Compiling cp2k serial on x86_64 Intel Xeon Intel Ifort Suse Enterprise 9 (PARALLEL)
Roberto Scipioni
robertino... at yahoo.it
Wed Oct 22 07:12:26 UTC 2008
Hi all,
Now I have been trying to make the parallel version work
I used the arch file (I used ifort 10.0 and mkl 10)
CC = icc
CPP = cpp
FC = /opt/ompi_ifort10/bin/mpif90 -FR
FC_fixed = /opt/ompi_ifort10/bin/mpif90 -FI
LD = /opt/ompi_ifort10/bin/mpif90 -i_dynamic -openmp
AR = ar -r
DFLAGS = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -D__FFTW3
CPPFLAGS = -traditional -C $(DFLAGS) -P
FCFLAGS = $(DFLAGS) -O3 -Vaxlib
LDFLAGS = $(FCFLAGS) -L/opt/intel/mkl/10.0.1.014/lib/em64t/
LIBS=/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_scalapack.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_blacs_openmpi_ilp64.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a /opt/FFTW/fftw-3.1.3/.libs/libfftw3.a -lguide -lpthread
OBJECTS_ARCHITECTURE = machine_intel.o
The compilation was fine
I produced the binary cp2k.popt
Then I went to the tests directory
and I use the script
#!/bin/sh
###########################################################
#PBS -N TEST
#PBS -l walltime=100:00:00
#PBS -l nodes=1:ppn=1:node0
############################################################
cd ${PBS_O_WORKDIR}
/opt/ompi_ifort10/bin/mpirun -np 1 -npernode 1 -x OMP_NUM_THREADS=1 ~/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt 3H2O-ep.inp > out
exit 0
############################################################
~
~
But I got the following error
[shizuwo:27227] *** Process received signal ***
[shizuwo:27227] Signal: Segmentation fault (11)
[shizuwo:27227] Signal code: Address not mapped (1)
[shizuwo:27227] Failing at address: 0x100
[shizuwo:27227] [ 0] /lib64/tls/libpthread.so.0 [0x2a957bd650]
[shizuwo:27227] [ 1] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(cp_blacs_env_mp_cp_blacs_env_create_+0x37f) [0xe0325d]
[shizuwo:27227] [ 2] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(qs_environment_types_mp_qs_env_create_+0x3bc) [0x849c2c]
[shizuwo:27227] [ 3] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(qs_main_mp_quickstep_create_force_env_+0x7d) [0x8e1ec9]
[shizuwo:27227] [ 4] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(f77_interface_mp_create_force_env_+0x1431) [0x4c2ce3]
[shizuwo:27227] [ 5] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(ep_methods_mp_ep_env_init_low_+0x66a) [0x13fa502]
[shizuwo:27227] [ 6] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(cp_ep_init_+0x8) [0xf35cbc]
[shizuwo:27227] [ 7] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(ep_types_mp_ep_env_create_+0x21b) [0xf0b783]
[shizuwo:27227] [ 8] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(force_env_methods_mp_ep_create_force_env_+0x46) [0x511210]
[shizuwo:27227] [ 9] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(f77_interface_mp_create_force_env_+0x1532) [0x4c2de4]
[shizuwo:27227] [10] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(cp2k_runs_mp_cp2k_run_+0x1498) [0x48dc5c]
[shizuwo:27227] [11] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(cp2k_runs_mp_run_input_+0x10a) [0x48c762]
[shizuwo:27227] [12] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(MAIN__+0xda5) [0x48b7c5]
[shizuwo:27227] [13] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(main+0x2a) [0x48aa12]
[shizuwo:27227] [14] /lib64/tls/libc.so.6(__libc_start_main+0xea) [0x2a96d91aaa]
[shizuwo:27227] [15] /home/robechan/cp2k_new2/cp2k/exe/TEST_64_2_ifort10_mkl10/cp2k.popt(for_write_seq_fmt_xmit+0x42) [0x48a94a]
[shizuwo:27227] *** End of error message ***
mpirun noticed that job rank 0 with PID 27227 on node shizuwo exited on signal 11 (Segmentation fault).
~
and the following output in the file out
----------------------------------------------------------------------------------------------------------------
@shizuwo has created process number 0 27227
**** **** ****** ** PROGRAM STARTED AT Wed Oct 22 15:24:26 2008
***** ** *** *** ** PROGRAM STARTED ON shizuwo
** **** ****** PROGRAM STARTED BY
***** ** ** ** ** PROGRAM PROCESS ID 27227
**** ** ******* ** PROGRAM STARTED IN /home/robechan/cp2k_new2/cp2k/tests/E
P
CP2K| version string: CP2K version 2.0.0 (Development Version)
CP2K| is freely available from http://cp2k.berlios.de/
CP2K| Program compiled at Wed Oct 22 15:11:53 JST 2008
CP2K| Program compiled on shizuwo
CP2K| Program compiled for TEST_64_2_ifort10_mkl10
CP2K| Last CVS entry xc_xwpbe.F/1.12/Tue Aug 26 23:46:48 2008
CP2K| Input file name 3H2O-ep.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name BASIS_SET
GLOBAL| Potential file name POTENTIAL
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name __STD_INPUT__
GLOBAL| Method name CP2K
GLOBAL| Project name H2O
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Run type MD
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level 1
GLOBAL| Total number of message passing processes 1
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
15:24:26 NOTE in ep_methods:ep_env_init_low ep_methods:ep_env_init_low
creating main_qs_env
-------------------------------------------------------------------------------
The segmentation occurs because the programs is probably looking for something and does not find it any idea ?
Thanks
Roberto
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