The ABINIT Users Mailing List ( CLOSED )

[James Johns <jej7x@xenon.cchem.berkeley.edu>]

Thanks for the help Alain, i took your advice and installed openmpi into 
/opt/openmpi and exported the paths as you said. I then compiled the simple hello world program below using mpifortran and 
ran the a.out using "mpirun a.out" and it worked just fine.  I then 
switched to my abinit directory  to try configure --enable-mpi 
--with-mpi-prefix=/opt/openmpi.  I thought the configuration script ran 
fine, and tried make multi and make multi_alt, but I kept getting this 
error.

ltypes.F90
 In file defs_wvltypes.F90:33

 use BigDFT_API
              1
Fatal Error: Can't open module file 'bigdft_api.mod' for reading at (1): 
No such  file or directory
make[1]: *** [defs_wvltypes.o] Error 1

I then checked the config.log file and found the following error:
configure:9388: /opt/openmpi//bin/mpicc -E  conftest.c
conftest.c:16:28: error: ac_nonexistent.h: No such file or directory
configure:9395: $? = 1
configure: failed program was:
| /* confdefs.h.  */

and

configure:11219: /opt/openmpi//bin/mpicc -c   conftest.c >&5
configure:11226: $? = 0
configure:11258: /opt/openmpi//bin/mpicc -c   conftest.c >&5
conftest.c: In function 'main':
conftest.c:34: error: 'not' undeclared (first use in this function)
conftest.c:34: error: (Each undeclared identifier is reported only once
conftest.c:34: error: for each function it appears in.)
conftest.c:34: error: expected ';' before 'big'
configure:11265: $? = 1
configure: failed program was:
| /* confdefs.h.  */


and one other one with confdefs.h.

I get the same result when I type gcc -v
gcc -v
Using built-in specs.
Target: x86_64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr 
--with-local-prefix=/usr/local --infodir=/usr/share/info 
--mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 
--enable-languages=c,c++,objc,fortran,obj-c++,java,ada 
--enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 
--enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 
--with-system-zlib --enable-shared --enable-__cxa_atexit 
--enable-libstdcxx-allocator=new --program-suffix= 
--enable-version-specific-runtime-libs --without-system-libunwind 
--with-cpu=generic --host=x86_64-suse-linux
Thread model: posix
gcc version 4.1.2 20070115 (SUSE Linux)


and when I type mpif90 -v or /opt/openmpi/bin/mpif90 -v
 /opt/openmpi/bin/mpif90 -v
Using built-in specs.
Target: x86_64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr 
--with-local-prefix=/usr/local --infodir=/usr/share/info 
--mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 
--enable-languages=c,c++,objc,fortran,obj-c++,java,ada 
--enable-checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 
--enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 
--with-system-zlib --enable-shared --enable-__cxa_atexit 
--enable-libstdcxx-allocator=new --program-suffix= 
--enable-version-specific-runtime-libs --without-system-libunwind 
--with-cpu=generic --host=x86_64-suse-linux
Thread model: posix
gcc version 4.1.2 20070115 (SUSE Linux)

Finally, you wanted to see the showme
/opt/openmpi/bin/mpif90 -showme
gfortran -I/opt/openmpi/include -pthread -I/opt/openmpi/lib 
-L/opt/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl 
-Wl,--export-dynamic -lnsl -lutil -lm -ldl


I'm working with abinit5.6.5 at the moment.
This is not a small post, so if you made it this far down, THANK YOU.

-Cheers,
James


On Mon, 16 Feb 2009, Alain Jacques wrote:

> Hello James,
>
> If you use the configure flags --enable-mpi --
> --with-mpi-prefix=/opt/mpich ... FC=ifort, the thing to look after is
> that the mpi environment uses the same fortran compiler. So your
> /opt/mpich/... should have been built with Intel ifort compiler; if
> mpich has been installed from a Suse distributed package, I assume it
> has been built with the default gcc/gfortran toolchain.
> Not recognized? ... look for the mpif90 wrapper; it should reside in
> /opt/mpich/bin and the right prefix is then
> --with-mpi-prefix=/opt/mpich. Are you working with a mpich(1) or mpich2?
> mpich is antiquated, use mpich2 (and btw I would recommend openmpi)
>
> Setup your build environment in order to find the mpi execs if it is not
> already done (export PATH=/opt/mpich/bin:$PATH) and libraries (export
> LD_LIBRARY_PATH=/opt/mpich/lib:$LD_LIBRARY_PATH)
> Do a simple parallalel fortran hello test with the following program ...
>
> PROGRAM HelloWorld
> include 'mpif.h'
>
> call mpi_init(ierr)
> call mpi_comm_size(MPI_COMM_WORLD,npes, ierr)
> call mpi_comm_rank(MPI_COMM_WORLD,irank,ierr)
>
> print*,'Hello World! I am ',irank,' of ',npes
>
> call mpi_finalize(ierr)
>
> END PROGRAM
>
> Save in hello.f90. Compile with mpif90 hello.f90. Does it produce a
        > working binary?
> If all of this work, go back to abinit. Try with a plain configure and
> let it find out the best setup. Do a configure --enable-mpi
> --with-mpi-prefix=/opt/mpich. Maybe add --enable-64bit-flags if you're
> working with a 64bit mpich lib. Any error during configure? Look for
> details in config.log. In case of difficulties, please mention your
> abinit version, the output of gcc -v, mpif90 -v and mpif90 -showme.
>
> Cheers,
>
> Alain
>
>
> > Hi,
> > I'm the relatively inexperienced system admin for a few computers in
> > my experimental lab.  I'm  using a SMP 4 intel xenon processor
> > SUSE10.1 machine, and have compiled and run abinit quite sucessfully,
> > but only in a serial capacity.  I'd like to use the larger power of my
> > machine by using the parallel version of the code.  To that end, I
> > installed the mpich package.  That, however, did not install a header
> > file mpi.h which the tutorial on abinip said to look for.  I then
> > installed the mpich development package/kit/thingy from SUSE.  This
> > has the mpich header, as well as a several libraries for the fortran
> > compiler.  First question, it is unclear from the tutorial if I should
> > still use the configuration flag FC=ifort (I had used the intel
> > fortran compiler to make the serial version).  Also, using the default
> > configuration script, it does not detect a native mpi support.    If I
> > use the command configure --with-mpi-prefix=/opt/mpich/include (this
> > is where mpi.h is) it also can't find anything.  If I use the
> > directory /opt/mpich/ch-p4 it can at least find that there is a
> > general parallel environment, but does not recognize it as mpi.  This
> > also does not put a copy of abinip in the ~abinit/src/main directory.
> > Attempting to run make and then make install or make multi and make
> > install both give errors.  In the tutorial, it says to replace a
> > directory in the line with a directory you have already written down,
> > but early in the same paragraph it says to take note of the location
> > of the mpi.h file, the name and location of the MPI library file
> > ending in .a (which of the many library files I'm not sure) and the
> > dependencies of the MPI Library.  The tutorial I'm reading from is
> > http://www.abinit.org/Infos_v5.5/tutorial/lesson_parallelism.html
> >
> > I know discussions of compilation of abinit, and specifically how to
> > compile and use the parallel version have come up before, but I have 4
> > years of this forum saved on my hard drive, and searching for parallel
> > or compilation problems yields far to many results.  If anyone has any
> > clarification, that would be greatly appreciated. Thanks,
> > James Johns
> > UC Berkeley