The ABINIT Users Mailing List ( CLOSED )

[<zhouy6@rpi.edu>]

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.