[molpro-user] 0:Segmentation Violation error, status=: 11

Thu Dec 3 16:41:29 GMT 2009

At least for the binary case, your job below probably does not run since starting with 2009.1 one can't
have the angstrom unit inside the geometry block.  Try:

molpro <<!
basis=vdz
angstrom
geometry={h1;h2,h1,0.74}
hf
!

-Kirk

On Dec 3, 2009, at 7:01 AM, G.Bradshaw wrote:

> Hi
> 
> I have spent many hours trying to get this software to run on our system
> Redhat 5.4
> Intel(R) Xeon(R) CPU           E5420  @ 2.50GHz
> 64Gb memory
> Intel cluster tools compiler 11.1
> ga-4-2 (compiled with intel compilers)
> 
> source = molpro.2009.1.tar
> binary = molpro-mpp-2009-1.1-20.Linux_x86_64.sh
> 
> the binary files when run with
> 
> 
> molpro <<!
>        basis=vdz;
>        geometry={angstrom;h1;h2,h1,.74}
>        hf
>        !
> 
> gives
> 
> 0:Segmentation Violation error, status=: 11
> (rank:0 hostname:naraku.open.ac.uk pid:798):ARMCI DASSERT fail. signaltrap.c:SigSegvHandler():301 cond:0
> Last System Error Message from Task 0:: Inappropriate ioctl for device
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
> 
> a recompile of the source code with the following config
> 
> Molpro CONFIG
> 
> # MOLPRO CONFIG generated at Thu Dec  3 14:34:59 GMT 2009, for host naraku.open.ac.uk<http://naraku.open.ac.uk>
> 
> CONFIGURE_OPTIONS="-mpp" "-mppbase" "/data/ga-4-2"
> 
> AR=ar
> ARCHNAME=Linux/x86_64
> ARFLAGS=-rS
> AWK=awk
> BIBTEX=/usr/bin/bibtex
> BLASLIB=-L/opt/intel/mkl/10.2.0.013/lib/em64t -lmkl_intel_ilp64 -lmkl_sequential -lmk
> l_core
> BUILD=p
> CAT=cat
> CC=/opt/intel/Compiler/11.1/038/bin/intel64/icc
> CCVERSION=11.1
> CC_FRONT=
> CDEBUG=-g
> CDEFINE=-D
> CFLAGS=-ftz -fPIC -vec-report0 -DMOLPROC_PAR -DINT64 -DZLIB
> CLEARSPEEDLIB=
> CMPPINCLUDE=/data/ga-4-2/include
> COPT=-O2
> COPT0=-O0
> COPT1=-O1
> COPT2=-O2
> COPT3=-O3
> CP=cp -p
> CPROFILE=-p
> CSCN=cscn
> CSFLAGS=-O3 -I. --dynamic
> C_OPT0=
> C_OPT1=
> C_OPT2=
> C_OPT3=
> DOXYGEN=/usr/bin/doxygen
> ECHO=echo
> EXPORT=export
> F90FLAGS=
> FC=/opt/intel/Compiler/11.1/038/bin/intel64/ifort
> FCVERSION=11.1
> FDEBUG=-g
> FDEFINE=-D
> FFLAGS=-i8 -r8 -pc64 -fPIC -auto -Vaxlib -vec-report0
> FOPT=-O3
> FOPT0=-O0
> FOPT1=-O1
> FOPT2=-O2
> FOPT3=-O3
> FPP=-fpp
> FPROFILE=-p
> FSTATIC=
> FTCFLAGS=molpro unix unix-i8 Linux lapack ga sf eaf mpi-io mpp blas1 blas2 blas3
> F_OPT0=
> F_OPT1=nevpt2_optrpc.f explicit_util.f artwo2.f drv2el_l3ext_lmp2g.f drv2el_l3ext_cen.f
> F_OPT2=integrals.f90 RL4gen1.f basis_integral_shells.f
> F_OPT3=
> GROUPPOS=4
> HDF5=
> HOSTFILE_FORMAT=%N
> INSTBIN=/usr/local/bin
> INSTHTML=/root/public_html/molpro/molpro2009.1
> INSTLIB=/usr/local/lib/molprop_2009_1_Linux_x86_64_i8
> INTEGER=8
> LAPACKLIB=
> LATEX2HTML=
> LAUNCHER=/opt/intel/impi/3.2.1.009/bin64/mpiexec -n %n %x
> LD_ENV=/opt/intel/Compiler/11.1/038/lib/intel64:/opt/intel/mkl/10.2.0.013/lib/em64t
> LD_ENVNAME=LD_LIBRARY_PATH
> LIBRARY_SUFFIX=a
> LIBS=-lstdc++ -lz
> LIBS_FRONT=
> LINKOPT=
> LINKOPT_FRONT=
> LN=ln -s
> LSFULL=ls -l
> MACROS=MOLPRO MOLPRO_ifort GA_TOOLS GA_TCGMSG_MPI _I8_ LAPACK_INT=8 _MOLCAS_MPP_
> MAKEDEPEND_OPTIONS=
> MAKEINDEX=/usr/bin/makeindex
> MAPLE=
> MKDIR=mkdir -p
> MODULE_FLAG=-I
> MODULE_SUFFIX=mod
> MOLPRO_CACHE=
> MOLPRO_FLOPDGM=
> MOLPRO_FLOPDGV=
> MOLPRO_FLOPMXM=
> MOLPRO_FLOPMXV=
> MOLPRO_MINDGC=
> MOLPRO_MINDGL=
> MOLPRO_MINDGM=
> MOLPRO_MINDGR=
> MOLPRO_MINDGV=
> MOLPRO_MXMBLK=
> MOLPRO_MXMBLN=
> MOLPRO_SHAREDLIB=1
> MOLPRO_UNROLL=
> MPILIB=-I/opt/intel/impi/3.2.1.009/include64 -I/opt/intel/impi/3.2.1.009/include64 -L/opt/inte
> l/impi/3.2.1.009/lib64 -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker $libdir -Xlinker -
> rpath -Xlinker /opt/intel/mpi-rt/3.2.1 -lmpi -lmpiif -lmpigi -lrt -lpthread -ldl
> MPPLIB=-L/data/ga-4-2/lib/LINUX64 -ltcgmsg-mpi -lglobal -lma -lpario -larmci
> OBJECT_SUFFIX=o
> OWNERPOS=3
> PAPER=a4paper
> PARSE=parse-Linux-x86_64-i8.o
> PATCHER=patcher.exe
> PDFLATEX=/usr/bin/pdflatex -halt-on-error
> PNAME=molprop_2009_1_Linux_x86_64_i8
> PTSIZE=11
> RANLIB=ranlib
> RM=rm -rf
> SHAREDLIBFLAGS=-shared --whole-archive ../lib/libmolpro.a --no-whole-archive -rpath-link . -L/
> opt/intel/Compiler/11.1/038/lib/intel64 -lsvml
> SHAREDLIBSUFFIX=so
> SHELL=/bin/sh
> STRIP=strip
> TAR=tar -cf
> UNTAR=tar -xf
> VERSION=2009.1
> XSD=/usr/bin/xmllint --noout --schema
> XSLT=/usr/bin/xsltproc
> YACC=bison -b y
> 
> .SUFFIXES:
> MAKEFLAGS+=-r
> 
> running make runs fine but make test gives the following errors again
> 
> make[1]: Entering directory `/data/molpro/src/molpro2009.1/testjobs'
> Running job Cs_DKH10.test
> 0:Segmentation Violation error, status=: 11
> (rank:0 hostname:naraku.open.ac.uk pid:24518):ARMCI DASSERT fail. signaltrap.c:SigSegvHandler():301 cond:0
> rank 0 in job 38  naraku.open.ac.uk_37166   caused collective abort of all ranks
>  exit status of rank 0: return code 0
> **** PROBLEMS WITH JOB Cs_DKH10.test
> **** For further information, look in the output file
> **** /data/molpro/src/molpro2009.1/testjobs/Cs_DKH10.errout
> 
> for every job and the log file Cs_DKH10.errout is a 0 length file
> i have compiled it in all sort of different ways but i am still getting the same result
> 
> any help would be appreciated  or anyone who has a working version for RedHat 5.4
> i have multipul versions of mpi including mpich1, 2 and openmpi each compiled with intel and gcc compilers
> in different areas   as well as intel mpi
> 
> 
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