[CP2K:3304] regression?
Alin Marin Elena
alinm... at gmail.com
Sat Jun 18 16:18:27 UTC 2011
Hi Urban,
it is indeed... that is for the binary generated with this arch
# this works on my setup on abbaton and baphomet
# intel toolchain/mkl/openmpi... parallel threaded and optimised
#
#
CC = icc
CPP =
FC = ifort
LD = ifort
AR = ar -r
DFLAGS = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -D__FFTMKL
-I$(MPI_ROOT)/include
CPPFLAGS =
FCFLAGS = $(DFLAGS) -O0 -heap-arrays -fpp -free -check all -debug all -g -
traceback
FCFLAGS2 = $(DFLAGS) -O0 -heap-arrays -fpp -free -check all -debug all -g -
traceback
LDFLAGS = $(FCFLAGS) -L{$MKLROOT}/lib/em64t
LIBS = -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -
lmkl_blacs_sgimpt_lp64 -lmpi
OBJECTS_ARCHITECTURE = machine_intel.o
graphcon.o: graphcon.F
$(FC) -c $(FCFLAGS2) $<
but I get the same problem when using openmpi
forrtl: severe (408): fort: (2): Subscript #1 of the array RECV_META has value
1 which is greater than the upper bound of 0
Image PC Routine Line Source
cp2k.pompidbg 0000000008A3424A Unknown Unknown Unknown
cp2k.pompidbg 0000000008A32DC5 Unknown Unknown Unknown
cp2k.pompidbg 00000000089D51F6 Unknown Unknown Unknown
cp2k.pompidbg 0000000008989565 Unknown Unknown Unknown
cp2k.pompidbg 00000000089899B9 Unknown Unknown Unknown
cp2k.pompidbg 0000000008334B9B dbcsr_transformat 2771
dbcsr_transformations.F
cp2k.pompidbg 00000000004DD414 cp_dbcsr_interfac 644
cp_dbcsr_interface.F
cp2k.pompidbg 0000000003975E4C cp_dbcsr_operatio 2170
cp_dbcsr_operations.F
cp2k.pompidbg 000000000394528D cp_dbcsr_operatio 640
cp_dbcsr_operations.F
cp2k.pompidbg 00000000058FEFDA qs_initial_guess_ 493
qs_initial_guess.F
cp2k.pompidbg 000000000189ED40 qs_scf_mp_scf_env 2264 qs_scf.F
cp2k.pompidbg 000000000188BB00 qs_scf_mp_init_sc 1791 qs_scf.F
cp2k.pompidbg 0000000001866370 qs_scf_mp_scf_ 366 qs_scf.F
cp2k.pompidbg 000000000114B2E4 qs_energy_mp_qs_e 224
qs_energy.F
cp2k.pompidbg 0000000001148AE5 qs_energy_mp_qs_e 115
qs_energy.F
cp2k.pompidbg 0000000001184C3A qs_force_mp_qs_fo 227 qs_force.F
cp2k.pompidbg 00000000006E3273 force_env_methods 219
force_env_methods.F
cp2k.pompidbg 00000000004C6BC2 cp2k_runs_mp_cp2k 331
cp2k_runs.F
cp2k.pompidbg 00000000004DA767 cp2k_runs_mp_run_ 1115
cp2k_runs.F
cp2k.pompidbg 00000000004C2464 MAIN__ 291 cp2k.F
cp2k.pompidbg 00000000004BF22C Unknown Unknown Unknown
libc.so.6 00007F9B92E07BC6 Unknown Unknown Unknown
cp2k.pompidbg 00000000004BF129 Unknown Unknown Unknown
this is the arch
alin at stokes1:~/playground/cp2k/makefiles> module list
Currently Loaded Modulefiles:
1) intel-mkl/10.3.1.107 2) openmpi/1.5.3 3) intel-fc/2011.1.107
4) intel-cc/2011.1.107
alin at stokes1:~/playground/cp2k/makefiles> cat ../arch/stokes-intel.pompidbg
# this works on my setup on abbaton and baphomet
# intel toolchain/mkl/openmpi... parallel threaded and optimised
#
#
CC = icc
CPP =
FC = mpif90
LD = mpif90
AR = ar -r
DFLAGS = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -D__FFTMKL
CPPFLAGS =
FCFLAGS = $(DFLAGS) -O0 -heap-arrays -fpp -free -g -traceback -check all -
debug all
FCFLAGS2 = $(DFLAGS) -O0 -heap-arrays -fpp -free -g -traceback -check all -
debug all
LDFLAGS = $(FCFLAGS) -L{$MKLROOT}/lib/intel64
LIBS = -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -
lmkl_blacs_openmpi_lp64
OBJECTS_ARCHITECTURE = machine_intel.o
graphcon.o: graphcon.F
$(FC) -c $(FCFLAGS2) $<
and exctaly the same error when I compile is serial
forrtl: severe (408): fort: (2): Subscript #1 of the array SEND_META has value
1 which is greater than the upper bound of 0
Image PC Routine Line Source
cp2k.sdbg 000000000872592A Unknown Unknown Unknown
cp2k.sdbg 00000000087244A5 Unknown Unknown Unknown
cp2k.sdbg 00000000086C6396 Unknown Unknown Unknown
cp2k.sdbg 000000000867A6F5 Unknown Unknown Unknown
cp2k.sdbg 000000000867AB49 Unknown Unknown Unknown
cp2k.sdbg 0000000007FE748C dbcsr_transformat 1339
dbcsr_transformations.F
cp2k.sdbg 0000000007FB3276 dbcsr_transformat 823
dbcsr_transformations.F
cp2k.sdbg 0000000007F2A955 dbcsr_operations_ 802
dbcsr_operations.F
cp2k.sdbg 0000000007F364B3 dbcsr_operations_ 1120
dbcsr_operations.F
cp2k.sdbg 000000000042F99D cp_dbcsr_interfac 2981
cp_dbcsr_interface.F
cp2k.sdbg 0000000005DF5197 qs_ot_mp_qs_ot_ge 817 qs_ot.F
cp2k.sdbg 0000000005F61700 qs_ot_scf_mp_ot_s 496
qs_ot_scf.F
cp2k.sdbg 00000000016B2CBB qs_scf_mp_init_sc 1564 qs_scf.F
cp2k.sdbg 00000000016968F2 qs_scf_mp_scf_env 547 qs_scf.F
cp2k.sdbg 0000000001693BDF qs_scf_mp_scf_ 374 qs_scf.F
cp2k.sdbg 0000000000F78944 qs_energy_mp_qs_e 224
qs_energy.F
cp2k.sdbg 0000000000F76145 qs_energy_mp_qs_e 115
qs_energy.F
cp2k.sdbg 0000000000FB229A qs_force_mp_qs_fo 227 qs_force.F
cp2k.sdbg 000000000062A1B3 force_env_methods 219
force_env_methods.F
cp2k.sdbg 000000000040DAA2 cp2k_runs_mp_cp2k 331
cp2k_runs.F
cp2k.sdbg 0000000000421647 cp2k_runs_mp_run_ 1115
cp2k_runs.F
cp2k.sdbg 0000000000409344 MAIN__ 291 cp2k.F
cp2k.sdbg 000000000040610C Unknown Unknown Unknown
libc.so.6 00007F60FB08EBFD Unknown Unknown Unknown
cp2k.sdbg 0000000000406009 Unknown Unknown Unknown
alin at baphomet:~/playground/HF24broken> module list
Currently Loaded Modulefiles:
1) intel-mkl/10.3.4.191 2) intel-comp/12.0.4 3) intel-openmpi/1.5.3
alin at baphomet:~/playground/HF24broken> cat ../cp2k/arch/baphomet-intel.sdbg
CC = icc
CPP =
FC = ifort
LD = ifort
AR = ar -r
DFLAGS = -D__INTEL -D__FFTSG -D__FFTMKL
CPPFLAGS = -C -traditional $(DFLAGS)
FCFLAGS = $(DFLAGS) -I$(INTEL_INC) -O0 -heap-arrays -fpp -free -g -
traceback -check all -debug all
FCFLAGS2 = $(DFLAGS) -I$(INTEL_INC) -O0 -heap-arrays -fpp -free -g -
traceback -check all -debug all
LDFLAGS = $(FCFLAGS)
LIBS = -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -
lmkl_core
OBJECTS_ARCHITECTURE = machine_intel.o
graphcon.o: graphcon.F
$(FC) -c $(FCFLAGS2) $<
regards,
Alin
On Sat 18 Jun 2011 17:42:17 Urban Borštnik wrote:
> Hi,
>
> On Sat, 2011-06-18 at 16:31 +0100, Alin Marin Elena wrote:
> > Hi Urban,
> >
> > I have got it running, thank you!
> > Using openmpi instead of mpt seems to have done the trick... for both
> > gcc
> > 4.5.1 and intel 2011.1.107
> >
> > Cause you mentioned bounds checking before...
> > when using the intel compilers both 2011.1.107 and 2011.4.191 it fails
> > with some backtrace of the form (for this example).
>
> Is this with the MPT MPI library?
>
> Cheers,
> Urban
>
> > forrtl: severe (408): fort: (2): Subscript #1 of the array RECV_META has
> > value 1 which is greater than the upper bound of 0
> >
> > Image PC Routine Line
> > Source cp2k.p0 000000000897FCEA Unknown
> > Unknown Unknown cp2k.p0 000000000897E865 Unknown
> > Unknown Unknown cp2k.p0 0000000008920C96 Unknown
> > Unknown Unknown cp2k.p0 00000000088D5005 Unknown
> > Unknown Unknown cp2k.p0 00000000088D5459
> > Unknown Unknown Unknown cp2k.p0
> > 000000000828160F dbcsr_transformat 2771 dbcsr_transformations.F
> > cp2k.p0 0000000000429E94 cp_dbcsr_interfac 644
> > cp_dbcsr_interface.F
> > cp2k.p0 00000000038C28C8 cp_dbcsr_operatio 2170
> > cp_dbcsr_operations.F
> > cp2k.p0 0000000003891D09 cp_dbcsr_operatio 640
> > cp_dbcsr_operations.F
> > cp2k.p0 000000000584BA56 qs_initial_guess_ 493
> > qs_initial_guess.F
> > cp2k.p0 00000000017EB7BC qs_scf_mp_scf_env 2264
> > qs_scf.F cp2k.p0 00000000017D857C qs_scf_mp_init_sc
> > 1791 qs_scf.F cp2k.p0 00000000017B2DEC qs_scf_mp_scf_
> > 366 qs_scf.F cp2k.p0 0000000001097D60
> > qs_energy_mp_qs_e 224 qs_energy.F
> > cp2k.p0 0000000001095561 qs_energy_mp_qs_e 115
> > qs_energy.F
> > cp2k.p0 00000000010D16B6 qs_force_mp_qs_fo 227
> > qs_force.F cp2k.p0 000000000062FCEF force_env_methods
> > 219 force_env_methods.F
> > cp2k.p0 0000000000413642 cp2k_runs_mp_cp2k 331
> > cp2k_runs.F
> > cp2k.p0 00000000004271E7 cp2k_runs_mp_run_ 1115
> > cp2k_runs.F
> > cp2k.p0 000000000040EEE4 MAIN__ 291
> > cp2k.F cp2k.p0 000000000040BCAC Unknown
> > Unknown Unknown libc.so.6 00007F07F4EBFBC6 Unknown
> > Unknown Unknown cp2k.p0 000000000040BBA9 Unknown
> > Unknown Unknown
> >
> >
> > any ideas?
> >
> > regards,
> >
> > Alin
> >
> > On Fri 17 Jun 2011 22:55:50 Urban Borštnik wrote:
> > > Dear Alin,
> > >
> > > I ran your input with a gfortran-compiled version of the latest cvs
> > > (the 2.2 development branch) with 24 and 48 processes and could not
> > > reproduce a crash (with bounds checking).
> > >
> > > The first thing I would try is to either reduce the optimization
> > > level
> > > for all files or selectively for "distribution_1d_types" and
> > > "distribution_methods.F" (in the same way as for "graphcon.F"--take
> > > a
> > > look at your arch file).
> > >
> > > The other thing is to get a stack trace to see where the
> > > segmentation
> > > fault occurs...
> > >
> > > Cheers,
> > > Urban
> > >
> > > On Fri, 2011-06-17 at 20:32 +0100, Alin Marin Elena wrote:
> > > > Hi All,
> > > >
> > > > I have just compiled cp2k, the last cvs and I discovered a very
> > > > strange behaviour...
> > > > I have a small system, 23 atoms and I want to perform some
> > > > simple DFT
> > > > calculation. I try to run it in parallel.
> > > > If I use 12 cores I get my numbers... (HF12good)
> > > > If I use 24 cores I get a segmentation fault... (HF24broken)
> > > > If I use 23 cores I get my numbers... (HF23good)
> > > >
> > > > When I use an older version of cp2k few months...
> > > > If I use 24 cores I get my numbers... (HF24good)
> > > >
> > > > for all the successfull runs I got the same energy
> > > > alin at stokes2:~/playground/alin> grep "ENERGY| " HF*good/HF.out
> > > > HF12good/HF.out: ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):
> > > > -146.062369186077234
> > > > HF23good/HF.out: ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):
> > > > -146.062369186076523
> > > > HF24good/HF.out: ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):
> > > > -146.062369186077234
> > > >
> > > > Inputs and outputs for all tests can be found in the attachement
> > > > (or
> > > > link,if the list rejects it)... to make the attach smaller I
> > > > removed
> > > > the .cube files.
> > > > https://rapidshare.com/files/1317606759/hftests.tar.bz2
> > > >
> > > > All the binaries are compiled with the same settings compilers
> > > > and libs alin at stokes2:~/playground/alin/HF24broken> module list
> > > >
> > > > Currently Loaded Modulefiles:
> > > > 1) intel-mkl/10.2.6.038 2) intel-fc/2011.1.107 3)
> > > > intel-cc/2011.1.107>
> > > >
> > > > 4) mpt/2.01 (sgi mpi implementation)
> > > >
> > > > alin at stokes2:~/playground/cp2k> cat arch/stokes-intel.popt
> > > > # this works on my setup on abbaton and baphomet
> > > > # intel toolchain/mkl/openmpi... parallel threaded and optimised
> > > > #
> > > > #
> > > > CC = icc
> > > > CPP =
> > > > FC = ifort
> > > > LD = ifort
> > > > AR = ar -r
> > > > DFLAGS = -D__INTEL -D__FFTSG -D__parallel -D__BLACS
> > > > -D__SCALAPACK
> > > > -D__FFTMKL -I$(MPI_ROOT)/include
> > > > CPPFLAGS =
> > > > FCFLAGS = $(DFLAGS) -O3 -xSSE4.2 -heap-arrays -fpp -free
> > > > FCFLAGS2 = $(DFLAGS) -O1 -heap-arrays -fpp -free
> > > > LDFLAGS = $(FCFLAGS) -L{$MKLROOT}/lib/em64t
> > > > LIBS = -lmkl_scalapack_lp64 -lmkl_intel_lp64
> > > > -lmkl_sequential
> > > > -lmkl_core - lmkl_blacs_sgimpt_lp64 -lmpi
> > > >
> > > > OBJECTS_ARCHITECTURE = machine_intel.o
> > > >
> > > >
> > > > graphcon.o: graphcon.F
> > > >
> > > > $(FC) -c $(FCFLAGS2) $<
> > > >
> > > > Any suggestion much appreciated,
> > > >
> > > > regards,
> > > >
> > > > Alin
--
Without Questions there are no Answers!
_____________________________________________________________________
Alin Marin ELENA
Advanced Molecular Simulation Research Laboratory
School of Physics, University College Dublin
----
Ardionsamblú Móilíneach Saotharlann Taighde
Scoil na Fisice, An Coláiste Ollscoile, Baile Átha Cliath
-----------------------------------------------------------------------------------
http://alin.elenaworld.net
______________________________________________________________________
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