lib64/libpcre.so.1...Reading symbols from /lib64/libpcre.s
> o.1...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libpcre.so.1
> Reading symbols from /lib64/liblzma.so.5...Reading symbols from /lib64/liblzma.so.5...(no debugging symbols found)...done.
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/liblzma.so.5
> Reading symbols from /lib64/libnss_files.so.2...(no debugging symbols found)...done.
> Loaded symbols for /lib64/libnss_files.so.2
> 0x00007faacd261470 in __nanosleep_nocancel () from /lib64/libc.so.6
> Missing separate debuginfos, use: debuginfo-install glibc-2.17-78.el7.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.12.2-14.el7.x86_64 libX11-1.6.0-2.1.el7.x86_64 libXau-1.0.8-2.1.el7.x86_64 libcom_err-1.42.9-7.el7.x86_64 libgcc-4.8.3-9.el7.x86_64 libgfortran-4.8.3-9.el7.x86_64 libquadmath-4.8.3-9.el7.x86_64 libselinux-2.2.2-6.el7.x86_64 libstdc++-4.8.3-9.el7.x86_64 libxcb-1.9-5.el7.x86_64 openssl-libs-1.0.1e-42.el7.9.x86_64 pcre-8.32-14.el7.x86_64 xz-libs-5.1.2-9alpha.el7.x86_64 zlib-1.2.7-13.el7.x86_64
> (gdb) continue
> Continuing.
> Detaching after fork from child process 30734.
> [Inferior 1 (process 30563) exited normally]
>