compiling with HP MPI & Open MPI

C. Va'rnai cv... at cam.ac.uk
Mon Jul 7 16:04:34 CEST 2008


Dear All,

I am trying to compile CP2K on a supercomputer, and this is my first 
experience with supercomputers, I have used clusters so far. 
(http://www.rz.uni-karlsruhe.de/ssck/hpxc)

The default mpif90 compiler is HP MPI. When I compile CP2K with HP MPI, 
after a nice compilation without error message (I know, it doesn't mean 
that it should run fine), it gives segmentation fault. I don't really know 
much about HP MPI, and after fiddling around with the compiler options, I 
decided to use Open MPI I use on a cluster machine with the same 
Linux-x86-64-intel architecture. Running CP2K in interactive mode was 
successful. However, I couldn't get CP2K run properly using the batch 
system. For the command

job_submit -t 10 -T 60 -m 500 -p 4/1 -c d 
"/home/ssck/wkhu00f/wkhu23e/openmpi/bin/mpirun -np 4 cp2k.popt H2O.inp"

I got the following error message:
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT
cannot allocate memory for thread-local data: ABORT

When I decreased the requested memory from 500 to 300 MegaBytes, running

job_submit -t 10 -T 60 -m 300 -p 4/1 -c d 
"/home/ssck/wkhu00f/wkhu23e/openmpi/bin/mpirun -np 4 cp2k.popt H2O.inp"

it got stuck when opening the BASIS_MOLOPT file:

 GENERATE| Preliminary Number of Bonds generated: 0
 GENERATE|  Achieved consistency in connectivity generation.
 GENERATE| Number of Bonds generated: 0
 GENERATE| Preliminary Number of Bends generated: 0
 GENERATE| Number of Bends generated: 0
 GENERATE| Number of UB generated: 0
 GENERATE| Preliminary Number of Torsions generated: 0
 GENERATE| Number of Torsions generated: 0
 GENERATE| Number of Impropers generated: 0
 GENERATE| Number of 1-4 interactions generated: 0
 CP2K: An error occurred opening the file <BASIS_MOLOPT> with the unit 
number
    1 (IOSTAT =     41)

I would be glad if you had any idea what is wrong with the HP MPI 
compilation or what I am doing wrong with the OPen MPI compiled version. 
Thanks,

Csilla

The test file is the H2O.inp in the tests/QS/ directory.
Here is my arch file for the Open MPI run:

INTEL_INC=/opt/intel/mkl/10.0.011/include
INTEL_LIB=/opt/intel/mkl/10.0.011/lib/em64t

FFTW3_INC=/software/all/fftw/include
FFTW3_LIB=/software/all/fftw/lib

ACML_INC=/software/all/acml/acml4.0/ifort64_mp/include
ACML_LIB=/software/all/acml/acml4.0/ifort64_mp/lib

CC = icc CPP = FC = mpif90 LD = mpif90 AR = ar -r DFLAGS = -D__INTEL 
-D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -D__FFTW3 -D__FFTACML 
CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC) #-I$(FFTW3_INC) 
-I$(ACML_INC) FCFLAGS = $(DFLAGS) -I$(INTEL_INC) -I$(FFTW3_INC) 
-I$(ACML_INC) -O0 -openmp -xW -heap-arrays 64 -fpp -free LDFLAGS = 
$(FCFLAGS) LIBS = -L$(INTEL_LIB) -L$(FFTW3_LIB) -L$(ACML_LIB) 
-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_intel_lp64 
-lmkl_sequential -lmkl_core -lfftw3 -lacml_mp -lpthread 
#$(ACML_LIB)/libacml_mp.a

OBJECTS_ARCHITECTURE = machine_intel.o

The one for HP MPI differs only in linking -lmkl_blacs_lp64 instead of the 
openmpi version.




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