[molpro-user] Fwd: Problems with parallel build on AMD Opteron(tm) Processor 6376

Thu Jan 29 11:40:55 GMT 2015

Dear Robert,

This is not Molpro related but OpenMPI related. From the mpirun man page (v1.8.4):

"Please note that mpirun automatically binds processes as of the start of the v1.8 series. Two binding patterns are used in the absence of any further directives:

Bind to core:
when the number of processes is <= 2
Bind to socket:
when the number of processes is > 2

If your application uses threads, then you probably want to ensure that you are either not bound at all (by specifying --bind-to none), or bound to multiple cores using an appropriate binding level or specific number of processing elements per application process."

You can make --bind-to none a global default by editing the openmpi-mca-params.conf file in the openmpi/etc folder and adding a line

orte_process_binding = none

to the end of the file.

After this all new calculations should use different cores.

Cheers,

Heikki

________________________________
Lähettäjä: Molpro-user [molpro-user-bounces at molpro.net] käyttäjän molpro-user [molpro-user at molpro.net] puolesta
Lähetetty: 29. tammikuuta 2015 12:26
Vastaanottaja: molpro-user at molpro4.chem.cf.ac.uk
Aihe: [molpro-user] Fwd: Problems with parallel build on AMD Opteron(tm) Processor 6376

== == == == == == Forwarded message == == == == == ==
>From : Robert Polly<polly at kit.edu>
To : <molpro-user at molpro.net>
Date : Fri, 23 Jan 2015 12:50:51 +0000
Subject : Problems with parallel build on AMD Opteron(tm) Processor 6376
== == == == == == Forwarded message == == == == == ==

Dear MOLPRO community,
we installed MOLPRO on our new Opteron cluster (64 CPUs per node)

CPU: AMD Opteron(tm) Processor 6376
Compiler: ifort/icc
Openmpi: openmpi-1.8.3
Molpro: 2012.1.18

CONFIG file:

# MOLPRO CONFIG generated at Fri Jan 9 10:31:38 MET 2015, for host
master.hpc1.ine, SHA1=50d6e5f7071a51146f1443020887856fd3d38933

CONFIGURE_OPTIONS="-icc" "-ifort" "-mpp" "-openmpi" "-mppbase"
"/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/openmpi-install/include"

AR=ar
ARCHNAME=Linux/x86_64
ARFLAGS=-rS
AWK=awk
BIBTEX=
BLASLIB=-L/pub/hpc/module/compilers/intel/xe2015/composer_xe_2015.0.090/mkl/lib/intel64
-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
BUILD=p
CAT=cat
CC=/pub/hpc/module/compilers/intel/xe2015/composer_xe_2015.0.090/bin/intel64/icc
CCVERSION=15.0.0
CC_FRONT=
CDEBUG=-g $(addprefix $(CDEFINE),_DEBUG)
CDEFINE=-D
CFLAGS=-ftz
-I/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/openmpi-install/include
CLDFLAGS=
CLEAN=echo 'target clean only available with git cloned versions, please
unpack the tarball again'
CMPPINCLUDE=/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/openmpi-install/include
COPT=-O2
COPT0=-O0
COPT1=-O1
COPT2=-O2
COPT3=-O3
CP=cp -p
CPROFILE=-p
CUDACC=
CUDACCVERSION=
CUDACDEBUG=-g $(addprefix $(CUDACDEFINE),_DEBUG)
CUDACDEFINE=-D
CUDACFLAGS=
CUDACOPT=
CUDACOPT0=-O0
CUDACOPT1=-O1
CUDACOPT2=-O2
CUDACOPT3=-O3
CUDACPROFILE=-p
CXX=/pub/hpc/module/compilers/intel/xe2015/composer_xe_2015.0.090/bin/intel64/icpc
CXXFLAGS=$(CFLAGS)
DOXYGEN=/bin/doxygen
ECHO=/bin/echo
EXPORT=export
F90FLAGS=-stand f03
FC=/pub/hpc/module/compilers/intel/xe2015/composer_xe_2015.0.090/bin/intel64/ifort
FCVERSION=15.0.0
FDEBUG=-g $(addprefix $(FDEFINE),_DEBUG)
FDEFINE=-D
FFLAGS=-i8 -pc64 -auto -warn nousage -align array32byte -cxxlib
FLDFLAGS=
FOPT=-O3
FOPT0=-O0
FOPT1=-O1
FOPT2=-O2
FOPT3=-O3
FPROFILE=-p
FSTATIC=
HOSTFILE_FORMAT=%N
INSTALL_FILES_EXTRA=src/openmpi-install/bin/mpirun
src/openmpi-install/bin/orterun
INSTBIN=
INST_PL=0
INTEGER=8
LAPACKLIB=
LATEX2HTML=
LAUNCHER=/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/openmpi-install/bin/mpirun
--mca mpi_warn_on_fork 0 -machinefile %h -np %n %x
LD_ENV=/pub/hpc/module/compilers/intel/xe2015/composer_xe_2015.0.090/compiler/lib/intel64:/pub/hpc/module/compilers/intel/xe2015/composer_xe_2015.0.090/mkl/lib/intel64
LD_ENVNAME=LD_LIBRARY_PATH
LIBRARY_SUFFIX=a
LIBS=-lpthread
/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/boost-install/lib/libboost_system.a
/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/boost-install/lib/libboost_thread.a
-lrt
LN=ln -s
MACROS=MOLPRO NDEBUG MOLPRO_f2003 MOLPRO_bug3990 MPI2 HAVE_BOOST_THREADS
HAVE_SSE2 _I8_ MOLPRO_INT=8 BLAS_INT=8 LAPACK_INT=8 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=-I/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/openmpi-install/lib
-Wl,-rpath
-Wl,/home/polly/molpro/TEST/Molpro.2012.1.18.par/src/openmpi-install/lib
-Wl,--enable-new-dtags -L/home/polly/molpro/TEST\
/Molpro.2012.1.18.par/src/openmpi-install/lib -lmpi_usempif08
-lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -lm
-lpciaccess -ldl -lrt -losmcomp -libverbs -lrdmacm -lutil -lpsm_infinipath
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_x86_64_i8
PREFIX=/usr/local/molpro/molprop_2012_1_Linux_x86_64_i8
PTSIZE=11
PYTHON=/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=/bin/xmllint --noout --schema
XSLT=/bin/xsltproc
YACC=bison -b y

.SUFFIXES:
MAKEFLAGS+=-r
ifneq ($(LD_ENVNAME),)
$(LD_ENVNAME):=$(LD_ENV):$($(LD_ENVNAME))
endif

We encounter the problem, that when 2 MOLPRO jobs run on one node
with 8 processors each, they run on the same 8 processors already
allocated by
thge first job, although there are still 56 free processors on the machine.

Any suggestions how to solve the problem?

Best regards,
Robert

--

*********************************************************************

Karlsruher Institut für Technologie (KIT)
Institut fuer Nukleare Entsorgung

Dr. Robert Polly

Quantenchemie

Institut fuer Nukleare Entsorgung (INE), Campus Nord, Gebaeude 712,
Postfach 3640, 76021 Karlsruhe, Germany

0049-(0)721-608-24396

email: polly at kit.edu<mailto:polly at kit.edu>
www: http://www.fzk.de/ine

KIT - Universität des Landes Baden-Württemberg und
nationales Großforschungszentrum in der Helmholtz-Gemeinschaft

*********************************************************************

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