[molpro-user] {SPAM}? Fwd: 0:Segmentation Violation error, status=: 11

Wed Dec 9 16:29:57 GMT 2009

G.Bradshaw wrote:
> 
> Begin forwarded message:
> 
> From: G.Bradshaw <gb275 at openmail.open.ac.uk<mailto:gb275 at openmail.open.ac.uk>>
> Date: 3 December 2009 15:01:14 GMT
> To: "molpro-user at molpro.net<mailto:molpro-user at molpro.net>" <molpro-user at molpro.net<mailto:molpro-user at molpro.net>>
> Subject: 0:Segmentation Violation error, status=: 11
> 
> 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 <http://naraku.open.ac.uk> 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<http://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
> 
> 

I'm not sure how much this will help you, but as a point of information, 
we are successfully using the binary version of 2009.1 (for serial and 
parallel calcs) on RHEL 5.4 on both Opteron and Xeon processors.

(I could compile from source, but not successfully run, 2009.1 using 
ifort, gcc, and ga-4.2.)

Peter Ruprecht
University of Colorado