I can't rerun without psf files. Could you try and compile with -Og -g -fbacktrace (without fcheck=all).
Then try again. :) Den man. 28. jun. 2021 kl. 22.01 skrev Karen Fidanyan < karen.fidan...@mpsd.mpg.de>: > Dear Siesta users, > > I'm having a hard time trying to run SIESTA on my Debian-9 laptop. > I have: > > GNU Fortran (Debian 6.3.0-18+deb9u1) 6.3.0 20170516 > OpenMPI-2.0.2-2 > libblas 3.7.0-2, liblapack 3.7.0-2 > libscalapack-openmpi1 1.8.0-13 > > My arch.make is the following: > ********************************************************************** > .SUFFIXES: > .SUFFIXES: .f .F .o .a .f90 .F90 .c > > SIESTA_ARCH = gfortran_openMPI > > FPP = $(FC) -E -P -x c > FC = mpifort > FC_SERIAL = gfortran > FFLAGS = -O0 -g -fbacktrace -fcheck=all #-Wall > FFLAGS_DEBUG = -g -O0 > > PP = gcc -E -P -C > CC = gcc > CFLAGS = -O0 -g -Wall > > AR = ar > RANLIB = ranlib > SYS = nag > > LDFLAGS = -static-libgcc -ldl > > BLASLAPACK_LIBS = -llapack -lblas \ > -lscalapack-openmpi -lblacs-openmpi > -lblacsF77init-openmpi \ > -lblacsCinit-openmpi \ > -lpthread -lm > > MPI_INTERFACE = libmpi_f90.a > MPI_INCLUDE = . > > FPPFLAGS_MPI = -DMPI -DMPI_TIMING -D_DIAG_WORK > FPPFLAGS = $(DEFS_PREFIX) -DFC_HAVE_FLUSH -DFC_HAVE_ABORT $(FPPFLAGS_MPI) > > INCFLAGS = $(MPI_INCLUDE) > > LIBS = $(BLASLAPACK_LIBS) $(MPI_LIBS) > > atom.o: atom.F > $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) > $(FPPFLAGS_fixed_F) $< > > > .c.o: > $(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $< > .F.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $< > .F90.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< > .f.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $< > .f90.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $< > ********************************************************************** > > The code compiles without errors. > If I run with Diag.ParallelOverK True, I can run on multiple cores, no > errors. > With Diag.ParallelOverK False, I can run `mpirun -np 1` without errors, > but if I try to use >=2 cores, it fails with: > ********************************************************************** > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > #0 0x2ba6eb754d1d in ??? > #1 0x2ba6eb753f7d in ??? > #2 0x2ba6ec95405f in ??? > #3 0x2ba70ec1cd8c in ??? > #4 0x2ba6eab438a4 in ??? > #5 0x2ba6eab44336 in ??? > #6 0x563b3f1cfead in __m_diag_MOD_diag_c > at /home/fidanyan/soft/siesta-4.1/Src/diag.F90:709 > #7 0x563b3f1d2ef9 in cdiag_ > at /home/fidanyan/soft/siesta-4.1/Src/diag.F90:2253 > #8 0x563b3ebc7c8d in diagk_ > at /home/fidanyan/soft/siesta-4.1/Src/diagk.F:195 > #9 0x563b3eb9d714 in __m_diagon_MOD_diagon > at /home/fidanyan/soft/siesta-4.1/Src/diagon.F:265 > #10 0x563b3ed897cb in __m_compute_dm_MOD_compute_dm > at /home/fidanyan/soft/siesta-4.1/Src/compute_dm.F:172 > #11 0x563b3edbfaa5 in __m_siesta_forces_MOD_siesta_forces > at /home/fidanyan/soft/siesta-4.1/Src/siesta_forces.F:315 > #12 0x563b3f9a4005 in siesta > at /home/fidanyan/soft/siesta-4.1/Src/siesta.F:73 > #13 0x563b3f9a408a in main > at /home/fidanyan/soft/siesta-4.1/Src/siesta.F:10 > -------------------------------------------------------------------------- > mpirun noticed that process rank 0 with PID 0 on node fenugreek exited > on signal 11 (Segmentation fault). > ********************************************************************** > > I ran it by > `mpirun -np 2 ~/soft/siesta-4.1/Obj-debug-O0/siesta control.fdf | tee > siesta.out` > > The header of the broken calculation: > -------------------------------------------------------------------------------------------- > > > Siesta Version : v4.1.5-1-g384057250 > Architecture : gfortran_openMPI > Compiler version: GNU Fortran (Debian 6.3.0-18+deb9u1) 6.3.0 20170516 > Compiler flags : mpifort -O0 -g -fbacktrace -fcheck=all > PP flags : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DMPI_TIMING > -D_DIAG_WORK > Libraries : -llapack -lblas -lscalapack-openmpi -lblacs-openmpi > -lblacsF77init-openmpi -lblacsCinit-openmpi -lpthread -lm > PARALLEL version > > * Running on 2 nodes in parallel > -------------------------------------------------------------------------------------------- > > > > I also attach the fdf file and the full output with an error. > Do you have an idea what is wrong? > > Sincerely, > Karen Fidanyan > PhD student > Max Planck Institute for the Structure and Dynamics of Matter > Hamburg, Germany > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
