The ABINIT Users Mailing List ( CLOSED )

["Anglade Pierre-Matthieu" <anglade@gmail.com>]

Hi,

That's just a little bit strange : your configure output tells that
the usual optimization for gfortran have been used. this should
provide a binary that is about 10% slower than the fastest possible
one in general.
1) Are you sure no other task could have interfered with your benchmarking ?
2) Does the other tests show the same discrepancy between your build
and the provided binary ? (for instance could you run and time "make
tests_acc") ?
3) you could always try to enforce the compilation flags you want. For
instance you can try something like : ./configure FC="gfotran -static
-march=native -O2" .
regards

PMA

On Tue, Oct 21, 2008 at 6:33 AM,  <zhouy6@rpi.edu> wrote:
> Hi dear all,
>
> I'm wondering if anybody has ever seen such a problem before. I'm running
> Abinit 5.4.4 on opteron clusters. and I downloaded both the source code and
> binary files.
>
> The provided abinis works fine, but the parallel version "abinip" doesn't 
> work
> properly because our machine is using a different type of MPI, so I have to
> recompile the source code.
>
> When compilation is done, I compared my abinis with the provided binary, and
> find that, the test job "tparal_1" took 23s to finish, while my abinis took
> 147s. The results from my abinis and provided one are exactly the same.
>
> Could anybody tell me what the problem is, and make the newly compiled one 
> as
> fast as the provided binary.
>
> Another way to solve it is: we are using OpenMPI, and the directory is, say,
> /opt/openmpi/, can I use somehow let the pre-compiled abinip know where the 
> MPI
> is?
>
> thanks in advance!
>
> p.s. here is the information after "./configure"
>  
> ==============================================================================
>  === Startup                                                                
> ===
>  
> ==============================================================================
>
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking target system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
>
>  
> ==============================================================================
>  === Option consistency checking                                            
> ===
>  
> ==============================================================================
>
> configure: checking consistency of MPI options
> configure:  |---> all OK
> configure:
> configure: checking consistency of external library options
> configure:  |---> all OK
> configure:
>
>  
> ==============================================================================
>  === Utilities                                                              
> ===
>  
> ==============================================================================
>
> checking whether make sets $(MAKE)... (cached) yes
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking for sh... /bin/sh
> checking for perl... /usr/bin/perl
> checking for python... /usr/bin/python
> checking for rm... /bin/rm
> checking for mv... /bin/mv
> checking for tar... /bin/tar
> checking for markdown... /usr/bin/markdown
> checking for latex... /usr/bin/latex
> checking for dvips... /usr/bin/dvips
> checking for dvipdf... /usr/bin/dvipdf
> checking for ps2pdf... /usr/bin/ps2pdf
> checking for egrep... grep -E
> configure: using internal version of MarkDown
>
>  
> ==============================================================================
>  === Libraries and linking                                                  
> ===
>  
> ==============================================================================
>
> checking for ranlib... ranlib
> checking for a sed that does not truncate output... /bin/sed
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking dependency style of gcc... gcc3
> checking for ld used by gcc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for ar... /usr/bin/ar
> checking for sed... /bin/sed
>
>  
> ==============================================================================
>  === Preprocessing                                                          
> ===
>  
> ==============================================================================
>
> checking how to run the C preprocessor... gcc -E
> checking for the true C preprocessor... /lib/cpp
> checking for C preprocessor options... -P -std=c89
>
>  
> ==============================================================================
>  === C support                                                              
> ===
>  
> ==============================================================================
>
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ANSI C... (cached) none needed
> checking dependency style of gcc... (cached) gcc3
> checking if we are using the Intel C compiler... no
> checking if we are using the GNU C compiler... yes
> checking whether byte ordering is bigendian... no
> configure: applying C compiler tricks (type: gnu, version: 3.4.6)
>
>  
> ==============================================================================
>  === C++ support                                                            
> ===
>  
> ==============================================================================
>
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking dependency style of g++... gcc3
> checking if we are using the Intel C++ compiler... no
> checking if we are using the GNU C++ compiler... yes
> configure: applying C++ compiler tricks (type: gnu, version: 3.4.6)
>
>  
> ==============================================================================
>  === Fortran support                                                        
> ===
>  
> ==============================================================================
>
> checking for f95... no
> checking for fort... no
> checking for xlf95... no
> checking for ifc... no
> checking for efc... no
> checking for pgf95... no
> checking for lf95... no
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran compiler... yes
> checking whether gfortran accepts -g... yes
> checking if we are using the G95 Fortran compiler... no
> checking if we are using the Intel Fortran compiler... no
> checking if we are using the GNU Fortran compiler... no
> checking if we are using the PathScale Fortran compiler... no
> checking if we are using the Portland Group Fortran compiler... no
> checking if we are using the Compaq Fortran compiler... no
> checking if we are using the ABSoft Fortran compiler... no
> checking if we are using the MIPSpro Fortran compiler... no
> checking if we are using the Fujitsu Fortran compiler... no
> checking if we are using the Sun WorkShop Fortran compiler... no
> checking if we are using the IBM XL Fortran compiler... no
> checking whether the Fortran compiler accepts exit()... yes
> checking whether to activate Fortran interfaces... yes
> checking whether to use C clock for timings... no
>
>  
> ==============================================================================
>  === Optimizations                                                          
> ===
>  
> ==============================================================================
>
> configure: applying optimizations for gnu_cc/all/opteron
> configure: applying optimizations for gnu_cxx/all/opteron
> configure: enabling per-directory Fortran optimizations
>
>  
> ==============================================================================
>  === MPI support                                                            
> ===
>  
> ==============================================================================
>
> checking for a native MPI support... no
> configure: using MPI prefix /opt/openmpi/1.2.6-V00/gcc/
> checking for a usable Open-MPI implementation... yes
> checking whether to build parallel code... yes
> checking if MPI is usable... yes
> checking for MPI type... open-mpi
> checking for MPI Fortran compiler... /opt/openmpi/1.2.6-V00/gcc//bin/mpif90
> checking for MPI CPPFLAGS... -DMPI=1
> checking for MPI FCFLAGS... none
> checking for MPI Fortran LDFLAGS... none
> checking for MPI run script... /opt/openmpi/1.2.6-V00/gcc//bin/mpirun
>
>  
> ==============================================================================
>  === External libraries                                                     
> ===
>  
> ==============================================================================
>
> checking whether to use the BIGDFT library... no
> checking whether to build the BIGDFT library... no
> checking whether to use the LINALG library... yes
> checking whether to build the LINALG library... yes
> checking whether to use the STRING_F library... no
> checking whether to build the STRING_F library... no
> checking whether to use the NETCDF library... no
> checking whether to build the NETCDF library... no
> checking whether to use the ETSF_IO library... no
> checking whether to build the ETSF_IO library... no
> checking whether to use the ETSF_XC library... no
> checking whether to build the ETSF_XC library... no
> checking whether to use the FOX library... no
> checking whether to build the FOX library... no
> checking whether to use the XMLF90 library... no
> checking whether to build the XMLF90 library... no
> checking whether to use the FFTW library... no
> checking whether to use the WANNIER90 library... no
> checking whether to build the WANNIER90 library... no
>
>  
> ==============================================================================
>  === Output                                                                 
> ===
>  
> ==============================================================================
>
> configure: creating ./config.status
> config.status: creating config.mk
> config.status: creating config.sh
> config.status: creating lib/xmlf90/build.mk
> config.status: creating src/defs/defs_infos.F90
> config.status: creating tests/tests.env
> config.status: creating config/wrappers/wrap-fc
> config.status: creating Makefile
> config.status: creating lib/Makefile
> config.status: creating src/Makefile
> config.status: creating lib/light/Makefile
> config.status: creating lib/macroav/Makefile
> config.status: creating lib/numeric/Makefile
> config.status: creating lib/numericf90/Makefile
> config.status: creating lib/linalg/Makefile
> config.status: creating lib/netcdf/Makefile
> config.status: creating lib/etsf_io/Makefile
> config.status: creating lib/string_f/Makefile
> config.status: creating lib/etsf_xc/Makefile
> config.status: creating lib/fox/Makefile
> config.status: creating lib/xmlf90/Makefile
> config.status: creating lib/wannier90/Makefile
> config.status: creating src/defs/Makefile
> config.status: creating src/lib01fftnew/Makefile
> config.status: creating src/lib01cg/Makefile
> config.status: creating src/lib01hidempi/Makefile
> config.status: creating src/00basis/Makefile
> config.status: creating src/01manage_mpi/Makefile
> config.status: creating src/11util/Makefile
> config.status: creating src/11contract/Makefile
> config.status: creating src/12spacepar/Makefile
> config.status: creating src/12parser/Makefile
> config.status: creating src/12geometry/Makefile
> config.status: creating src/12ffts/Makefile
> config.status: creating src/12nlstrain/Makefile
> config.status: creating src/13xml/Makefile
> config.status: creating src/13xc/Makefile
> config.status: creating src/13recipspace/Makefile
> config.status: creating src/13paw/Makefile
> config.status: creating src/13iovars/Makefile
> config.status: creating src/13nonlocal/Makefile
> config.status: creating src/13psp/Makefile
> config.status: creating src/13ionetcdf/Makefile
> config.status: creating src/13io_mpi/Makefile
> config.status: creating src/14poisson/Makefile
> config.status: creating lib/bigdft/Makefile
> config.status: creating src/14wfs/Makefile
> config.status: creating src/14wvl_wfs/Makefile
> config.status: creating src/14iowfdenpot/Makefile
> config.status: creating src/14bader/Makefile
> config.status: creating src/14occeig/Makefile
> config.status: creating src/15common/Makefile
> config.status: creating src/15gw/Makefile
> config.status: creating src/15rsprc/Makefile
> config.status: creating src/16response/Makefile
> config.status: creating src/16geomoptim/Makefile
> config.status: creating src/17suscep/Makefile
> config.status: creating src/17lwf/Makefile
> config.status: creating src/17ddb/Makefile
> config.status: creating src/18seqpar/Makefile
> config.status: creating src/19cut3d/Makefile
> config.status: creating src/21paral_md/Makefile
> config.status: creating src/21drive/Makefile
> config.status: creating src/21rdm/Makefile
> config.status: creating src/main/Makefile
> config.status: creating doc/Makefile
> config.status: creating tests/Makefile
> config.status: creating vms/Makefile
> config.status: creating config.h
> config.status: executing depfiles commands
> config.status: executing build-exec commands
>
> Configuration complete.
> You may now type "make" (or "make multi" or "make multi_alt" on a SMP 
> machine)
> to build ABINIT.
>



-- 
Pierre-Matthieu Anglade