The ABINIT Users Mailing List ( CLOSED )

[hyello25@gmail.com]

Dear Abinit users:
    When I do SCF calculations for supercell BZO/BTO, if ecut<=160Ha,it is 
OK. However, when I use ecut>=170Ha, it gives a error message like this: 
      ITER STEP NUMBER     1
 vtorho : nnsclo_now=  2, note that nnsclo,dbl_nnsclo,istep=  0 0  1
-P-0000  leave_test : synchronization done...
 vtorho: loop on k-points and spins done in parallel
    /opt/mpich/bin/mpirun.ch_shmem: line 91: 16625 Segmentation fault      
/opt/etsf/abinit/5.4/bin/abinip

    I test different pps, Teter-extended-norm-conserving and HGH, for both 
two, this problem appears. Then I use different K-point mesh, this problem 
appears too.

    Also, When I do optimization of cell geometry(optcell=1) for cubic 
ferromagnetic LaMnO3 with HGH pps, when ecut >= 130Ha, this problem emerge 
again! And the erroe message gives:
 ETOT  1  -158.14103404663    -1.58E+02 1.01E+00 1.91E+06 0.0E+00 0.00E+00 
0.318
 scprqt: <Vxc>= -4.2423491E-01 hartree
/opt/mpich/bin/mpirun.ch_shmem: line 91:  3691 Segmentation fault      
/opt/etsf/abinit/5.4/bin/abinip

    I do the calculation  using the version of abinit 5.4.4, operated on 
RHEL4.
    I don't know what is wrong with it and what does "Segmentation fault" 
mean.....
    Can you give me a hand?
PS: the file /opt/mpich/bin/mpirun.ch_shmem is given below and I mark the 
line 91. Also I give the input file of BZO/BTO supercell and LaMnO3.
          Best Regards,
                                                  Chen Zhu
                                                 Jan. 07. 2008

-----------------------------------------------------------------------------------------
The file /opt/mpich/bin/mpirun.ch_shmem:

#! /bin/sh
exitstatus=1
if [ "$argsset" = "" ] ; then
   . $MPIRUN_HOME/mpirun.args
   argsset=1
fi
# ch_shmem device
#
# Pass to mpirun that this is a shared memory device.  Since there
# may be several, try using the default value.
# This may not be what we want....
MPIRUN_DEVICE=$default_device
export MPIRUN_DEVICE
#
#
# Handle debuggers
#
#startpgm="eval"
MPICH_NP=$np
export MPICH_NP
# If MPICH_NP doesn't work, use -np $np
startpgm="$progname $cmdLineArgs"

if [ "$debugger" != "" ] ; then
    if [ "$debugger" = "totalview" ] ; then
        if [ "$TOTALVIEW" = "" ] ; then
           TOTALVIEW="totalview"
        fi
        # We need to put -mpichtv into an environment variable
        startpgm="$TOTALVIEW $progname -a $cmdLineArgs -mpichtv"
    else
        # There should be a way to specify a debugger startup method, for
        # special vendor-specific debuggers (like SGI's cvd) etc.
        # gdb or dbx-like debuggers
        dbgfile=$PWD_TRIAL/PId$$
        echo "Test" > $dbgfile
        if [ -s $dbgfile ] ; then
            /bin/rm -f $dbgfile
        else
            dbgfile=$HOME/PId$$
        fi
        # If gdb has an equivalent, the documentation is well hidden.
        #  - .gdbinit - and the documentation IS well hidden.  Fortunately,
        # the .gbdinit file is read; gdb provides the -nx (instead of -x)
        # command if you don't want to read the default init file.
        if [ "$debugger" = "dbx" -a -r $HOME/.dbxinit ] ; then
            cat $HOME/.dbxinit > $dbgfile
        fi
        # Regretably, xxgdb does NOT provide this argument (even though it
        # claims to).
    #    if [ "$debugger" = "xxgdb" -a -r $HOME/.gdbinit ] ; then
    #   cat $HOME/.gdbini > $dbgfile
    #    fi
        # handle USR1 pass for gdb; add an initial break
        if [ "$debugger" = "gdb" -o "$debugger" = "xxgdb" -o \
             "$debugger" = "ddd" ] ; then
            echo "handle SIGUSR1 nostop pass" >> $dbgfile
            echo "br MPI_Init" >> $dbgfile
            #echo "set args $cmdLineArgs -np $np" >> $dbgfile
            echo "set args $cmdLineArgs" >> $dbgfile
            echo "run" >> $dbgfile
        else
            echo "ignore USR1" >> $dbgfile
            # This may not work, depending on when the symbol table is read.
            # An alternative is to use the startup file to load the
            # program with "debug $progname" ,followed with this, followed
            # with run command args.
            echo "debug $progname" >> $dbgfile
            echo "stop in MPI_Init" >> $dbgfile
#           echo "run $cmdLineArgs -np $np" >> $dbgfile
            echo "run $cmdLineArgs" >> $dbgfile
        fi
    #   cat >> $dbgfile <<.
    ## Use this command to start your programm:
    #run  $cmdLineArgs -p4pg $p4pgfile
    #.
            commandfile=`echo $commandfile | sed -e s@%f@$dbgfile@g`
            startpgm="$debugger $commandfile $progname"
    fi
fi

#
# Build a suitable command for the whole thing
#
if [ $just_testing = 1 ] ; then
  doitall="echo"
else
  doitall="eval"
fi
#
$doitall $startpgm           #### line 91#####
exitstatus=$?
exit $exitstatus
-------------------------------------------------------------
The input file for BZO/BTO(with Teter-extended-noem-conserving pps given on 
abinit.org website):

iscf 5
toldfe  1.0d-10

#Definition of the k-point grids
kptopt  1
nshiftk  1
shiftk  0.5  0.5  0.5
ngkpt  6 6 3


#Definition of the unit cell
acell  7.6881721615E+00  7.6881721615E+00  1.5229661071E+01
rprim  1.0  0.0  0.0
       0.0  1.0  0.0
       0.0  0.0  1.0

#atoms types
ntypat  4
znucl  56  40  22  8
natom   10
typat  1  1  2  3  4  4  4  4  4  4
xred    0.0000000000E+00  0.0000000000E+00 -9.4442195375E-03
        0.0000000000E+00  0.0000000000E+00  5.1272810994E-01
        5.0000000000E-01  5.0000000000E-01  2.5165554212E-01
        5.0000000000E-01  5.0000000000E-01  7.5161181164E-01
        5.0000000000E-01  5.0000000000E-01 -1.1128669085E-02
        5.0000000000E-01  0.0000000000E+00  2.5093260203E-01
        0.0000000000E+00  5.0000000000E-01  2.5093260203E-01
        5.0000000000E-01  5.0000000000E-01  5.1361827983E-01
        5.0000000000E-01  0.0000000000E+00  7.5124697051E-01
        0.0000000000E+00  5.0000000000E-01  7.5124697051E-01

ecut 170
ixc   3
nband  48
nstep  200
diemac  12.0

--------------------------------------------------------------
The input file for LaMnO3(with HGH pps given on abinit.org website):

toldfe  1.0d-10
kptopt 1
nshiftk 1
shiftk  0.5  0.5  0.5

#Definition of the unit cell
acell 3*3.880  angstrom     
rprim  1  0  0  
       0  1  0
       0  0  1

#Definition of the atom types
ntypat 3         
znucl 57 8 25
          
occopt 7
tsmear 0.005

#Definition of the atoms
natom 5           
typat 1 2 2 2 3         
xred               
   0.0  0.0  0.0  
   1/2  1/2  0.0  
   1/2  0.0  1/2
   0.0  1/2  1/2
   1/2  1/2  1/2

#Definition of the planewave basis set
ecut 120

nspinor 1
nsppol 2
nspden 2
spinat 0.0 0.0 0.0
       0.0 0.0 0.0
       0.0 0.0 0.0
       0.0 0.0 0.0
       0.0 0.0 4.0

ixc  1
nband 53
#Definition of the SCF procedure
nstep 100          
diemac 1.0d6       


!---------------------------!

G.R. Qian
Physics Dept. NJU CN
!---------------------------!