[molpro-user] SVD failing on cray xc40 (UNCLASSIFIED)
Andy May
MayAJ1 at cardiff.ac.uk
Tue Apr 14 16:05:18 BST 2015
James,
I just tried on swan.cray.com and found that there are error messages
during configure.
The reason is that the -v option to ifort, on swan.cray.com at least,
gives output with lots of extra garbage that meant configure didn't
parse it correctly. If that happened on your system it will mean that
configure didn't determine the ifort version correctly, so some files
that should have been deoptimized were not.
I've made a commit to fix it, at least for that system, but the process
of parsing that output is not robust so it could break again. In our
master version we've changed to using the compiler CPP predefined macros
to determine the version, so this problem will disappear one day. If you
wait 24 hours then download the 'nightly' tarball it should contain the fix.
I then built with Intel 15.0.1 compilers with:
module swap PrgEnv-cray PrgEnv-intel
cd /lus/scratch/${LOGNAME}
tar -xzf molpro.tar.gz
cd Molpro
./configure -batch -mpp -mppbase ${MPICH_DIR}/include
make
For reference I attach the resulting CONFIG file. I then used the
following job script to run:
#!/bin/sh
#PBS -q large
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -N Molpro
export TMPDIR="/lus/scratch/${LOGNAME}/Molpro/tmp"
wfudir="/lus/scratch/${LOGNAME}/Molpro/wfu"
mkdir ${wfudir} ${TMPDIR}
cd /lus/scratch/${LOGNAME}/Molpro
make -C lib MOLPRO_OPTIONS="-W ${wfudir}" init.log
make -C examples MOLPRO_OPTIONS="-n8 -W ${wfudir}" butane_opt_transition.out
which ran as expected.
Best wishes,
Andy
On 09/02/15 19:21, Ianni, James C CTR (US) wrote:
> Classification: UNCLASSIFIED
> Caveats: NONE
>
> I have Molpro compiled with Intel 15.0.1 compiler with cray-mpich/7.1.0 on a
> Cray XC40. When I run the butane_opt_transition.com example (or any other
> example) molpro on two nodes under PBS, molpro starts up, runs for a little
> bit, then I see SVD errors and molpro errors out. Here's my run line:
> TMPD=a directory on a lustre mount that all nodes can see
> LIBMOL points to ./lib/ that does exists with MOLPRO libs
> molpro -N 16 -n 8 -d ${TMPD} -L ${LIBMOL} ${input} >& molpro.out
>
> Here is the output:
>
> cat butane_opt_transition.out
>
> Primary working directories : /work1/ianni/187
> Secondary working directories : /work1/ianni/187
> Wavefunction directory : /usr/people/ianni/wfu/
> Main file repository : /work1/ianni/187/
>
> SHA1 : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> NAME : 2012.1.20
> ARCHNAME : Linux/XT
> FC : ftn
> FCVERSION : 15.0
> BLASLIB :
> id : xxxxxx
>
> Nodes nprocs
> nid00016 7
> Number of processes for MPI-2 version of Molpro: nprocs(total)= 8
> nprocs(compute)= 7 nprocs(helper)= 1
> ga_uses_ma=false, calling ma_init with nominal heap.
> GA-space will be limited to 8.0 MW (determined by -G option)
>
> Using customized tuning parameters: mindgm=1; mindgv=20; mindgc=4;
> mindgr=1; noblas=0; minvec=7
> default implementation of scratch files=sf
>
> ***, Bicyclo-[1.1.0]-butane Transition State
> memory,1,m
> basis=3-21G
>
> L1=1.495 ang
> ! Define Active Variables
> L2=1.418 ang
> L3=1.463 ang
> L4=1.093 ang
> L5=1.111 ang
> L6=1.098 ang
> L7=1.097 ang
> L8=1.110 ang
> L9=1.106 ang
> A1=92.1 degree
> A2=62.1 degree
> A3=136.0 degree
> A4=123.5 degree
> A5=122.4 degree
> A6=124.7 degree
> A7=126.7 degree
> A8=117.9 degree
> D1=-120.4 degree
> D2=4.4 degree
> D3=108.8 degree
> D4=-107.5 degree
> D5=84.2 degree
> D6=109.3 degree
> D7=-106.1 degree
>
> geometry={C1
> ! Geometry Specification Z-Matrix
> C2 1 L1
> C3 2 L2 1 A1
> C4 1 L3 2 A2 3 D1
> H5 1 L4 2 A3 3 D2
> H6 2 L5 1 A4 4 D3
> H7 3 L6 2 A5 1 D4
> H8 3 L7 2 A6 1 D5
> H9 4 L8 1 A7 2 D6
> H10 4 L9 1 A8 2 D7}
> int
> rhf
> optg
> root,2
> ! Transition State search
> method,qsd
> ! Use Quadratic Steepest Descent Method
>
> Variables initialized (782), CPU time= 0.00 sec
> Commands initialized (547), CPU time= 0.01 sec, 517 directives.
> Default parameters read. Elapsed time= 0.14 sec
>
> Checking input...
> Passed
> 1
>
>
> *** PROGRAM SYSTEM MOLPRO ***
> Copyright, University College Cardiff Consultants
> Limited, 2008
>
> Version 2012.1 linked Feb 9 2015
> 11:53:33
>
>
>
> ****************************************************************************
> ******************************************************
> LABEL *
> Linux-3.0xxxxxx-cray_xxxxx/nid00016(x86_64) 64 bit mpp version
> DATE: 09-Feb-15 TIME: 12:56:10
>
> ****************************************************************************
> ******************************************************
>
> SHA1: xxxxxxxxxxxxxxxxxxxxxxxxxxx
>
> ****************************************************************************
> ******************************************************
>
> Variable memory set to 1000000 words, buffer space 230000 words
>
> SETTING BASIS = 3-21G
> SETTING L1 = 1.49500000 ANG
> SETTING L2 = 1.41800000 ANG
> SETTING L3 = 1.46300000 ANG
> SETTING L4 = 1.09300000 ANG
> SETTING L5 = 1.11100000 ANG
> SETTING L6 = 1.09800000 ANG
> SETTING L7 = 1.09700000 ANG
> SETTING L8 = 1.11000000 ANG
> SETTING L9 = 1.10600000 ANG
> SETTING A1 = 92.10000000 DEGREE
> SETTING A2 = 62.10000000 DEGREE
> SETTING A3 = 136.00000000 DEGREE
> SETTING A4 = 123.50000000 DEGREE
> SETTING A5 = 122.40000000 DEGREE
> SETTING A6 = 124.70000000 DEGREE
> SETTING A7 = 126.70000000 DEGREE
> SETTING A8 = 117.90000000 DEGREE
> SETTING D1 = -120.40000000 DEGREE
> SETTING D2 = 4.40000000 DEGREE
> SETTING D3 = 108.80000000 DEGREE
> SETTING D4 = -107.50000000 DEGREE
> SETTING D5 = 84.20000000 DEGREE
> SETTING D6 = 109.30000000 DEGREE
> SETTING D7 = -106.10000000 DEGREE
>
>
> Using spherical harmonics
>
> Library entry C S 3-21G selected for orbital group 1
> Library entry C P 3-21G selected for orbital group 1
> Library entry H S 3-21G selected for orbital group 2
>
> 1PROGRAM * SEWARD (Integral evaluation for generally contracted gaussian
> basis sets) Author: Roland Lindh, 1990
>
> Geometry written to block 1 of record 700
>
> Orientation using atomic masses
> Molecule type: Asymmetric top
> Rotational constants: 7.8042247 7.0211678 17.5553961 GHz
> (calculated with average atomic masses)
>
> Point group C1
>
>
>
> ATOMIC COORDINATES
>
> NR ATOM CHARGE X Y Z
>
> 1 C1 6.00 -1.640579909 0.342559831 -0.904560907
> 2 C2 6.00 0.824024883 0.863916589 0.374239143
> 3 C3 6.00 0.084380924 -0.486625311 2.567271106
> 4 C4 6.00 0.668647928 -0.555867676 -2.130811827
> 5 H5 1.00 -3.419409756 -0.570397278 -0.386446301
> 6 H6 1.00 1.684650173 2.774997780 0.496440331
> 7 H7 1.00 -0.391230728 0.462658513 4.349949947
> 8 H8 1.00 0.249887640 -2.539815746 2.800655226
> 9 H9 1.00 1.295661019 -2.548968182 -2.316052099
> 10 H10 1.00 1.337443926 0.467435373 -3.826045695
>
> Bond lengths in Bohr (Angstrom)
>
> 1-2 2.825140566 1-3 3.964423717 1-4 2.764669330 1-5 2.065470662 2-3
> 2.679631654
> ( 1.495000000) ( 2.097882678) ( 1.463000000) ( 1.093000000)
> ( 1.418000000)
>
> 2-4 2.883610535 2-6 2.099485732 3-7 2.074919292 3-8 2.073029566 4-9
> 2.097596006
> ( 1.525940975) ( 1.111000000) ( 1.098000000) ( 1.097000000)
> ( 1.110000000)
>
> 4-10 2.090037101
> ( 1.106000000)
>
> Bond angles
>
> 1-2-3 92.10000000 1-2-4 57.92057221 1-2-6 123.50000000 1-3-2
> 45.40967985
>
> 1-3-7 123.84702362 1-3-8 109.90647887 1-4-2 59.97942779 1-4-9
> 126.70000000
>
> 1- 4-10 117.90000000 2- 1- 3 42.49032015 2- 1- 4 62.10000000 2-
> 1- 5 136.00000000
>
> 2- 3- 7 122.40000000 2- 3- 8 124.70000000 2- 4- 9 121.90052635 2-
> 4-10 116.50736785
>
> 3-1-4 87.53730416 3-1-5 93.58906654 3-2-4 116.61172912 3-2-6
> 121.62027136
>
> 4- 1- 5 133.39075532 4- 2- 6 121.38803225 7- 3- 8 112.00585093 9-
> 4-10 107.33380036
>
> NUCLEAR CHARGE: 30
> NUMBER OF PRIMITIVE AOS: 78
> NUMBER OF SYMMETRY AOS: 78
> NUMBER OF CONTRACTIONS: 48 ( 48A )
> NUMBER OF CORE ORBITALS: 4 ( 4A )
> NUMBER OF VALENCE ORBITALS: 22 ( 22A )
>
>
> NUCLEAR REPULSION ENERGY 111.39771670
>
>
> Eigenvalues of metric
>
> 1 0.118E-01 0.150E-01 0.249E-01 0.364E-01 0.476E-01 0.589E-01
> 0.607E-01 0.655E-01
>
>
> Contracted 2-electron integrals neglected if value below 1.0D-11
> AO integral compression algorithm 1 Integral accuracy 1.0D-11
>
> 4.719 MB (compressed) written to integral file ( 67.2%)
>
> Node minimum: 0.524 MB, node maximum: 0.786 MB
>
>
> NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 99372. BUFFER LENGTH:
> 32768
> NUMBER OF SEGMENTS: 1 SEGMENT LENGTH: 99372 RECORD LENGTH:
> 262144
>
> Memory used in sort: 0.39 MW
>
> SORT1 READ 853217. AND WROTE 97357. INTEGRALS IN 1 RECORDS.
> CPU TIME: 0.01 SEC, REAL TIME: 0.03 SEC
> SORT2 READ 672700. AND WROTE 692076. INTEGRALS IN 14 RECORDS.
> CPU TIME: 0.01 SEC, REAL TIME: 0.06 SEC
>
> Node minimum: 98364. Node maximum: 99372. integrals
>
> OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000
> 0.000000
>
>
>
> ****************************************************************************
> ******************************************************
> DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
> 1 18 14.43 500 610 700 900
> 950 970 1000 129 960 1100
> VAR BASINP GEOM SYMINP
> ZMAT AOBASIS BASIS P2S ABASIS S
> 1400 1410 1200 1210
> 1080 1600 1650 1700
> T V H0 H01
> AOSYM SMH MOLCAS OPER
>
> PROGRAMS * TOTAL INT
> CPU TIMES * 0.13 0.04
> REAL TIME * 0.48 SEC
> DISK USED * 17.85 MB
> GA USED * 0.00 MB (max) 0.00 MB (current)
>
> ****************************************************************************
> ******************************************************
>
> 1PROGRAM * RHF-SCF (CLOSED SHELL) Authors: W. Meyer, H.-J. Werner
>
>
> NUMBER OF ELECTRONS: 15+ 15- SPACE SYMMETRY=1 SPIN SYMMETRY:
> Singlet
> CONVERGENCE THRESHOLDS: 1.00E-06 (Density) 1.00E-07 (Energy)
> MAX. NUMBER OF ITERATIONS: 60
> INTERPOLATION TYPE: DIIS
> INTERPOLATION STEPS: 2 (START) 1 (STEP)
> LEVEL SHIFTS: 0.00 (CLOSED) 0.00 (OPEN)
>
>
>
> Orbital guess generated from atomic densities. Full valence occupancy: 15
>
> Molecular orbital dump at record 2100.2
>
> ITERATION DDIFF GRAD ENERGY 2-EL.EN.
> DIPOLE MOMENTS DIIS ORB.
> 1 0.000D+00 0.000D+00 NaN NaN
> NaN NaN NaN 0 start
> 2 0.000D+00 NaN NaN NaN
> NaN NaN NaN 1 diag
> ? Error
> ? SVD solve failed
> ? The problem occurs in rmp2f12/LinearSolveGenSvd
>
> ______________________________
>
>
>
> Classification: UNCLASSIFIED
> Caveats: NONE
>
>
>
>
> _______________________________________________
> Molpro-user mailing list
> Molpro-user at molpro.net
> http://www.molpro.net/mailman/listinfo/molpro-user
>
-------------- next part --------------
# MOLPRO CONFIG generated at Tue Apr 14 09:08:47 CDT 2015, for host swan, SHA1=89c4732a0b2b3cf0560d69a42b84eb4ee468be9e
CONFIGURE_OPTIONS= "-mpp" "-mppbase" "/opt/cray/mpt/7.2.0/gni/mpich2-intel/140/include"
AR=ar
ARCHNAME=Linux/XT
ARFLAGS=-rS
AWK=awk
BIBTEX=
BLASLIB=
BUILD=p
CAT=cat
CC=/opt/cray/craype/2.3.0/bin/cc
CCVERSION=15.0.1
CC_FRONT=/opt/intel/composer_xe_2015.1.133/bin/intel64/icc
CDEBUG=-g $(addprefix $(CDEFINE),_DEBUG)
CDEFINE=-D
CFLAGS=-ftz
CLDFLAGS=
CLEAN=echo 'target clean only available with git cloned versions, please unpack the tarball again'
CMPPINCLUDE=/opt/cray/mpt/7.2.0/gni/mpich2-intel/140/include
COPT=-O2
COPT0=-O0
COPT1=-O1
COPT2=-O2
COPT3=-O3
CP=cp -p
CPROFILE=-p
CUDACC=
CUDACCVERSION=
CUDACDEBUG=-g $(addprefix $(CUDACDEFINE),_DEBUG)
CUDACDEFINE=-D
CUDACFLAGS=
CUDACOPT=
CUDACOPT0=-O0
CUDACOPT1=-O1
CUDACOPT2=-O2
CUDACOPT3=-O3
CUDACPROFILE=-p
CXX=/opt/cray/craype/2.3.0/bin/CC
CXXFLAGS=$(CFLAGS)
DOXYGEN=/usr/bin/doxygen
ECHO=/bin/echo
EXPORT=export
F90FLAGS=-stand f03
FC=/opt/cray/craype/2.3.0/bin/ftn
FCVERSION=15.0.1
FDEBUG=-g $(addprefix $(FDEFINE),_DEBUG)
FDEFINE=-D
FFLAGS=-i8 -pc64 -auto -warn nousage -cxxlib
FLDFLAGS=
FOPT=-O3
FOPT0=-O0
FOPT1=-O1
FOPT2=-O2
FOPT3=-O3
FPROFILE=-p
FSTATIC=
HOSTFILE_FORMAT=
INSTALL_FILES_EXTRA=
INSTBIN=
INST_PL=0
INTEGER=8
LAPACKLIB=
LATEX2HTML=
LAUNCHER=/opt/cray/alps/5.2.1-2.0502.9041.11.6.ari/bin/aprun -n %n %x
LD_ENV=/opt/cray/craype/2.3.0/compiler/lib/intel64
LD_ENVNAME=LD_LIBRARY_PATH
LIBRARY_SUFFIX=a
LIBS=-lpthread /lus/scratch/${LOGNAME}/Molpro/src/boost-install/lib/libboost_system.a /lus/scratch/${LOGNAME}/Molpro/src/boost-install/lib/libboost_thread.a -lrt
LN=ln -s
MACROS=MOLPRO NDEBUG MOLPRO_f2003 MPI2 HAVE_BOOST_THREADS HAVE_SSE2 _I8_ MOLPRO_INT=8 BLAS_INT=4 LAPACK_INT=4 MOLPRO_AIMS MOLPRO_NECI _MOLCAS_MPP_ MOLPRO_BLAS MOLPRO_LAPACK
MAKEDEPEND_OPTIONS=
MAKEINDEX=
MAPLE=
MAX_INCREMENT_LIBRARY=0
MKDIR=mkdir -p
MODULE_FLAG=-I
MODULE_SUFFIX=mod
MPILIB=
MPPLIB=
OBJECT_SUFFIX=o
OPT0=B88.F copyc6.F
OPT1=explicit_util.F avcc.F koopro4.F dlaed4.F frequencies.F optg.F
OPT2=tstfnc.F dftgrid.F mrf12_singles.F90 basis_integral_shells.F integrals.F90 geminal.F surface.F gcc.F90
OPT3=
PAPER=a4paper
PARSE=parse-Linux-x86_64-i8.o
PDFLATEX=
PNAME=molprop_2012_1_Linux_XT_i8
PREFIX=/usr/local/molpro/molprop_2012_1_Linux_XT_i8
PTSIZE=11
PYTHON=/usr/bin/python
RANLIB=ranlib
RM=rm -rf
SHELL=/bin/sh
STRIP=strip
SUFFIXES=F F90 c cpp
TAR=tar -cf
UNTAR=tar -xf
VERBOSE=@
VERSION=2012.1
XSD=/usr/bin/xmllint --noout --schema
XSLT=/usr/bin/xsltproc
YACC=bison -b y
.SUFFIXES:
MAKEFLAGS+=-r
ifneq ($(LD_ENVNAME),)
$(LD_ENVNAME):=$(LD_ENV):$($(LD_ENVNAME))
endif
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