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

Thu Dec 10 14:16:39 GMT 2009

After following this up it was in fact an issue with the license token.
The license token must not be split over several lines, but appear on
one single line.

Best wishes,

Andy

On 09/12/09 19:14, Andy May wrote:
> 
> This looks like a problem with the MPI launcher. If you run, for instance:
> 
> ./molpro -v test.mol
> 
> it should show you the command it is attempting to run. Looking at your
> CONFIG file, it will probably be something like:
> 
> /opt/intel/impi/3.2.1.009/bin64/mpiexec -n 1 /path/to/molpro.exe
> 
> The first thing to try is that the Global Arrays testjob runs with this
> command, i.e.:
> 
> /opt/intel/impi/3.2.1.009/bin64/mpiexec -n 1
> /data/ga-4-2/global/testing/test.x
> 
> If the above job does not run successfully then you must fix either the
> GA installation or the options to mpiexec which are needed.
> 
> Best wishes,
> 
> Andy
> 
> On 08/12/09 21:57, 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
>>
>>
>> ________________________________
>>
>> The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England & Wales and a charity registered in Scotland (SC 038302).
>> _______________________________________________
>> Molpro-user mailing list
>> Molpro-user at molpro.net
>> http://www.molpro.net/mailman/listinfo/molpro-user