I have now tried to rerun it with 4.1. And I get no error, even in debug mode.
My bet is that the scalapack library is an old and buggy one. But I could be wrong. Could you rerun with the different possibilities for Diag.Algorithm? I.e. try them all and see which ones works, and which doesn't, then report back. Den ons. 30. jun. 2021 kl. 11.16 skrev Karen Fidanyan < karen.fidan...@mpsd.mpg.de>: > Dear Nick, > > thanks for helping! > > I redid it with -Og flag. The input, *.psf and the output are attached. I > also attach debug.* files obtained with -DDEBUG. > I run as `mpirun -np 2 ~/soft/siesta-4.1/Obj-dbg-Og/siesta control.fdf > 2>&1 | tee siesta.out`. > > Sincerely, > Karen Fidanyan > On 6/28/21 10:22 PM, Nick Papior wrote: > > 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 > > -- 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/)
