[molpro-user] Parallel molpro
Manhui Wang
wangm9 at cardiff.ac.uk
Thu Oct 13 15:39:50 BST 2011
Hello,
(1)For the question about pre-compiled binaries, there is a run-time
option --tcgssh to set ssh as access mode instead of the default rsh.
The pre-compiled binaries are built with GA-TCGMSG. Since Molpro runs
well interactively on your machine according to your email, the problem
in your case appears bin/molpro script couldn't pick up the right node
list from the PBS environment variables (eg $PBS_NODEFILE). The
bin/molpro script attempts to parse the node information from some
standard job schedulers, but might not cover your case. Could you add
some debugging command in bin/molpro script? It might work by slightly
changing the script. Another option -v will more more information, eg
.../bin/molpro -v --tcgssh -n 16 yourtest.mol
(2)About building Molpro from source code, some options seem to be
duplicative and unnecessary. In addition, /opt/sgi/mpt/mpt-2.04 and
/opt/sgi/mpt/mpt-2.0.4 are two different directories, which one is for
your SGI MPI? In your CONFIG
LAUNCHER=
there is nothing set for it, while in an successful CONFIG it should
direct to the mpi command, eg (for Intel MPI)
LAUNCHER=/software/intel/mpi/4.0.0.025/intel64/bin/mpiexec -machinefile
%h -n %n %x
Could you please try a fresh build with your right SGI MPI path using
the following options(or similar):
./configure -ifort -icc -mpp -mppbase /path-to-SGIMPI -var
PREFIX=/usr/local/packages/molpro
I couldn't get access to an SGI machine, so have no chance to test them.
Best wishes,
Manhui
On 13/10/11 12:14, Marcela Madrid wrote:
>
>>>
>>> hi,
>>>
>>> I am trying to install molpro on an SGI UV to run in parallel by submitting from a PBS job.
>>> I got the LINUX binary
>>>
>>> molpro-mpp-2010.1-24.Linux_x86_64.sh
>>>
>>> and installed without problems. When I type
>>> /usr/local/packages/molpro/bin/molpro -n 16 fci.test
>>> interactively it runs to completion on 16 processors.
>>> However, when I include this line in the PBS job it runs to completion, but only in 1 PE. I read that this has to do with the pre-compiled binaries using GA and needing to access each node with rsh. If this is the case it might not have a solution for us. But just in case I thought I would ask. Also, I am assuming this is mpi and not openmp?
>>> (I tried everything). How is one suppose to run it?
>>>
>>> Another thing I tried is to compile my own, using MPI. Ideally this is what I would prefer to do, but the test does not run, it dies with
>>>
>>> SORT1 READ 123. AND WROTE 100. INTEGRALS IN 1 RECORDS. CPU TIME: 0.00 SEC, REAL TIME: 0.01 SEC
>>> SORT2 READ 100. AND WROTE 120. INTEGRALS IN 1 RECORDS. CPU TIME: 0.01 SEC, REAL TIME: 0.02 SEC
>>>
>>> FILE SIZES: FILE 1: 2.5 MBYTE, FILE 4: 4.2 MBYTE, TOTAL: 6.8 MBYTE
>>>
>>> OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000
>>> ?ERROR IN GLOBAL_DESTROY FOR IHANDLE= 0
>>>
>>> GLOBAL ERROR fehler on processor 0
>>>
>>> Here is the CONFIG file: Can someone please tell me what I am missing? thanks so much, Marcela
>>>
>>> CONFIGURE_OPTIONS="-mpp" "-mppbase" "/opt/sgi/mpt/mpt-2.04" "-var" "MPPLIB=-lmpi" "-var" "PREFIX=/usr/local/packages/molpro" "-mpp" "-mpp
>>> base" "/opt/sgi/mpt/mpt-2.0.4"
>>>
>>> AR=ar
>>> ARCHNAME=Linux/x86_64
>>> ARFLAGS=-rS
>>> AWK=awk
>>> BIBTEX=
>>> BLASLIB=-L/opt/intel/Compiler/11.1/072/mkl/lib/em64t -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core
>>> BOOSTVERSION=1_47_0
>>> BUILD=p
>>> CAT=cat
>>> CC=/usr/bin/gcc
>>> CCVERSION=4.3
>>> CC_FRONT=
>>> CDEBUG=-g $(addprefix $(CDEFINE),_DEBUG)
>>> CDEFINE=-D
>>> CFLAGS=-m64 -Waddress -Wcast-align -Wchar-subscripts -Wcomment -Wdeclaration-after-statement -Wformat -Wimplicit -Wimplicit-function-decl
>>> aration -Wimplicit-int -Wmain -Wmissing-braces -Wmultichar -Wnested-externs -Wparentheses -Wpointer-arith -Wpointer-sign -Wreturn-type -W
>>> sequence-point -Wsign-compare -Wstrict-aliasing -Wstrict-overflow=1 -Wswitch -Wtrigraphs -Wunknown-pragmas -Wunused-function -Wunused-lab
>>> el -Wunused-value -Wunused-variable -Wvolatile-register-var -pedantic -Wno-long-long
>>> CLEAN=echo 'target clean only available with git cloned versions, please unpack the tarball again'
>>> CLEARSPEEDLIB=
>>> CMPPINCLUDE=
>>> COPT=-O3
>>> COPT0=-O0
>>> COPT1=-O1
>>> COPT2=-O2
>>> COPT3=-O3
>>> CP=cp -p
>>> CPROFILE=-p
>>> CSCN=cscn
>>> CSFLAGS=-O3 -I. --dynamic
>>> CUDACC=
>>> CUDACCVERSION=
>>> CUDACDEBUG=-g $(addprefix $(CUDACDEFINE),_DEBUG)
>>> CUDACDEFINE=-D
>>> CUDACFLAGS=
>>> CUDACOPT=
>>> CUDACOPT0=-O0
>>> CUDACOPT1=-O1
>>> CUDACOPT2=-O2
>>> CUDACOPT3=-O3
>>> CUDACPROFILE=-p
>>> CXX=/usr/bin/g++
>>> CXXFLAGS=$(filter-out -Wdeclaration-after-statement -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wnested-externs -Wpointer-
>>> sign,$(CFLAGS))
>>> DOXYGEN=
>>> ECHO=echo
>>> EXPORT=export
>>> F90FLAGS=-stand f03
>>> FC=/opt/intel/Compiler/11.1/072/bin/intel64/ifort
>>> FCVERSION=11.1
>>> FDEBUG=-g $(addprefix $(FDEFINE),_DEBUG)
>>> FDEFINE=-D
>>> FFLAGS=-i8 -r8 -pc64 -auto -Vaxlib -vec-report0 -cxxlib
>>> FOPT=-O3
>>> FOPT0=-O0
>>> FOPT1=-O1
>>> FOPT2=-O2
>>> FOPT3=-O3
>>> FPP=-fpp
>>> FPROFILE=-p
>>> FSTATIC=
>>> FTCFLAGS=molpro unix unix-i8 Linux mpp
>>> HDF5INCLUDE=
>>> HDF5LIB=
>>> HOSTFILE_FORMAT=
>>> INSTBIN=
>>> INST_PL=0
>>> INTEGER=8
>>> LAPACKLIB=
>>> LATEX2HTML=
>>> LAUNCHER=
>>> LD_ENV=/opt/intel/Compiler/11.1/072/lib/intel64:/opt/intel/Compiler/11.1/072/mkl/lib/em64t
>>> LD_ENVNAME=LD_LIBRARY_PATH
>>> LIBRARY_SUFFIX=a
>>> LIBS=
>>> LIBS_FRONT=
>>> LINKOPT=
>>> LINKOPT_FRONT=
>>> LN=ln -s
>>> MACROS=MOLPRO MOLPRO_ifort MOLPRO_f2003 _I8_ BLAS_INT=8 LAPACK_INT=8 MOLPRO_FORCE_VECTOR MOLPRO_NEXTSCALAR MOLPRO_NO_RECURRENCE MOLPRO_NO
>>> VECTOR MOLPRO_SHORTLOOP _MOLCAS_MPP_ MOLPRO_BLAS MOLPRO_LAPACK
>>> MAKEDEPEND_OPTIONS=
>>> MAKEINDEX=
>>> MAPLE=
>>> MKDIR=mkdir -p
>>> MODULE_FLAG=-I
>>> MODULE_SUFFIX=mod
>>> MPILIB=
>>> MPPLIB=-lmpi
>>> OBJECT_SUFFIX=o
>>> OPT0=copyc6.F
>>> OPT1=nevpt2_optrpc.F explicit_util.F artwo2.F drv2el_l3ext_lmp2g.F drv2el_l3ext_cen.F rmp2_f12_drv2.F90 ri_lmp2g.F df_llmp2.F readdump.F
>>> OPT2=integrals.F90 RL4gen1.F basis_integral_shells.F
>>> OPT3=
>>> PAPER=a4paper
>>> PARSE=parse-Linux-x86_64-i8.o
>>> PDFLATEX=
>>> PNAME=molprop_2010_1_Linux_x86_64_i8
>>> PREFIX=/usr/local/packages/molpro/molprop_2010_1_Linux_x86_64_i8
>>> PTSIZE=11
>>> RANLIB=ranlib
>>> RM=rm -rf
>>> SHELL=/bin/sh
>>> STRIP=strip
>>> SUFFIXES=F F90 c cpp
>>> TAR=tar -cf
>>> UNTAR=tar -xf
>>> VERBOSE=@
>>> VERSION=2010.1
>>> XSD=/usr/bin/xmllint --noout --schema
>>> XSLT=/usr/bin/xsltproc
>>> YACC=bison -b y
>>>
>>> .SUFFIXES:
>>> MAKEFLAGS+=-r
>>> MPPLIB=-lmpi
>>> OBJECT_SUFFIX=o
>>> OPT0=copyc6.F
>>> OPT1=nevpt2_optrpc.F explicit_util.F artwo2.F drv2el_l3ext_lmp2g.F drv2el_l3ext_cen.F rmp2_f12_drv2.F90 ri_lmp2g.F df_llmp2.F readdump.F
>>> OPT2=integrals.F90 RL4gen1.F basis_integral_shells.F
>>> OPT3=
>>> PAPER=a4paper
>>> PARSE=parse-Linux-x86_64-i8.o
>>> PDFLATEX=
>>> PNAME=molprop_2010_1_Linux_x86_64_i8
>>> PREFIX=/usr/local/packages/molpro/molprop_2010_1_Linux_x86_64_i8
>>> PTSIZE=11
>>> RANLIB=ranlib
>>> RM=rm -rf
>>> SHELL=/bin/sh
>>> STRIP=strip
>>> SUFFIXES=F F90 c cpp
>>> TAR=tar -cf
>>> UNTAR=tar -xf
>>> VERBOSE=@
>>> VERSION=2010.1
>>> 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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--
-----------
Manhui Wang
School of Chemistry, Cardiff University,
Main Building, Park Place,
Cardiff CF10 3AT, UK
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