Cp2k compiled but some test files fail

Samuel Lamphier samuell... at gmail.com
Fri Sep 27 20:52:29 CEST 2013


Hello,
I have compiled cp2k-2.4 on Centos OS 6, this is a custom built system. We 
installed http://software.intel.com/en-us/intel-cluster-studio-xe. Our ARCH 
file is below, no errors compiling. When running the test files in the QS 
folder, we received the error segmentation fault. We used gdb to help find 
the error (below). Could someone please help us fix this?

INTEL_MKL = ~/Shared/intel/mkl
INTEL_INC = 
/home/cormackgroup/Shared/intel/composer_xe_2013_sp1.0.080/mkl/interfaces/fftw3xf
INTEL_LIB = $(INTEL_MKL)/lib/intel64/

CC       = mpicc 
CPP      = cpp 
FC       = mpiifort -FR  
LD       = mpiifort -mkl 
AR       = ar -r
DFLAGS   = -D__INTEL -D__FFTMKL -D__FFTW3 -D__parallel -D__BLACS 
-D__SCALAPACK
CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
FCFLAGS  = $(DFLAGS) -I$(INTEL_INC) -FR -O2 -xhost -heap-arrays -fpp -free 
-g #-check bounds -fp-stack-check -check arg_temp_created
FCFLAGS2 = $(DFLAGS) -I$(INTEL_INC) -FR -O1 -xhost -heap-arrays -fpp -free 
-g #-check bounds -fp-stack-check -check arg_temp_created
LDFLAGS  = $(FCFLAGS) -I$(INTEL_INC)
LIBS     
=-L/home/cormackgroup/Shared/intel/composer_xe_2013_sp1.0.080/mkl/interfaces/fftw3xf 
-lfftw3 #/home/cormackgroup/Archive/scalapack-2.0.2/libscalapack.a \
          
  

#/home/cormackgroup/Archive/scalapack-2.0.2/libscalapack.a
# home/cormackgroup/Shared/intel/mkl/lib/intel64/libmkl_scalapack_lp64.a   
       -mkl
#/home/cormackgroup/Shared/intel/mkl/lib/intel64/libmkl_blacs_lp64.a 

OBJECTS_ARCHITECTURE = machine_intel.o


graphcon.o: graphcon.F
$(FC) -c $(FCFLAGS2) $<
 




Reported Error: The matrix is empty?


Program received signal SIGSEGV, Segmentation fault.
0x000000000240bc2f in DBCSR_INDEX_OPERATIONS::transpose_index_local 
(new_col_p=..., new_row_i=..., old_row_p=Cannot access memory at address 0x1
) at 
/home/cormackgroup/Simulation.01/cp2k-2.4.0/makefiles/../src/dbcsr_lib/dbcsr_index_operations.F:904
904    CALL dbcsr_sort_indices (nblks, new_col_i, new_row_i, new_blk_p)
Missing separate debuginfos, use: debuginfo-install 
glibc-2.12-1.107.el6_4.4.x86_64 libgcc-4.4.7-3.el6.x86_64
(gdb) quit
A debugging session is active.

Inferior 1 [process 5513] will be killed.

Quit anyway? (y or n) y   
[cormackgroup at n01ib0 QS]$ ./cp2k.popt -i C.inp -o C1.out
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source 
            
cp2k.popt          00000000026E5579  Unknown               Unknown  Unknown
cp2k.popt          00000000026E3EF0  Unknown               Unknown  Unknown
cp2k.popt          0000000002674A42  Unknown               Unknown  Unknown
cp2k.popt          0000000002625133  Unknown               Unknown  Unknown
cp2k.popt          000000000262936B  Unknown               Unknown  Unknown
libpthread.so.0    0000003B8DA0F500  Unknown               Unknown  Unknown
cp2k.popt          000000000240BC2F  Unknown               Unknown  Unknown
cp2k.popt          00000000024CB483  Unknown               Unknown  Unknown
cp2k.popt          000000000249210B  Unknown               Unknown  Unknown
cp2k.popt          000000000248F240  Unknown               Unknown  Unknown
cp2k.popt          00000000004170A2  Unknown               Unknown  Unknown
cp2k.popt          0000000001369991  Unknown               Unknown  Unknown
cp2k.popt          00000000009EAB09  Unknown               Unknown  Unknown
cp2k.popt          0000000001D2E498  Unknown               Unknown  Unknown
cp2k.popt          0000000000AD25FD  Unknown               Unknown  Unknown
cp2k.popt          0000000000ACED47  Unknown               Unknown  Unknown
cp2k.popt          000000000090545C  Unknown               Unknown  Unknown
cp2k.popt          0000000000922EF0  Unknown               Unknown  Unknown
cp2k.popt          000000000054BDF1  Unknown               Unknown  Unknown
cp2k.popt          000000000040DDFD  Unknown               Unknown  Unknown
cp2k.popt          000000000040B9DD  Unknown               Unknown  Unknown
cp2k.popt          0000000000406FF2  Unknown               Unknown  Unknown
cp2k.popt          00000000004060D6  Unknown               Unknown  Unknown
libc.so.6          0000003B8D21ECDD  Unknown               Unknown  Unknown
cp2k.popt          0000000000405FC9  Unknown               Unknown  Unknown
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