The ABINIT Users Mailing List ( CLOSED )

["matthieu verstraete" <matthieu.jean.verstraete@gmail.com>]

For 5.6.4 the configuration of etsfio does not always work: add

--disable-etsf-io --disable-netcdf 

to the configure line. You'll probably also have to make clean to remove the calls to netcdf which were already compiled

Matthieu

On Fri, Dec 26, 2008 at 6:36 PM, Physics fany <physicsfany@yahoo.com> wrote:

Hello,

thanks for replying.

1. I went through "ldd abinip" the following message appeared:

    linux-gate.so.1 =>  (0xffffe000)
    libmpi_f90.so.0 => /usr/local/lib/libmpi_f90.so.0 (0xb8078000)
    libmpi_f77.so.0 => /usr/local/lib/libmpi_f77.so.0 (0xb804a000)
    libmpi.so.0 => /usr/local/lib/libmpi.so.0 (0xb7fc4000)
    libopen-rte.so.0 => /usr/local/lib/libopen-rte.so.0 (0xb7f6f000)
    libopen-pal.so.0 => /usr/local/lib/libopen-pal.so.0 (0xb7f17000)
    libdl.so.2 => /lib/libdl.so.2 (0xb7f13000)
    libnsl.so.1 => /lib/libnsl.so.1 (0xb7efb000)
    libutil.so.1 => /lib/libutil.so.1 (0xb7ef7000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb7e44000)
    libm.so.6 => /lib/libm.so.6 (0xb7e1e000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7e10000)
    libpthread.so.0 => /lib/libpthread.so.0 (0xb7df8000)
    libc.so.6 => /lib/libc.so.6 (0xb7cb4000)
    /lib/ld-linux.so.2 (0xb8099000)

although didn't see any unreferenced libraries, I executed "export  LD_LIBRARY_PATH=/usr/local/lib" and configured again, make and make install, I did what you said about making a parallel test and I recievd the following log:
STOP INIT
STOP INIT
STOP INIT
STOP INIT

These were all for abinit.5.6.3, but I went for installing the source for abinit 5.6.4 as well, but I received the folowing error:

LDFLAGS was  -L/home/sara/abinit-5.6.4/plugins/netcdf
Action: install NetCDF and set the library link path with --with-netcdf-ldflags.
configure: error: "No 'NetCDF' library found."
make[4]: *** [configure-stamp] Error 1
make[4]: Leaving directory `/home/sara/abinit-5.6.4/plugins/etsf_io'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/sara/abinit-5.6.4/plugins/etsf_io'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/sara/abinit-5.6.4/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/sara/abinit-5.6.4'
make: *** [all] Error 2

Sorry to take your time :-(

---

From: Alain Jacques <ajs.jacques@gmail.com>
To: forum@abinit.org
Sent: Friday, December 26, 2008 7:10:18 PM
Subject: Re: [abinit-forum] parallel tune

Hello again,

Physics fany wrote:

1. opensuse comes with gcc-4.3.2 (?) yes, it does.
2. but what kind of MPI implementation are you using? openmpi-1.2.8

Nice. It is the system I am using for development - abinit 5.6.4 builds nicely on it, including parallelization. I realized that you work with version 5.4.4. 5.6.4 is out and is the recommended production release. But 5.4.4 should work

3. A copy of your abinit configure or the head of the config.log would be useful. Please find it below.

4. Maybe you need to specify a transport with mpirun suitable for your hardware setup. in abinit 5.4.4 I made the abinip by manually enabling mpi and some libraries, I did the same for some libraries, still the made abinip does not work!

Check with a "ldd abinip" that the exec links to the correct libraries; you should see references to /usr/local/lib/libmpi... right? Abinit's configure picks a mpi implementation you probably build yourself and install in /usr/local. If ldd finds unreferenced libraries you may have to add an "export  LD_LIBRARY_PATH=/usr/local/lib" i.e. where the libmpi reside.
Lets try a test. Make a test directory, cd to it, copy the content of the abinit distribution tests/paral/Input/ directory in it. Copy tests/Psps_for_tests/26fe.pspnc in your test directory. Make a test.files containing the following lines:

t_kpt+spin.int_kpt+spin.out
t.i
t.o
t
26fe.pspnc

and run it with "mpirun --mca btl sm,self -np 2 abinip < test.files >& log_mpi"
You may have to replace abinip with the full path to the exec. Follow the log_mpi output; this test takes a few minutes to  run. I assume you have at least a dual core CPU system therefore asking for 2 processes. From another terminal window, "top" should display 2 abinip tasks and plenty of CPU use :-) Does it work or do you have errors in the log?
If it doesn't, please show the error ... and the configure invocation line.

Kind regards,

Alain

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Matthieu Verstraete

European Theoretical Spectroscopy Facility (ETSF) 
Dpto. Fisica de Materiales, 
U. del Pais Vasco,            
Centro Joxe Mari Korta, Av. de Tolosa, 72,   Phone: +34-943018393
E-20018 Donostia-San Sebastian, Spain        Fax  : +34-943018390

Mail : matthieu.jean.verstraete@gmail.com
http://www-users.york.ac.uk/~mjv500