[molpro-user] Can I compile molpro2009.1 parallel version without GA?
He Ping
heping at sccas.cn
Sat Oct 10 07:34:46 BST 2009
Dear Manhui,
Thanks for your patience and explicit answer. Let me do some tests and give
you feedback.
On Fri, Oct 9, 2009 at 10:56 PM, Manhui Wang <wangm9 at cardiff.ac.uk> wrote:
> Dear He Ping,
> GA may take full advantage of shared memory on an MPP node, but
> MPI-2 doesn't. On the other hand, MPI-2 may take advantage of the
> built-in MPI-2 library with fast connection. The performance depends on
> lots of facts, including MPI library, machine, network etc. It is better
> to build both versions of Molpro, and then choose the better one on that
> machine.
> It doesn't seem to be hard to make GA4-2 work on machine like
> yours. Details were shown in my previous email.
>
> Best wishes,
> Manhui
>
> He Ping wrote:
> > Hi Manhui,
> >
> > Thanks. I will try these patches first.
> > But would you like to tell me something about GA's effect on molpro? So
> > far I can not get a GA version molpro, so I can not know the performance
> > of GA version. If GA version is not much better than non-GA version, I
> > will not take much time building it.
> > Thanks a lot
> >
> > On Fri, Oct 9, 2009 at 7:25 PM, Manhui Wang <wangm9 at cardiff.ac.uk
> > <mailto:wangm9 at cardiff.ac.uk>> wrote:
> >
> > Dear He Ping,
> > Recent patches include some bugfixes for intel compiler 11,
> > OopenMPI, and running molpro across nodes with InfiniBand. If you
> have
> > not updated them, please do it now. It may resolve your existing
> > problems.
> >
> > He Ping wrote:
> > > Dear Manhui,
> > >
> > > Thanks a lot for your detailed reply, that's very helpful. Very
> > sorry to
> > > answer later, for I have to do a lot of tests. So far, one version
> of
> > > molpro2009.1 is basically ok, but I still have some questions.
> > >
> > > 1. Compile Part.
> > > Openmpi 1.3.3 can pass compile and link for both w GA and w/o
> GA
> > > 4.2. I do not use my own blas, so I use default, this is my
> > > configure step,
> > >
> > > ./configure -batch -ifort -icc -mppbase $MPI_HOME/include64
> -var
> > > LIBS="-L/usr/lib64 -libverbs -lm" -mpp (in your letter, I
> guess
> > > you forget this necessary option.)
> > >
> > > But *intelmpi failed for both*, I can show the err message
> > > seperately below.
> > >
> > > *Intelmpi w/o GA: *
> > >
> > > make[1]: Nothing to be done for `default'.
> > > make[1]: Leaving directory
> > >
> >
> `/datastore/workspace/scheping/molpro2009.1_intelmpi/molpro2009.1/utilities'
> > > make[1]: Entering directory
> > >
> >
> `/datastore/workspace/scheping/molpro2009.1_intelmpi/molpro2009.1/src'
> > > Preprocessing include files
> > > make[1]: *** [common.log] Error 1
> > > make[1]: *** Deleting file `common.log'
> > > make[1]: Leaving directory
> > >
> >
> `/datastore/workspace/scheping/molpro2009.1_intelmpi/molpro2009.1/src'
> > > make: *** [src] Error 2
> > >
> > > *Intelmpi w GA:*
> > >
> > > compiling molpro_cvb.f
> > > failed
> > > molpro_cvb.f(1360): error #5102: Cannot open include file
> > > 'common/ploc'
> > > include "common/ploc"
> > > --------------^
> > > compilation aborted for molpro_cvb.f (code 1)
> > > make[3]: *** [molpro_cvb.o] Error 1
> > > preprocessing perfloc.f
> > > compiling perfloc.f
> > > failed
> > > perfloc.f(14): error #5102: Cannot open include file
> > 'common/ploc'
> > > include "common/ploc"
> > > --------------^
> > > perfloc.f(42): error #6385: The highest data type rank
> permitted
> > > is INTEGER(KIND=8). [VARIAT]
> > > if(.not.variat)then
> > > --------------^
> > > perfloc.f(42): error #6385: The highest data type rank
> permitted
> > > is INTEGER(KIND=8).
> >
> > Which version of intel compilers are you using? Has your GA worked
> fine?
> > We have tested Molpro2009.1 with
> > (1) intel/compilers/10.1.015 (11.0.074), GA 4-2 hosted by
> intel/mpi/3.1
> > (3.2)
> > (2) without GA, intel/compilers/10.1.015 (11.0.074), intel/mpi/3.1
> (3.2)
> >
> > all work fine. CONFIG files will be helpful to see the problems.
> > >
> > > 2. No .out file when I use more than about 12 processes, but I
> can
> > > get .xml file. It's very strange, everything is ok when
> process
> > > number is less than 12, but once exceed this number, such as
> 16
> > > cpus, molpro always gets this err message,
> > >
> > > orrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine
> > > Line Source
> > > libopen-pal.so.0 00002AAAAB4805C6 Unknown
> > > Unknown Unknown
> > > libopen-pal.so.0 00002AAAAB482152 Unknown
> > > Unknown Unknown
> > > libc.so.6 000000310FC5F07A Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 00000000005A4C36 Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 00000000005A4B84 Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 000000000053E57B Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 0000000000540A8C Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 000000000053C5E5 Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 00000000004BCA5C Unknown
> > > Unknown Unknown
> > > libc.so.6 000000310FC1D8A4 Unknown
> > > Unknown Unknown
> > > molprop_2009_1_Li 00000000004BC969 Unknown
> > > Unknown Unknown
> > >
> > > Can I ignore this message?
> > Have you seen this on one or multiple nodes? If on multiple nodes,
> the
> > problem has been fixed by recent patches. By default, both *.out and
> > .xml can be obtained, but you can use option --no-xml-output to
> disable
> > the *xml.
> > In addition, OpenMPI seems to be unstable sometime. When lots of jobs
> > are run with OpenMPI, some jobs hang up unexpectedly. This behavior
> is
> > not seen for Intel MPI.
> >
> > >
> > > 3. Script Err. For molpro openmpi version, the script
> > > molpro_openmpi1.3.3/bin/molprop_2009_1_Linux_x86_64_i8 seems
> not
> > > to work.
> > > When I call this script, only one process is started, even if
> I
> > > use -np 8. So I have to run it manually, such as
> > > mpirun -np 8 -machinefile ./hosts
> > > molprop_2009_1_Linux_x86_64_i8.exe test.com
> > <http://test.com> <http://test.com>
> > Have your ./bin/molpro worked?. For me, it works fine. In
> ./bin/molpro,
> > some environmental settings are included. In the case that
> ./bin/molpro
> > doesn't work properly, you might want to directly use
> > molprop_2009_1_Linux_x86_64_i8.exe, then it is your responsibility to
> > set up these environmental variables.
> > > 4. Molpro w GA can not cross over nodes. One node is ok, but if
> > cross
> > > over nodes, I will get "molpro ARMCI DASSERT fail" err, and
> > molpro
> > > can not be terminated normally. Do you know the difference
> > between
> > > w GA and w/o GA? If GA is not better than w/o GA, I will
> > pass this
> > > GA version.
> > I think this problem has been fixed by recent patches.
> > As the difference between molpro w GA and w/o GA, it is hard to make
> a
> > simple conclusion. For calculations with a small number of processes(
> > eg. < 8), molpro w GA might be somewhat fast, but molpro without GA
> is
> > quite competitive in performance when it is run with a large number
> of
> > processes. Please refer to the benchmark
> > results(http://www.molpro.net/info/bench.php).
> > >
> > >
> > >
> > > Sorry for packing up so many questions, answer is any one
> > question
> > > will help me a lot. And I think question 1 and 2 will be more
> > > important to me. Thanks.
> > >
> > >
> > >
> >
> > Best wishes,
> > Manhui
> >
> >
> >
> > > On Thu, Sep 24, 2009 at 5:33 PM, Manhui Wang <wangm9 at cardiff.ac.uk
> > <mailto:wangm9 at cardiff.ac.uk>
> > > <mailto:wangm9 at cardiff.ac.uk <mailto:wangm9 at cardiff.ac.uk>>>
> wrote:
> > >
> > > Hi He Ping,
> > > Yes, you can build parallel Molpro wthout GA for 2009.1.
> > Please see
> > > the manual A..3.3 Configuration
> > >
> > > For the case of using the MPI-2 library, one example can be
> > >
> > > ./configure -mpp -mppbase /usr/local/mpich2-install/include
> > >
> > > and the -mppbase directory should contain file mpi.h. Please
> > ensure the
> > > built-in or freshly built MPI-2 library fully supports MPI-2
> > standard
> > > and works properly.
> > >
> > >
> > > Actually we have tested molpro2009.1 on almost the same system
> > as what
> > > you mentioned (EMT64, Red Hat Enterprise Linux Server release
> 5.3
> > > (Tikanga), Intel MPI, ifort, icc, Infiniband). For both GA and
> > MPI-2
> > > buildings, all work fine. The configurations are shown as
> > follows(beware
> > > of lines wrapping):
> > > (1) For Molpro2009.1 built with MPI-2
> > > ./configure -batch -ifort -icc -blaspath
> > > /software/intel/mkl/10.0.1.014/lib/em64t
> > <http://10.0.1.014/lib/em64t>
> > > <http://10.0.1.014/lib/em64t> -mppbase $MPI_HOME/include64
> > > -var LIBS="-L/usr/lib64 -libverbs -lm"
> > >
> > > (2) For Molpro built with GA 4-2:
> > > Build GA4-2:
> > > make TARGET=LINUX64 USE_MPI=y CC=icc FC=ifort COPT='-O3'
> > > FOPT='-O3' \
> > > MPI_INCLUDE=$MPI_HOME/include64 MPI_LIB=$MPI_HOME/lib64 \
> > > ARMCI_NETWORK=OPENIB MA_USE_ARMCI_MEM=y
> > > IB_INCLUDE=/usr/include/infiniband IB_LIB=/usr/lib64
> > >
> > > mpirun ./global/testing/test.x
> > > Build Molpro
> > > ./configure -batch -ifort -icc -blaspath
> > > /software/intel/mkl/10.0.1.014/lib/em64t
> > <http://10.0.1.014/lib/em64t>
> > > <http://10.0.1.014/lib/em64t> -mppbase /GA4-2path -var
> > > LIBS="-L/usr/lib64 -libverbs -lm"
> > >
> > > (LIBS="-L/usr/lib64 -libverbs -lm" will make molpro link with
> > Infiniband
> > > library)
> > >
> > > (some note about MOLPRO built with MPI-2 library can also been
> > in manual
> > > 2.2.1 Specifying parallel execution)
> > > Note: for MOLPRO built with MPI-2 library, when n processes are
> > > specified, n-1 processes are used to compute and one process
> > is used to
> > > act as shared counter server (in the case of n=1, one process
> > is used to
> > > compute and no shared counter server is needed). Even so, it
> > is quite
> > > competitive in performance when it is run with a large number
> of
> > > processes.
> > > If you have built both versions, you can also compare the
> > performance
> > > yourself.
> > >
> > >
> > > Best wishes,
> > > Manhui
> > >
> > > He Ping wrote:
> > > > Hello,
> > > >
> > > > I want to run molpro2009.1 parallel version on infiniband
> > network.
> > > I met
> > > > some problems when using GA, from the manual, section 3.2,
> there
> > > is one
> > > > line to say,
> > > >
> > > > If the program is to be built for parallel execution then
> > the Global
> > > > Arrays toolkit *or* the
> > > > MPI-2 library is needed.
> > > >
> > > > Does that mean I can build molpro parallel version without
> > GA? If so,
> > > > who can tell me some more about how to configure?
> > > > My system is EM64T, Red Hat Enterprise Linux Server release
> 5.1
> > > > (Tikanga), intel mpi, intel ifort and icc.
> > > >
> > > > Thanks a lot.
> > > >
> > > > --
> > > >
> > > > He Ping
> > > >
> > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------
> > > >
> > > > _______________________________________________
> > > > Molpro-user mailing list
> > > > Molpro-user at molpro.net <mailto:Molpro-user at molpro.net>
> > <mailto:Molpro-user at molpro.net <mailto:Molpro-user at molpro.net>>
> > > > http://www.molpro.net/mailman/listinfo/molpro-user
> > >
> > > --
> > > -----------
> > > Manhui Wang
> > > School of Chemistry, Cardiff University,
> > > Main Building, Park Place,
> > > Cardiff CF10 3AT, UK
> > > Telephone: +44 (0)29208 76637
> > >
> > >
> > >
> > >
> > > --
> > >
> > > He Ping
> > > [O] 010-58813311
> >
> > --
> > -----------
> > Manhui Wang
> > School of Chemistry, Cardiff University,
> > Main Building, Park Place,
> > Cardiff CF10 3AT, UK
> > Telephone: +44 (0)29208 76637
> >
> >
> >
> >
> > --
> >
> > He Ping
> > [O] 010-58813311
>
> --
> -----------
> Manhui Wang
> School of Chemistry, Cardiff University,
> Main Building, Park Place,
> Cardiff CF10 3AT, UK
> Telephone: +44 (0)29208 76637
>
>
--
He Ping
[O] 010-58813311
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