[CP2K:4644] Cp2k compiled but some test files fail

Iain Bethune ibet... at epcc.ed.ac.uk
Fri Sep 27 21:58:10 CEST 2013


Hi Samuel. We have also just upgraded to the intel 14.0 compiler in compeer ex 2013 sp 1 and saw the same problem for various test cases. I've reported a bug to Intel and am currently waiting for them to investigate.  For now it's better to use the 13.1 compiler!

- Iain 

Sent from my iPad

On 27 Sep 2013, at 19:52, Samuel Lamphier <samuell... at gmail.com> wrote:

> 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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