[molpro-user] Can I compile molpro2009.1 parallel version without GA?

He Ping heping at sccas.cn
Fri Oct 9 10:12:51 BST 2009 

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).

   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?

   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
   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.



   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.




On Thu, Sep 24, 2009 at 5:33 PM, Manhui Wang <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 -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 -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
> > 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
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