[petsc-users] gnu debugger

[Anthony Haas]

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


Is the command continue that I have used suitable here?
Does the [Inferior 1 (process 30563) exited normally] means that no bug 
was detected?
Or does [0]PETSC ERROR: PETSC: Attaching gdb to ... means that something 
is going wrong?


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]