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

[Gregory Magoon]

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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