Hi everyone:
My name is Yunkun Xie and I´m a Ph.D. student at the University of
Virginia. I tried to compile parallel version of Siesta on our school's
linux server. The system I´m working on is a Intel Xeon cluster with MPICH2
and intel compiler. I have compiled Siesta 1.3f1p using
mpich2-eth-intel/1.3. There was no error in compiling. However, when I
tried to run the example calculation for Fe and MgO, on one processor it
worked fine but when I tried to run it on several processors I got
segmentation fault errors. Then I recompiled Smeagol with -CB(So that I can
have more information about the error) and run again. It gave me messages
like this: forrtl: severe (408): fort: (2): Subscript #1 of the array
INDXUO has value 16 which is greater than the upper bound of 15 (Different
numbers for different systems, basis size etc.) Is this a problem you
recognize and know how to solve?
I've attached the output of Siesta and also the arch.make file. Hope
they can help you find out where goes wrong.
P.S: I installed the old version because I want to install Smeagol. I
also tried the newest version of Siesta but the error still exists.
Output:
* ......*
* ......*
* **siesta: Atomic coordinates (Bohr) and species*
*siesta: 0.00000 0.00000 0.00000 1 1*
*
*
*initatomlists: Number of atoms, orbitals, and projectors: 1 15
16*
*
*
** ProcessorY, Blocksize: 1 8*
*
*
*
*
*siesta: System type = bulk*
*
*
*siesta: k-grid: Number of k-points = 1183*
*siesta: k-grid: Cutoff = 16.156 Ang*
*siesta: k-grid: Supercell and displacements*
*siesta: k-grid: 13 0 0 0.000*
*siesta: k-grid: 0 13 0 0.000*
*siesta: k-grid: 0 0 13 0.000*
*
*
*superc: Internal auxiliary supercell: 7 x 7 x 7 = 343*
*superc: Number of atoms, orbitals, and projectors: 343 5145 5488*
*
*
** Maximum dynamic memory allocated = 2 MB*
*
*
*siesta: ==============================*
* Begin CG move = 0*
* ==============================*
*
*
*outcoor: Atomic coordinates (fractional):*
* 0.00000000 0.00000000 0.00000000 1 Fe 1*
*
*
*superc: Internal auxiliary supercell: 7 x 7 x 7 = 343*
*superc: Number of atoms, orbitals, and projectors: 343 5145 5488*
*
*
*InitMesh: MESH = 16 x 16 x 16 = 4096*
*InitMesh: Mesh cutoff (required, used) = 150.000 171.794 Ry*
*forrtl: severe (408): fort: (2): Subscript #1 of the array INDXUO has
value 16 which is greater than the upper bound of 15*
*
*
*Image PC Routine Line Source
*
*libintlc.so.5 00002B551014CF7A Unknown Unknown Unknown
*
*libintlc.so.5 00002B551014BAF5 Unknown Unknown Unknown
*
*libifcore.so.5 00002B550F5271F2 Unknown Unknown Unknown
*
*libifcore.so.5 00002B550F49C5FB Unknown Unknown Unknown
*
*libifcore.so.5 00002B550F49CA87 Unknown Unknown Unknown
*
*siesta 000000000085152F Unknown Unknown Unknown
*
*siesta 0000000000637009 Unknown Unknown Unknown
*
*siesta 0000000000A37F51 Unknown Unknown Unknown
*
*siesta 000000000040B1EC Unknown Unknown Unknown
*
*libc.so.6 000000333781D994 Unknown Unknown Unknown
*
*siesta 000000000040B0F9 Unknown Unknown Unknown
*
*[[email protected]] ONE OF THE PROCESSES TERMINATED BADLY:
CLEANING UP*
*APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)*
*-bash-3.2$*
arch.make:
SIESTA_ARCH=x86_64
#
FC=mpif90
FC_ASIS=$(FC)
FFLAGS=-g -O0 -CB
LDFLAGS=
COMP_LIBS=dc_lapack.a
SOURCE_DIR=/home/yx3ga/DFT/siesta-1.3f1_test/siesta-1.3f1
EXEC = siesta
#NETCDF_LIBS=/usr/local/netcdf-3.5/lib/pgi/libnetcdf.a
#NETCDF_INTERFACE=libnetcdf_f90.a
#DEFS_CDF=-DCDF
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.
DEFS_MPI=-DMPI
HOME_LIB=/share/apps
BLAS_LIBS=-lblas
LAPACK_LIBS=-llapack
BLACS_LIBS=$(HOME_LIB)/blacsmpi/blacsmpi-1.2/intel/lib/libblacs.a
/share/apps/blacsmpi/blacsmpi-1.2/intel/lib/libblacsCinit.a
/share/apps/blacsmpi/blacsmpi-1.2/intel/lib/libblacsF77init.a
$(HOME_LIB)/blacsmpi/blacsmpi-1.2/intel/lib/libblacs.a
SCALAPACK_LIBS=/share/apps/scalapack/scalapack-1.8.0/intel/lib/libscalapack.a
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
$(NETCDF_LIBS)
RANLIB=echo
SYS=bsd
DEFS= $(DEFS_CDF) $(DEFS_MPI)
#
.F.o:
$(FC) -c $(FFLAGS) $(DEFS) $<
.f.o:
$(FC) -c $(FFLAGS) $<
.F90.o:
$(FC) -c $(FFLAGS) $(DEFS) $<
.f90.o:
$(FC) -c $(FFLAGS) $<
Sincerely,
-Yunkun
