[molpro-user] ARMCI test errors after compiling with GA/MPICH2, gfortran, ATLAS on Ubuntu 11.04

Tue May 24 13:22:00 BST 2011

Hello all,
I am faceing problem installing molpro2010 with the command
./configure -batch -gcc -ifort -mpp -auto-ga-tcgmsg-mpich2 -instroot
/usr/local/molpro2010
its creating the CONFIG file without any error but when i am going to
execute a command
make install
it showing me an error given below
please help me
thanks in advance

Updating ../lib/libmolpro.a
ar -rS ../lib/libmolpro.a util/licence.o
make[2]: Leaving directory `/root/.molpro/Molpro/src'
make[2]: Entering directory `/root/.molpro/Molpro/src'
make[3]: Entering directory `/root/.molpro/Molpro/src'
make[4]: Entering directory `/root/.molpro/Molpro/src'
link date: 25 May 2011 01:41:52 ; version: 2010.1
SHA1 : 297cac099cefd7e93f9e8d4e83c3300f69c4946f
make[4]: Leaving directory `/root/.molpro/Molpro/src'
compiling molver.f90
make[3]: Leaving directory `/root/.molpro/Molpro/src'
linking ../bin/molpro.exe
failed
/root/.molpro/Molpro/src/ga-install/lib/libga.a(farg.o): In function
`f2c_getarg_':
farg.F:(.text+0x5): undefined reference to `_gfortran_getarg_i8'
/root/.molpro/Molpro/src/ga-install/lib/libga.a(farg.o): In function
`f2c_iargc_':
farg.F:(.text+0x13): undefined reference to `_gfortran_iargc'
make[2]: [../bin/molpro.exe] Error 1 (ignored)
failure
/root/.molpro/Molpro/src/ga-install/lib/libga.a(farg.o): In function
`f2c_getarg_':
farg.F:(.text+0x5): undefined reference to `_gfortran_getarg_i8'
/root/.molpro/Molpro/src/ga-install/lib/libga.a(farg.o): In function
`f2c_iargc_':
farg.F:(.text+0x13): undefined reference to `_gfortran_iargc'
make[2]: *** [../bin/molpro.exe] Error 1
make[2]: Leaving directory `/root/.molpro/Molpro/src'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/root/.molpro/Molpro/src'
make: *** [src] Error 2

On Mon, May 23, 2011 at 10:53 PM, Gregory Magoon <gmagoon at mit.edu> wrote:

> I was able to narrow this down to an issue with ATLAS. Andy, could you
> elaborate
> on your previous comments regarding Molpro not working with the
> unmodified ATLAS
> libraries? Is this a compile-time or run-time issue? If it is a
> run-time issue,
> would something like the procedure described below help address the issue
> I'm
> having? (I have taken this from the ATLAS documentation):
>
> "ATLAS does not provide a full lapack library.  However, there is a simple
> way
> to get ATLAS to provide its faster LAPACK routines to a full LAPACK
> library.
> ATLAS's internal routines are distinct from LAPACK's, so it is safe to
> compile
> ATLAS's LAPACK routines directly into a netlib-style LAPACK library.
> If you install LAPACK before ATLAS, this can be automated as described in
> ATLAS/INSTALL.txt.  The following describes adding netlib LAPACK to an
> already built ATLAS library:
>
> First, obtain the LAPACK src from netlib and build the LAPACK library as
> normal.  Then, in the lib/ subdirectory of your ATLAS build directory
> (where you should have a liblapack.a), issue the following commands:
>  mkdir tmp
>  cd tmp
>  ar x ../liblapack.a
>  cp <your LAPACK path & lib> ../liblapack.a
>  ar d ../liblapack.a lsame.o xerbla.o csrot.o zdrot.o
>  ar r ../liblapack.a *.o
>  cd ..
>  rm -rf tmp
>
> Just linking in ATLAS's liblapack.a first will not get you the best LAPACK
> performance, mainly because LAPACK's untuned ILAENV will be used instead
> of ATLAS's slightly tuned one."
>
> Thanks again,
> Greg
>
> Quoting Gregory Magoon <gmagoon at mit.edu>:
>
> > An update: although the original command you suggested didn't work,
> > as explained
> > in my earlier e-mail, I tried the same command with the -noblas and
> -nolapack
> > options that you proposed and the tests seem to be working properly:
> >
> > ./configure -batch -gcc -gfortran -mpp -auto-ga-tcgmsg-mpich2 -instroot
> > /usr/local/molpro2010.1 -noblas -nolapack
> >
> > So, it seems our ATLAS, BLAS and/or LAPACK libraries were causing the
> issue.
> > However, it is still not clear why. I had just installed these libraries
> as
> > Ubuntu packages:
> > sudo apt-get install libatlas-base-dev
> > sudo apt-get install liblapack-dev
> > Perhaps there is some critical step I omitted or these are not the
> correct
> > packages?
> >
> > Thanks again,
> > Greg
> >
> > user at kamet:~/Molpro$ ./configure -batch -gcc -gfortran -mpp
> > -auto-ga-tcgmsg-mpich2 -instroot /usr/local/molpro2010.1 -noblas
> -nolapack
> >
> > machine type recognized as x86_64 (Generic 64-bit)
> > kernel recognized as Linux
> >
> > user request compiler gfortran
> > GNU Fortran Compiler, Version 4.5.2
> > FC=/usr/bin/gfortran
> >
> > user request compiler gcc
> > GNU Compiler Collection, Version 4.5.2
> > CC=/usr/bin/gcc
> >
> > starting auto-build of prerequisites
> >
> > building MPICH2 version 1.3.3rc1, each step could take a few minutes
> >
> > ./configure --prefix=/home/user/Molpro/src/mpich2-install
> > --with-device=ch3:nemesis --with-pm=hydra --enable-f77
> F77=/usr/bin/gfortran
> > --enable-fc FC=/usr/bin/gfortran --enable-cc CC=/usr/bin/gcc --enable-cxx
> > CXX=/usr/bin/g++
> > make
> > make install
> > MPICH2 built, if you want to test the MPICH2 build, please run:
> >
> > cd /home/user/Molpro/src/mpich2-1.3.3rc1; make testing
> >
> > building Global Arrays version 5-0-2, each step could take a few minutes
> >
> > ./configure --prefix=/home/user/Molpro/src/ga-install --with-scalapack=no
> > --enable-f77 F77=/usr/bin/gfortran CC=/usr/bin/gcc CXX=/usr/bin/g++
> > --with-tcgmsg --with-mpi='/home/user/Molpro/src/mpich2-install/lib
> -lmpich
> > -lopa -lmpl -lrt -I/home/user/Molpro/src/mpich2-install/include'
> > make
> > make install
> > Global Arrays built, if you want to test the Global Arrays build, please
> run:
> >
> > cd /home/user/Molpro/src/ga-5-0-2; make checkprogs; make check
> > MPIEXEC="/home/user/Molpro/src/mpich2-install/bin/mpiexec -np 4"
> >
> > ./configure -batch "-gcc" "-gfortran" "-mpp" "-instroot"
> > "/usr/local/molpro2010.1" "-noblas" "-nolapack" -mppbase
> > /home/user/Molpro/src/ga-5-0-2
> >
> > machine type recognized as x86_64 (Generic 64-bit)
> > kernel recognized as Linux
> >
> > user request compiler gfortran
> > GNU Fortran Compiler, Version 4.5.2
> > FC=/usr/bin/gfortran
> >
> > user request compiler gcc
> > GNU Compiler Collection, Version 4.5.2
> > CC=/usr/bin/gcc
> >
> > ga_GA_MP_LIBS            = -lmpich -lopa -lmpl -lrt
> > ga_GA_MP_LDFLAGS         = -L/home/user/Molpro/src/mpich2-install/lib
> > ga_GA_MP_CPPFLAGS        = -I/home/user/Molpro/src/mpich2-install/include
> > ga_TARGET                = LINUX64
> > ga_MSG_COMMS             = TCGMSGMPI
> > ga_prefix                = /home/user/Molpro/src/ga-install
> > ga_ARMCI_NETWORK_LDFLAGS =
> > ga_ARMCI_NETWORK_LIBS    =
> > ga_BLAS_SIZE             = 4
> >
> > Use MPP library - Global Arrays version 5 or higher
> > MPPLIB=-L/home/user/Molpro/src/ga-install/lib -lga -larmci
> >
> > MPILIB=-L/home/user/Molpro/src/mpich2-install/lib -lmpich -lopa -lmpl
> -lrt
> >
> > parallel=mpich2
> >
> > parse-Linux-x86_64-i8.o is your object
> >
> > CONFIG file created; proceed to compilation
> >
> > Quoting Andy May <MayAJ1 at cardiff.ac.uk>:
> >
> >> Greg,
> >>
> >> I can't seem to replicate this problem using options as close as
> >> possible to yours.
> >>
> >> One thing I have noticed is that linking only the routines that come
> >> with ATLAS does not work anymore with Molpro. I have fixed this, and
> >> there will be an update sometime in the future, but this leads me to
> >> conclude the -lapack you are using is either a supplemented ATLAS
> >> library, or a system one.
> >>
> >> I don't think the BLAS/LAPACK will be the problem, but perhaps
> >> configure has not correctly determined the integer size in these
> >> libraries, you can always try using Molpro internal ones with
> >> -noblas -nolapack options.
> >>
> >> There may be problems with the MPICH2 version which ships with
> >> Ubuntu, certainly there were problems with hydra around 1.3.1, but
> >> if you say that ifort works then maybe it's okay. To eliminate this
> >> I would suggest to use a newer version (no need to do this by hand,
> >> see below).
> >>
> >> Also, we are now at PL21 (there is a new tarball).
> >>
> >> Can I therefore suggest you first try the following with 2010.1.21:
> >>
> >> ./configure -batch -gcc -gfortran -mpp -auto-ga-tcgmsg-mpich2
> >> -instroot /usr/local/molpro2010.1
> >>
> >> and see if this then gives you a working build.
> >>
> >> Best wishes,
> >>
> >> Andy
> >>
> >
> >
> >
> >
>
>
> _______________________________________________
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> Molpro-user at molpro.net
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>

-- 
Thanks & Regards
Chanchal Kumar Haldar
B.E (Electronics and Telecommunication)
Linux System Administrator.
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