Difference between revisions of "Identify what's causing segmentation fault in Yambo"

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## for intel fortran  <code>./configure FCFLAGS="-O1 -g -CB -CA -debug" UFLAGS="-O0 -g -CB -CA -debug" FFLAGS="-O1 -g  -CB -CA -debug"  --enable-keep-src"</code>
## for intel fortran  <code>./configure FCFLAGS="-O1 -g -CB -CA -debug" UFLAGS="-O0 -g -CB -CA -debug" FFLAGS="-O1 -g  -CB -CA -debug"  --enable-keep-src"</code>
# '''Use a debugger''': Compile with debugging options, "-O1 -g" for gfortran "-O1 -g -debug for ifortran, plus the <code>--enable-keep-src</code> flag, then execute your job in a debugger for example <code>gdb --args yambo -F yambo_input.in</code>. It can work also in parallel see [https://www.open-mpi.org/faq/?category=debugging here] and [https://stackoverflow.com/questions/329259/how-do-i-debug-an-mpi-program here]
# '''Use a debugger''': Compile with debugging options, "-O1 -g" for gfortran "-O1 -g -debug for ifortran, plus the <code>--enable-keep-src</code> flag, then execute your job in a debugger for example <code>gdb --args yambo -F yambo_input.in</code>. It can work also in parallel see [https://www.open-mpi.org/faq/?category=debugging here] and [https://stackoverflow.com/questions/329259/how-do-i-debug-an-mpi-program here]
# '''Memory leaks''': [only for experts] compile Yambo with debugging option then run your job with valgrind: <code>valgrind --tool=memcheck --leak-check=summary ./yambo</code>
# '''Memory leaks''': [only for experts] compile Yambo with debugging options then run your job with [https://valgrind.org/ valgrind]: <code>valgrind --tool=memcheck --leak-check=summary ./yambo</code>

Revision as of 18:07, 10 January 2021

There may be different reasons why the Yambo code generates segmentation faults in a run.
To help Yambo developers understand where the problem lies and help you, please follow the steps below. If one of the step solves your problem and please report the result in the forum.


Rule out possible causes of the segmentation fault:

  1. GPU: recompile without GPU support, remove the --enable-cuda flag. If this solve the problem report the bug in forum GPU section Yambo on GPU machines.
  2. OPEN-MP: compile and run Yambo without open-mp support, no --enable-open-mp flag in compilation and OMP_NUM_THREADS="1".
  3. Lapack/Blas: use internal Lapack/Blas. Reconfigure and recompile Yambo with the flag --enable-int-linalg.
  4. FFT: compile Yambo with internal FFT libraries --enable-internal-fftsg .
  5. Scalapack: compile without Scalpack, unset the flag --with-scalapack-libs.
  6. Parallelism
    1. Change the number of processors
    2. Use automatic parallelization, unset all parallel variable input
    3. Run in serial
  7. Optimization: use a lower optimization level for example O1 or O0, by doing ./configure FCFLAGS="-O0" F77FLAGS="-O1"
  8. Compilers: change C/Fortran compiler if it is possible, move form intel fortran to gfortran or vice-versa.
    In order to set compilers in the configure use ./configure FC=ifort F77=ifort CC=icc for Intel and ./configure FC=gfortran F77=gfortran CC=gcc for gfortran.


If no one of the previous steps solved your problem, report the problem in the forum.
If you want you can try to debug Yambo and identity from where the segmentation fault following the steps below, this will help developers to find a solution to your problem more quickly:

Debugging the segmentation fault:

  1. Checking options: compile Yambo with the compiler checking options and run again your simulation, report the result in the forum:
    1. for g-fortran compiler ./configure FCFLAGS="-O1 -g -fcheck=all" UFLAGS="-O0 -g -fcheck=all" FFLAGS="-O1 -g -fcheck=all" --enable-keep-src"
    2. for intel fortran ./configure FCFLAGS="-O1 -g -CB -CA -debug" UFLAGS="-O0 -g -CB -CA -debug" FFLAGS="-O1 -g -CB -CA -debug" --enable-keep-src"
  2. Use a debugger: Compile with debugging options, "-O1 -g" for gfortran "-O1 -g -debug for ifortran, plus the --enable-keep-src flag, then execute your job in a debugger for example gdb --args yambo -F yambo_input.in. It can work also in parallel see here and here
  3. Memory leaks: [only for experts] compile Yambo with debugging options then run your job with valgrind: valgrind --tool=memcheck --leak-check=summary ./yambo